references.bib

@misc{center_for_history_and_new_media_zotero_????,
	title = {Zotero {Quick} {Start} {Guide}},
	url = {http://zotero.org/support/quick_start_guide},
	author = {{Center for History and New Media}}
}

@article{jacques_optical_2013,
	title = {Optical properties of biological tissues: a review},
	volume = {58},
	issn = {0031-9155, 1361-6560},
	shorttitle = {Optical properties of biological tissues},
	url = {http://stacks.iop.org/0031-9155/58/i=11/a=R37?key=crossref.e58b67eb50f9f6507dd5e75b7744fa07},
	doi = {10.1088/0031-9155/58/11/R37},
	number = {11},
	urldate = {2016-06-28},
	journal = {Physics in Medicine and Biology},
	author = {Jacques, Steven L},
	month = jun,
	year = {2013},
	pages = {R37--R61},
	file = {Jacques_PMB2013.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WBNNDFW8/Jacques_PMB2013.pdf:application/pdf}
}

@article{rivera_use_2012,
	title = {Use of a lensed fiber for a large-field-of-view, high-resolution, fiber-scanning microendoscope},
	volume = {37},
	issn = {0146-9592, 1539-4794},
	url = {https://www.osapublishing.org/abstract.cfm?URI=ol-37-5-881},
	doi = {10.1364/OL.37.000881},
	language = {en},
	number = {5},
	urldate = {2016-06-22},
	journal = {Optics Letters},
	author = {Rivera, David R. and Brown, Christopher M. and Ouzounov, Dimitre G. and Webb, Watt W. and Xu, Chris},
	month = mar,
	year = {2012},
	pages = {881},
	file = {ol-37-5-881.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U9KT9N8D/ol-37-5-881.pdf:application/pdf}
}

@article{provenzano_collagen_2006,
	title = {Collagen fibril morphology and organization: {Implications} for force transmission in ligament and tendon},
	volume = {25},
	issn = {0945-053X},
	shorttitle = {Collagen fibril morphology and organization},
	url = {http://www.sciencedirect.com/science/article/pii/S0945053X05001332},
	doi = {10.1016/j.matbio.2005.09.005},
	abstract = {Connective tissue mechanical behavior is primarily determined by the composition and organization of collagen. In ligaments and tendons, type I collagen is the principal structural element of the extracellular matrix, which acts to transmit force between bones or bone and muscle, respectively. Therefore, characterization of collagen fibril morphology and organization in fetal and skeletally mature animals is essential to understanding how tissues develop and obtain their mechanical attributes. In this study, tendons and ligaments from fetal rat, bovine, and feline, and mature rat were examined with scanning electron microscopy. At early fetal developmental stages, collagen fibrils show fibril overlap and interweaving, apparent fibril ends, and numerous bifurcating/fusing fibrils. Late in fetal development, collagen fibril ends are still present and fibril bundles (fibers) are clearly visible. Examination of collagen fibrils from skeletally mature tissues, reveals highly organized regions but still include fibril interweaving, and regions that are more randomly organized. Fibril bifurcations/fusions are still present in mature tissues but are less numerous than in fetal tissue. To address the continuity of fibrils in mature tissues, fibrils were examined in individual micrographs and consecutive overlaid micrographs. Extensive microscopic analysis of mature tendons and ligaments detected no fibril ends. These data strongly suggest that fibrils in mature ligament and tendon are either continuous or functionally continuous. Based upon this information and published data, we conclude that force within these tissues is directly transferred through collagen fibrils and not through an interfibrillar coupling, such as a proteoglycan bridge.},
	number = {2},
	urldate = {2014-11-04},
	journal = {Matrix Biology},
	author = {Provenzano, Paolo P. and Vanderby Jr., Ray},
	month = mar,
	year = {2006},
	keywords = {Cell–matrix interaction, Extracellular matrix, Scanning electron microscopy, Structure-function, Three-dimensional matrix organization},
	pages = {71--84},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DAB3G7F6/Provenzano and Vanderby Jr. - 2006 - Collagen fibril morphology and organization Impli.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/86ID5DXR/S0945053X05001332.html:text/html}
}

@article{wojcik_interaction_2008,
	title = {Interaction of a {DNA} intercalator {DRAQ}5, and a minor groove binder {SYTO}17, with chromatin in live cells-{Influence} on chromatin organization and histone-{DNA} interactions},
	volume = {73A},
	issn = {15524922, 15524930},
	url = {http://doi.wiley.com/10.1002/cyto.a.20573},
	doi = {10.1002/cyto.a.20573},
	language = {en},
	number = {6},
	urldate = {2016-06-29},
	journal = {Cytometry Part A},
	author = {Wojcik, Krzysztof and Dobrucki, Jurek W.},
	month = jun,
	year = {2008},
	pages = {555--562},
	file = {20573_ftp.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5CHVPAG4/20573_ftp.pdf:application/pdf}
}

@article{zhang_proteomic_2005,
	title = {Proteomic {Study} {Reveals} {That} {Proteins} {Involved} in {Metabolic} and {Detoxification} {Pathways} {Are} {Highly} {Expressed} in {HER}-2/neu-positive {Breast} {Cancer}*},
	volume = {4},
	issn = {1535-9476, 1535-9484},
	url = {http://www.mcponline.org/content/4/11/1686},
	doi = {10.1074/mcp.M400221-MCP200},
	abstract = {The receptor tyrosine kinase ErbB2 (HER-2/neu) is overexpressed in up to 30\% of breast cancers and is associated with poor prognosis and an increased likelihood of metastasis especially in node-positive tumors. In this proteomic study, to identify the proteins that are associated with the aggressive phenotype of HER-2/neu-positive breast cancer, tumor cells from both HER-2/neu-positive and -negative tumors were procured by laser capture microdissection. Differentially expressed proteins in the two subsets of tumors were identified by two-dimensional electrophoresis and MALDI-TOF/TOF MS/MS. We found differential expression of several key cell cycle modulators, which were linked with increased proliferation of the HER-2/neu-overexpressing cells. Nine proteins involved in glycolysis (triose-phosphate isomerase (TPI), phosphoglycerate kinase 1 (PGK1), and enolase 1 (ENO1)), lipid synthesis (fatty acid synthase (FASN)), stress-mediated chaperonage (heat shock protein 27 (Hsp27)), and antioxidant and detoxification pathways (haptoglobin, aldo-keto reductase (AKR), glyoxalase I (GLO), and prolyl-4-hydrolase β-isoform (P4HB)) were found to be up-regulated in HER-2/neu-positive breast tumors. HER-2/neu-dependent differential expression of PGK1, FASN, Hsp27, and GLO was further validated in four breast cancer cell lines and 12 breast tumors by immunoblotting and confirmed by partially switching off the HER-2/neu signaling in the high HER-2/neu-expressing SKBr3 cell line with Herceptin treatment. Statistical correlations of these protein expressions with HER-2/neu status were further verified by immunohistochemistry on a tissue microarray comprising 97 breast tumors. Our findings suggest that HER-2/neu signaling may result, directly or indirectly, in enhanced activation of various metabolic, stress-responsive, antioxidative, and detoxification processes within the breast tumor microenvironment. We hypothesize that these identified changes in the cellular proteome are likely to drive cell proliferation and tissue invasion and that the key cell cycle modulators involved, when uncovered by future research, would serve as naturally useful targets for the development of therapeutic strategies to negate the metastatic potential of HER-2/neu-positive breast tumors.},
	language = {en},
	number = {11},
	urldate = {2015-03-07},
	journal = {Molecular \& Cellular Proteomics},
	author = {Zhang, DaoHai and Tai, Lee Kian and Wong, Lee Lee and Chiu, Lily-Lily and Sethi, Sunil K. and Koay, Evelyn S. C.},
	month = nov,
	year = {2005},
	pmid = {16048908},
	pages = {1686--1696},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Q9N7AQKK/Q9N7AQKK.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3P5CM33C/Zhang et al. - 2005 - Proteomic Study Reveals That Proteins Involved in .html:text/html}
}

@article{bydlon_advancing_2012,
	title = {Advancing {Optical} {Imaging} for {Breast} {Margin} {Assessment}: {An} {Analysis} of {Excisional} {Time}, {Cautery}, and {Patent} {Blue} {Dye} on {Underlying} {Sources} of {Contrast}},
	volume = {7},
	issn = {1932-6203},
	shorttitle = {Advancing {Optical} {Imaging} for {Breast} {Margin} {Assessment}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519619/},
	doi = {10.1371/journal.pone.0051418},
	abstract = {Breast conserving surgery (BCS) is a recommended treatment for breast cancer patients where the goal is to remove the tumor and a surrounding rim of normal tissue. Unfortunately, a high percentage of patients return for additional surgeries to remove all of the cancer. Post-operative pathology is the gold standard for evaluating BCS margins but is limited due to the amount of tissue that can be sampled. Frozen section analysis and touch-preparation cytology have been proposed to address the surgical needs but also have sampling limitations. These issues represent an unmet clinical need for guidance in resecting malignant tissue intra-operatively and for pathological sampling. We have developed a quantitative spectral imaging device to examine margins intra-operatively. The context in which this technology is applied (intra-operative or post-operative setting) is influenced by time after excision and surgical factors including cautery and the presence of patent blue dye (specifically Lymphazurin™, used for sentinel lymph node mapping). Optical endpoints of hemoglobin ([THb]), fat ([β-carotene]), and fibroglandular content via light scattering ({\textless}µs’{\textgreater}) measurements were quantified from diffuse reflectance spectra of lumpectomy and mastectomy specimens using a Monte Carlo model. A linear longitudinal mixed-effects model was used to fit the optical endpoints for the cautery and kinetics studies. Monte Carlo simulations and tissue mimicking phantoms were used for the patent blue dye experiments. [THb], [β-carotene], and {\textless}µs’{\textgreater} were affected by {\textless}3.3\% error with {\textless}80 µM of patent blue dye. The percent change in [β-carotene], {\textless}µs’{\textgreater}, and [β-carotene]/{\textless}µs’{\textgreater} was {\textless}14\% in 30 minutes, while percent change in [THb] was {\textgreater}40\%. [β-carotene] and [β-carotene]/{\textless}µs’{\textgreater} were the only parameters not affected by cautery. This work demonstrates the importance of understanding the post-excision kinetics of ex-vivo tissue and the presence of cautery and patent blue dye for breast tumor margin assessment, to accurately interpret data and exploit underling sources of contrast.},
	number = {12},
	urldate = {2016-06-24},
	journal = {PLoS ONE},
	author = {Bydlon, Torre M. and Barry, William T. and Kennedy, Stephanie A. and Brown, J. Quincy and Gallagher, Jennifer E. and Wilke, Lee G. and Geradts, Joseph and Ramanujam, Nimmi},
	month = dec,
	year = {2012},
	pmid = {23251526},
	pmcid = {PMC3519619},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7NJG4IH3/Bydlon et al. - 2012 - Advancing Optical Imaging for Breast Margin Assess.pdf:application/pdf}
}

@article{mendez_influence_2006,
	series = {{PAPERS} {FROM} {THE} {AMERICAN} {SOCIETY} {OF} {BREAST} {SURGEONS}7th {Annual} {Meeting}},
	title = {Influence of breast cancer margin assessment method on the rates of positive margins and residual carcinoma},
	volume = {192},
	issn = {0002-9610},
	url = {http://www.sciencedirect.com/science/article/pii/S0002961006004430},
	doi = {10.1016/j.amjsurg.2006.06.009},
	abstract = {Background
We hypothesized that the method of breast cancer margin assessment may be associated with different rates of positive margins and residual carcinoma.
Methods
A total of 178 breast cancer specimens were divided into 2 groups (A and B) based on the margin assessment method used. Rates of positive margins, re-excision, and residual carcinoma at re-excision were compared and analyzed statistically.
Results
At least 1 margin was positive in 64.7\% in group A and in 65.2\% in group B. At directed re-excision 54\% in group A and 51\% in group B had residual carcinoma. The lateral margin was positive in 44\% in group A compared with 26\% in group B (P = .06). The posterior margin was positive in 19\% in group A and in 51\% in group B (P = .001).
Conclusions
Two different breast cancer specimen margin assessment methods had comparable rates of positive margins and residual carcinoma at re-excision. Different patterns of specific margin positivity suggest that the method of margin assessment may alter results.},
	number = {4},
	urldate = {2016-06-24},
	journal = {The American Journal of Surgery},
	author = {Méndez, Jane E. and Lamorte, Wayne W. and de las Morenas, Antonio and Cerda, Sandra and Pistey, Robert and King, Thomas and Kavanah, Maureen and Hirsch, Erwin and Stone, Michael D.},
	month = oct,
	year = {2006},
	keywords = {Breast cancer margin assessment, Breast cancer positive margins, Breast cancer re-excision},
	pages = {538--540},
	file = {1-s2.0-S0002961006004430-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UPWM7DI5/1-s2.0-S0002961006004430-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PBX4IV4J/S0002961006004430.html:text/html}
}

@article{walsh_optical_2013,
	title = {Optical {Metabolic} {Imaging} {Identifies} {Glycolytic} {Levels}, {Subtypes}, and {Early}-{Treatment} {Response} in {Breast} {Cancer}},
	volume = {73},
	issn = {0008-5472, 1538-7445},
	url = {http://cancerres.aacrjournals.org/content/73/20/6164},
	doi = {10.1158/0008-5472.CAN-13-0527},
	abstract = {Abnormal cellular metabolism is a hallmark of cancer, yet there is an absence of quantitative methods to dynamically image this powerful cellular function. Optical metabolic imaging (OMI) is a noninvasive, high-resolution, quantitative tool for monitoring cellular metabolism. OMI probes the fluorescence intensities and lifetimes of the autofluorescent metabolic coenzymes reduced NADH and flavin adenine dinucleotide. We confirm that OMI correlates with cellular glycolytic levels across a panel of human breast cell lines using standard assays of cellular rates of glucose uptake and lactate secretion (P {\textless} 0.05, r = 0.89). In addition, OMI resolves differences in the basal metabolic activity of untransformed from malignant breast cells (P {\textless} 0.05) and between breast cancer subtypes (P {\textless} 0.05), defined by estrogen receptor and/or HER2 expression or absence. In vivo OMI is sensitive to metabolic changes induced by inhibition of HER2 with the antibody trastuzumab (herceptin) in HER2-overexpressing human breast cancer xenografts in mice. This response was confirmed with tumor growth curves and stains for Ki67 and cleaved caspase-3. OMI resolved trastuzumab-induced changes in cellular metabolism in vivo as early as 48 hours posttreatment (P {\textless} 0.05), whereas fluorodeoxyglucose-positron emission tomography did not resolve any changes with trastuzumab up to 12 days posttreatment (P {\textgreater} 0.05). In addition, OMI resolved cellular subpopulations of differing response in vivo that are critical for investigating drug resistance mechanisms. Importantly, OMI endpoints remained unchanged with trastuzumab treatment in trastuzumab-resistant xenografts (P {\textgreater} 0.05). OMI has significant implications for rapid cellular-level assessment of metabolic response to molecular expression and drug action, which would greatly accelerate drug development studies. Cancer Res; 73(20); 6164–74. ©2013 AACR.},
	language = {en},
	number = {20},
	urldate = {2015-03-06},
	journal = {Cancer Research},
	author = {Walsh, Alex J. and Cook, Rebecca S. and Manning, H. Charles and Hicks, Donna J. and Lafontant, Alec and Arteaga, Carlos L. and Skala, Melissa C.},
	month = oct,
	year = {2013},
	pmid = {24130112},
	pages = {6164--6174},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4WCPZSBM/Walsh et al. - 2013 - Optical Metabolic Imaging Identifies Glycolytic Le.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/D57FAMBV/Walsh et al. - 2013 - Optical Metabolic Imaging Identifies Glycolytic Le.html:text/html}
}

@article{paul_mitosis_2015,
	title = {Mitosis {Detection} for {Invasive} {Breast} {Cancer} {Grading} in {Histopathological} {Images}},
	volume = {24},
	issn = {1057-7149},
	doi = {10.1109/TIP.2015.2460455},
	abstract = {Histopathological grading of cancer not only offers an insight to the patients' prognosis but also helps in making individual treatment plans. Mitosis counts in histopathological slides play a crucial role for invasive breast cancer grading using the Nottingham grading system. Pathologists perform this grading by manual examinations of a few thousand images for each patient. Hence, finding the mitotic figures from these images is a tedious job and also prone to observer variability due to variations in the appearances of the mitotic cells. We propose a fast and accurate approach for automatic mitosis detection from histopathological images. We employ area morphological scale space for cell segmentation. The scale space is constructed in a novel manner by restricting the scales with the maximization of relative-entropy between the cells and the background. This results in precise cell segmentation. The segmented cells are classified in mitotic and non-mitotic category using the random forest classifier. Experiments show at least 12\% improvement in F1 score on more than 450 histopathological images at 40× magnification.},
	number = {11},
	journal = {IEEE Transactions on Image Processing},
	author = {Paul, A. and Mukherjee, D. P.},
	month = nov,
	year = {2015},
	keywords = {area morphological scale space, area morphology, automatic mitosis detection, biological organs, BREAST cancer, Breast cancer grading, Cancer, cell segmentation, cellular biophysics, Entropy, F1 score, histopathological imaging, histopathological slides, Image edge detection, Image segmentation, invasive breast cancer grading, Manuals, maximization, medical image processing, Mitosis detection, Mitosis detection,, mitotic cells, nonmitotic category, Nottingham grading system, optimisation, patient prognosis, random forest classifier, relative-entropy, relative-entropy maximization, scale space, Shape, treatment planning},
	pages = {4041--4054},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/28F6H2EQ/articleDetails.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U6EC5BAS/Paul and Mukherjee - 2015 - Mitosis Detection for Invasive Breast Cancer Gradi.pdf:application/pdf}
}

@misc{_dapi_????,
	title = {{DAPI} {Counterstaining} {Protocols} {\textbar} {Thermo} {Fisher} {Scientific}},
	url = {https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/dapi-protocol/basic-dapi-counterstaining-protocols.html},
	urldate = {2016-06-29},
	file = {DAPI Counterstaining Protocols | Thermo Fisher Scientific:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S9SKBDUS/basic-dapi-counterstaining-protocols.html:text/html}
}

@article{amato_surgical_2012,
	title = {Surgical margins of resection for breast cancer: current evidence},
	volume = {67},
	issn = {0026-4733},
	shorttitle = {Surgical margins of resection for breast cancer},
	abstract = {Breast cancer is the most common form of cancer and second main cause of death in women in western countries. Breast-conserving therapy, consisting of lumpectomy and radiation therapy, has become the standard local treatment for T1-T2 breast tumors. There is general agreement that successful breast conservation requires complete tumor excision with a "tumor-free" or "negative" margin of resection, but the definition of a negative margin is controversial. A commonly accepted definition of adequate margins requires a 2-mm distance between ink and tumor but opinions range from the original National Surgical Adjuvant Breast and Bowel Project definition of "no ink on tumor", to a recommended width of 10 mm or more. The ability to perform real-time molecular imaging analysis of margins during surgery would clearly be a significant advance; several groups have engaged in this effort, with encouraging reports of preliminary data. Further development of such techniques promises to lead to a point at which accurate intraoperative margin evaluation may be possible and may even be combined with therapeutic interventions, using techniques such as photodynamic therapy.},
	language = {eng},
	number = {5},
	journal = {Minerva Chirurgica},
	author = {Amato, B. and Rispoli, C. and Iannone, L. and Testa, S. and Compagna, R. and Rocco, N.},
	month = oct,
	year = {2012},
	pmid = {23232484},
	keywords = {Breast neoplasms, Female, Humans},
	pages = {445--452}
}

@patent{liu_high_2014,
	title = {High resolution structured illumination microscopy},
	url = {http://www.google.com/patents/US8836948},
	abstract = {Disclosed are systems, apparatus, methods and devices, including a method that includes generating two or more sequential surface plasmon interference patterns, at least one of the two or more sequential surface plasmon interference patterns being different from another of the two or more sequential surface plasmon interference patterns, and capturing respective images of a specimen resulting from the interference patterns. Also disclosed is a method that includes generating two or more sequential optical interference patterns, at least one of the two or more sequential optical interference patterns being different from another of the interference patterns, and removing from each of the generated interference patterns, using a beam stopper, a corresponding zero-order diffraction light component included in the respective generated patterns to obtain resultant corresponding two or more sequential optical interference patterns, directed at a specimen, with missing respective zero-order light components.},
	nationality = {United States},
	assignee = {The Regents Of The University Of California},
	number = {US8836948 B2},
	urldate = {2016-07-05},
	author = {Liu, Zhaowei},
	month = sep,
	year = {2014},
	note = {U.S. Classification 356/450, 356/445; International Classification G02B21/16, G01N21/64, G01B9/04, G01B11/24, G02B5/00, G01B9/02, G02B27/60, G01N21/55; Cooperative Classification G01N2201/0675, G01N2201/0635, G01N21/6458, G01B11/2441, G01B9/04, G01N21/648, G02B21/16, G02B5/008, G02B27/60},
	file = {Google Patents PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/98VHN5HJ/Liu - 2014 - High resolution structured illumination microscopy.pdf:application/pdf}
}

@article{fujikawa_natural_2005,
	title = {Natural history of human prostate gland: {Morphometric} and histopathological analysis of {Japanese} men},
	volume = {65},
	copyright = {Copyright © 2005 Wiley-Liss, Inc.},
	issn = {1097-0045},
	shorttitle = {Natural history of human prostate gland},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/pros.20208/abstract},
	doi = {10.1002/pros.20208},
	abstract = {BACKGROUND
To clarify the pathology of the development of prostatic disorders such as inflammation, cancer, and hyperplasia, we compared histopathological findings of the prostate according to age group.
METHODS
Whole-mount sections of prostates were used to assess the relationship between age and prostate weight (n = 962), prostate histological composition in the transition zone (TZ) and in the peripheral zone (PZ) (n = 68), prostate histopathological findings by zone (n = 102), and comparison of latent tumor development by age group (n = 1,815).
RESULTS
A rapid increase in prostate weight from birth to the 20s was followed by a slow rise thereafter. Volume increases (P {\textless} 0.01) were observed in all components of glandular epithelium, glandular lumen, and stroma in the TZ from the 40s to 70s inclusive. In the PZ, the epithelial and stromal volumes tended to decrease in an age-dependent manner (P {\textless} 0.05). Calculi and lymphocyte infiltration were detected at a relatively early age, with a tendency towards an age-dependent increase. Glandular dilation and nodular hyperplasia were noted first in the 30s group, also with a tendency towards age-dependent increase. Latent tumors were first detected in the 30s group (5.6\%), and slowly increased thereafter.
CONCLUSIONS
There was an age-dependent trend towards prostate glandular dilation and prostate enlargement with inflammation. It was demonstrated that tumor and hyperplasia have a long natural history, usually starting in the fourth decade of life, accompanied by dynamic changes with age in glandular tissue composition as well as cell proliferation activity. © 2005 Wiley-Liss, Inc.},
	language = {en},
	number = {4},
	urldate = {2016-04-21},
	journal = {The Prostate},
	author = {Fujikawa, Shinji and Matsuura, Hiroshi and Kanai, Masahiro and Fumino, Miki and Ishii, Kenichiro and Arima, Kiminobu and Shiraishi, Taizo and Sugimura, Yoshiki},
	month = dec,
	year = {2005},
	keywords = {benign prostatic hyperplasia, morphometric analysis, natural history, PROSTATE cancer},
	pages = {355--364},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZCH7E4ZZ/Fujikawa et al. - 2005 - Natural history of human prostate gland Morphomet.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UXBCXDPD/abstract.html:text/html}
}

@article{kroemer_natural_2015,
	title = {Natural and therapy-induced immunosurveillance in breast cancer},
	volume = {21},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1078-8956},
	url = {http://www.nature.com/nm/journal/v21/n10/full/nm.3944.html},
	doi = {10.1038/nm.3944},
	abstract = {The immunosurveillance theory postulates that tumors evolve and progress in an uncontrolled fashion only when anticancer immune responses fail. Natural immunosurveillance clearly influences human breast cancer (BC) progression because the prognosis of BC patients is dictated by the density, composition and activity of the tumor immune infiltrate at diagnosis. Moreover, chemotherapeutic and radiotherapeutic regimens commonly employed for the treatment of BC affect the tumor immune infiltrate, and accumulating data suggest that the clinical efficacy of these treatments is largely determined by T cell–dependent tumor-specific immune responses. In addition, the mechanism of action of targeted anticancer therapeutics, such as the erb-b2 receptor tyrosine kinase 2 (ERBB2)-targeting agent trastuzumab, involves the innate and adaptive arms of the immune system. In this Review, we discuss these findings as well as preliminary evidence indicating that immunotherapy constitutes a promising option for the treatment of BC. Moreover, we point out that the successful implementation of immunotherapy to BC management requires the optimization of current immunotherapeutic regimens and the identification of immunological biomarkers that enable improved risk stratification and the design of personalized, dynamic treatment plans.},
	language = {en},
	number = {10},
	urldate = {2016-06-23},
	journal = {Nature Medicine},
	author = {Kroemer, Guido and Senovilla, Laura and Galluzzi, Lorenzo and André, Fabrice and Zitvogel, Laurence},
	month = oct,
	year = {2015},
	keywords = {BREAST cancer, Immunosurveillance},
	pages = {1128--1138},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3IKPGCNA/Kroemer et al. - 2015 - Natural and therapy-induced immunosurveillance in .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MVS5BRRD/nm.3944.html:text/html}
}

@misc{_combination_????,
	type = {{WebContent}},
	title = {Combination {Products}},
	url = {http://www.fda.gov/CombinationProducts/},
	language = {en},
	urldate = {2015-11-23},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2JH8MCIM/CombinationProducts.html:text/html}
}

@misc{_health_????,
	title = {Health {Policy} {Advisory} {Committee} on {Technology} - {Home} {Page}},
	url = {https://www.health.qld.gov.au/healthpact/},
	urldate = {2016-07-04},
	file = {Health Policy Advisory Committee on Technology - Home Page:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/R5RXQ3HH/healthpact.html:text/html}
}

@misc{_draq5_????,
	title = {{DRAQ}5 {Fluorescent} {Probe} {Solution} (5 {mM}) - {Thermo} {Fisher} {Scientific}},
	url = {https://www.thermofisher.com/order/catalog/product/62251},
	urldate = {2016-06-29},
	file = {DRAQ5 Fluorescent Probe Solution (5 mM) - Thermo Fisher Scientific:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4MHCE26B/62251.html:text/html}
}

@article{haloua_nationwide_2016,
	title = {A nationwide pathology study on surgical margins and excision volumes after breast-conserving surgery: {There} is still much to be gained},
	volume = {25},
	issn = {09609776},
	shorttitle = {A nationwide pathology study on surgical margins and excision volumes after breast-conserving surgery},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0960977615002532},
	doi = {10.1016/j.breast.2015.11.003},
	language = {en},
	urldate = {2016-07-04},
	journal = {The Breast},
	author = {Haloua, M.H. and Volders, J.H. and Krekel, N.M.A. and Barbé, E. and Sietses, C. and Jóźwiak, K. and Meijer, S. and van den Tol, M.P.},
	month = feb,
	year = {2016},
	pages = {14--21},
	file = {fgd.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HJDETZ3K/fgd.pdf:application/pdf}
}

@article{dan_dmd-based_2013,
	title = {{DMD}-based {LED}-illumination {Super}-resolution and optical sectioning microscopy},
	volume = {3},
	issn = {2045-2322},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552285/},
	doi = {10.1038/srep01116},
	abstract = {Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×107 pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.},
	urldate = {2016-07-08},
	journal = {Scientific Reports},
	author = {Dan, Dan and Lei, Ming and Yao, Baoli and Wang, Wen and Winterhalder, Martin and Zumbusch, Andreas and Qi, Yujiao and Xia, Liang and Yan, Shaohui and Yang, Yanlong and Gao, Peng and Ye, Tong and Zhao, Wei},
	month = jan,
	year = {2013},
	pmid = {23346373},
	pmcid = {PMC3552285},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RBXU98G8/Dan et al. - 2013 - DMD-based LED-illumination Super-resolution and op.pdf:application/pdf}
}

@article{njoh_spectral_2006,
	title = {Spectral analysis of the {DNA} targeting bisalkylaminoanthraquinone {DRAQ}5 in intact living cells},
	volume = {69},
	issn = {1552-4922},
	doi = {10.1002/cyto.a.20308},
	abstract = {BACKGROUND: We report on the potential DNA binding modes and spectral characteristics of the cell-permeant far red fluorescent DNA dye, DRAQ5, in solution and bound within intact cells. Our aim was to determine the constraints for its use in flow cytometry and bioimaging.
METHODS: Solution characteristics and quantum yields were determined by spectroscopy. DRAQ5 binding to nuclear DNA was analyzed using fluorescence quenching of Hoechst 33342 dye, emission profiling by flow cytometry, and spectral confocal laser scanning microscopy of the complex DRAQ5 emission spectrum. Cell cycle profiling utilized an EGFP-cyclin B1 reporter as an independent marker of cell age. Molecular modeling was used to explore the modes of DNA binding.
RESULTS: DRAQ5 showed a low quantum yield in solution and a spectral shift upon DNA binding, but no significant fluorescence enhancement. DRAQ5 caused a reduction in the fluorescence intensity of Hoechst 33342 in live cells prelabeled with the UV excitable dye, consistent with molecular modeling that suggests AT preference and an engagement of the minor groove. In vivo spectral analysis of DRAQ5 demonstrated shifts to longer wavelengths upon binding with DNA. Analysis of spectral windows of the dual emission peaks at 681 and 707 nm in cells showed that cell cycle compartment recognition was independent of the far red-near IR emission wavelengths monitored.
CONCLUSIONS: The study provides new clues to modes of DNA binding of the modified anthraquinone molecule in vivo, and its AT base-pair selectivity. The combination of low quantum yield but high DNA affinity explains the favorable signal-to-noise profile of DRAQ5-nuclear fluorescence. The robust nature of cell cycle reporting using DRAQ5, even when restricted spectral windows are selected, facilitates the analysis of encroaching spectral emissions from other fluorescent reporters, including GFP-tagged proteins.},
	language = {eng},
	number = {8},
	journal = {Cytometry. Part A: The Journal of the International Society for Analytical Cytology},
	author = {Njoh, Kerenza L. and Patterson, Laurence H. and Zloh, Mire and Wiltshire, Marie and Fisher, Janet and Chappell, Sally and Ameer-Beg, Simon and Bai, Yanhong and Matthews, Daniel and Errington, Rachel J. and Smith, Paul J.},
	month = aug,
	year = {2006},
	pmid = {16969814},
	keywords = {Anthraquinones, Benzimidazoles, Bone Neoplasms, Cell Cycle, Cell Line, Tumor, Cyclin B, Cyclin B1, DNA-Binding Proteins, DNA, Neoplasm, Flow cytometry, Fluorescent Dyes, Humans, Image Cytometry, Ligands, Microscopy, Confocal, Nitrogen Oxides, Osteosarcoma, Spectrometry, Fluorescence, Spectrum Analysis},
	pages = {805--814}
}

@article{boonin-vail_defense_1997,
	title = {A defense of `{A} {Defense} of {Abortion}': {On} the responsibility objection to {Thomson}'s argument},
	volume = {107},
	issn = {00141704},
	shorttitle = {A defense of `{A} {Defense} of {Abortion}'},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=rlh&AN=9707151148&site=ehost-live&scope=site},
	abstract = {Defends Judith Jarvis Thomson's argument for abortion known as Responsibility Objection.  1971 article `A Defense of Abortion,' by Thomson; Thomson's premise on the impermissibility of abortion; Analogy of pregnancy to a woman plugged into a violinist; Argument for abortion establishing permissibility only in rape cases; Versions of Responsibility Objection.},
	number = {2},
	urldate = {2016-05-07},
	journal = {Ethics},
	author = {Boonin-Vail, David},
	month = jan,
	year = {1997},
	keywords = {ABORTION -- Moral \& ethical aspects, THOMSON, Judith},
	pages = {286},
	file = {abortion.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6DM97NG9/6DM97NG9.pdf:application/pdf}
}

@article{huston_influence_2006,
	series = {{PAPERS} {FROM} {THE} {AMERICAN} {SOCIETY} {OF} {BREAST} {SURGEONS}7th {Annual} {Meeting}},
	title = {The influence of additional surgical margins on the total specimen volume excised and the reoperative rate after breast-conserving surgery},
	volume = {192},
	issn = {0002-9610},
	url = {http://www.sciencedirect.com/science/article/pii/S0002961006004302},
	doi = {10.1016/j.amjsurg.2006.06.021},
	abstract = {Background
It is unclear whether the additional removal of breast tissue during breast-conserving therapy (BCT) for breast cancer beyond the standard lumpectomy reduces the incidence of inadequate microscopic margins found at pathological examination and subsequent reoperation. This study compares the reoperative rates after initial BCT in 3 groups of patients who underwent lumpectomy with complete resection of 4 to 6 additional margins, lumpectomy with selective resection of 1 to 3 additional margins, or standard lumpectomy.
Methods
Retrospective data were reviewed from 171 selected cases of BCT, from May 2000 to February 2006. Forty-five cases involved lumpectomy with complete resection of 4 to 6 additional margins; 77 involved lumpectomy with selective resection of 1 to 3 additional margins, whereas 49 involved standard lumpectomy. All samples underwent pathologic analysis of inked resection margins by permanent section. The 3 groups were compared for patient demographics, tumor size and histologic subtype, tumor stage, margin status, excised specimen volume, and eventual subsequent reoperation. Adequate surgical margin was defined as any negative margin greater than 2 mm.
Results
The group with complete resection of 4 to 6 additional margins had a subsequent reoperation rate of 17.7\%, whereas the group with selective resection of 1 to 3 additional margins and the standard lumpectomy group had a subsequent reoperation rate of 32.5\% and 38.7\%, respectively, because of inadequate margins. The mean total excised specimen volume in the 3 groups was 129.19, 46.04, and 37.44 cm3, respectively.
Conclusions
The complete resection of 4 to 6 additional margins during the initial BCT resulted in the lowest subsequent reoperation rate, and the largest total volume specimen excised among the 3 techniques studied.},
	number = {4},
	urldate = {2016-06-30},
	journal = {The American Journal of Surgery},
	author = {Huston, Tara L. and Pigalarga, Rodolfo and Osborne, Michael P. and Tousimis, Eleni},
	month = oct,
	year = {2006},
	keywords = {BREAST cancer, breast-conserving surgery, Margins, Re-excision rate, Specimen volume},
	pages = {509--512},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XZC4QJZM/S0002961006004302.html:text/html}
}

@article{lin_tendon_2006,
	title = {Tendon healing in interleukin-4 and interleukin-6 knockout mice},
	volume = {39},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S0021929004005494},
	doi = {10.1016/j.jbiomech.2004.11.009},
	abstract = {Cytokines have been shown to play an important role in tendon and ligament healing by regulating cellular differentiation and activity. The majority of studies that have investigated the role of cytokines in tendon and ligament healing have added them to injured tissue and assessed their effect. Because the efficacy of exogenously applying cytokines is dependent upon many factors such as the correct dosage, timing, and frequency, conflicting results are often reported. To avoid these factors, this study used transgenic mice with knockouts of interleukin-4 (IL4 −/−) and interleukin-6 (IL6 −/−) to investigate their role in tendon healing. Because of the reported roles of both of these cytokines in inflammation and fibroplasia, it was hypothesized that the order of organizational, geometric, and mechanical properties would be (greatest to least) injured IL6 −/−, injured control, and injured IL4 −/− mice. In addition, it was hypothesized that specific cytokines would be upregulated in each knockout group, but not compensate for the lack of IL-4 or IL-6. Mechanical and organizational properties of injured tendons from IL6 −/− mice were inferior to that of control and IL4 −/− mice despite the upregulation of the pro-inflammatory cytokine TNF-α. Temporal levels of IL-10 and IL-13 in the IL4 −/− mice resulted in comparable and even superior properties when compared to CTL mice. This study shows that IL-6 could not be compensated for and plays an important role in tendon healing. This study also supports the use of this animal model to further investigate tendon healing.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Lin, Tony W. and Cardenas, Luis and Glaser, David L. and Soslowsky, Louis J.},
	year = {2006},
	keywords = {Cytokines, Interleukins, Knockout mice, Tendon, Tendon healing, Transgenic mice},
	pages = {61--69},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DH24DTWS/Lin et al. - 2006 - Tendon healing in interleukin-4 and interleukin-6 .pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Z3Z3JB8D/S0021929004005494.html:text/html}
}

@misc{_jurisdictional_????,
	type = {{WebContent}},
	title = {Jurisdictional {Updates} - {Jurisdictional} {Update}: {Drug}-{Eluting} {Cardiovascular} {Stents}},
	shorttitle = {Jurisdictional {Updates} - {Jurisdictional} {Update}},
	url = {http://www.fda.gov/CombinationProducts/JurisdictionalInformation/JurisdictionalUpdates/ucm106552.htm},
	language = {en},
	urldate = {2015-11-23},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/V5A49PU2/ucm106552.html:text/html}
}

@book{ibanez_itk_2005,
	address = {New York, NY},
	edition = {2. ed},
	title = {The {ITK} software guide: updated for {ITK} version 2.4 ; [the insight segmentation and registration toolkit ; covers installing and programming with {ITK}, includes {C}++ source code examples and data, shows how to use {ITK} in your own application]},
	isbn = {978-1-930934-15-3},
	shorttitle = {The {ITK} software guide},
	language = {eng},
	publisher = {Kitware},
	editor = {Ibáñez, Luis},
	year = {2005},
	note = {OCLC: 255488656},
	keywords = {C},
	file = {saahpc09.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GUJIRXG9/saahpc09.pdf:application/pdf}
}

@article{salvadori_reoperation_1999,
	title = {Reoperation for locally recurrent breast cancer in patients previously treated with conservative surgery},
	volume = {86},
	copyright = {© 1999 British Journal of Surgery Society Ltd},
	issn = {1365-2168},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1046/j.1365-2168.1999.00961.x/abstract},
	doi = {10.1046/j.1365-2168.1999.00961.x},
	abstract = {Background:
This study aimed to analyse the possibility of surgical rescue of intrabreast tumour recurrence (IBTR) following conservative operation for breast cancer, i.e. quadrantectomy, axillary dissection and radiotherapy.
Methods:
Of 2544 patients treated with this approach, 209 presented with an IBTR as the first and only sign of relapse. Some 197 patients were considered suitable for further surgery; 12 were inoperable. Six patients declined operation.
Results:
Reoperative surgery was total mastectomy in 134 patients (70 per cent) and further local resection in 57 (30 per cent). Median follow-up after second surgery was 73 (range 1–192) months. The overall survival probability at 60 months was 70 per cent after mastectomy and 85 per cent following further local excision. There was no difference in disease-free survival between the two operative groups. Second IBTR was more common at 5 years in the re-excision group (19 versus 4 per cent).
Conclusion:
Since the type of surgery did not seem to affect survival, breast conservation can be considered in selected patients with IBTR. © 1999 British Journal of Surgery Society Ltd},
	language = {en},
	number = {1},
	urldate = {2016-06-30},
	journal = {British Journal of Surgery},
	author = {Salvadori, B. and Marubini, E. and Miceli, R. and Conti, A. R. and Cusumano, F. and Andreola, S. and Zucali, R. and Veronesi, U.},
	month = jan,
	year = {1999},
	pages = {84--87},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AGFQUJQP/Salvadori et al. - 1999 - Reoperation for locally recurrent breast cancer in.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JGSWKUWM/abstract.html:text/html}
}

@article{demir_automated_2005,
	title = {Automated cancer diagnosis based on histopathological images: a systematic survey},
	shorttitle = {Automated cancer diagnosis based on histopathological images},
	url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.61.1199&rep=rep1&type=pdf},
	urldate = {2016-07-04},
	journal = {Rensselaer Polytechnic Institute, Tech. Rep},
	author = {Demir, Cigdem and Yener, Bülent},
	year = {2005},
	file = {05-09.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RS4SIKW9/05-09.pdf:application/pdf}
}

@article{thomopoulos_localized_2002,
	title = {The localized expression of extracellular matrix components in healing tendon insertion sites: an in situ hybridization study},
	volume = {20},
	copyright = {Copyright © 2002 Orthopaedic Research Society},
	issn = {1554-527X},
	shorttitle = {The localized expression of extracellular matrix components in healing tendon insertion sites},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1016/S0736-0266(01)00144-9/abstract},
	doi = {10.1016/S0736-0266(01)00144-9},
	abstract = {The localized expression of a number of extracellular matrix genes was evaluated over time in a novel rat rotator cuff injury model. The supraspinatus tendons of rats were severed at the bony insertion and repaired surgically. The healing response was evaluated at 1, 2, 4, and 8 weeks post-injury using histologic and in situ hybridization techniques. Expression patterns of collagens (I, II, III, IX, X, XII), proteoglycans (decorin, aggrecan, versican, biglycan, fibromodulin), and other extracellular matrix proteins (elastin, osteocalcin, alkaline phosphatase) were evaluated at the healing tendon to bone insertion site. Histologic results indicate a poor healing response to the injury, with only partial recreation of the insertion site by 8 weeks. In situ hybridization results indicate a specific pattern of genes expressed in each zone of the insertion site (i.e., tendon, fibrocartilage, mineralized cartilage, bone). Overall, expression of collagen types I and XII, aggrecan, and biglycan was increased, while expression of collagen type X and decorin was decreased. Expression of collagen type I, collagen type XII, and biglycan decreased over time, but remained above normal at 8 weeks. Results indicate that the rat supraspinatus tendon is ineffective in recreating the original insertion site, even at 8 weeks post-injury, in the absence of biological or biomechanical enhancements. © 2002 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved.},
	language = {en},
	number = {3},
	urldate = {2014-11-03},
	journal = {Journal of Orthopaedic Research},
	author = {Thomopoulos, S. and Hattersley, G. and Rosen, V. and Mertens, M. and Galatz, L. and Williams, G. R. and Soslowsky, L. J.},
	month = may,
	year = {2002},
	pages = {454--463},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/48H3MJN4/Thomopoulos et al. - 2002 - The localized expression of extracellular matrix c.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4TK3UZQU/abstract\;jsessionid=1F78527C017CDB9B57D2B3C34E9210B8.html:text/html}
}

@article{yang_survey_2008,
	title = {A survey of shape feature extraction techniques},
	url = {https://hal.archives-ouvertes.fr/hal-00446037/},
	urldate = {2016-07-02},
	journal = {Pattern recognition},
	author = {Yang, Mingqiang and Kpalma, Kidiyo and Ronsin, Joseph},
	year = {2008},
	pages = {43--90},
	file = {ARS-Journal-SurveyPatternRecognition.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TNJXX7PJ/ARS-Journal-SurveyPatternRecognition.pdf:application/pdf}
}

@article{narod_breast_2012,
	title = {Breast cancer in young women},
	volume = {9},
	copyright = {© 2012 Nature Publishing Group},
	issn = {1759-4774},
	url = {http://www.nature.com/nrclinonc/journal/v9/n8/full/nrclinonc.2012.102.html},
	doi = {10.1038/nrclinonc.2012.102},
	abstract = {About one in 300 women will be diagnosed with breast cancer before the age of 40. Advances in screening have not had an impact on mortality in women who are too young to be candidates for screening. Risk factors for early breast cancer include a lean body habitus and recent use of an oral contraceptive. Breast cancers in very young women are typically aggressive, in part owing to the over-representation of high-grade, triple-negative tumours, but young age is an independent negative predictor of cancer-specific survival. Very early age-of-onset also correlates strongly with the risk of local recurrence and with the odds of contralateral breast cancer. Given the high risks of local and distant recurrence in young women with invasive breast cancer, most (if not all) young patients are candidates for chemotherapy. It is hoped that by increasing breast cancer awareness, the proportion of invasive breast cancers that are diagnosed at 2.0 cm or smaller will increase and that this will lead to a reduction in mortality.},
	language = {en},
	number = {8},
	urldate = {2016-06-23},
	journal = {Nature Reviews Clinical Oncology},
	author = {Narod, Steven A.},
	month = aug,
	year = {2012},
	pages = {460--470},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KGTMN8U7/Narod - 2012 - Breast cancer in young women.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UQGDH45R/nrclinonc.2012.102.html:text/html}
}

@misc{_types_????,
	title = {Types of breast cancers},
	url = {http://www.cancer.org/cancer/breastcancer/detailedguide/breast-cancer-breast-cancer-types},
	urldate = {2016-06-23},
	file = {Types of breast cancers:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GZ5Q5ZJR/breast-cancer-breast-cancer-types.html:text/html}
}

@article{harryman_cohesive_2016,
	title = {The {Cohesive} {Metastasis} {Phenotype} in {Human} {Prostate} {Cancer}},
	volume = {1866},
	issn = {0304-419X},
	url = {http://www.sciencedirect.com/science/article/pii/S0304419X16300671},
	doi = {10.1016/j.bbcan.2016.09.005},
	abstract = {A critical barrier for the successful prevention and treatment of recurrent prostate cancer is detection and eradication of metastatic and therapy-resistant disease. Despite the fall in diagnoses and mortality, the reported incidence of metastatic disease has increased 72\% since 2004. Prostate cancer arises in cohesive groups as intraepithelial neoplasia, migrates through muscle and leaves the gland via perineural invasion for hematogenous dissemination. Current technological advances have shown cohesive-clusters of tumor (also known as microemboli) within the circulation. Circulating tumor cell (CTC) profiles are indicative of disseminated prostate cancer, and disseminated tumor cells (DTC) are found in cohesive-clusters, a phenotypic characteristic of both radiation- and drug-resistant tumors. Recent reports in cell biology and informatics, coupled with mass spectrometry, indicate that the integrin adhesome network provides an explanation for the biophysical ability of cohesive-clusters of tumor cells to invade thorough muscle and nerve microenvironments while maintaining adhesion-dependent therapeutic resistance. Targeting cohesive-clusters takes advantage of the known ability of extracellular matrix (ECM) adhesion to promote tumor cell survival and represents an approach that has the potential to avoid the progression to drug- and radiotherapy-resistance. In the following review we will examine the evidence for development and dissemination of cohesive-clusters in metastatic prostate cancer.},
	number = {2},
	urldate = {2016-11-28},
	journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
	author = {Harryman, William L. and Hinton, James P. and Rubenstein, Cynthia P. and Singh, Parminder and Nagle, Raymond B. and Parker, Sarah J. and Knudsen, Beatrice S. and Cress, Anne E.},
	month = dec,
	year = {2016},
	keywords = {adhesome, circulating tumor cells, cohesive-clusters, integrins, metastasis, PROSTATE cancer},
	pages = {221--231},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JDCIXZXJ/JDCIXZXJ.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S2B6C2PM/S0304419X16300671.html:text/html}
}

@article{fiolka_time-lapse_2012,
	title = {Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination},
	volume = {109},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325651/},
	doi = {10.1073/pnas.1119262109},
	abstract = {Previous implementations of structured-illumination microscopy (SIM) were slow or designed for one-color excitation, sacrificing two unique and extremely beneficial aspects of light microscopy: live-cell imaging in multiple colors. This is especially unfortunate because, among the resolution-extending techniques, SIM is an attractive choice for live-cell imaging; it requires no special fluorophores or high light intensities to achieve twice diffraction-limited resolution in three dimensions. Furthermore, its wide-field nature makes it light-efficient and decouples the acquisition speed from the size of the lateral field of view, meaning that high frame rates over large volumes are possible. Here, we report a previously undescribed SIM setup that is fast enough to record 3D two-color datasets of living whole cells. Using rapidly programmable liquid crystal devices and a flexible 2D grid pattern algorithm to switch between excitation wavelengths quickly, we show volume rates as high as 4 s in one color and 8.5 s in two colors over tens of time points. To demonstrate the capabilities of our microscope, we image a variety of biological structures, including mitochondria, clathrin-coated vesicles, and the actin cytoskeleton, in either HeLa cells or cultured neurons.},
	number = {14},
	urldate = {2016-06-25},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Fiolka, Reto and Shao, Lin and Rego, E. Hesper and Davidson, Michael W. and Gustafsson, Mats G. L.},
	month = apr,
	year = {2012},
	pmid = {22431626},
	pmcid = {PMC3325651},
	pages = {5311--5315},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9KUI6ECQ/Fiolka et al. - 2012 - Time-lapse two-color 3D imaging of live cells with.pdf:application/pdf}
}

@article{johantgen_treating_1995,
	title = {Treating early-stage breast cancer: {Hospital} characteristics associated with breast-conserving surgery},
	volume = {85},
	copyright = {Copyright American Public Health Association Oct 1995},
	issn = {00900036},
	shorttitle = {Treating early-stage breast cancer},
	url = {http://search.proquest.com.libproxy.tulane.edu:2048/docview/215107814/abstract/2611BCF4DF024E32PQ/1},
	abstract = {Despite growing acceptance of the fact that women with early-stage breast cancer have similar outcomes with lumpectomy plus radiation as with mastectomy, many studies have revealed the uneven adoption of such breast-conserving surgery. Discharge data from the Hospital Cost and Utilization Project, representing multiple payers, locations, and hospital types, demonstrate increasing trends in breast-conserving surgery as a proportion of breast cancer surgeries from 1981 to 1987. Women with axillary node involvement were less likely to have a lumpectomy, even though consensus recommendations do not preclude this form of treatment when local metastases are present. Non-White race, urban hospital location, and hospital teaching were associated with an increased likelihood of having breast-conserving surgery.},
	language = {English},
	number = {10},
	urldate = {2016-07-04},
	journal = {American Journal of Public Health},
	author = {Johantgen, Mary E. and Coffey, Rosanna M. and Harris, Robert and Levy, Helen and Clinton, J. Jarrett},
	month = oct,
	year = {1995},
	keywords = {BREAST cancer, Breasts, Hospitals, Medical Sciences, Public Health And Safety, Surgery},
	pages = {1432--4},
	file = {Full Text Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/I7A249QE/1.html:text/html}
}

@misc{_rfd_????,
	type = {{WebContent}},
	title = {{RFD} {Process}},
	url = {http://www.fda.gov/CombinationProducts/RFDProcess/},
	language = {en},
	urldate = {2015-11-22},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NMGAFJ4I/RFDProcess.html:text/html}
}

@article{karthikeyan_concept_2008,
	title = {The concept of ocular inserts as drug delivery systems: {An} overview},
	volume = {2},
	issn = {09738398},
	shorttitle = {The concept of ocular inserts as drug delivery systems},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=37336005&site=ehost-live&scope=site},
	abstract = {Ocular diseases require localized administration of drugs to the tissues around the ocular cavity. The existing ocular drug delivery systems are fairly primitive and inefficient. However, the design of ocular system is undergoing gradual transition from an empirical to rational basis. In the recent years, there has been explosion of interest in the polymer based delivery devices. Utilization of the principles of controlled release as embodied by ocular inserts offers an attractive approach to the problem of prolonging pre-corneal drug residence times. In the present update, the authors discuss the basic concept of ocular inserts as drug delivery system and examine the few inserts, which are available in the market or are being developed by pharmaceutical companies for drug delivery. The article discusses soluble ocular drug insert, Ocusert, Collagen Shields, Ocufit, Minidisc and new ophthalmic delivery system with special attention to biological/clinical performances, and potential for future applications and developments.},
	number = {4},
	urldate = {2015-11-22},
	journal = {Asian Journal of Pharmaceutics},
	author = {Karthikeyan, Deivasigamani and Bhowmick, Mithun and Pandey, Vijay Prakesh and Nandhakumar, Jothivel and Sengottuvelu, Singaravel and Sonkar, Sandeep and Sivakumar, Thangavel},
	month = oct,
	year = {2008},
	keywords = {ADMINISTRATION of drugs, Basic concept, collagen shields, Drug Delivery Systems, EYE -- Diseases, MEDICAL equipment, minidisc, new ophthalmic delivery system, ocufit, ocular diseases, ocusert, POLYMERS, soluble ocular drug insert, TISSUES},
	pages = {192--200}
}

@article{derenzini_nucleolar_2000,
	title = {Nucleolar size indicates the rapidity of cell proliferation in cancer tissues},
	volume = {191},
	copyright = {Copyright © 2000 John Wiley \& Sons, Ltd.},
	issn = {1096-9896},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-9896(200006)191:2<181::AID-PATH607>3.0.CO;2-V/abstract},
	doi = {10.1002/(SICI)1096-9896(200006)191:2<181::AID-PATH607>3.0.CO;2-V},
	abstract = {In order to define the importance of the nucleolus in tumour pathology, the relationship between nucleolar size and function and tumour mass growth rate was studied in vivo. Ten established human cancer cell lines from colon carcinomas and neuroblastomas were inoculated subcutaneously in athymic mice and the doubling time (DT) of the xenograft tumour mass was calculated. The tumour DTs ranged from 3.2 to 15.7 days. Nucleolar size was evaluated in sections from formalin-fixed and paraffin-embedded tumour samples after silver staining for AgNOR proteins, using a specific image analysis system. The nucleolar area values were inversely related to the xenograft tumour mass DTs (r=−0.90; p{\textless}0.001). Nucleolar functional activity was also evaluated using rapid, intermediate, and slow growing tumours (one each). The values of RNA polymerase I activity measured in vitro were strongly related to the corresponding tumour DTs (r=−0.99; p=0.03). The labelling indices (LIs) of three proliferation markers, MIB1, PCNA, and bromodeoxyuridine (BrdU), were also evaluated. As revealed by the MIB1 and PCNA LIs, almost all the cells of the xenograft tumours were cycling (86.6±5.6 SD and 95.5±2.0 SD, respectively). Neither the MIB1, PCNA or BrdU LIs were related to the xenograft tumour mass DT, showing that the different growth rates of tumour xenografts were not due to different growth fractions, but were mainly related to different cell proliferation rates. The present data demonstrate that the size and function of the nucleolus are related to the cell proliferation rate of cancer tissue. Evaluation of nucleolar size after silver staining of AgNOR proteins represents a unique parameter for the histological assessment of rapidity of cell proliferation in tumour lesions. Copyright © 2000 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {2},
	urldate = {2016-06-26},
	journal = {The Journal of Pathology},
	author = {Derenzini, Massimo and Trerè, Davide and Pession, Annalisa and Govoni, Marzia and Sirri, Valentina and Chieco, Pasquale},
	month = jun,
	year = {2000},
	keywords = {AgNOR proteins, cancer cells, cell proliferation rate, nucleolus, quantitation, ribosome biogenesis},
	pages = {181--186},
	file = {path.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZGT3CT5G/path.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P44V4XIB/abstract.html:text/html}
}

@article{gustafsson_three-dimensional_2008,
	title = {Three-{Dimensional} {Resolution} {Doubling} in {Wide}-{Field} {Fluorescence} {Microscopy} by {Structured} {Illumination}},
	volume = {94},
	issn = {0006-3495},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397368/},
	doi = {10.1529/biophysj.107.120345},
	abstract = {Structured illumination microscopy is a method that can increase the spatial resolution of wide-field fluorescence microscopy beyond its classical limit by using spatially structured illumination light. Here we describe how this method can be applied in three dimensions to double the axial as well as the lateral resolution, with true optical sectioning. A grating is used to generate three mutually coherent light beams, which interfere in the specimen to form an illumination pattern that varies both laterally and axially. The spatially structured excitation intensity causes normally unreachable high-resolution information to become encoded into the observed images through spatial frequency mixing. This new information is computationally extracted and used to generate a three-dimensional reconstruction with twice as high resolution, in all three dimensions, as is possible in a conventional wide-field microscope. The method has been demonstrated on both test objects and biological specimens, and has produced the first light microscopy images of the synaptonemal complex in which the lateral elements are clearly resolved.},
	number = {12},
	urldate = {2016-06-29},
	journal = {Biophysical Journal},
	author = {Gustafsson, Mats G. L. and Shao, Lin and Carlton, Peter M. and Wang, C. J. Rachel and Golubovskaya, Inna N. and Cande, W. Zacheus and Agard, David A. and Sedat, John W.},
	month = jun,
	year = {2008},
	pmid = {18326650},
	pmcid = {PMC2397368},
	pages = {4957--4970},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F5VWF2ET/Gustafsson et al. - 2008 - Three-Dimensional Resolution Doubling in Wide-Fiel.pdf:application/pdf}
}

@article{veta_assessment_2015,
	title = {Assessment of algorithms for mitosis detection in breast cancer histopathology images},
	volume = {20},
	issn = {1361-8415},
	url = {http://www.sciencedirect.com/science/article/pii/S1361841514001807},
	doi = {10.1016/j.media.2014.11.010},
	abstract = {The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues.

In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists.},
	number = {1},
	urldate = {2016-06-30},
	journal = {Medical Image Analysis},
	author = {Veta, Mitko and van Diest, Paul J. and Willems, Stefan M. and Wang, Haibo and Madabhushi, Anant and Cruz-Roa, Angel and Gonzalez, Fabio and Larsen, Anders B. L. and Vestergaard, Jacob S. and Dahl, Anders B. and Cireşan, Dan C. and Schmidhuber, Jürgen and Giusti, Alessandro and Gambardella, Luca M. and Tek, F. Boray and Walter, Thomas and Wang, Ching-Wei and Kondo, Satoshi and Matuszewski, Bogdan J. and Precioso, Frederic and Snell, Violet and Kittler, Josef and de Campos, Teofilo E. and Khan, Adnan M. and Rajpoot, Nasir M. and Arkoumani, Evdokia and Lacle, Miangela M. and Viergever, Max A. and Pluim, Josien P. W.},
	month = feb,
	year = {2015},
	keywords = {BREAST cancer, Cancer grading, digital pathology, Mitosis detection, whole slide imaging},
	pages = {237--248},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/I7X3Q3NG/Veta et al. - 2015 - Assessment of algorithms for mitosis detection in .pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8DWRM7JH/S1361841514001807.html:text/html}
}

@article{curd_construction_2015,
	series = {Super-resolution {Light} {Microscopy}},
	title = {Construction of an instant structured illumination microscope},
	volume = {88},
	issn = {1046-2023},
	url = {http://www.sciencedirect.com/science/article/pii/S1046202315300293},
	doi = {10.1016/j.ymeth.2015.07.012},
	abstract = {A challenge in biological imaging is to capture high-resolution images at fast frame rates in live cells. The “instant structured illumination microscope” (iSIM) is a system designed for this purpose. Similarly to standard structured illumination microscopy (SIM), an iSIM provides a twofold improvement over widefield microscopy, in x, y and z, but also allows much faster image acquisition, with real-time display of super-resolution images.

The assembly of an iSIM is reasonably complex, involving the combination and alignment of many optical components, including three micro-optics arrays (two lenslet arrays and an array of pinholes, all with a pitch of 222 μm) and a double-sided scanning mirror. In addition, a number of electronic components must be correctly controlled. Construction of the system is therefore not trivial, but is highly desirable, particularly for live-cell imaging.

We report, and provide instructions for, the construction of an iSIM, including minor modifications to a previous design in both hardware and software. The final instrument allows us to rapidly acquire fluorescence images at rates faster than 100 fps, with approximately twofold improvement in resolution in both x–y and z; sub-diffractive biological features have an apparent size (full width at half maximum) of 145 nm (lateral) and 320 nm (axial), using a 1.49 NA objective and 488 nm excitation.},
	urldate = {2016-08-26},
	journal = {Methods},
	author = {Curd, Alistair and Cleasby, Alexa and Makowska, Katarzyna and York, Andrew and Shroff, Hari and Peckham, Michelle},
	month = oct,
	year = {2015},
	keywords = {Construction, Fluorescence microscopy, Instant structured illumination microscope, Super-resolution},
	pages = {37--47},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UFEV6P4I/Curd et al. - 2015 - Construction of an instant structured illumination.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/747DXS9M/S1046202315300293.html:text/html}
}

@article{ignatiadis_luminal_2013,
	title = {Luminal breast cancer: from biology to treatment},
	volume = {10},
	copyright = {© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1759-4774},
	shorttitle = {Luminal breast cancer},
	url = {http://www.nature.com/nrclinonc/journal/v10/n9/full/nrclinonc.2013.124.html},
	doi = {10.1038/nrclinonc.2013.124},
	abstract = {Oestrogen receptor (ER)-positive—or luminal—tumours represent around two-thirds of all breast cancers. Luminal breast cancer is a highly heterogeneous disease comprising different histologies, gene-expression profiles and mutational patterns, with very varied clinical courses and responses to systemic treatment. Despite adjuvant endocrine therapy and chemotherapy treatment for patients at high risk of relapse, both early and late relapses still occur, a fact that highlights the unmet medical needs of these patients. Ongoing research aims to identify those patients who can be spared adjuvant chemotherapy and who will benefit from extended adjuvant hormone therapy. This research also aims to explore the role of adjuvant bisphosphonates, to interrogate new agents for targeting minimal residual disease, and to address endocrine resistance. Data from next-generation sequencing studies have given us new insight into the biology of luminal breast cancer and, together with advances in preclinical models and the availability of newer targeted agents, have led to the testing of rationally chosen combination treatments in clinical trials. However, a major challenge will be to make sense of the large amount of patient genomic data that is becoming increasingly available. This analysis will be critical to our understanding how intertumour and intratumour heterogeneity can influence treatment response and resistance.},
	language = {en},
	number = {9},
	urldate = {2016-06-23},
	journal = {Nature Reviews Clinical Oncology},
	author = {Ignatiadis, Michail and Sotiriou, Christos},
	month = sep,
	year = {2013},
	keywords = {BREAST cancer, Drug development, Targeted therapies, Tumour heterogeneity},
	pages = {494--506},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UQQ5FCNQ/Ignatiadis and Sotiriou - 2013 - Luminal breast cancer from biology to treatment.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BG8GINWK/nrclinonc.2013.124.html:text/html}
}

@article{espina_what_2011,
	title = {What is the malignant nature of human ductal carcinoma in situ?},
	volume = {11},
	copyright = {© 2010 Nature Publishing Group},
	issn = {1474-175X},
	url = {http://www.nature.com/nrc/journal/v11/n1/full/nrc2950.html},
	doi = {10.1038/nrc2950},
	abstract = {Invasive, genetically abnormal carcinoma progenitor cells have been propagated from human and mouse breast ductal carcinoma in situ (DCIS) lesions, providing new insights into breast cancer progression. The survival of DCIS cells in the hypoxic, nutrient-deprived intraductal niche could promote genetic instability and the derepression of the invasive phenotype. Understanding potential survival mechanisms, such as autophagy, that might be functioning in DCIS lesions provides strategies for arresting invasion at the pre-malignant stage. A new, open trial of neoadjuvant therapy for patients with DCIS constitutes a model for testing investigational agents that target malignant progenitor cells in the intraductal niche.},
	language = {en},
	number = {1},
	urldate = {2016-06-23},
	journal = {Nature Reviews Cancer},
	author = {Espina, Virginia and Liotta, Lance A.},
	month = jan,
	year = {2011},
	pages = {68--75},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8FSBVMCV/Espina and Liotta - 2011 - What is the malignant nature of human ductal carci.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F6VEIT6W/nrc2950.html:text/html}
}

@misc{_kernel_????,
	title = {The {Kernel} {Trick}},
	url = {http://www.eric-kim.net/eric-kim-net/posts/1/kernel_trick.html},
	urldate = {2016-07-11},
	file = {The Kernel Trick:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U68IDI3N/kernel_trick.html:text/html}
}

@article{dowarah_title_????,
	title = {{TITLE} {OF} {THE} {STUDY}: {Physiotherapy} services and its impact on the {Quality} of life in {Breast} {Cancer} patients},
	shorttitle = {{TITLE} {OF} {THE} {STUDY}},
	url = {http://www.academia.edu/download/34797147/Braest_cancer.docx},
	urldate = {2016-07-04},
	author = {Dowarah, Bhatri Pratim},
	file = {acspc-042725.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NGRAAMH3/acspc-042725.pdf:application/pdf}
}

@article{izu_dysfunctional_2011,
	title = {Dysfunctional tendon collagen fibrillogenesis in collagen {VI} null mice},
	volume = {30},
	issn = {0945-053X},
	url = {http://www.sciencedirect.com/science/article/pii/S0945053X10001514},
	doi = {10.1016/j.matbio.2010.10.001},
	abstract = {Tendons are composed of fibroblasts and collagen fibrils. The fibrils are organized uniaxially and grouped together into fibers. Collagen VI is a non-fibrillar collagen expressed in developing and adult tendons. Human collagen VI mutations result in muscular dystrophy, joint hyperlaxity and contractures. The purpose of this study is to determine the functional roles of collagen VI in tendon matrix assembly. During tendon development, collagen VI was expressed throughout the extracellular matrix, but enriched around fibroblasts and their processes. To analyze the functional roles of collagen VI a mouse model with a targeted inactivation of Col6a1 gene was utilized. Ultrastructural analysis of Col6a1−/− versus wild type tendons demonstrated disorganized extracellular micro-domains and associated collagen fibers in the Col6a1−/− tendon. In Col6a1−/− tendons, fibril structure and diameter distribution were abnormal compared to wild type controls. The diameter distributions were shifted significantly toward the smaller diameters in Col6a1−/− tendons compared to controls. An analysis of fibril density (number/μm2) demonstrated a {\textasciitilde} 2.5 fold increase in the Col6a1−/− versus wild type tendons. In addition, the fibril arrangement and structure were aberrant in the peri-cellular regions of Col6a1−/− tendons with frequent very large fibrils and twisted fibrils observed restricted to this region. The biomechanical properties were analyzed in mature tendons. A significant decrease in cross-sectional area was observed. The percent relaxation, maximum load, maximum stress, stiffness and modulus were analyzed and Col6a1−/− tendons demonstrated a significant reduction in maximum load and stiffness compared to wild type tendons. An increase in matrix metalloproteinase activity was suggested in the absence of collagen VI. This suggests alterations in tenocyte expression due to disruption of cell–matrix interactions. The changes in expression may result in alterations in the peri-cellular environment. In addition, the absence of collagen VI may alter the sequestering of regulatory molecules such as leucine rich proteoglycans. These changes would result in dysfunctional regulation of tendon fibrillogenesis indirectly mediated by collagen VI.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Matrix Biology},
	author = {Izu, Yayoi and Ansorge, Heather L. and Zhang, Guiyun and Soslowsky, Louis J. and Bonaldo, Paolo and Chu, Mon-Li and Birk, David E.},
	month = jan,
	year = {2011},
	keywords = {Collagen VI, Collagen VI-null mouse, development, Fibrillogenesis, Tendon, Tendon biomechanics},
	pages = {53--61},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5ZGE7469/Izu et al. - 2011 - Dysfunctional tendon collagen fibrillogenesis in c.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/K4HQ5QXX/S0945053X10001514.html:text/html}
}

@article{isaacs_association_2016,
	title = {Association of {Breast} {Conservation} {Surgery} for {Cancer} {With} 90-{Day} {Reoperation} {Rates} in {New} {York} {State}},
	issn = {2168-6254},
	url = {http://archsurg.jamanetwork.com/article.aspx?doi=10.1001/jamasurg.2015.5535},
	doi = {10.1001/jamasurg.2015.5535},
	language = {en},
	urldate = {2016-07-10},
	journal = {JAMA Surgery},
	author = {Isaacs, Abby J. and Gemignani, Mary L. and Pusic, Andrea and Sedrakyan, Art},
	month = feb,
	year = {2016},
	file = {margin-probe.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9CCW2IHI/margin-probe.pdf:application/pdf}
}

@article{niziolek_what_2013,
	title = {What {Does} {Motor} {Efference} {Copy} {Represent}? {Evidence} from {Speech} {Production}},
	volume = {33},
	issn = {0270-6474, 1529-2401},
	shorttitle = {What {Does} {Motor} {Efference} {Copy} {Represent}?},
	url = {http://www.jneurosci.org/content/33/41/16110},
	doi = {10.1523/JNEUROSCI.2137-13.2013},
	abstract = {How precisely does the brain predict the sensory consequences of our actions? Efference copy is thought to reflect the predicted sensation of self-produced motor acts, such as the auditory feedback heard while speaking. Here, we use magnetoencephalographic imaging (MEG-I) in human speakers to demonstrate that efference copy prediction does not track movement variability across repetitions of the same motor task. Specifically, spoken vowels were less accurately predicted when they were less similar to a speaker's median production, even though the prediction is thought to be based on the very motor commands that generate each vowel. Auditory cortical responses to less prototypical speech productions were less suppressed, resembling responses to speech errors, and were correlated with later corrective movement, suggesting that the suppression may be functionally significant for error correction. The failure of the motor system to accurately predict less prototypical speech productions suggests that the efferent-driven suppression does not reflect a sensory prediction, but a sensory goal.},
	language = {en},
	number = {41},
	urldate = {2015-02-20},
	journal = {The Journal of Neuroscience},
	author = {Niziolek, Caroline A. and Nagarajan, Srikantan S. and Houde, John F.},
	month = oct,
	year = {2013},
	pmid = {24107944},
	pages = {16110--16116},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GV3HVTMQ/Niziolek et al. - 2013 - What Does Motor Efference Copy Represent Evidence.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PIDIUHKG/Niziolek et al. - 2013 - What Does Motor Efference Copy Represent Evidence.html:text/html}
}

@article{pannek_nuclear_1999,
	title = {Nuclear shape and nuclear matrix protein composition in prostate and seminal vesicles},
	volume = {54},
	issn = {0090-4295},
	url = {http://www.sciencedirect.com/science/article/pii/S0090429599002757},
	doi = {10.1016/S0090-4295(99)00275-7},
	abstract = {Objectives. The nucleus controls cell function and behavior. The nuclear matrix determines internal nuclear changes. Two-dimensional gel electrophoresis is the reference standard for the analysis of nuclear matrix protein (NMP) composition. Differences in NMP composition should therefore be reflected by changes in nuclear shape. We investigated the differences in NMP composition and nuclear morphometry of the prostate and seminal vesicles. Both tissues are androgen-dependent sex accessory organs with completely different biologic behavior.

Methods. High-resolution two-dimensional gel electrophoresis and silver staining were used to evaluate NMP composition from histologically normal prostate and seminal vesicle epithelial cells. Nuclear morphometry, performed using a computer-assisted image analysis system, described the distribution, variability, and extremes of nuclear shape.

Results. NMP composition analysis demonstrated that both tissues have a similar NMP composition, and tissue-specific NMPs that were consistently present in all specimens of each tissue could not be demonstrated. Nuclear morphometry showed a significantly greater heterogeneity in nuclear shape in the seminal vesicles than in the prostate.

Conclusions. The striking similarity of the NMP composition demonstrates the close biologic relationship between prostate and seminal vesicle tissue. The similar NMP composition does not correlate with the marked alterations in nuclear shape and structure between these tissues. Therefore, nuclear morphometry may depict differences in the functional state of a similar set of NMPs, shown by two-dimensional gel electrophoresis, which may be responsible for the different biologic behavior of these tissues.},
	number = {5},
	urldate = {2016-04-21},
	journal = {Urology},
	author = {Pannek, Jürgen and Lakshmanan, Yegappan and Pound, Charles R and Lemkin, Peter F and Epstein, Jonathan I and Partin, Alan W},
	month = nov,
	year = {1999},
	pages = {934--939},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XDHQWU4K/Pannek et al. - 1999 - Nuclear shape and nuclear matrix protein compositi.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QMWD49A9/S0090429599002757.html:text/html}
}

@incollection{singh_topological_2014,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Topological {Descriptors} of {Histology} {Images}},
	copyright = {©2014 Springer International Publishing Switzerland},
	isbn = {978-3-319-10580-2 978-3-319-10581-9},
	url = {http://link.springer.com/chapter/10.1007/978-3-319-10581-9_29},
	abstract = {The purpose of this study is to investigate architectural characteristics of cell arrangements in breast cancer histology images. We propose the use of topological data analysis to summarize the geometric information inherent in tumor cell arrangements. Our goal is to use this information as signatures that encode robust summaries of cell arrangements in tumor tissue as captured through histology images. In particular, using ideas from algebraic topology we construct topological descriptors based on cell nucleus segmentations such as persistency charts and Betti sequences. We assess their performance on the task of discriminating the breast cancer subtypes Basal, Luminal A, Luminal B and HER2. We demonstrate that the topological features contain useful complementary information to image-appearance based features that can improve discriminatory performance of classifiers.},
	language = {en},
	number = {8679},
	urldate = {2015-03-02},
	booktitle = {Machine {Learning} in {Medical} {Imaging}},
	publisher = {Springer International Publishing},
	author = {Singh, Nikhil and Couture, Heather D. and Marron, J. S. and Perou, Charles and Niethammer, Marc},
	editor = {Wu, Guorong and Zhang, Daoqiang and Zhou, Luping},
	month = sep,
	year = {2014},
	keywords = {Artificial Intelligence (incl. Robotics), Computer Graphics, Data Mining and Knowledge Discovery, Health Informatics, Image Processing and Computer Vision, Pattern Recognition},
	pages = {231--239},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RZ9E86PU/Singh et al. - 2014 - Topological Descriptors of Histology Images.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U5KTBU9W/Singh et al. - 2014 - Topological Descriptors of Histology Images.html:text/html}
}

@article{lopez-otin_breast_1998,
	title = {Breast and {Prostate} {Cancer}: {An} {Analysis} of {Common} {Epidemiological}, {Genetic}, and {Biochemical} {Features}},
	volume = {19},
	issn = {0163-769X},
	shorttitle = {Breast and {Prostate} {Cancer}},
	url = {http://press.endocrine.org/doi/abs/10.1210/edrv.19.4.0337},
	doi = {10.1210/edrv.19.4.0337},
	abstract = {AffiliationsDepartamento de Bioquímica y Biología Molecular
(C.L.-O.), Facultad de Medicina, Universidad de Oviedo 33006, Oviedo,
Spain; and Department of Pathology and Laboratory Medicine, Mount Sinai
Hospital, Toronto, Ontario, Canada, M5G 1X5 and Department of
Laboratory Medicine and Pathobiology, University of Toronto (E.P.D.),
Toronto, Ontario M5G 1L5, Canada},
	number = {4},
	urldate = {2015-08-31},
	journal = {Endocrine Reviews},
	author = {López-Otín, Carlos and Diamandis, Eleftherios P.},
	month = aug,
	year = {1998},
	pages = {365--396},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8X3P337H/López-Otín and Diamandis - 1998 - Breast and Prostate Cancer An Analysis of Common .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P8FQS8WB/López-Otín and Diamandis - 1998 - Breast and Prostate Cancer An Analysis of Common .html:text/html}
}

@misc{_how_????,
	title = {How is breast cancer staged?},
	url = {http://www.cancer.org/cancer/breastcancer/detailedguide/breast-cancer-staging},
	urldate = {2016-06-24},
	file = {How is breast cancer staged?:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BWZN8FJM/breast-cancer-staging.html:text/html}
}

@article{nedjar_continuum_2011,
	title = {On a continuum thermodynamics formulation and computational aspects of finite growth in soft tissues},
	volume = {27},
	issn = {20407939},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=66794058&site=ehost-live&scope=site},
	doi = {10.1002/cnm.1448},
	abstract = {In this paper, we try to settle the bases of a concise modelling of growth within the unified framework of continuum thermodynamics. Special emphasis is placed on the modelling of soft biological tissues at finite strains. For this, we adopt the nowadays well-known kinematic assumption of a multiplicative decomposition of the deformation gradient into an elastic part and a growth part. It is shown how continuum thermodynamics is crucial in setting convenient forms for the coupling between stress and growth in general. The particularization to isotropy simplifies considerably the growth modelling from both the theoretical and the numerical points of view. Simple growth constitutive equations are proposed and embedded into a finite element context. Finally, representative numerical examples examining stress-dependent growth and residual stress arising from growth and resorption close this study. Copyright © 2011 John Wiley \& Sons, Ltd.},
	number = {11},
	urldate = {2014-11-09},
	journal = {International Journal for Numerical Methods in Biomedical Engineering},
	author = {Nedjar, B.},
	month = nov,
	year = {2011},
	keywords = {ELASTOPLASTICITY, FINITE element method, FINITE groups, GIBBS' free energy, HYDROSTATIC pressure},
	pages = {1850--1866},
	file = {grow.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2AMMUFAJ/grow.pdf:application/pdf}
}

@article{visvader_keeping_2009,
	title = {Keeping abreast of the mammary epithelial hierarchy and breast tumorigenesis},
	volume = {23},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/23/22/2563},
	doi = {10.1101/gad.1849509},
	abstract = {The epithelium of the mammary gland exists in a highly dynamic state, undergoing dramatic morphogenetic changes during puberty, pregnancy, lactation, and regression. The recent identification of stem and progenitor populations in mouse and human mammary tissue has provided evidence that the mammary epithelium is organized in a hierarchical manner. Characterization of these normal epithelial subtypes is an important step toward understanding which cells are predisposed to oncogenesis. This review summarizes progress in the field toward defining constituent cells and key molecular regulators of the mammary epithelial hierarchy. Potential relationships between normal epithelial populations and breast tumor subtypes are discussed, with implications for understanding the cellular etiology underpinning breast tumor heterogeneity.},
	language = {en},
	number = {22},
	urldate = {2016-07-12},
	journal = {Genes \& Development},
	author = {Visvader, Jane E.},
	month = nov,
	year = {2009},
	pmid = {19933147},
	keywords = {BRCA1, BREAST cancer, development, luminal progenitor, mammary gland, Stem cell},
	pages = {2563--2577},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BUZZ582I/Visvader - 2009 - Keeping abreast of the mammary epithelial hierarch.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S3RDUSG5/2563.html:text/html}
}

@article{dillon_factors_2007,
	title = {Factors {Affecting} {Successful} {Breast} {Conservation} for {Ductal} {Carcinoma} in {Situ}},
	volume = {14},
	issn = {1068-9265, 1534-4681},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1245/s10434-006-9246-y},
	doi = {10.1245/s10434-006-9246-y},
	abstract = {Background Successful breast-conserving therapy in DCIS is restricted by high rates of residual disease resulting in the need for radiotherapy and/or re-excision. This study identifies patients with DCIS who are most at risk of compromised margins and of residual disease. Methods All patients undergoing breast-conserving surgery for DCIS over a 6-year period were included. Method of diagnosis, mammographic size, pathological size, DCIS-margin distance and residual disease on re-excision were analysed. Results One hundred and thirty-five patients underwent initial breast-conserving surgery for DCIS. The compromised margin rate was 72\%, and the rate of residual disease on re-operation was 54\%. On univariate analysis, underestimation of pathological size by mammography by {\textgreater}1 cm occurred in 40\% of those with compromised margins undergoing a therapeutic operation compared to only 14\% of those with clear margins (P = 0.02). However, on multivariate analysis only pathological size (P {\textless} 0.0001, OR = 1.0,95\% CI 1.037–1.128) and lack of a preoperative diagnosis by core biopsy (P {\textless} 0.0001, OR = 5.3,95\% CI 1.859–15.08) were predictive of compromised margins. The presence of residual disease on re-excision was associated with increasing pathological size (P {\textless} 0.0001, OR = 1.085,95\% CI 1.038–1.134) and decreasing DCIS-margin distance (P = 0.03, OR = 6.694,95\% CI 1.84–37.855). Twenty-nine percent (n = 13/45) of lesions ≤3 cm compared to 84\% (n = 27/32) of lesions {\textgreater}3 cm had residual disease on re-operation (P {\textless} 0.0001). Residual disease was present in 62\% (n = 34/55), 64\% (n = 7/11) and 17\% (n = 2/12) of patients with DCIS-margin distances ≤1, 1–2 and 2–5 mm, respectively. Conclusion Considerable underestimation of DCIS extent by mammography occurs in a high proportion of patients with compromised margins in breast conservation. Patients at particularly high risk of residual disease on re-excision are those with lesions {\textgreater}3 cm and those with DCIS-margin distances of ≤ 2mm.},
	language = {en},
	number = {5},
	urldate = {2016-06-30},
	journal = {Annals of Surgical Oncology},
	author = {Dillon, Mary F. and Dermott, Enda W. Mc and O’Doherty, Ann and Quinn, Cecily M. and Hill, Arnold D. and O’Higgins, Niall},
	month = feb,
	year = {2007},
	pages = {1618--1628},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GAQFETTA/s10434-006-9246-y.html:text/html}
}

@misc{_basic_????,
	title = {The {Basic} {Chemistry} of {Hematoxylin}: {Leica} {Biosystems}},
	url = {http://www.leicabiosystems.com/pathologyleaders/the-basic-chemistry-of-hematoxylin/},
	urldate = {2016-06-29},
	file = {The Basic Chemistry of Hematoxylin\: Leica Biosystems:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GMWT6K8U/the-basic-chemistry-of-hematoxylin.html:text/html}
}

@article{ware_prostate_1987,
	title = {Prostate tumor progression and metastasis},
	volume = {907},
	issn = {0304-419X},
	url = {http://www.sciencedirect.com/science/article/pii/0304419X87900102},
	doi = {10.1016/0304-419X(87)90010-2},
	number = {3},
	urldate = {2016-11-28},
	journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
	author = {Ware, Joy L.},
	month = nov,
	year = {1987},
	pages = {279--298},
	file = {1-s2.0-0304419X87900102-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/A67HCC96/1-s2.0-0304419X87900102-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/THS447B6/0304419X87900102.html:text/html}
}

@article{technow_genomic_2013,
	title = {Genomic {Prediction} of {Northern} {Corn} {Leaf} {Blight} {Resistance} in {Maize} with {Combined} or {Separated} {Training} {Sets} for {Heterotic} {Groups}},
	volume = {3},
	issn = {, 2160-1836},
	url = {http://www.g3journal.org/content/3/2/197},
	doi = {10.1534/g3.112.004630},
	abstract = {Northern corn leaf blight (NCLB), a severe fungal disease causing yield losses worldwide, is most effectively controlled by resistant varieties. Genomic prediction could greatly aid resistance breeding efforts. However, the development of accurate prediction models requires large training sets of genotyped and phenotyped individuals. Maize hybrid breeding is based on distinct heterotic groups that maximize heterosis (the dent and flint groups in Central Europe). The resulting allocation of resources to parallel breeding programs challenges the establishment of sufficiently sized training sets within groups. Therefore, using training sets combining both heterotic groups might be a possibility of increasing training set sizes and thereby prediction accuracies. The objectives of our study were to assess the prospect of genomic prediction of NCLB resistance in maize and the benefit of a training set that combines two heterotic groups. Our data comprised 100 dent and 97 flint lines, phenotyped for NCLB resistance per se and genotyped with high-density single-nucleotide polymorphism marker data. A genomic BLUP model was used to predict genotypic values. Prediction accuracies reached a maximum of 0.706 (dent) and 0.690 (flint), and there was a strong positive response to increases in training set size. The use of combined training sets led to significantly greater prediction accuracies for both heterotic groups. Our results encourage the application of genomic prediction in NCLB-resistance breeding programs and the use of combined training sets.},
	language = {en},
	number = {2},
	urldate = {2015-02-10},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Technow, Frank and Bürger, Anna and Melchinger, Albrecht E.},
	month = feb,
	year = {2013},
	pmid = {23390596},
	keywords = {disease resistance, genomic prediction, GenPred, heterotic groups, maize, northern corn leaf blight, Shared data resources},
	pages = {197--203},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HPZFN66A/Technow et al. - 2013 - Genomic Prediction of Northern Corn Leaf Blight Re.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QDHBBCDT/197.html:text/html}
}

@unpublished{_grant_????,
	title = {Grant {Proposal} {Persistent} {Homology}},
	file = {proj-description.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8SHGSDNH/proj-description.pdf:application/pdf}
}

@article{colen_nci_2014,
	title = {{NCI} {Workshop} {Report}: {Clinical} and {Computational} {Requirements} for {Correlating} {Imaging} {Phenotypes} with {Genomics} {Signatures}},
	volume = {7},
	issn = {1936-5233},
	shorttitle = {{NCI} {Workshop} {Report}},
	url = {http://www.transonc.com/article/S1936523314000801/abstract},
	doi = {10.1016/j.tranon.2014.07.007},
	abstract = {The National Cancer Institute (NCI) Cancer Imaging Program organized two related workshops on June 26–27, 2013, entitled “Correlating Imaging Phenotypes with Genomics Signatures Research” and “Scalable Computational Resources as Required for Imaging-Genomics Decision Support Systems.” The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently advanced to correlate with imaging phenotypes that underpin genomics and clinical outcomes, and exploring new scientific methods to extract phenotypic features from medical images and relate them to genomics analyses. The second workshop focused on computational methods that explore informatics and computational requirements to extract phenotypic features from medical images and relate them to genomics analyses and improve the accessibility and speed of dissemination of existing NIH resources. These workshops linked clinical and scientific requirements of currently known phenotypic and genotypic cancer biology characteristics with imaging phenotypes that underpin genomics and clinical outcomes. The group generated a set of recommendations to NCI leadership and the research community that encourage and support development of the emerging radiogenomics research field to address short-and longer-term goals in cancer research.},
	language = {English},
	number = {5},
	urldate = {2015-11-30},
	journal = {Translational Oncology},
	author = {Colen, Rivka and Foster, Ian and Gatenby, Robert and Giger, Mary Ellen and Gillies, Robert and Gutman, David and Heller, Matthew and Jain, Rajan and Madabhushi, Anant and Madhavan, Subha and Napel, Sandy and Rao, Arvind and Saltz, Joel and Tatum, James and Verhaak, Roeland and Whitman, Gary},
	month = oct,
	year = {2014},
	pages = {556--569},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QNWZ6IVX/Colen et al. - 2014 - NCI Workshop Report Clinical and Computational Re.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2X248U4M/abstract.html:text/html}
}

@article{martin_dna_2005,
	title = {{DNA} labeling in living cells},
	volume = {67A},
	copyright = {Copyright © 2005 Wiley-Liss, Inc.},
	issn = {1552-4930},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/cyto.a.20172/abstract},
	doi = {10.1002/cyto.a.20172},
	abstract = {Background
Live cell fluorescence microscopy experiments often require visualization of the nucleus and the chromatin to determine the nuclear morphology or the localization of nuclear compartments.
Methods
We compared five different DNA dyes, TOPRO-3, TOTO-3, propidium iodide, Hoechst 33258, and DRAQ5, to test their usefulness in live cell experiments with continuous imaging and photobleaching in widefield epifluorescence and confocal laser scanning microscopy. In addition, we compared the DNA stainings with fluorescent histones as an independent fluorescent label to mark chromatin.
Results
From the dyes tested, only Hoechst and DRAQ5 could be used to stain DNA in living cells. However, DRAQ5 had several advantages, namely low photobleaching, labeling of the chromatin compartments comparable to that of H2B-GFP fusion proteins, and deep red excitation/emission compatible with available genetically encoded fluorescent proteins such as C/G/YFP or mRFP.
Conclusions
The DNA dye DRAQ5 is well suited for chromatin visualization in living cells and can easily be combined with other fluorophores with blue to orange emission. © 2005 Wiley-Liss, Inc.},
	language = {en},
	number = {1},
	urldate = {2016-06-25},
	journal = {Cytometry Part A},
	author = {Martin, Robert M. and Leonhardt, Heinrich and Cardoso, M. Cristina},
	month = sep,
	year = {2005},
	keywords = {chromatin, DNA dyes, DRAQ5, Fluorescence microscopy, live cell imaging, nuclear structure},
	pages = {45--52},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WCPX6KUR/Martin et al. - 2005 - DNA labeling in living cells.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KRNA666E/abstract.html:text/html}
}

@article{schnabel_randomized_2014,
	title = {A {Randomized} {Prospective} {Study} of {Lumpectomy} {Margin} {Assessment} with {Use} of {MarginProbe} in {Patients} with {Nonpalpable} {Breast} {Malignancies}},
	volume = {21},
	issn = {1068-9265},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975090/},
	doi = {10.1245/s10434-014-3602-0},
	abstract = {Background
The presence of tumor cells at the margins of breast lumpectomy specimens is associated with an increased risk of ipsilateral tumor recurrence. Twenty to 30 \% of patients undergoing breast-conserving surgery require second procedures to achieve negative margins. This study evaluated the adjunctive use of the MarginProbe device (Dune Medical Devices Ltd, Caesarea, Israel) in providing real-time intraoperative assessment of lumpectomy margins.

Methods
This multicenter randomized trial enrolled patients with nonpalpable breast malignancies. The study evaluated MarginProbe use in addition to standard intraoperative methods for margin assessment. After specimen removal and inspection, patients were randomized to device or control arms. In the device arm, MarginProbe was used to examine the main lumpectomy specimens and direct additional excision of positive margins. Intraoperative imaging was used in both arms; no intraoperative pathology assessment was permitted.

Results

In total, 596 patients were enrolled. False-negative rates were 24.8 and 66.1 \% and false-positive rates were 53.6 and 16.6 \% in the device and control arms, respectively. All positive margins on positive main specimens were resected in 62 \% (101 of 163) of cases in the device arm, versus 22 \% (33 of 147) in the control arm (p {\textless} 0.001). A total of 19.8 \% (59 of 298) of patients in the device arm underwent a reexcision procedure compared with 25.8 \% (77 of 298) in the control arm (6 \% absolute, 23 \% relative reduction). The difference in tissue volume removed was not significant.

Conclusions
Adjunctive use of the MarginProbe device during breast-conserving surgery improved surgeons’ ability to identify and resect positive lumpectomy margins in the absence of intraoperative pathology assessment, reducing the number of patients requiring reexcision. MarginProbe may aid performance of breast-conserving surgery by reducing the burden of reexcision procedures for patients and the health care system.},
	number = {5},
	urldate = {2016-07-04},
	journal = {Annals of Surgical Oncology},
	author = {Schnabel, Freya and Boolbol, Susan K. and Gittleman, Mark and Karni, Tami and Tafra, Lorraine and Feldman, Sheldon and Police, Alice and Friedman, Neil B. and Karlan, Scott and Holmes, Dennis and Willey, Shawna C. and Carmon, Moshe and Fernandez, Kristen and Akbari, Stephanie and Harness, Jay and Guerra, Lisa and Frazier, Thomas and Lane, Karen and Simmons, Rache M. and Estabrook, Alison and Allweis, Tanir},
	year = {2014},
	pmid = {24595800},
	pmcid = {PMC3975090},
	pages = {1589--1595},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JKJ4SURQ/Schnabel et al. - 2014 - A Randomized Prospective Study of Lumpectomy Margi.pdf:application/pdf}
}

@misc{_next_????,
	title = {Next {Generation} {Cancer} {Diagnostics} {Market} {Size}, {And} {Forecast} {To} 2022},
	url = {http://www.briskinsights.com/report/next-generation-cancer-diagnostics-market},
	urldate = {2016-07-04},
	file = {Next Generation Cancer Diagnostics Market Size, And Forecast To 2022:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BSZHNCW6/next-generation-cancer-diagnostics-market.html:text/html}
}

@article{fu_structured_2016,
	title = {Structured {Illumination} {Microscopy} and a {Quantitative} {Image} {Analysis} for the {Detection} of {Positive} {Margins} in a {Pre}-{Clinical} {Genetically} {Engineered} {Mouse} {Model} of {Sarcoma}},
	volume = {11},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723137/},
	doi = {10.1371/journal.pone.0147006},
	abstract = {Intraoperative assessment of surgical margins is critical to ensuring residual tumor does not remain in a patient. Previously, we developed a fluorescence structured illumination microscope (SIM) system with a single-shot field of view (FOV) of 2.1×1.6 mm (3.4 mm2) and sub-cellular resolution (4.4 μm). The goal of this study was to test the utility of this technology for the detection of residual disease in a genetically engineered mouse model of sarcoma. Primary soft tissue sarcomas were generated in the hindlimb and after the tumor was surgically removed, the relevant margin was stained with acridine orange (AO), a vital stain that brightly stains cell nuclei and fibrous tissues. The tissues were imaged with the SIM system with the primary goal of visualizing fluorescent features from tumor nuclei. Given the heterogeneity of the background tissue (presence of adipose tissue and muscle), an algorithm known as maximally stable extremal regions (MSER) was optimized and applied to the images to specifically segment nuclear features. A logistic regression model was used to classify a tissue site as positive or negative by calculating area fraction and shape of the segmented features that were present and the resulting receiver operator curve (ROC) was generated by varying the probability threshold. Based on the ROC curves, the model was able to classify tumor and normal tissue with 77\% sensitivity and 81\% specificity (Youden’s index). For an unbiased measure of the model performance, it was applied to a separate validation dataset that resulted in 73\% sensitivity and 80\% specificity. When this approach was applied to representative whole margins, for a tumor probability threshold of 50\%, only 1.2\% of all regions from the negative margin exceeded this threshold, while over 14.8\% of all regions from the positive margin exceeded this threshold.},
	number = {1},
	urldate = {2016-06-24},
	journal = {PLoS ONE},
	author = {Fu, Henry L. and Mueller, Jenna L. and Whitley, Melodi J. and Cardona, Diana M. and Willett, Rebecca M. and Kirsch, David G. and Brown, J. Quincy and Ramanujam, Nimmi},
	month = jan,
	year = {2016},
	pmid = {26799613},
	pmcid = {PMC4723137},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BZRSBAVE/Fu et al. - 2016 - Structured Illumination Microscopy and a Quantitat.pdf:application/pdf}
}

@article{singer_margins_2016,
	title = {Margins in breast conserving surgery: {The} financial cost \& potential savings associated with the new margin guidelines},
	volume = {28},
	issn = {0960-9776},
	shorttitle = {Margins in breast conserving surgery},
	url = {http://www.sciencedirect.com/science/article/pii/S0960977616300376},
	doi = {10.1016/j.breast.2016.04.007},
	abstract = {Introduction
In this study, we compare the indications for re-excision, the findings of additional tumor in the re-excision specimen as they relate to margin status, and costs associated with re-excision based on recent new consensus statements.
Materials and methods
A retrospective analysis was performed on 462 patients with invasive breast carcinoma who underwent at least one lumpectomy between January 2011 and December 2013. Postoperative data was analyzed based on where additional disease was found, as it relates to the margin status of the initial lumpectomy and the additional direct costs associated with additional procedures.
Results
Of the 462 patients sampled, 149 underwent a re-excision surgery (32.2\%). Four patients underwent mastectomy as their second operation. In the 40 patients with additional disease found on re-excision, 36 (90.0\%) of them had a positive margin on their initial lumpectomy. None of the four mastectomy patients had residual disease. The mean cost of the initial lumpectomy for all 462 patients was \$2118.01 plus an additional \$1801.92 for those who underwent re-excision.
Discussion
A positive margin was most predictive of finding residual tumor on re-excision as would be expected. Using old criteria only 0.07\% (4/61) of patients who had undergone re-excision with a ‘clear’ margin, had additional tumor found, at a total cost of \$106,354.11. Thus, the new consensus guidelines will lead to less overall cost, at no clinical risk to patients while reducing a patient's surgical risk and essentially eliminating delays in adjuvant care.},
	urldate = {2016-07-04},
	journal = {The Breast},
	author = {Singer, Lauren and Brown, Eric and Lanni Jr., Thomas},
	month = aug,
	year = {2016},
	keywords = {BREAST cancer, Cost, Re-excision},
	pages = {1--4},
	file = {1-s2.0-S0960977616300376-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2RT4556I/1-s2.0-S0960977616300376-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RHJMDMUP/S0960977616300376.html:text/html}
}

@incollection{berry_imaging_2014,
	title = {Imaging of {Adipose} {Tissue}},
	volume = {537},
	isbn = {978-0-12-411619-1},
	url = {http://linkinghub.elsevier.com/retrieve/pii/B9780124116191000045},
	language = {en},
	urldate = {2016-07-03},
	booktitle = {Methods in {Enzymology}},
	publisher = {Elsevier},
	author = {Berry, Ryan and Church, Christopher D. and Gericke, Martin T. and Jeffery, Elise and Colman, Laura and Rodeheffer, Matthew S.},
	year = {2014},
	pages = {47--73},
	file = {1-s2.0-B9780124116191000045-main(1).pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/82XMT8G2/1-s2.0-B9780124116191000045-main(1).pdf:application/pdf}
}

@article{civier_computational_2013,
	title = {Computational modeling of stuttering caused by impairments in a basal ganglia thalamo-cortical circuit involved in syllable selection and initiation},
	volume = {126},
	issn = {1090-2155},
	doi = {10.1016/j.bandl.2013.05.016},
	abstract = {Atypical white-matter integrity and elevated dopamine levels have been reported for individuals who stutter. We investigated how such abnormalities may lead to speech dysfluencies due to their effects on a syllable-sequencing circuit that consists of basal ganglia (BG), thalamus, and left ventral premotor cortex (vPMC). "Neurally impaired" versions of the neurocomputational speech production model GODIVA were utilized to test two hypotheses: (1) that white-matter abnormalities disturb the circuit via corticostriatal projections carrying copies of executed motor commands and (2) that dopaminergic abnormalities disturb the circuit via the striatum. Simulation results support both hypotheses: in both scenarios, the neural abnormalities delay readout of the next syllable's motor program, leading to dysfluency. The results also account for brain imaging findings during dysfluent speech. It is concluded that each of the two abnormality types can cause stuttering moments, probably by affecting the same BG-thalamus-vPMC circuit.},
	language = {eng},
	number = {3},
	journal = {Brain and Language},
	author = {Civier, Oren and Bullock, Daniel and Max, Ludo and Guenther, Frank H.},
	month = sep,
	year = {2013},
	pmid = {23872286},
	pmcid = {PMC3775364},
	keywords = {Basal Ganglia, Brain, Computer Simulation, Dopamine, Humans, Motor Cortex, Nerve Net, Phonetics, Stuttering, Thalamus},
	pages = {263--278}
}

@article{mcdowell_generalized_2007,
	title = {A generalized noise variance analysis model and its application to the characterization of 1/f noise},
	volume = {15},
	issn = {1094-4087},
	url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-15-7-3833},
	doi = {10.1364/OE.15.003833},
	language = {en},
	number = {7},
	urldate = {2016-07-08},
	journal = {Optics Express},
	author = {McDowell, Emily J. and Cui, Xiquan and Yaqoob, Zahid and Yang, Changhuei},
	year = {2007},
	pages = {3833}
}

@article{thorpe_aspartic_2010,
	title = {Aspartic {Acid} {Racemization} and {Collagen} {Degradation} {Markers} {Reveal} an {Accumulation} of {Damage} in {Tendon} {Collagen} {That} {Is} {Enhanced} with {Aging}},
	volume = {285},
	issn = {0021-9258},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871433/},
	doi = {10.1074/jbc.M109.077503},
	abstract = {Little is known about the rate at which protein turnover occurs in living tendon and whether the rate differs between tendons with different physiological roles. In this study, we have quantified the racemization of aspartic acid to calculate the age of the collagenous and non-collagenous components of the high strain injury-prone superficial digital flexor tendon (SDFT) and low strain rarely injured common digital extensor tendon (CDET) in a group of horses with a wide age range. In addition, the turnover of collagen was assessed indirectly by measuring the levels of collagen degradation markers (collagenase-generated neoepitope and cross-linked telopeptide of type I collagen). The fractional increase in d-Asp was similar (p = 0.7) in the SDFT (5.87 × 10−4/year) and CDET (5.82 × 10−4/year) tissue, and d/l-Asp ratios showed a good correlation with pentosidine levels. We calculated a mean (±S.E.) collagen half-life of 197.53 (±18.23) years for the SDFT, which increased significantly with horse age (p = 0.03) and was significantly (p {\textless} 0.001) higher than that for the CDET (34.03 (±3.39) years). Using similar calculations, the half-life of non-collagenous protein was 2.18 (±0.41) years in the SDFT and was significantly (p = 0.04) lower than the value of 3.51 (±0.51) years for the CDET. Collagen degradation markers were higher in the CDET and suggested an accumulation of partially degraded collagen within the matrix with aging in the SDFT. We propose that increased susceptibility to injury in older individuals results from an inability to remove partially degraded collagen from the matrix leading to reduced mechanical competence.},
	number = {21},
	urldate = {2014-11-04},
	journal = {The Journal of Biological Chemistry},
	author = {Thorpe, Chavaunne T. and Streeter, Ian and Pinchbeck, Gina L. and Goodship, Allen E. and Clegg, Peter D. and Birch, Helen L.},
	month = may,
	year = {2010},
	pmid = {20308077},
	pmcid = {PMC2871433},
	pages = {15674--15681}
}

@misc{_ibisworld_????,
	title = {{IBISWorld} {US} - {Industry}, {Company} and {Business} {Research} {Reports} and {Information}},
	url = {http://clients1.ibisworld.com.libproxy.tulane.edu:2048/reports/us/industry/ataglance.aspx?indid=5772},
	urldate = {2016-07-04},
	file = {IBISWorld US - Industry, Company and Business Research Reports and Information:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/V7ZAJ7Z2/ataglance.html:text/html}
}

@misc{_seer_????,
	title = {{SEER} {Training}:{Introduction} to {Breast} {Cancer}},
	url = {http://training.seer.cancer.gov/breast/intro/},
	urldate = {2016-06-23},
	file = {SEER Training\:Introduction to Breast Cancer:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NFKZISS3/intro.html:text/html}
}

@article{rashid_frequencies_2011,
	title = {Frequencies of different nuclear morphological features in prostate adenocarcinoma},
	volume = {15},
	issn = {1092-9134},
	url = {http://www.sciencedirect.com/science/article/pii/S109291341100089X},
	doi = {10.1016/j.anndiagpath.2011.06.002},
	abstract = {Diagnosis of prostate adenocarcinoma is primarily based on morphological analysis. Nucleomegaly, prominent nucleoli, and hyperchromasia constitute current nuclear diagnostic parameters but are seen in benign conditions, vary with Gleason grade, and pose diagnostic challenge in well-differentiated tumors with accompanying inflammation or equivocal architectural features. In such cases, other pleomorphic nuclear features such as variation in size and shape, irregular contours, nuclear membrane infoldings, and nonuniform chromatin, which are not incorporated in formal evaluation, may prove helpful. Our aim was to study different nuclear morphological features of prostate adenocarcinoma (including currently practiced ones) and highlight their variation with Gleason grades. We examined 84 cases of prostate adenocarcinoma using oil immersion microscopy where necessary. Commonest Gleason pattern observed was grade 4a accounting for 42.8\% of cases. Nuclear enlargement (moderate to marked in 93.8\%), nucleolar enlargement (62.1\%), and nonuniform chromatin distribution (100\%) could serve as useful diagnostic features but did not vary with tumor differentiation. Pleomorphism (moderate in 58.6\%), nuclear overlapping (62.8\%), nuclear membrane infoldings (66.2\%), and irregular contours (frequent in 94.5\%) were significant diagnostic features that increased in frequency and extent with increasing grade and could be used to differentiate low-grade from high-grade tumors. Worsening of nuclear morphology with advancing tumor grades indicated that nuclear anaplasia accompanies poor architectural differentiation. Coexistence of pale and dark nuclei signified variable chromatin density of no diagnostic significance.},
	number = {6},
	urldate = {2016-04-21},
	journal = {Annals of Diagnostic Pathology},
	author = {Rashid, Farhat and Ul Haque, Anwar},
	month = dec,
	year = {2011},
	keywords = {Gleason grades, Nuclear morphology, Prostate adenocarcinoma},
	pages = {414--421},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UFWUFSNW/Rashid and Ul Haque - 2011 - Frequencies of different nuclear morphological fea.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/K8K9DCGJ/S109291341100089X.html:text/html}
}

@misc{singh_topological_2014-1,
	title = {Topological {Descriptors} of {Histology} {Images}},
	author = {{Singh}},
	year = {2014},
	file = {Untitled Attachment:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5U7NJGQD/Singh - 2014 - Topological Descriptors of Histology Images.html:text/html}
}

@article{bodilsen_abstract_2016,
	title = {Abstract {S}2-01: {Importance} of margin width and re-excision in breast conserving treatment of early breast cancer; a {Danish} breast cancer cooperative group study of 11,900 women},
	volume = {76},
	copyright = {©2016 American Association for Cancer Research.},
	issn = {0008-5472, 1538-7445},
	shorttitle = {Abstract {S}2-01},
	url = {http://cancerres.aacrjournals.org/content/76/4_Supplement/S2-01},
	doi = {10.1158/1538-7445.SABCS15-S2-01},
	abstract = {Background: The majority of women with invasive breast cancer are treated surgically by breast conserving surgery (BCS). A significant proportion subsequently undergo re-excision to obtain clear margins. However what constitutes a sufficient negative margin continues to be subject of controversy. The purpose of the study was to investigate the association between margin width and ipsilateral breast tumour recurrence (IBTR) as well as identifying factors associated with residual disease after repeat surgery, and to determine the effect of re-excision on IBTR in a population-based nationwide cohort.
Method: 11,900 patients treated with breast conserving therapy for unilateral invasive cancer in Denmark between 2000 and 2009 were included. All patients received whole breast irradiation and were offered systemic adjuvant treatment according to the guidelines of the Danish Breast Cancer Cooperative Group.
Results: The median follow-up was 4.9 years. The cumulative incidence of IBTR at 5 and 9 year was 2.4\% and 5.9\%, respectively. No decrease in IBTR with a wider negative margin compared to a narrow but negative margin was seen in adjusted analysis ({\textgreater}0-1 mm vs. 2-4 mm vs. ≥5 mm (reference): HR 1.54 (CI 95\% 0.81-2.93) vs 0.95 (CI 95\% 0.56-1.62) vs. 1). A final positive margin did however increase the risk of IBTR (HR 2.51; 95\% CI 1.02-6.23). Other factors associated with increased IBTR were young age (HR 3.10; 95\% CI 1.89-5.10), more than 4 positive lymph nodes (HR 1.80; 95\% CI 1.24-2.62), and re-excision (HR 1.53; 95\% CI 1.16-2.02). Receiving chemotherapy (HR 0.45; 95\% CI 0.33-0.61) or boost (HR 0.43; 95\% CI 0.31-0.60) reduced risk of IBTR as did being oestrogen receptor positive treated with (HR 0.35; 95\% CI 0.25-0.49) or without (HR 0.43; 95\% CI 0.31-0.60) adjuvant endocrine therapy.
Within two months of initial BCS 1342 women (11\%) had a re-excision. Residual disease was found in 20\% of re-excisions. In adjusted analysis DCIS outside the invasive tumour (OR 2.69; 95\% CI 1.99-3.63), positive initial margin (OR 2.26, 95\% CI 1.70-2.99, p{\textless}0.001), and age {\textless}50 years (OR 1.53; 95\% CI 1.00-2.31) was associated with increased risk of residual disease. Patients with residual disease after re-excision had in the adjusted analysis an increased risk of ipsilateral breast tumour recurrence (IBTR), regardless of whether residual findings were invasive carcinoma (HR 2.97, CI 95\% 1.57-5.62) or DCIS (HR 2.58, CI 95\% 1.50-4.45). However no difference was seen for overall survival comparing one procedure with repeat surgery with or without residual disease (p=0.96).
Conclusion: An overall low rate of IBTR was seen. While a final positive margin was associated with a more than two-fold risk of IBTR, no evidence of improved local control was found with wider negative margins compared to narrow. However the finding of residual disease at re-excision was associated with an increased risk of IBTR.
Citation Format: Bodilsen A, Bjerre K, Offersen BV, Vahl P, Mele M, Dixon MJ, Ejlertsen B, Overgaard J, Christiansen P. Importance of margin width and re-excision in breast conserving treatment of early breast cancer; a Danish breast cancer cooperative group study of 11,900 women. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S2-01.},
	language = {en},
	number = {4 Supplement},
	urldate = {2016-06-22},
	journal = {Cancer Research},
	author = {Bodilsen, A. and Bjerre, K. and Offersen, B. V. and Vahl, P. and Mele, M. and Dixon, M. J. and Ejlertsen, B. and Overgaard, J. and Christiansen, P.},
	month = feb,
	year = {2016},
	pages = {S2--01--S2--01},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PT7KDM2Q/S2-01.html:text/html}
}

@article{azuma_evaluation_2013,
	title = {Evaluation of the effectiveness of simple nuclei-segmentation methods on {Caenorhabditis} elegans embryogenesis images},
	volume = {14},
	issn = {1471-2105},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077036/},
	doi = {10.1186/1471-2105-14-295},
	abstract = {Background
For the analysis of spatio-temporal dynamics, various automated processing methods have been developed for nuclei segmentation. These methods tend to be complex for segmentation of images with crowded nuclei, preventing the simple reapplication of the methods to other problems. Thus, it is useful to evaluate the ability of simple methods to segment images with various degrees of crowded nuclei.

Results
Here, we selected six simple methods from various watershed based and local maxima detection based methods that are frequently used for nuclei segmentation, and evaluated their segmentation accuracy for each developmental stage of the Caenorhabditis elegans. We included a 4D noise filter, in addition to 2D and 3D noise filters, as a pre-processing step to evaluate the potential of simple methods as widely as possible. By applying the methods to image data between the 50- to 500-cell developmental stages at 50-cell intervals, the error rate for nuclei detection could be reduced to ≤ 2.1\% at every stage until the 350-cell stage. The fractions of total errors throughout the stages could be reduced to ≤ 2.4\%. The error rates improved at most of the stages and the total errors improved when a 4D noise filter was used. The methods with the least errors were two watershed-based methods with 4D noise filters. For all the other methods, the error rate and the fraction of errors could be reduced to ≤ 4.2\% and ≤ 4.1\%, respectively. The minimum error rate for each stage between the 400- to 500-cell stages ranged from 6.0\% to 8.4\%. However, similarities between the computational and manual segmentations measured by volume overlap and Hausdorff distance were not good. The methods were also applied to Drosophila and zebrafish embryos and found to be effective.

Conclusions
The simple segmentation methods were found to be useful for detecting nuclei until the 350-cell stage, but not very useful after the 400-cell stage. The incorporation of a 4D noise filter to the simple methods could improve their performances. Error types and the temporal biases of errors were dependent on the methods used. Combining multiple simple methods could also give good segmentations.},
	urldate = {2016-06-30},
	journal = {BMC Bioinformatics},
	author = {Azuma, Yusuke and Onami, Shuichi},
	month = oct,
	year = {2013},
	pmid = {24090283},
	pmcid = {PMC4077036},
	pages = {295},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Q44FH24G/Azuma and Onami - 2013 - Evaluation of the effectiveness of simple nuclei-s.pdf:application/pdf}
}

@article{mazhar_structured_2010,
	title = {Structured illumination enhances resolution and contrast in thick tissue fluorescence imaging},
	volume = {15},
	issn = {1083-3668},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917462/},
	doi = {10.1117/1.3299321},
	abstract = {We introduce a noncontact imaging method utilizing multifrequency structured illumination for improving lateral and axial resolution and contrast of fluorescent molecular probes in thick, multiple-scattering tissue phantoms. The method can be implemented rapidly using a spatial light modulator and a simple image demodulation scheme similar to structured light microscopy in the diffraction regime. However, imaging is performed in the multiple-scattering regime utilizing spatially modulated scalar photon density waves. We demonstrate that by increasing the structured light spatial frequency, fluorescence from deeper structures is suppressed and signals from more superficial objects enhanced. By measuring the spatial frequency dependence of fluorescence, background can be reduced by localizing the signal to a buried fluorescent object. Overall, signal-to-background ratio (SBR) and resolution improvements are dependent on spatial frequency and object depth∕dimension with as much as sevenfold improvement in SBR and 33\% improvement in resolution for ∼1-mm objects buried 3 mm below the surface in tissue-like media with fluorescent background.},
	number = {1},
	urldate = {2016-07-08},
	journal = {Journal of Biomedical Optics},
	author = {Mazhar, Amaan and Cuccia, David J. and Gioux, Sylvain and Durkin, Anthony J. and Frangioni, John V. and Tromberg, Bruce J.},
	year = {2010},
	pmid = {20210421},
	pmcid = {PMC2917462},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JITVEBBB/Mazhar et al. - 2010 - Structured illumination enhances resolution and co.pdf:application/pdf}
}

@article{chan_effects_2000,
	title = {Effects of basic fibroblast growth factor ({bFGF}) on early stages of tendon healing: {A} rat patellar tendon model},
	volume = {71},
	issn = {1745-3674},
	shorttitle = {Effects of basic fibroblast growth factor ({bFGF}) on early stages of tendon healing},
	url = {http://informahealthcare.com/doi/abs/10.1080/000164700317381234},
	doi = {10.1080/000164700317381234},
	abstract = {We studied the effects of basic fibroblast growth factor (bFGF) on cell proliferation, type III collagen expression, ultimate stress and the pyridinoline content in the early stages of healing in rat patellar tendon. 96 male Sprague Dawley rats were injected with increasing doses of basic fibroblast growth factor (bFGF) at 3 days after a "window defect" was induced in the mid-part of the patellar tendon. They were killed at 7 and 14 days after the injury. A dose-dependent increase in the number of proliferating cells and the level of expression of type III collagen was demonstrated at only 7 days post-injury. On the other hand, we found no effects of bFGF on ultimate stress and the pyridinoline content of healing tendons. Only time significantly affected both strength-associated parameters. We showed that in vivo supplementation with bFGF affected the initial events of healing such as cell proliferation and type III collagen expression.},
	number = {5},
	urldate = {2014-11-03},
	journal = {Acta Orthopaedica},
	author = {Chan, Barbara P and Fu, Sai-chuen and Qin, Ling and Lee, Kwong-man and Rolf, Chriter G and Chan, Kai-ming},
	month = jan,
	year = {2000},
	pages = {513--518},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RTAWUPDK/Chan et al. - 2000 - Effects of basic fibroblast growth factor (bFGF) o.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DHCVNA3S/000164700317381234.html:text/html}
}

@article{jensen_tumor_2008,
	title = {Tumor volume in subcutaneous mouse xenografts measured by {microCT} is more accurate and reproducible than determined by 18F-{FDG}-{microPET} or external caliper},
	volume = {8},
	copyright = {2008 Jensen et al; licensee BioMed Central Ltd.},
	issn = {1471-2342},
	url = {http://www.biomedcentral.com/1471-2342/8/16/abstract},
	doi = {10.1186/1471-2342-8-16},
	abstract = {PMID: 18925932},
	language = {en},
	number = {1},
	urldate = {2015-03-08},
	journal = {BMC Medical Imaging},
	author = {Jensen, Mette M. and Jørgensen, Jesper T. and Binderup, Tina and Kjær, Andreas},
	month = oct,
	year = {2008},
	pmid = {18925932},
	pages = {16},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KJ58ZNNR/Jensen et al. - 2008 - Tumor volume in subcutaneous mouse xenografts meas.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HNQEDTXF/Jensen et al. - 2008 - Tumor volume in subcutaneous mouse xenografts meas.html:text/html}
}

@misc{_ibisworld_????-1,
	title = {{IBISWorld} {US} - {Industry}, {Company} and {Business} {Research} {Reports} and {Information}},
	url = {http://clients1.ibisworld.com.libproxy.tulane.edu:2048/reports/us/industry/default.aspx?entid=5612},
	urldate = {2016-07-04},
	file = {IBISWorld US - Industry, Company and Business Research Reports and Information:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6FF2NXF6/default.html:text/html}
}

@article{esbona_intraoperative_2012,
	title = {Intraoperative {Imprint} {Cytology} and {Frozen} {Section} {Pathology} for {Margin} {Assessment} in {Breast} {Conservation} {Surgery}: {A} {Systematic} {Review}},
	volume = {19},
	issn = {1068-9265, 1534-4681},
	shorttitle = {Intraoperative {Imprint} {Cytology} and {Frozen} {Section} {Pathology} for {Margin} {Assessment} in {Breast} {Conservation} {Surgery}},
	url = {http://link.springer.com/article/10.1245/s10434-012-2492-2},
	doi = {10.1245/s10434-012-2492-2},
	abstract = {Background Achieving negative surgical margins is critical to minimizing the risk of tumor recurrence in patients undergoing breast conservation surgery (BCS) for a breast malignancy. Our objective was to perform a systematic review comparing reexcision rates, sensitivity and specificity of the intraoperative use of the margin assessment techniques of imprint cytology (IC) and frozen section analysis (FSA), against permanent histopathologic section (PS). Methods The databases PubMed, Web of Knowledge, Cochrane Library and CINAHL Plus were searched for literature published from 1997 to 2011. Original investigations of patients who underwent BCS for breast cancer that evaluated margin assessment with PS and/or IC or FSA were included. Of 182 titles identified, 41 patient cohorts from 37 articles met inclusion criteria: PS (n = 19), IC (n = 7) and FSA (n = 15). Studies were summarized qualitatively using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist for cohort studies and the Strength of Recommendation Taxonomy (SORT) numerical scale for diagnostic studies. Results The final reexcision rates after primary BCS were 35 \% for PS, 11 \% for IC (p = 0.001 vs. PS) and 10 \% for FSA (p {\textless} 0.0001 vs. PS). For IC, reexcision rates decreased from 26 to 4 \% (p = 0.18) and for FSA, reexcision rates decreased from 27 to 6 \% (p {\textless} 0.0001). The pooled sensitivity of IC and FSA were 72 and 83 \%. The pooled specificity of IC and FSA were 97 and 95 \%. The average length of each technique was 13 min for IC and 27 min for FSA. Conclusions Patients who underwent BCS with intraoperative IC or FSA to assess negative surgical margins had significantly fewer secondary surgical procedures for excision of their breast malignancies.},
	language = {en},
	number = {10},
	urldate = {2016-06-22},
	journal = {Annals of Surgical Oncology},
	author = {Esbona, Karla and Li, Zhanhai and Wilke, Lee G.},
	month = jul,
	year = {2012},
	pages = {3236--3245},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Q3G893B2/Esbona et al. - 2012 - Intraoperative Imprint Cytology and Frozen Section.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AUP9N3EM/s10434-012-2492-2.html:text/html}
}

@article{schnitt_classification_2010,
	title = {Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy},
	volume = {23},
	copyright = {© 2010 Nature Publishing Group},
	issn = {0893-3952},
	shorttitle = {Classification and prognosis of invasive breast cancer},
	url = {http://www.nature.com.libproxy.tulane.edu:2048/modpathol/journal/v23/n2s/full/modpathol201033a.html},
	doi = {10.1038/modpathol.2010.33},
	abstract = {For many years, patient age, axillary lymph node status, tumor size, histological features (especially histological grade and lymphovascular invasion), hormone receptor status, and HER2 status have been the major factors used to categorize patients with breast cancer in order to assess prognosis and determine the appropriate therapy. These factors are most often viewed in combination to group patients into various risk categories. Although these risk categories are useful for assessing prognosis and risk in groups of patients with breast cancer, their role in determining prognosis and evaluating risk in an individual patient is more limited. Therefore, better methods are required to help assess prognosis and determine the most appropriate treatment for patients on an individual basis. Recently, various molecular techniques, particular gene expression profiling, have been increasingly used to help refine breast cancer classification and to assess prognosis and response to therapy. Although the precise role of these newer techniques in the daily management of patients with breast cancer continues to evolve, it is clear that they have the potential to provide value above and beyond that provided by the traditional clinical and pathological prognostic and predictive factors.},
	number = {S2},
	urldate = {2016-07-07},
	journal = {Modern Pathology},
	author = {Schnitt, Stuart J.},
	month = may,
	year = {2010},
	keywords = {BREAST cancer, classification, gene expression profiling, molecular, Prognosis},
	pages = {S60--S64},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U8QRQRAG/Schnitt - 2010 - Classification and prognosis of invasive breast ca.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QAFJMI7N/modpathol201033a.html:text/html}
}

@article{cheng_estrogen_2001,
	title = {Estrogen augments glucose transporter and {IGF}1 expression in primate cerebral cortex},
	volume = {15},
	issn = {0892-6638},
	abstract = {Estrogen has many positive effects on neural tissue in experimental model systems, including stimulation of neurite growth and neurotransmitter synthesis and protection against diverse types of neural injury. In humans, estrogen treatment is reputed to protect against Alzheimer's disease. To investigate potential mediators of estrogen's action and determine whether selective estrogen receptor modulators (SERMs) such as tamoxifen have estrogen-like effects in the primate brain, we evaluated the expression of glucose transporters and insulin-like growth factor 1 (IGF1) and its receptor in the frontal cortex of ovariectomized rhesus monkeys. We treated one group for 3 days with vehicle, another with 17 beta estradiol (E2), and a third with tamoxifen. The expression of facilitative glucose transporters (Gluts) 1, 3, and 4 was investigated using in situ hybridization, immunohistochemistry, and immunoblot analysis. Gluts 3 and 4 were concentrated in cortical neurons and Glut1 in capillaries and glial cells. E2 treatment induced two- to fourfold increases in Glut3 and Glut4 mRNA levels and lesser but significant increases in Glut3 and 4 protein levels. E2 treatment induced an approximately 70\% increase in parenchymal Glut1 mRNA levels, but did not appreciably affect vascular Glut1 gene expression. IGF1 and IGF1 receptor mRNAs were concentrated in cortical neurons in a distribution similar to Gluts 3 and 4. IGF1 mRNA levels were significantly increased in E2-treated animals but IGF1 receptor mRNA levels were not altered by hormone treatment. Tamoxifen increased cerebral cortical Glut3 and 4 mRNA levels, but did not affect Glut1, IGF1, or IGF1 receptor expression. This study provides novel data showing that Gluts 3 and 4 and IGF1 are coexpressed by primate cerebral cortical neurons, where their expression is enhanced by estrogen. These findings suggest that up-regulation of glucose transporter and IGF1 expression may contribute to estrogen's salutary effects on neural tissue. Tamoxifen, an antiestrogen at the breast, is shown to have estrogen-like effects on higher brain centers in the monkey, suggesting that some SERMs may share estrogen's neuroprotective potential for menopausal women.},
	language = {eng},
	number = {6},
	journal = {FASEB journal: official publication of the Federation of American Societies for Experimental Biology},
	author = {Cheng, C. M. and Cohen, M. and Wang, J. and Bondy, C. A.},
	month = apr,
	year = {2001},
	pmid = {11292650},
	keywords = {Animals, Antineoplastic Agents, Hormonal, Cerebral Cortex, Estradiol, Female, Gene Expression, Glucose Transporter Type 3, Glucose Transporter Type 4, Insulin-Like Growth Factor I, Macaca mulatta, Monosaccharide Transport Proteins, Muscle Proteins, Nerve Tissue Proteins, Receptor, IGF Type 1, RNA, Messenger, Tamoxifen},
	pages = {907--915}
}

@article{osako_efficacy_2015,
	title = {Efficacy of intraoperative entire-circumferential frozen section analysis of lumpectomy margins during breast-conserving surgery for breast cancer},
	volume = {20},
	issn = {1341-9625, 1437-7772},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1007/s10147-015-0827-2},
	doi = {10.1007/s10147-015-0827-2},
	abstract = {Background Intraoperative frozen section analysis of the surgical margins during breast-conserving surgery (BCS) for breast cancer can reliably achieve clear surgical margins and prevent re-operations. The aim of this study was to assess intraoperative entire-circumferential frozen section analysis (IEFSA) of the lumpectomy margins during BCS. Methods A total of 1029 patients who underwent BCS with IEFSA between June 2007 and July 2013 were available for assessment. The inner surfaces of the shaved lumpectomy margins were examined as frozen sections during BCS. The margins were defined as positive when the cancer cells were present within 5 mm from the edge of the outermost margins of the specimens. Results Out of 1029 patients, 312 patients (30.3 \%) had positive margins after the initial lumpectomy and underwent additional resections during BCS. Fourteen patients (1.4 \%) underwent mastectomy following the results of additional resections during the first surgery. Of 1015 patients who completed BCS, 60 patients (5.9 \%) were found to have positive margins in the final pathology. One patient (0.1 \%) underwent re-operation after BCS while the residual diseases of the other 59 patients were judged to be minimal. Of the 312 patients who were judged to have positive margins after the initial lumpectomy with IEFSA, 53 patients (16.9 \%) were found to have negative margins in the final pathology. At a median follow-up time of 54.1 months, one patient (0.1 \%) had a recurrence of breast cancer in the preserved breast. Conclusion IEFSA is useful for preventing the need for re-operation and local recurrence after BCS.},
	language = {en},
	number = {6},
	urldate = {2016-06-24},
	journal = {International Journal of Clinical Oncology},
	author = {Osako, Tomofumi and Nishimura, Reiki and Nishiyama, Yasuyuki and Okumura, Yasuhiro and Tashima, Rumiko and Nakano, Masahiro and Fujisue, Mamiko and Toyozumi, Yasuo and Arima, Nobuyuki},
	month = apr,
	year = {2015},
	pages = {1093--1101},
	file = {art%3A10.1007%2Fs10147-015-0827-2.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/G7NUHIZ5/art%3A10.1007%2Fs10147-015-0827-2.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KWJXC3VA/s10147-015-0827-2.html:text/html}
}

@article{beal_auditory_2010,
	title = {Auditory evoked fields to vocalization during passive listening and active generation in adults who stutter},
	volume = {52},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2010.04.277},
	abstract = {We used magnetoencephalography to investigate auditory evoked responses to speech vocalizations and non-speech tones in adults who do and do not stutter. Neuromagnetic field patterns were recorded as participants listened to a 1 kHz tone, playback of their own productions of the vowel /i/ and vowel-initial words, and actively generated the vowel /i/ and vowel-initial words. Activation of the auditory cortex at approximately 50 and 100 ms was observed during all tasks. A reduction in the peak amplitudes of the M50 and M100 components was observed during the active generation versus passive listening tasks dependent on the stimuli. Adults who stutter did not differ in the amount of speech-induced auditory suppression relative to fluent speakers. Adults who stutter had shorter M100 latencies for the actively generated speaking tasks in the right hemisphere relative to the left hemisphere but the fluent speakers showed similar latencies across hemispheres. During passive listening tasks, adults who stutter had longer M50 and M100 latencies than fluent speakers. The results suggest that there are timing, rather than amplitude, differences in auditory processing during speech in adults who stutter and are discussed in relation to hypotheses of auditory-motor integration breakdown in stuttering.},
	language = {eng},
	number = {4},
	journal = {NeuroImage},
	author = {Beal, Deryk S. and Cheyne, Douglas O. and Gracco, Vincent L. and Quraan, Maher A. and Taylor, Margot J. and De Nil, Luc F.},
	month = oct,
	year = {2010},
	pmid = {20452437},
	keywords = {Adult, Auditory Perception, Brain, Brain Mapping, Evoked Potentials, Auditory, Humans, Male, Speech, Stuttering},
	pages = {1645--1653}
}

@article{legesse_seamless_2015,
	title = {Seamless stitching of tile scan microscope images: {STITCHING} {OF} {TILE} {SCAN} {IMAGES}},
	volume = {258},
	issn = {00222720},
	shorttitle = {Seamless stitching of tile scan microscope images},
	url = {http://doi.wiley.com/10.1111/jmi.12236},
	doi = {10.1111/jmi.12236},
	language = {en},
	number = {3},
	urldate = {2016-07-01},
	journal = {Journal of Microscopy},
	author = {Legesse, F.B. and Chernavskaia, O. and Heuke, S. and Bocklitz, T. and Meyer, T. and Popp, J. and Heintzmann, R.},
	month = jun,
	year = {2015},
	pages = {223--232},
	file = {jmi12236.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KFSK57IF/jmi12236.pdf:application/pdf}
}

@article{mandula_line_2012,
	title = {Line scan - structured illumination microscopy super-resolution imaging in thick fluorescent samples},
	volume = {20},
	issn = {1094-4087},
	url = {https://www.osapublishing.org/abstract.cfm?URI=oe-20-22-24167},
	doi = {10.1364/OE.20.024167},
	language = {en},
	number = {22},
	urldate = {2016-06-22},
	journal = {Optics Express},
	author = {Mandula, Ondrej and Kielhorn, Martin and Wicker, Kai and Krampert, Gerhard and Kleppe, Ingo and Heintzmann, Rainer},
	month = oct,
	year = {2012},
	pages = {24167},
	file = {linescan.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KWVWF4T4/linescan.pdf:application/pdf}
}

@article{walsh_quantitative_2014,
	title = {Quantitative {Optical} {Imaging} of {Primary} {Tumor} {Organoid} {Metabolism} {Predicts} {Drug} {Response} in {Breast} {Cancer}},
	volume = {74},
	issn = {0008-5472, 1538-7445},
	url = {http://cancerres.aacrjournals.org/content/74/18/5184},
	doi = {10.1158/0008-5472.CAN-14-0663},
	abstract = {There is a need for technologies to predict the efficacy of cancer treatment in individual patients. Here, we show that optical metabolic imaging of organoids derived from primary tumors can predict the therapeutic response of xenografts and measure antitumor drug responses in human tumor–derived organoids. Optical metabolic imaging quantifies the fluorescence intensity and lifetime of NADH and FAD, coenzymes of metabolism. As early as 24 hours after treatment with clinically relevant anticancer drugs, the optical metabolic imaging index of responsive organoids decreased (P {\textless} 0.001) and was further reduced when effective therapies were combined (P {\textless} 5 × 10−6), with no change in drug-resistant organoids. Drug response in xenograft-derived organoids was validated with tumor growth measurements in vivo and staining for proliferation and apoptosis. Heterogeneous cellular responses to drug treatment were also resolved in organoids. Optical metabolic imaging shows potential as a high-throughput screen to test the efficacy of a panel of drugs to select optimal drug combinations. Cancer Res; 74(18); 5184–94. ©2014 AACR.},
	language = {en},
	number = {18},
	urldate = {2015-03-06},
	journal = {Cancer Research},
	author = {Walsh, Alex J. and Cook, Rebecca S. and Sanders, Melinda E. and Aurisicchio, Luigi and Ciliberto, Gennaro and Arteaga, Carlos L. and Skala, Melissa C.},
	month = sep,
	year = {2014},
	pmid = {25100563},
	pages = {5184--5194},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6G2BZ8FI/Walsh et al. - 2014 - Quantitative Optical Imaging of Primary Tumor Orga.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NV9IWAGC/Walsh et al. - 2014 - Quantitative Optical Imaging of Primary Tumor Orga.html:text/html}
}

@article{suh_cost_2005,
	title = {A cost comparison analysis of partial versus whole-breast irradiation after breast-conserving surgery for early-stage breast cancer},
	volume = {62},
	issn = {0360-3016},
	url = {http://www.sciencedirect.com/science/article/pii/S0360301604028494},
	doi = {10.1016/j.ijrobp.2004.10.039},
	abstract = {Purpose: To assess, if and for whom, there are cost savings associated with alternate breast radiotherapy (RT) techniques when compared with the conventional external beam-based whole-breast RT with a boost (WBRT-B).

Methods and Materials: Treatment planning and delivery utilization data were modeled for eight different breast RT techniques: (1) WBRT-B: 60 Gy in 30 fractions; (2) WBRT: 50 Gy in 25 fractions; (3) WBRT-accelerated (AC): 42.5 Gy in 16 fractions; (4) WBRT-intensity-modulated RT (IMRT): 60 Gy in 30 fractions; (5) accelerated partial breast irradiation (APBI)-IC, MammoSite: 34 Gy in 10 twice-daily fractions; (6) APBI-IT, HDR interstitial: 34 Gy in 10 twice-daily fractions; (7) APBI three-dimensional conformal RT (3D-CRT): 38.5 Gy in 10 twice-daily fractions; or (8) APBI-IMRT: 38.5 Gy in 10 twice-daily fractions. Costs incurred by payer (i.e., direct medical costs; 2003 Medicare Fee Schedule) and patient (i.e., direct nonmedical costs; time and travel) were estimated. Total societal costs were then calculated for each treatment approach.

Results: Not all efforts to reduce overall treatment time result in total cost savings. The least expensive partial breast-based RT approaches were the external beam techniques (APBI-3D-CRT, APBI-IMRT). Any reduced cost to patients for the HDR brachytherapy-based APBI regimens were overshadowed by substantial increases in cost to payers, resulting in higher total societal costs; the cost of HDR treatment delivery was primarily responsible for the increased direct medical cost. For the whole breast-based RT approaches, treating without a boost (WBRT) or with WBRT-AC reduced total costs. Overall, WBRT-AC was the least costly of all the regimens, in terms of costs to society; APBI approaches, in general, were favored over whole-breast techniques when only considering costs to patients.

Conclusions: Based on societal cost considerations, WBRT-AC appears to be the preferred approach. If one were to pursue a partial-breast RT regimen to minimize patient costs, it would be more advantageous from a societal perspective to pursue external beam-based approaches such as APBI-3D-CRT or APBI-IMRT in lieu of the brachytherapy-based regimens.},
	number = {3},
	urldate = {2016-07-04},
	journal = {International Journal of Radiation Oncology*Biology*Physics},
	author = {Suh, W. Warren and Pierce, Lori J. and Vicini, Frank A. and Hayman, James A.},
	month = jul,
	year = {2005},
	keywords = {BREAST cancer, Costs, Radiation},
	pages = {790--796},
	file = {1-s2.0-S0360301604028494-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JC3MIZDF/1-s2.0-S0360301604028494-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NP4DN435/S0360301604028494.html:text/html}
}

@article{ghaznavi_digital_2013,
	title = {Digital imaging in pathology: whole-slide imaging and beyond.},
	volume = {8},
	issn = {1553-4014},
	shorttitle = {Digital imaging in pathology},
	doi = {10.1146/annurev-pathol-011811-120902},
	journal = {Annual review of pathology},
	author = {Ghaznavi, Farzad},
	year = {2013},
	file = {Digital imaging in pathology\: whole-slide imaging and beyond. | Center for Computational Imaging and Personalized Diagnostics:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/42BI4C62/digital-imaging-pathology-whole-slide-imaging-and-beyond-0.html:text/html;Digital-imaging-in-pathology---whole-slide-imaging-and-beyond.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8QQRTW2I/Digital-imaging-in-pathology---whole-slide-imaging-and-beyond.pdf:application/pdf}
}

@article{yang_proliferation_2004,
	title = {Proliferation and collagen production of human patellar tendon fibroblasts in response to cyclic uniaxial stretching in serum-free conditions},
	volume = {37},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S002192900400034X},
	doi = {10.1016/j.jbiomech.2004.01.005},
	abstract = {We studied the effect of cyclic mechanical stretching on the proliferation and collagen mRNA expression and protein production of human patellar tendon fibroblasts under serum-free conditions. The role of transforming growth factor-β1 (TGF-β1) in collagen production by cyclically stretched tendon fibroblasts was also investigated. The tendon fibroblasts were grown in microgrooved silicone dishes, where the cells were highly elongated and aligned with the microgrooves. Cyclic uniaxial stretching with constant frequency and duration (0.5 Hz, 4 h) but varying magnitude of stretch (no stretch, 4\%, and 8\%) was applied to the silicone dishes. Following the period of stretching, the cells were rested for 20 h in stretching-conditioned medium to allow for cell proliferation. In separate experiments, the cells were stretched for 4 h and then rested for another 4 h. Samples of the medium, total cellular RNA and protein were used for analysis of collagen and TGF-β1 gene expression and production. It was found that there was a slight increase in fibroblast proliferation at 4\% and 8\% stretch, compared to that of non-stretched fibroblasts, where at 8\% stretch the increase was significant. It was also found that the gene expression and protein production of collagen type I and TGF-β1 increased in a stretching-magnitude-dependent manner. And, levels of collagen type III were not changed, despite gene expression levels of the protein being slightly increased. Furthermore, the exogenous addition of anti-TGF-β1 antibody eliminated the increase in collagen type I production under cyclic uniaxial stretching conditions. The results suggest that mechanical stretching can modulate proliferation of human tendon fibroblasts in the absence of serum and increase the cellular production of collagen type I, which is at least in part mediated by TGF-β1.},
	number = {10},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Yang, Guoguang and Crawford, Richard C. and Wang, James H-C.},
	month = oct,
	year = {2004},
	keywords = {Alternatives, collagen, Mechanobiology, Proliferation, Stretching, Tendon fibroblasts, TGF-β1},
	pages = {1543--1550},
	file = {collprolif.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ESN3FX6Q/collprolif.pdf:application/pdf}
}

@incollection{veltri_nuclear_2014,
	series = {Advances in {Experimental} {Medicine} and {Biology}},
	title = {Nuclear {Morphometry}, {Epigenetic} {Changes}, and {Clinical} {Relevance} in {Prostate} {Cancer}},
	copyright = {©2014 Springer Science+Business Media New York},
	isbn = {978-1-4899-8031-1 978-1-4899-8032-8},
	url = {http://link.springer.com/chapter/10.1007/978-1-4899-8032-8_4},
	abstract = {Nuclear structure alterations in cancer involve global genetic (mutations, amplifications, copy number variations, translocations, etc.) and epigenetic (DNA methylation and histone modifications) events that dramatically and dynamically spatially change chromatin, nuclear body, and chromosome organization. In prostate cancer (CaP) there appears to be early ({\textless}50 years) versus late ({\textgreater}60 years) onset clinically significant cancers, and we have yet to clearly understand the hereditary and somatic-based molecular pathways involved. We do know that once cancer is initiated, dedifferentiation of the prostate gland occurs with significant changes in nuclear structure driven by numerous genetic and epigenetic processes. This review focuses upon the nuclear architecture and epigenetic dynamics with potential translational clinically relevant applications to CaP. Further, the review correlates changes in the cancer-driven epigenetic process at the molecular level and correlates these alterations to nuclear morphological quantitative measurements. Finally, we address how we can best utilize this knowledge to improve the efficacy of personalized treatment of cancer.},
	language = {en},
	number = {773},
	urldate = {2016-04-21},
	booktitle = {Cancer {Biology} and the {Nuclear} {Envelope}},
	publisher = {Springer New York},
	author = {Veltri, Robert W. and Christudass, Christhunesa S.},
	editor = {Schirmer, Eric C. and Heras, Jose I. de las},
	year = {2014},
	note = {DOI: 10.1007/978-1-4899-8032-8\_4},
	keywords = {Biomedicine general, Cancer Research, Epigenetics, Medical Microbiology, Membrane Biology, Nuclear morphology, Nuclear roundness, PROSTATE cancer, Protein Science},
	pages = {77--99},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8ACBIDTA/Veltri and Christudass - 2014 - Nuclear Morphometry, Epigenetic Changes, and Clini.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZPQAT8MD/10.html:text/html}
}

@article{guo_image_2014,
	title = {An image processing pipeline to detect and segment nuclei in muscle fiber microscopic images},
	volume = {77},
	issn = {1097-0029},
	doi = {10.1002/jemt.22373},
	abstract = {Muscle fiber images play an important role in the medical diagnosis and treatment of many muscular diseases. The number of nuclei in skeletal muscle fiber images is a key bio-marker of the diagnosis of muscular dystrophy. In nuclei segmentation one primary challenge is to correctly separate the clustered nuclei. In this article, we developed an image processing pipeline to automatically detect, segment, and analyze nuclei in microscopic image of muscle fibers. The pipeline consists of image pre-processing, identification of isolated nuclei, identification and segmentation of clustered nuclei, and quantitative analysis. Nuclei are initially extracted from background by using local Otsu's threshold. Based on analysis of morphological features of the isolated nuclei, including their areas, compactness, and major axis lengths, a Bayesian network is trained and applied to identify isolated nuclei from clustered nuclei and artifacts in all the images. Then a two-step refined watershed algorithm is applied to segment clustered nuclei. After segmentation, the nuclei can be quantified for statistical analysis. Comparing the segmented results with those of manual analysis and an existing technique, we find that our proposed image processing pipeline achieves good performance with high accuracy and precision. The presented image processing pipeline can therefore help biologists increase their throughput and objectivity in analyzing large numbers of nuclei in muscle fiber images.},
	language = {eng},
	number = {8},
	journal = {Microscopy Research and Technique},
	author = {Guo, Yanen and Xu, Xiaoyin and Wang, Yuanyuan and Wang, Yaming and Xia, Shunren and Yang, Zhong},
	month = aug,
	year = {2014},
	pmid = {24777764},
	keywords = {Animals, Bayesian network, Bayes Theorem, Cell Nucleus, clustered nuclei, identification, Image Processing, Computer-Assisted, Mice, muscle fiber images, Muscle Fibers, Skeletal, watershed},
	pages = {547--559}
}

@article{azu_what_2009,
	title = {What is an {Adequate} {Margin} for {Breast}-{Conserving} {Surgery}? {Surgeon} {Attitudes} and {Correlates}},
	volume = {17},
	issn = {1068-9265, 1534-4681},
	shorttitle = {What is an {Adequate} {Margin} for {Breast}-{Conserving} {Surgery}?},
	url = {http://link.springer.com/article/10.1245/s10434-009-0765-1},
	doi = {10.1245/s10434-009-0765-1},
	abstract = {Background Re-excision is common in breast-conserving surgery (BCS), partly due to lack of consensus on margin definitions. A population-based surgeon sample was used to determine current attitudes toward margin width and identify characteristics associated with margin choice. Methods Breast cancer patients treated from 2005 to 2007 were identified from Los Angeles and Detroit Surveillance, Epidemiology, and End Results (SEER) registries. Pathology reports were used to identify their surgeons, who were surveyed (n = 418). Response rate was 74.6\% (n = 312). Mean surgeon age was 51.9 years, 17.8\% were female, and mean number of years in practice was 18.5. Results Wide variation in margin selection was noted among surgeons, and did not differ for invasive cancer and ductal carcinoma in situ (DCIS). In a scenario of T1 invasive cancer, 11\% of surgeons endorsed margins of tumor not touching ink (TNTI), 42\% of 1–2 mm, 28\% of ≥5 mm, and 19\% {\textgreater}1 cm as precluding need for re-excision before radiotherapy. On multivariate analysis, having 50\% or more of practice devoted to breast cancer independently predicted smaller margin choice (p = 0.03). For a patient with a 1.4-cm grade 2 estrogen receptor (ER)-positive DCIS without radiotherapy (RT) planned, 3\% of surgeons chose TNTI, 12\% 1–2 mm, 25\% ≥5 mm, and 61\% {\textgreater}1 cm as sufficient without re-excision. In the scenario of DCIS without RT, breast specialization independently predicted larger margin choice (p = 0.03). Gender and years in practice were not predictive of margin choice. Conclusions Wide variation in BCS margin definition exists. Variation is similar for invasive cancer and DCIS with RT, with more specialized surgeons choosing smaller margins. In DCIS without RT, more specialized surgeons favored larger margins. A standardized margin definition may significantly affect re-excision rates.},
	language = {en},
	number = {2},
	urldate = {2016-06-22},
	journal = {Annals of Surgical Oncology},
	author = {Azu, Michelle and Abrahamse, Paul and Katz, Steven J. and Jagsi, Reshma and Morrow, Monica},
	month = oct,
	year = {2009},
	pages = {558--563},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7B62524X/Azu et al. - 2009 - What is an Adequate Margin for Breast-Conserving S.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SDHIKJBT/s10434-009-0765-1.html:text/html}
}

@article{cowin_tissue_2004,
	title = {Tissue {Growth} and {Remodeling}},
	volume = {6},
	url = {http://dx.doi.org/10.1146/annurev.bioeng.6.040803.140250},
	doi = {10.1146/annurev.bioeng.6.040803.140250},
	abstract = {The growth and remodeling of a tissue depends on certain features in the history of its mechanical environment as well as its genetic makeup. The mechanical environment influences the tissue's developing morphology, the process of simply increasing the size of existing morphological structures, and the formation of the proteins of which the tissue is constructed. The relationships between genetic information, various epigenetic mechanisms and tissue development are discussed. The developmental growth and remodeling of most structural tissues are enhanced by the use of those tissues and retarded by their disuse. The mechanical or mathematical modeling of tissue growth and development using cellular automata models and continuum mechanical models is reviewed.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Annual Review of Biomedical Engineering},
	author = {Cowin, Stephen C.},
	year = {2004},
	pmid = {15255763},
	keywords = {adaptation, development, modeling, morphogenesis, simulation},
	pages = {77--107},
	file = {gandr.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TMR6VENG/gandr.pdf:application/pdf}
}

@article{schnitt_should_2012,
	title = {Should {Intraoperative} {Frozen} {Section} {Evaluation} of {Breast} {Lumpectomy} {Margins} {Become} {Routine} {Practice}?},
	volume = {138},
	copyright = {© American Society for Clinical Pathology},
	issn = {0002-9173, 1943-7722},
	url = {http://ajcp.oxfordjournals.org/content/138/5/635},
	doi = {10.1309/AJCPPQ1JGV0GJIAB},
	abstract = {In this issue of the Journal , Jorns et al1 report that intraoperative frozen section examination of breast lumpectomy margins was associated with a substantial reduction in the rate of reexcision. In their retrospective study, at some time after the initial lumpectomy a reexcision was performed in 48.9\% of patients who did not have frozen section margin evaluation compared with only 14.9\% of those in whom frozen section evaluation of the margins was performed. Further, these investigators developed a technique to overcome the methodological difficulties of attempting to cut frozen sections of fatty tissue such as margins of breast specimens. So if it is now technically feasible to obtain adequate frozen sections from lumpectomy margins and if intraoperative frozen section evaluations of these margins can reduce the need for a subsequent reexcision by almost 70\%, should pathologists the world over be gearing up to routinely freeze margins of breast lumpectomy specimens? To answer this question, we must first review some fundamental data on lumpectomy margins and their association with local recurrence, and put these data into current clinical context.

Various patient factors, treatment factors, and pathologic factors have been reported to be associated with an increased risk of recurrence in the ipsilateral breast (local recurrence) after breast-conserving treatment for invasive breast cancer and ductal carcinoma in situ (DCIS). Arguably the most important of these is the status of the microscopic margins of excision of the resected breast specimen. Positive margins (ie, invasive carcinoma or DCIS at an inked tissue edge) have consistently been associated with a higher risk of local recurrence than negative margins.2 Therefore, obtaining negative margins is the primary goal of breast-conserving surgery. Unfortunately, there is far from universal agreement as to what constitutes an adequate negative margin. In fact, results of surveys of surgeons and …},
	language = {en},
	number = {5},
	urldate = {2016-06-23},
	journal = {American Journal of Clinical Pathology},
	author = {Schnitt, Stuart J. and Morrow, Monica},
	month = nov,
	year = {2012},
	pmid = {23086762},
	pages = {635--638},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VKST2CB4/Schnitt and Morrow - 2012 - Should Intraoperative Frozen Section Evaluation of.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GX9G7S9X/635.html:text/html}
}

@article{fleming_intraoperative_2004,
	title = {Intraoperative margin assessment and re-excision rate in breast conserving surgery},
	volume = {30},
	issn = {0748-7983},
	url = {http://www.sciencedirect.com/science/article/pii/S0748798303002713},
	doi = {10.1016/j.ejso.2003.11.008},
	abstract = {Aim: The aim of this study was to assess the efficacy of intraoperative margin assessment in obtaining clear margins in conserving surgery for breast cancer.

Methods: Two hundred and twenty patients undergoing wide local excision (WLE) for core biopsy proven primary invasive breast cancer, during a 30 months period, were included in the study. Following surgical excision the breast specimen was orientated with sutures, inked using India ink and coloured pigments and incised to identify the tumour, maintaining orientation. The distance to the individual radial margins were estimated macroscopically by the pathologist and conveyed intraoperatively to the surgeon. A macroscopic tumour-margin distance of less than 10 mm was considered compromised and the margin(s) in question was then excised if feasible.

Results: Eighty-one patients (37\%) were judged to have compromised margins following intraoperative macroscopic evaluation and had at least one margin re-excised. Sixteen of the 81 patients (20\%) in this subgroup had compromised margins on microscopy and required a second operation. One hundred and thirty-nine patients (63\%) were deemed to have clear margins intraoperatively, subsequently confirmed on microscopic examination in 135 patients (97\%). Intraoperative macroscopic assessment of margin status was associated with 9.1\% of patients requiring a second operation. In the absence of intraoperative assessment of margin status a further 47 patients (21.4\%) would have required a second operation.

Conclusion: Intraoperative macroscopic margin assessment is an effective technique in reducing the number of second operative procedures in patients undergoing conserving surgery for primary invasive breast cancer.},
	number = {3},
	urldate = {2016-06-30},
	journal = {European Journal of Surgical Oncology (EJSO)},
	author = {Fleming, F. J and Hill, A. D. K and Mc Dermott, E. W and O'Doherty, A and O'Higgins, N. J and Quinn, C. M},
	month = apr,
	year = {2004},
	keywords = {BREAST cancer, Intraoperative, Margin assessment},
	pages = {233--237},
	file = {1-s2.0-S0748798303002713-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/R495B3XD/1-s2.0-S0748798303002713-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MR2FFR2B/S0748798303002713.html:text/html}
}

@article{morris_breast-conserving_1997,
	title = {Breast-conserving therapy vs mastectomy in early-stage breast cancer: a meta-analysis of 10-year survival},
	volume = {3},
	issn = {1081-4442},
	shorttitle = {Breast-conserving therapy vs mastectomy in early-stage breast cancer},
	abstract = {BACKGROUND: The randomized trials comparing breast-conserving therapy (BCT), i.e., surgery and radiation to the breast, with mastectomy in early-stage breast cancer use a variety of protocols. Meta-analysis may assist in understanding the impact of these differences on survival.
PURPOSE: To evaluate the possible variations of the relative efficacy of BCT and mastectomy in terms of overall survival according to tumor size, nodal status, and use of adjuvant radiation therapy.
METHODS: The most recent published results and, where available, updated patient-level data from randomized controlled trials of BCT and mastectomy for early-stage breast cancer were combined in a meta-analysis using a random effects model. Pooled survival rates and odds ratios were generated according to subgroups of nodal status and tumor size. Five- and 10-year odds ratios were also determined according to adjuvant radiation protocol.
RESULTS: The pooled odds ratio comparing 10-year survival for BCT and mastectomy was 0.91. The odds ratios comparing the two treatment regimens were not significant after grouping according to tumor size and nodal status. When more than 50\% of node-positive patients in both the mastectomy and BCT arms received adjuvant radiation, both arms had similar survival rates. When less than 50\% of node-positive patients in both arms received adjuvant nodal radiation, the odds ratio was 0.69, and patients receiving BCT had a survival advantage.
CONCLUSIONS: Patients allocated to BCT have survival rates at least as high as patients allocated to mastectomy. When all protocols were combined, nodal status and tumor size did not significantly alter the relative survival rates. However, under some conditions, particularly for node-positive patients, BCT may confer a relative survival advantage over mastectomy. In particular, mastectomy without adjuvant radiation appears to be inferior to BCT for node-positive patients.},
	language = {eng},
	number = {1},
	journal = {The Cancer Journal from Scientific American},
	author = {Morris, A. D. and Morris, R. D. and Wilson, J. F. and White, J. and Steinberg, S. and Okunieff, P. and Arriagada, R. and Lê, M. G. and Blichert-Toft, M. and van Dongen, J. A.},
	month = feb,
	year = {1997},
	pmid = {9072310},
	keywords = {Breast neoplasms, Combined Modality Therapy, Demography, Female, Humans, Mastectomy, Mastectomy, Segmental, Odds Ratio, Randomized Controlled Trials as Topic, Survival Analysis},
	pages = {6--12}
}

@article{provost_3d_2014,
	title = {3D ultrafast ultrasound imaging in vivo},
	volume = {59},
	issn = {1361-6560},
	doi = {10.1088/0031-9155/59/19/L1},
	abstract = {Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra--and inter-observer variability.},
	language = {eng},
	number = {19},
	journal = {Physics in Medicine and Biology},
	author = {Provost, Jean and Papadacci, Clement and Arango, Juan Esteban and Imbault, Marion and Fink, Mathias and Gennisson, Jean-Luc and Tanter, Mickael and Pernot, Mathieu},
	month = oct,
	year = {2014},
	pmid = {25207828},
	pages = {L1--L13}
}

@article{broker_cell_2005,
	title = {Cell {Death} {Independent} of {Caspases}: {A} {Review}},
	volume = {11},
	issn = {1078-0432, 1557-3265},
	shorttitle = {Cell {Death} {Independent} of {Caspases}},
	url = {http://clincancerres.aacrjournals.org/content/11/9/3155},
	doi = {10.1158/1078-0432.CCR-04-2223},
	abstract = {Patterns of cell death have been divided into apoptosis, which is actively executed by specific proteases, the caspases, and accidental necrosis. However, there is now accumulating evidence indicating that cell death can occur in a programmed fashion but in complete absence and independent of caspase activation. Alternative models of programmed cell death (PCD) have therefore been proposed, including autophagy, paraptosis, mitotic catastrophe, and the descriptive model of apoptosis-like and necrosis-like PCD. Caspase-independent cell death pathways are important safeguard mechanisms to protect the organism against unwanted and potential harmful cells when caspase-mediated routes fail but can also be triggered in response to cytotoxic agents or other death stimuli. As in apoptosis, the mitochondrion can play a key role but also other organelles such as lysosomes and the endoplasmic reticulum have an important function in the release and activation of death factors such as cathepsins, calpains, and other proteases. Here we review the various models of PCD and their death pathways at molecular and organelle level and discuss the relevance of the growing knowledge of caspase-independent cell death pathways for cancer.},
	language = {en},
	number = {9},
	urldate = {2015-03-06},
	journal = {Clinical Cancer Research},
	author = {Bröker, Linda E. and Kruyt, Frank A. E. and Giaccone, Giuseppe},
	month = may,
	year = {2005},
	pmid = {15867207},
	keywords = {apoptosis, death pathway, programmed cell death},
	pages = {3155--3162},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6VNE9XQK/Bröker et al. - 2005 - Cell Death Independent of Caspases A Review.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/88A639M9/Bröker et al. - 2005 - Cell Death Independent of Caspases A Review.html:text/html}
}

@article{taber_towards_2009,
	title = {Towards a unified theory for morphomechanics},
	volume = {367},
	issn = {1364-503X, 1471-2962},
	url = {http://rsta.royalsocietypublishing.org/content/367/1902/3555},
	doi = {10.1098/rsta.2009.0100},
	abstract = {Mechanical forces are closely involved in the construction of an embryo. Experiments have suggested that mechanical feedback plays a role in regulating these forces, but the nature of this feedback is poorly understood. Here, we propose a general principle for the mechanics of morphogenesis, as governed by a pair of evolution equations based on feedback from tissue stress. In one equation, the rate of growth (or contraction) depends on the difference between the current tissue stress and a target (homeostatic) stress. In the other equation, the target stress changes at a rate that depends on the same stress difference. The parameters in these morphomechanical laws are assumed to depend on stress rate. Computational models are used to illustrate how these equations can capture a relatively wide range of behaviours observed in developing embryos, as well as show the limitations of this theory. Specific applications include growth of pressure vessels (e.g. the heart, arteries and brain), wound healing and sea urchin gastrulation. Understanding the fundamental principles of tissue construction can help engineers design new strategies for creating replacement tissues and organs in vitro.},
	language = {en},
	number = {1902},
	urldate = {2014-11-10},
	journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
	author = {Taber, Larry A.},
	month = sep,
	year = {2009},
	pmid = {19657011},
	keywords = {Biomechanics, computational models, development, growth, Mechanobiology, morphogenesis},
	pages = {3555--3583},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RXNNI94K/Taber - 2009 - Towards a unified theory for morphomechanics.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/X4I6A94K/3555.html:text/html}
}

@article{ameye_abnormal_2002,
	title = {Abnormal collagen fibrils in tendons of biglycan/fibromodulin-deficient mice lead to gait impairment, ectopic ossification, and osteoarthritis},
	volume = {16},
	issn = {0892-6638, 1530-6860},
	url = {http://www.fasebj.org/content/16/7/673},
	doi = {10.1096/fj.01-0848com},
	abstract = {Small leucine-rich proteoglycans (SLRPs) regulate extracellular matrix organization, a process essential in development, tissue repair, and metastasis. In vivo interactions of biglycan and fibromodulin, two SLRPs highly expressed in tendons and bones, were investigated by generating biglycan/fibromodulin double-deficient mice. Here we show that collagen fibrils in tendons from mice deficient in biglycan and/or fibromodulin are structurally and mechanically altered resulting in unstable joints. As a result, the mice develop successively and progressively 1) gait impairment, 2) ectopic tendon ossification, and 3) severe premature osteoarthritis. Forced use of the joints increases ectopic ossification and osteoarthritis in the double-deficient mice, further indicating that structurally weak tendons cause the phenotype. The study shows that mutations in SLRPs may predispose to osteoarthritis and offers a valuable and unique animal model for spontaneous osteoarthritis characterized by early onset and a rapid progression of the disease—Ameye, L., Aria, D., Jepsen, K., Oldberg, A., Xu, T., Young, M. F. Abnormal collagen fibrils in tendons of biglycan/fibromodulin-deficient mice lead to gait impairment, ectopic ossification, and osteoarthritis.},
	language = {en},
	number = {7},
	urldate = {2014-11-03},
	journal = {The FASEB Journal},
	author = {Ameye, Laurent and Aria, Dean and Jepsen, Karl and Oldberg, Ake and Xu, Tianshun and Young, Marian F.},
	month = may,
	year = {2002},
	pmid = {11978731},
	keywords = {bone, cartilage, leucine-rich, matrix, proteoglycans},
	pages = {673--680},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SMX7UADI/f.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FDRECCFM/Ameye et al. - 2002 - Abnormal collagen fibrils in tendons of biglycanf.html:text/html}
}

@misc{_measureobjectsizeshape_????,
	title = {{MeasureObjectSizeShape}},
	url = {http://d1zymp9ayga15t.cloudfront.net/CPmanual/MeasureObjectSizeShape.html},
	urldate = {2016-07-02},
	file = {MeasureObjectSizeShape:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PPE9FBNI/MeasureObjectSizeShape.html:text/html}
}

@article{hino_rapid_2016,
	title = {Rapid {Cancer} {Fluorescence} {Imaging} {Using} {A} γ-{Glutamyltranspeptidase}-{Specific} {Probe} {For} {Primary} {Lung} {Cancer}},
	volume = {9},
	issn = {1936-5233},
	url = {http://www.sciencedirect.com/science/article/pii/S1936523316300080},
	doi = {10.1016/j.tranon.2016.03.007},
	abstract = {BACKGROUND: We set out to examine the activity of γ-glutamyltranspeptidase (GGT) in lung cancer and the validity of γ-glutamyl hydroxymethyl rhodamine green (gGlu-HMRG) for intraoperative imaging of primary lung cancer. METHODS: GGT activities and mRNA expression levels of GGT1 (one of the GGT subtypes) in five human lung cancer cell lines were examined by fluorescence imaging and quantitative reverse transcription polymerase chain reaction. In vivo imaging of an orthotopic A549 xenograft model in nude mice was performed to confirm its applicability to intraoperative imaging. Furthermore, ex vivo imaging of 73 specimens from lung cancer patients were performed and analyzed to calculate the sensitivity/specificity of gGlu-HMRG for lung cancer diagnosis. RESULTS: GGT activities and mRNA expression levels of GGT1 are diverse depending on cell type; A549, H441, and H460 showed relatively high GGT activities and expression levels, whereas H82 and H226 showed lower values. In the in vivo mouse model study, tiny pleural dissemination and hilar/mediastinal lymph node metastasis (less than 1 mm in diameter) were clearly detected 15 minutes after topical application of gGlu-HMRG. In the ex vivo study of specimens from patients, the sensitivity and specificity of gGlu-HMRG were calculated to be 43.8\% (32/73) and 84.9\% (62/73), respectively. When limited to female patients, never smokers, and adenocarcinomas, these values were 78.9\% (15/19) and 73.7\% (14/19), respectively. CONCLUSIONS: Although GGT activity of lung cancer cells vary, gGlu-HMRG can serve as an intraoperative imaging tool to detect small foci of lung cancer when such cells have sufficient GGT activity.},
	number = {3},
	urldate = {2016-06-24},
	journal = {Translational Oncology},
	author = {Hino, Haruaki and Kamiya, Mako and Kitano, Kentaro and Mizuno, Kazue and Tanaka, Sayaka and Nishiyama, Nobuhiro and Kataoka, Kazunori and Urano, Yasuteru and Nakajima, Jun},
	month = jun,
	year = {2016},
	pages = {203--210},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UTUEHJV8/Hino et al. - 2016 - Rapid Cancer Fluorescence Imaging Using A γ-Glutam.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QE277FZM/S1936523316300080.html:text/html}
}

@article{down_oncological_2013,
	title = {Oncological {Advantages} of {Oncoplastic} {Breast}-{Conserving} {Surgery} in {Treatment} of {Early} {Breast} {Cancer}},
	volume = {19},
	copyright = {© 2013 Wiley Periodicals, Inc.},
	issn = {1524-4741},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1111/tbj.12047/abstract},
	doi = {10.1111/tbj.12047},
	abstract = {The standard approach to breast-conserving surgery is wide local excision of the tumor and radiotherapy. However, a significant number of patients require further surgery to obtain oncologically clear margins, and may obtain a poor cosmetic result following adjuvant radiotherapy. Oncoplastic techniques may result in improved cosmesis, but few studies have investigated the oncological advantage of this approach. The aim of this retrospective study was to compare tumor clearance and the need for further margin excision following standard wide local excision (group A, 121 patients), and oncoplastic breast-conserving surgery (group B, 37 patients). These techniques included therapeutic mammoplasty, sub-axillary fat pad rotation mammoplasty, thoraco-epigastric flap, and central flap. Compared to standard surgery (group A), oncoplastic techniques (group B) can be employed for significantly larger tumors (17.6 mm versus 23.9 mm, p = 0.002). Oncoplastic breast-conserving surgery results in higher mean specimen weights (58.1 g versus 231.1 g, p {\textless} 0.0001), higher specimen volumes (112.3 cm3 versus 484.5 cm3, p {\textless} 0.0001), and wider clear margins (6.1 mm versus 14.3 mm, p {\textless} 0.0001), resulting in lower rates of further surgery (28.9\% versus 5.4\%, p = 0.002). There was no statistical increase in complication rates following oncoplastic surgery. Oncoplastic breast-conserving surgery is more successful than standard wide local excision in treating larger tumors and obtaining wider radial margins, thus reducing the need for further margin excision, which delays adjuvant therapy. There was no increase in postoperative complication rate using an oncoplastic approach.},
	language = {en},
	number = {1},
	urldate = {2016-06-23},
	journal = {The Breast Journal},
	author = {Down, Sue K. and Jha, Pankaj K., MBBS MS MSc and Burger, Amy and Hussien, Maged I.},
	month = jan,
	year = {2013},
	keywords = {breast-conserving surgery, breast reconstruction, mammoplasty},
	pages = {56--63},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GXBA64WD/Down et al. - 2013 - Oncological Advantages of Oncoplastic Breast-Conse.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QNQS5WSU/abstract.html:text/html}
}

@article{ambrosi_perspectives_2011,
	title = {Perspectives on biological growth and remodeling},
	volume = {59},
	issn = {0022-5096},
	url = {http://www.sciencedirect.com/science/article/pii/S0022509610002516},
	doi = {10.1016/j.jmps.2010.12.011},
	abstract = {The continuum mechanical treatment of biological growth and remodeling has attracted considerable attention over the past fifteen years. Many aspects of these problems are now well-understood, yet there remain areas in need of significant development from the standpoint of experiments, theory, and computation. In this perspective paper we review the state of the field and highlight open questions, challenges, and avenues for further development.},
	number = {4},
	urldate = {2014-11-04},
	journal = {Journal of the Mechanics and Physics of Solids},
	author = {Ambrosi, D. and Ateshian, G. A. and Arruda, E. M. and Cowin, S. C. and Dumais, J. and Goriely, A. and Holzapfel, G. A. and Humphrey, J. D. and Kemkemer, R. and Kuhl, E. and Olberding, J. E. and Taber, L. A. and Garikipati, K.},
	month = apr,
	year = {2011},
	keywords = {Chemo-mechanics, Computational mechanics, Mechanotransduction, morphogenesis, Thermodynamics},
	pages = {863--883},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FW834D6V/Ambrosi et al. - 2011 - Perspectives on biological growth and remodeling.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MX2F2MDN/S0022509610002516.html:text/html}
}

@article{richardson_abstract_2013,
	title = {Abstract {P}5-15-05: {The} impact of a change in margin width policy on rates of re-operation for breast conserving surgery},
	volume = {73},
	copyright = {©2013 American Association for Cancer Research.},
	issn = {0008-5472, 1538-7445},
	shorttitle = {Abstract {P}5-15-05},
	url = {http://cancerres.aacrjournals.org/content/73/24_Supplement/P5-15-05},
	doi = {10.1158/0008-5472.SABCS13-P5-15-05},
	abstract = {Background: The definition of a negative surgical margin in prospective randomized trials of breast conserving surgery (BCS) is ‘no tumour at ink’ with no conclusive evidence that wider margins of 1mm, 2mm or 5mm are essential for optimal outcomes in the era of modern radiotherapy techniques and systemic therapy. Our group have previously shown that residual tumour is present in only 6\% of specimens when re-excision is prompted by a margin of 2 – 5mm compared with 40\% for when primary tumour margins are ≤2mm. An audit was undertaken to determine the effect of a change in margin mandate from 5mm to 2mm on rates of re-excision and residual disease in re-excision specimens.
Methods: Data were collected retrospectively from 410 women undergoing BCS for symptomatic and screen-detected invasive and non-invasive disease between November 1st 2009 and October 31st 2011. Rates of re-excision and residual disease in re-excision specimens were compared for 215 patients in the 12 months immediately before (Group 1) and 195 patients in a similar time period after (Group 2) a change in margin policy. All impalpable lesions had conventional intra-operative specimen imaging. Statistical analysis was performed using Fisher's exact test.
Results: Amongst these 410 BCS patients, there were similar proportions of symptomatic and screen-detected cases in each group, but slightly more wire-localized procedures in group 2 (59.5\% versus 48.4\%; p = 0.029). Rates of patient re-excision were 21.9\% (47/215) for group 1 and 25.6\% (50/195) for group 2 with no significant difference between margin mandates of 5mm and 2mm respectively (p = 0.42). Eleven patients in each group had a completion mastectomy with 6 and 4 patients in Groups 1 and 2 respectively undergoing {\textgreater}1 re-excision. There was a trend for an increased proportion of residual disease following a change in margin policy (30.2\% group 1, 40.7\% Group2; p = 0.32) and the majority of re-excision cases had ductal carcinoma in situ alone or combined with invasive cancer in the primary specimen ({\textgreater}80\%). There was no significant difference in the proportion of wire-localizations for all re-excisions (≥1) between Group 1 (31/42 = 74\%) and Group 2 (25/43 = 58\%) (p = 0.17).
Conclusion: A reduction in target surgical margin width from 5mm to 2mm has not decreased rates of re-excision but yields a trend towards an increase in proportion of specimens with residual disease. Longer follow up is required to assess rates of local control and further analyses will ascertain whether a less stringent margin policy is more appropriate for contemporary BCS where adjuvant treatments contribute to local control.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-15-05.},
	language = {en},
	number = {24 Supplement},
	urldate = {2016-06-22},
	journal = {Cancer Research},
	author = {Richardson, C. E. and Arima, Y. and Wishart, G. C. and Ambler, G. K. and Benson, J. R.},
	month = dec,
	year = {2013},
	pages = {P5--15--05--P5--15--05},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AD2FIT9T/P5-15-05.html:text/html}
}

@techreport{curran_medical_2015,
	address = {Melbourne, Australia},
	type = {{IBISWorld} {Industry} {Report} 33451b},
	title = {Medical {Device} {Manufacturing} in the {US}},
	url = {http://clients1.ibisworld.com.libproxy.tulane.edu:2048/reports/us/industry/default.aspx?entid=764},
	urldate = {2015-11-22},
	institution = {IBISWorld Services},
	author = {Curran, Jack},
	month = oct,
	year = {2015},
	file = {IBISWorld Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UQ7TKK73/login.html:text/html}
}

@patent{chiang_optical_2013,
	title = {Optical imaging system using structured illumination},
	url = {http://www.google.com/patents/US20130100525},
	abstract = {The present invention discloses an optical system to generate incoherent structured illumination and an optical imaging system using incoherent structured illumination. The optical system includes: at least one coherent light source, a spatial light modulator, a plurality of optical lenses, a rotating diffuser for destroying the coherence of the structured illumination pattern, an objective, and a stage accommodating samples. The optical imaging system using incoherent structured illumination includes: an optical microscope having an objective and a beam splitter, a charge-coupled device camera for recording a sequence of images of the samples, a stage for accommodating and moving samples; a coherent light source; a spatial light modulator; a quarter wave plate, a plurality of optical lenses and mirrors; and a diffuser rotating 360 degrees or vibrating rapidly around the axis of the optical path continuously.},
	nationality = {United States},
	assignee = {Su Yu CHIANG,},
	number = {US20130100525 A1},
	urldate = {2016-07-05},
	author = {CHIANG, Su Yu and CHANG, Bo Jui and YUH, Jih Young and CHOU, Li Jun},
	month = apr,
	year = {2013},
	note = {U.S. Classification 359/385; International Classification G02B21/06; Cooperative Classification G02B27/58, G02B27/48, G02B21/14, G02B21/082},
	file = {Google Patents PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZNGM6KXW/CHIANG et al. - 2013 - Optical imaging system using structured illuminati.pdf:application/pdf}
}

@article{kunos_breast_2006,
	title = {Breast {Conservation} {Surgery} {Achieving} ≥ 2 mm {Tumor}-{Free} {Margins} {Results} in {Decreased} {Local}-{Regional} {Recurrence} {Rates}},
	volume = {12},
	issn = {1524-4741},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1075-122X.2006.00181.x/abstract},
	doi = {10.1111/j.1075-122X.2006.00181.x},
	abstract = {Abstract:  Whether cosmetically acceptable tumor-free (≥2 mm) surgical margins reduce the local-regional recurrence risk for patients treated with fractionated radiation therapy, chemotherapy, and hormonal therapy is unknown. The benefit of a minimum cosmetically acceptable tumor-free margin remains speculative because no contemporary studies have investigated the extent of invasive disease infiltration within the breast beyond the primary tumor. To address these clinical issues, we conducted a retrospective study of 341 women diagnosed with stage I or II invasive breast cancer to determine the rate of local in-breast, elsewhere in-breast, and ipsilateral regional lymph node recurrences of breast cancer after conservation surgery achieving either tumor-free (≥2 mm) or close ({\textgreater}0 mm to {\textless}2 mm) surgical margins followed by whole breast radiation therapy over a 6-year period from January 1996 to December 2002. Women may have received adjuvant chemotherapy or hormonal therapy as clinically indicated. After a median follow-up of 56 months from the completion of breast conservation surgery, 14 of the 341 women (4.1\%) developed breast cancer recurrences. Crude ipsilateral recurrence rates were 1.8\% (4 of 222) for tumor-free (≥2 mm) versus 8.4\% (10 of 119) for close ({\textgreater}0 mm to {\textless}2 mm) surgical margins (p = 0.007). The estimated 5-year cumulative local recurrence rate was significantly less for women with tumor-free margins (2.1\%) as compared to close surgical margins (8.9\%) (p = 0.004). Multivariate analyses identified negative estrogen receptor expression (p = 0.004), close surgical margins (p = 0.012), and the presence of angiolymphatic invasion (p = 0.040) as prognostic factors for local-regional recurrences. Microscopically the extent of invasive disease infiltration beyond the primary tumor was on average 1 mm, with all measured invasive disease less than 1 cm. Based on our findings, cosmetically acceptable tumor-free (≥2 mm) surgical margins significantly reduce local in-breast and regional lymph node recurrences with fractionated radiation therapy, chemotherapy, and hormonal therapy.},
	language = {en},
	number = {1},
	urldate = {2016-06-28},
	journal = {The Breast Journal},
	author = {Kunos, Charles and Latson, Larry and Overmoyer, Beth and Silverman, Paula and Shenk, Robert and Kinsella, Timothy and Lyons, Janice},
	month = jan,
	year = {2006},
	keywords = {breast radiation therapy, breast recurrence, breast surgical margins},
	pages = {28--36},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W6EU95X9/Kunos et al. - 2006 - Breast Conservation Surgery Achieving ≥ 2 mm Tumor.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4IKAGRSP/abstract\;jsessionid=DFEBB0F0E5D60335F36F04BB6730A6E4.html:text/html}
}

@misc{year_infographic:_????,
	title = {Infographic: {More} {Cyclists} {In} {A} {Country} {Means} {Fewer} {Fatal} {Crashes}},
	shorttitle = {Infographic},
	url = {http://www.statista.com/chart/3261/more-cyclists-in-a-country-means-fewer-fatal-crashes/},
	abstract = {This chart shows bicycle travel per inhabitant per year (km) and number of cyclists killed per billion km.},
	urldate = {2015-03-10},
	journal = {Statista Infographics},
	author = {year, This chart shows bicycle travel per inhabitant per and Km, Number of Cyclists Killed Per Billion},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JPKAXKG8/year and Km - Infographic More Cyclists In A Country Means Fewe.html:text/html}
}

@article{searle_introduction:_2014,
	title = {Introduction: {Addressing} the hard problem},
	volume = {13},
	issn = {02196352},
	shorttitle = {Introduction},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=96984468&site=ehost-live&scope=site},
	doi = {10.1142/S0219635214020014},
	abstract = {The article discusses the connection between consciousness and the brain. It provides overview of the factors that motivate the person's conscious state and the role of the lower level neuronal process of the brain. The author also mentions the main elements of the history that describe the relationship of consciousness and the brain which should be overcome to understand them.},
	number = {2},
	urldate = {2016-12-05},
	journal = {Journal of Integrative Neuroscience},
	author = {Searle, John R.},
	month = jun,
	year = {2014},
	keywords = {Brain, Brain damage, Consciousness, Mind \& body, Perception},
	pages = {vii--xi},
	file = {EBSCO Full Text:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3IQCI2PA/Searle - 2014 - Introduction Addressing the hard problem.pdf:application/pdf}
}

@article{delorme_eeglab:_2004,
	title = {{EEGLAB}: an open source toolbox for analysis of single-trial {EEG} dynamics including independent component analysis},
	volume = {134},
	issn = {0165-0270},
	shorttitle = {{EEGLAB}},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027003003479},
	doi = {10.1016/j.jneumeth.2003.10.009},
	abstract = {We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive ‘pop’ functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A ‘plug-in’ facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and open source development, together with sample data, user tutorial and extensive documentation.},
	number = {1},
	urldate = {2015-02-18},
	journal = {Journal of Neuroscience Methods},
	author = {Delorme, Arnaud and Makeig, Scott},
	month = mar,
	year = {2004},
	keywords = {EEG, ERP, ICA, Matlab, Single-trial, Software, Spectral decomposition},
	pages = {9--21},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AR8P452P/AR8P452P.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZVBWCDCA/Delorme and Makeig - 2004 - EEGLAB an open source toolbox for analysis of sin.html:text/html}
}

@article{maxmen_hard_2012,
	title = {The hard facts},
	volume = {485},
	copyright = {© 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v485/n7400_supp/full/485S50a.html},
	doi = {10.1038/485S50a},
	abstract = {For women worldwide, breast cancer is the most common cancer diagnosed and has the highest death toll. With improvements in screening and treatments over the past 50 years, more women are living longer, but the numbers reveal some tough challenges. By Amy Maxmen.},
	language = {en},
	number = {7400},
	urldate = {2015-08-31},
	journal = {Nature},
	author = {Maxmen, Amy},
	month = may,
	year = {2012},
	keywords = {Cancer, Epidemiology, Molecular biology},
	pages = {S50--S51},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SQT4VZFT/Maxmen - 2012 - The hard facts.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7F8HNVSZ/Maxmen - 2012 - The hard facts.html:text/html}
}

@article{desantis_breast_2014,
	title = {Breast cancer statistics, 2013},
	volume = {64},
	copyright = {© 2013 American Cancer Society, Inc.},
	issn = {1542-4863},
	url = {http://onlinelibrary.wiley.com/doi/10.3322/caac.21203/abstract},
	doi = {10.3322/caac.21203},
	abstract = {In this article, the American Cancer Society provides an overview of female breast cancer statistics in the United States, including data on incidence, mortality, survival, and screening. Approximately 232,340 new cases of invasive breast cancer and 39,620 breast cancer deaths are expected to occur among US women in 2013. One in 8 women in the United States will develop breast cancer in her lifetime. Breast cancer incidence rates increased slightly among African American women; decreased among Hispanic women; and were stable among whites, Asian Americans/Pacific Islanders, and American Indians/Alaska Natives from 2006 to 2010. Historically, white women have had the highest breast cancer incidence rates among women aged 40 years and older; however, incidence rates are converging among white and African American women, particularly among women aged 50 years to 59 years. Incidence rates increased for estrogen receptor-positive breast cancers in the youngest white women, Hispanic women aged 60 years to 69 years, and all but the oldest African American women. In contrast, estrogen receptor-negative breast cancers declined among most age and racial/ethnic groups. These divergent trends may reflect etiologic heterogeneity and the differing effects of some factors, such as obesity and parity, on risk by tumor subtype. Since 1990, breast cancer death rates have dropped by 34\% and this decrease was evident in all racial/ethnic groups except American Indians/Alaska Natives. Nevertheless, survival disparities persist by race/ethnicity, with African American women having the poorest breast cancer survival of any racial/ethnic group. Continued progress in the control of breast cancer will require sustained and increased efforts to provide high-quality screening, diagnosis, and treatment to all segments of the population. CA Cancer J Clin 2014;64:52–62. © 2013 American Cancer Society, Inc.},
	language = {en},
	number = {1},
	urldate = {2016-06-23},
	journal = {CA: A Cancer Journal for Clinicians},
	author = {DeSantis, Carol and Ma, Jiemin and Bryan, Leah and Jemal, Ahmedin},
	month = jan,
	year = {2014},
	keywords = {Breast neoplasms, Epidemiology, health disparities, screening and early detection},
	pages = {52--62},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZIAN9WUT/DeSantis et al. - 2014 - Breast cancer statistics, 2013.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TQCG6BIB/abstract.html:text/html}
}

@article{selman_mcneal_2011,
	title = {The {McNeal} {Prostate}: {A} {Review}},
	volume = {78},
	issn = {0090-4295},
	shorttitle = {The {McNeal} {Prostate}},
	url = {http://www.sciencedirect.com/science/article/pii/S0090429511021376},
	doi = {10.1016/j.urology.2011.07.1395},
	abstract = {Prostate anatomy has been the subject of controversy for 200 years. In the 19th and early 20th centuries, lobar anatomy was accepted. Beginning in 1968 and for the next 25 years, John E. McNeal presented his view of prostate anatomy in terms of 4 anatomic zones. The transition zone was introduced in 1978 as the site of development of benign prostatic hyperplasia. This review was undertaken to describe the evolution of McNeal’s anatomic concepts.},
	number = {6},
	urldate = {2016-12-12},
	journal = {Urology},
	author = {Selman, Steven H.},
	month = dec,
	year = {2011},
	pages = {1224--1228},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RCNWKRW8/Selman - 2011 - The McNeal Prostate A Review.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S63FJ649/S0090429511021376.html:text/html}
}

@article{ryerson_annual_2016,
	title = {Annual {Report} to the {Nation} on the {Status} of {Cancer}, 1975-2012, featuring the increasing incidence of liver cancer},
	volume = {122},
	copyright = {© 2016 American Cancer Society},
	issn = {1097-0142},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/cncr.29936/abstract},
	doi = {10.1002/cncr.29936},
	abstract = {BACKGROUND

Annual updates on cancer occurrence and trends in the United States are provided through an ongoing collaboration among the American Cancer Society (ACS), the Centers for Disease Control and Prevention (CDC), the National Cancer Institute (NCI), and the North American Association of Central Cancer Registries (NAACCR). This annual report highlights the increasing burden of liver and intrahepatic bile duct (liver) cancers.


METHODS

Cancer incidence data were obtained from the CDC, NCI, and NAACCR; data about cancer deaths were obtained from the CDC's National Center for Health Statistics (NCHS). Annual percent changes in incidence and death rates (age-adjusted to the 2000 US Standard Population) for all cancers combined and for the leading cancers among men and women were estimated by joinpoint analysis of long-term trends (incidence for 1992-2012 and mortality for 1975-2012) and short-term trends (2008-2012). In-depth analysis of liver cancer incidence included an age-period-cohort analysis and an incidence-based estimation of person-years of life lost because of the disease. By using NCHS multiple causes of death data, hepatitis C virus (HCV) and liver cancer-associated death rates were examined from 1999 through 2013.


RESULTS

Among men and women of all major racial and ethnic groups, death rates continued to decline for all cancers combined and for most cancer sites; the overall cancer death rate (for both sexes combined) decreased by 1.5\% per year from 2003 to 2012. Overall, incidence rates decreased among men and remained stable among women from 2003 to 2012. Among both men and women, deaths from liver cancer increased at the highest rate of all cancer sites, and liver cancer incidence rates increased sharply, second only to thyroid cancer. Men had more than twice the incidence rate of liver cancer than women, and rates increased with age for both sexes. Among non-Hispanic (NH) white, NH black, and Hispanic men and women, liver cancer incidence rates were higher for persons born after the 1938 to 1947 birth cohort. In contrast, there was a minimal birth cohort effect for NH Asian and Pacific Islanders (APIs). NH black men and Hispanic men had the lowest median age at death (60 and 62 years, respectively) and the highest average person-years of life lost per death (21 and 20 years, respectively) from liver cancer. HCV and liver cancer-associated death rates were highest among decedents who were born during 1945 through 1965.


CONCLUSIONS

Overall, cancer incidence and mortality declined among men; and, although cancer incidence was stable among women, mortality declined. The burden of liver cancer is growing and is not equally distributed throughout the population. Efforts to vaccinate populations that are vulnerable to hepatitis B virus (HBV) infection and to identify and treat those living with HCV or HBV infection, metabolic conditions, alcoholic liver disease, or other causes of cirrhosis can be effective in reducing the incidence and mortality of liver cancer. Cancer 2016;122:1312–1337. © 2016 American Cancer Society.},
	language = {en},
	number = {9},
	urldate = {2016-06-23},
	journal = {Cancer},
	author = {Ryerson, A. Blythe and Eheman, Christie R. and Altekruse, Sean F. and Ward, John W. and Jemal, Ahmedin and Sherman, Recinda L. and Henley, S. Jane and Holtzman, Deborah and Lake, Andrew and Noone, Anne-Michelle and Anderson, Robert N. and Ma, Jiemin and Ly, Kathleen N. and Cronin, Kathleen A. and Penberthy, Lynne and Kohler, Betsy A.},
	month = may,
	year = {2016},
	keywords = {and End Results (SEER), Cancer, Epidemiology, incidence, liver cancer, mortality, National Program of Cancer Registries (NPCR), North American Association of Central Cancer Registries (NAACCR), Surveillance, survival, trends, viral hepatitis},
	pages = {1312--1337},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XC9JU6HK/Ryerson et al. - 2016 - Annual Report to the Nation on the Status of Cance.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9KZUKMF5/abstract.html:text/html}
}

@article{kummerow_kl_nationwide_2015,
	title = {{NAtionwide} trends in mastectomy for early-stage breast cancer},
	volume = {150},
	issn = {2168-6254},
	url = {http://dx.doi.org/10.1001/jamasurg.2014.2895},
	doi = {10.1001/jamasurg.2014.2895},
	abstract = {Importance 
Accredited breast centers in the United States are measured on performance of breast conservation surgery (BCS) in the majority of women with early-stage breast cancer. Prior research in regional and limited national cohorts suggests a recent shift toward increasing performance of mastectomy in patients eligible for BCS.Objective
To examine whether mastectomy rates in patients eligible for BCS are increasing over time nationwide, and are associated with coincident increases in breast reconstruction and bilateral mastectomy for unilateral disease.Design, Setting, and Participants
We performed a retrospective cohort study of temporal trends in performance of mastectomy for early-stage breast cancer using multivariable logistic regression modeling to adjust for pertinent covariates and interactions. We studied more than 1.2 million adult women treated at centers accredited by the American Cancer Society and the American College of Surgeons Commission on Cancer from January 1, 1998, to December 31, 2011, using the National Cancer Data Base.Exposures
Year of breast cancer diagnosis.Main Outcomes and Measures
Proportion of women with early-stage breast cancer who underwent mastectomy. Secondary outcome measures include temporal trends in breast reconstruction and bilateral mastectomy for unilateral disease.Results
A total of 35.5\% of the study cohort underwent mastectomy. The adjusted odds of mastectomy in BCS-eligible women increased 34\% during the most recent 8 years of the cohort, with an odds ratio of 1.34 (95\% CI, 1.31-1.38) in 2011 relative to 2003. Rates of increase were greatest in women with clinically node-negative disease (odds ratio, 1.38; 95\% CI, 1.34-1.41) and in situ disease (odds ratio, 2.05; 95\% CI, 1.95-2.15). In women undergoing mastectomy, rates of breast reconstruction increased from 11.6\% in 1998 to 36.4\% in 2011 (P {\textless} .001 for trend). Rates of bilateral mastectomy for unilateral disease increased from 1.9\% in 1998 to 11.2\% in 2011 (P {\textless} .001).Conclusions and Relevance
In the past decade, there have been marked trends toward higher proportions of BCS-eligible patients undergoing mastectomy, breast reconstruction, and bilateral mastectomy. The greatest increases are seen in women with node-negative and in situ disease. Mastectomy rates do not yet exceed current American Cancer Society/American College of Surgeons Commission on Cancer accreditation benchmarks. Further research is needed to understand factors associated with these trends and their implications for performance measurement in American Cancer Society/American College of Surgeons Commission on Cancer centers.},
	number = {1},
	urldate = {2016-07-04},
	journal = {JAMA Surgery},
	author = {{Kummerow KL} and {Du L} and {Penson DF} and {Shyr Y} and {Hooks MA}},
	month = jan,
	year = {2015},
	pages = {9--16}
}

@article{pavot_new_2012,
	title = {New insights in mucosal vaccine development},
	volume = {30},
	issn = {0264-410X},
	url = {http://www.sciencedirect.com/science/article/pii/S0264410X11017579},
	doi = {10.1016/j.vaccine.2011.11.003},
	abstract = {Mucosal surfaces are the major entrance for infectious pathogens and therefore mucosal immune responses serve as a first line of defence. Most current immunization procedures are obtained by parenteral injection and only few vaccines are administered by mucosal route, because of its low efficiency. However, targeting of mucosal compartments to induce protective immunity at both mucosal sites and systemic level represents a great challenge. Major efforts are made to develop new mucosal candidate vaccines by selecting appropriate antigens with high immunogenicity, designing new mucosal routes of administration and selecting immune-stimulatory adjuvant molecules. The aim of mucosal vaccines is to induce broad potent protective immunity by specific neutralizing antibodies at mucosal surfaces and by induction of cellular immunity. Moreover, an efficient mucosal vaccine would make immunization procedures easier and be better suited for mass administration. This review focuses on contemporary developments of mucosal vaccination approaches using different routes of administration.},
	number = {2},
	urldate = {2014-11-07},
	journal = {Vaccine},
	author = {Pavot, Vincent and Rochereau, Nicolas and Genin, Christian and Verrier, Bernard and Paul, Stéphane},
	month = jan,
	year = {2012},
	keywords = {Antigen, Delivery, Mucosal, Routes, Vaccines},
	pages = {142--154},
	file = {vacc.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8IDFDAUN/vacc.pdf:application/pdf}
}

@article{soltanzadeh_extraction_2012,
	title = {Extraction of {Nucleolus} {Candidate} {Zone} in {White} {Blood} {Cells} of {Peripheral} {Blood} {Smear} {Images} {Using} {Curvelet} {Transform}},
	volume = {2012},
	issn = {1748-670X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361198/},
	doi = {10.1155/2012/574184},
	abstract = {The main part of each white blood cell (WBC) is its nucleus which contains chromosomes. Although white blood cells (WBCs) with giant nuclei are the main symptom of leukemia, they are not sufficient to prove this disease and other symptoms must be investigated. For example another important symptom of leukemia is the existence of nucleolus in nucleus. The nucleus contains chromatin and a structure called the nucleolus. Chromatin is DNA in its active form while nucleolus is composed of protein and RNA, which are usually inactive. In this paper, to diagnose this symptom and in order to discriminate between nucleoli and chromatins, we employ curvelet transform, which is a multiresolution transform for detecting 2D singularities in images. For this reason, at first nuclei are extracted by means of K-means method, then curvelet transform is applied on extracted nuclei and the coefficients are modified, and finally reconstructed image is used to extract the candidate locations of chromatins and nucleoli. This method is applied on 100 microscopic images and succeeds with specificity of 80.2\% and sensitivity of 84.3\% to detect the nucleolus candidate zone. After nucleolus candidate zone detection, new features that can be used to classify atypical and blast cells such as gradient of saturation channel are extracted.},
	urldate = {2016-06-30},
	journal = {Computational and Mathematical Methods in Medicine},
	author = {Soltanzadeh, Ramin and Rabbani, Hossein and Talebi, Ardeshir},
	year = {2012},
	pmid = {22666305},
	pmcid = {PMC3361198},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SRKIIQMV/Soltanzadeh et al. - 2012 - Extraction of Nucleolus Candidate Zone in White Bl.pdf:application/pdf}
}

@article{wang_gigapixel_2016,
	title = {Gigapixel surface imaging of radical prostatectomy specimens for comprehensive detection of cancer-positive surgical margins using structured illumination microscopy},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891779/},
	doi = {10.1038/srep27419},
	abstract = {Achieving cancer-free surgical margins in oncologic surgery is critical to reduce the need for additional adjuvant treatments and minimize tumor recurrence; however, there is a delicate balance between completeness of tumor removal and preservation of adjacent tissues critical for normal post-operative function. We sought to establish the feasibility of video-rate structured illumination microscopy (VR-SIM) of the intact removed tumor surface as a practical and non-destructive alternative to intra-operative frozen section pathology, using prostate cancer as an initial target. We present the first images of the intact human prostate surface obtained with pathologically-relevant contrast and subcellular detail, obtained in 24 radical prostatectomy specimens immediately after excision. We demonstrate that it is feasible to routinely image the full prostate circumference, generating gigapixel panorama images of the surface that are readily interpreted by pathologists. VR-SIM confirmed detection of positive surgical margins in 3 out of 4 prostates with pathology-confirmed adenocarcinoma at the circumferential surgical margin, and furthermore detected extensive residual cancer at the circumferential margin in a case post-operatively classified by histopathology as having negative surgical margins. Our results suggest that the increased surface coverage of VR-SIM could also provide added value for detection and characterization of positive surgical margins over traditional histopathology.},
	urldate = {2016-06-24},
	journal = {Scientific Reports},
	author = {Wang, Mei and Tulman, David B. and Sholl, Andrew B. and Kimbrell, Hillary Z. and Mandava, Sree H. and Elfer, Katherine N. and Luethy, Samuel and Maddox, Michael M. and Lai, Weil and Lee, Benjamin R. and Brown, J. Quincy},
	month = jun,
	year = {2016},
	pmid = {27257084},
	pmcid = {PMC4891779},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TCMFF6HU/Wang et al. - 2016 - Gigapixel surface imaging of radical prostatectomy.pdf:application/pdf}
}

@article{tambasco_quantifying_2009,
	title = {Quantifying the architectural complexity of microscopic images of histology specimens},
	volume = {40},
	issn = {0968-4328},
	url = {http://www.sciencedirect.com/science/article/pii/S0968432808002588},
	doi = {10.1016/j.micron.2008.12.004},
	abstract = {Tumour grade (a measure of the degree of cellular differentiation of malignant neoplasm) is an important prognostic factor in many types of cancer. In general, poorly differentiated tumours are characterized by a higher degree of architectural irregularity and complexity of histological structures. Fractal dimension is a useful parameter for characterizing complex irregular structures. However, one of the difficulties of estimating the fractal dimension from microscopic images is the segmentation of pathologically relevant structures for analysis. A commonly used technique to segment structures of interest is to apply a pixel intensity threshold to convert the original image to binary and extract pixel outline structures from the binary representation. The difficulty with this approach is that the value of the threshold required to segment the histological structures is highly dependent on the staining technique chosen and imaging conditions (i.e., illumination time, intensity, and uniformity) of the microscopic system. In this work, we present a method for finding the optimal intensity threshold by maximizing the corresponding fractal dimension. This method results in the segmentation of histological structures and the estimation of their fractal dimension (independent of imaging conditions). We applied our technique to 164 prostate histology sections from 82 prostate core biopsy specimens (two serial sections from each of the 63 benign prostate tissues and 19 high grade prostate carcinoma). We stained one of the serial sections with conventional hemotoxylin and eosin (H\&amp;E) and the other with pan-keratin, and found that the difference in mean fractal dimension between the two groups was statistically significant (p \&lt; 0.0001) for both stains. However, using receiver operating characteristics (ROC) analysis, we conclude that our fractal dimension method applied to the images of pan-keratin stained sections provides greater classification performance (benign versus high grade) than with those stained with H\&amp;E when compared to the original histological diagnosis. The sensitivity and specificity achieved with the pan-keratin images were 89.5\% and 90.5\%, respectively.},
	number = {4},
	urldate = {2016-04-21},
	journal = {Micron},
	author = {Tambasco, Mauro and Costello, Bridget M. and Kouznetsov, Alexei and Yau, Annie and Magliocco, Anthony M.},
	month = jun,
	year = {2009},
	keywords = {Architectural complexity, Fractal analysis, morphometry, PROSTATE cancer, reproducibility, Tumour grade},
	pages = {486--494},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GE7HQ2RE/Tambasco et al. - 2009 - Quantifying the architectural complexity of micros.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ACP58T63/S0968432808002588.html:text/html}
}

@article{veta_assessment_2015-1,
	title = {Assessment of algorithms for mitosis detection in breast cancer histopathology images},
	volume = {20},
	issn = {1361-8415},
	url = {http://www.sciencedirect.com/science/article/pii/S1361841514001807},
	doi = {10.1016/j.media.2014.11.010},
	abstract = {The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues.

In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists.},
	number = {1},
	urldate = {2016-06-25},
	journal = {Medical Image Analysis},
	author = {Veta, Mitko and van Diest, Paul J. and Willems, Stefan M. and Wang, Haibo and Madabhushi, Anant and Cruz-Roa, Angel and Gonzalez, Fabio and Larsen, Anders B. L. and Vestergaard, Jacob S. and Dahl, Anders B. and Cireşan, Dan C. and Schmidhuber, Jürgen and Giusti, Alessandro and Gambardella, Luca M. and Tek, F. Boray and Walter, Thomas and Wang, Ching-Wei and Kondo, Satoshi and Matuszewski, Bogdan J. and Precioso, Frederic and Snell, Violet and Kittler, Josef and de Campos, Teofilo E. and Khan, Adnan M. and Rajpoot, Nasir M. and Arkoumani, Evdokia and Lacle, Miangela M. and Viergever, Max A. and Pluim, Josien P. W.},
	month = feb,
	year = {2015},
	keywords = {BREAST cancer, Cancer grading, digital pathology, Mitosis detection, whole slide imaging},
	pages = {237--248},
	file = {1-s2.0-S1361841514001807-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VS7R5JWE/1-s2.0-S1361841514001807-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JSI4MBW6/S1361841514001807.html:text/html}
}

@article{liu_incorporating_2013,
	title = {Incorporating clinical metadata with digital image features for automated identification of cutaneous melanoma},
	volume = {169},
	copyright = {© 2013 British Association of Dermatologists},
	issn = {1365-2133},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1111/bjd.12550/abstract},
	doi = {10.1111/bjd.12550},
	abstract = {Background

Computer-assisted diagnosis (CAD) of malignant melanoma (MM) has been advocated to help clinicians to achieve a more objective and reliable assessment. However, conventional CAD systems examine only the features extracted from digital photographs of lesions. Failure to incorporate patients' personal information constrains the applicability in clinical settings.


Objectives

To develop a new CAD system to improve the performance of automatic diagnosis of melanoma, which, for the first time, incorporates digital features of lesions with important patient metadata into a learning process.


Methods

Thirty-two features were extracted from digital photographs to characterize skin lesions. Patients' personal information, such as age, gender and, lesion site, and their combinations, was quantified as metadata. The integration of digital features and metadata was realized through an extended Laplacian eigenmap, a dimensionality-reduction method grouping lesions with similar digital features and metadata into the same classes.


Results

The diagnosis reached 82·1\% sensitivity and 86·1\% specificity when only multidimensional digital features were used, but improved to 95·2\% sensitivity and 91·0\% specificity after metadata were incorporated appropriately. The proposed system achieves a level of sensitivity comparable with experienced dermatologists aided by conventional dermoscopes. This demonstrates the potential of our method for assisting clinicians in diagnosing melanoma, and the benefit it could provide to patients and hospitals by greatly reducing unnecessary excisions of benign naevi.


Conclusions

This paper proposes an enhanced CAD system incorporating clinical metadata into the learning process for automatic classification of melanoma. Results demonstrate that the additional metadata and the mechanism to incorporate them are useful for improving CAD of melanoma.},
	language = {en},
	number = {5},
	urldate = {2016-07-04},
	journal = {British Journal of Dermatology},
	author = {Liu, Z. and Sun, J. and Smith, M. and Smith, L. and Warr, R.},
	month = nov,
	year = {2013},
	pages = {1034--1040},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C7GXZIT6/Liu et al. - 2013 - Incorporating clinical metadata with digital image.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CI8MVT52/abstract.html:text/html}
}

@article{tromberg_non-invasive_2000,
	title = {Non-{Invasive} {In} {Vivo} {Characterization} of {Breast} {Tumors} {Using} {Photon} {Migration} {Spectroscopy}},
	volume = {2},
	issn = {1522-8002},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1531865/},
	abstract = {Frequency-domain photon migration (FDPM) is a non-invasive optical technique that utilizes intensity-modulated, near-infrared (NIR) light to quantitatively measure optical properties in thick tissues. Optical properties (absorption, µa, and scattering, µs′, parameters) derived from FDPM measurements can be used to construct low-resolution (0.5 to 1 cm) functional images of tissue hemoglobin (total, oxy-, and deoxyforms), oxygen saturation, blood volume fraction, water content, fat content and cellular structure. Unlike conventional NIR transillumination, FDPM enables quantitative analysis of tissue absorption and scattering parameters in a single non-invasive measurement. The unique functional information provided by FDPM makes it well-suited to characterizing tumors in thick tissues. In order to test the sensitivity of FDPM for cancer diagnosis, we have initiated clinical studies to quantitatively determine normal and malignant breast tissue optical and physiological properties in human subjects. Measurements are performed using a non-invasive, multi-wavelength, diode-laser FDPM device optimized for clinical studies. Results show that ductal carcinomas (invasive and in situ) and benign fibroadenomas exhibit 1.25 to 3-fold higher absorption than normal breast tissue. Within this group, absorption is greatest for measurements obtained from sites of invasive cancer. Optical scattering is approximately 20\% greater in pre-menopausal versus post-menopausal subjects due to differences in gland/cell proliferation and collagen/fat content. Spatial variations in tissue scattering reveal the loss of differentiation associated with breast disease progression. Overall, the metabolic demands of hormonal stimulation and tumor growth are detectable using photon migration techniques. Measurements provide quantitative optical property values that reflect changes in tissue perfusion, oxygen consumption, and cell/matrix development.},
	number = {1-2},
	urldate = {2016-06-28},
	journal = {Neoplasia (New York, N.Y.)},
	author = {Tromberg, Bruce J and Shah, Natasha and Lanning, Ryan and Cerussi, Albert and Espinoza, Jennifer and Pham, Tuan and Svaasand, Lars and Butler, John},
	month = jan,
	year = {2000},
	pmid = {10933066},
	pmcid = {PMC1531865},
	pages = {26--40},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IC6KQCGA/Tromberg et al. - 2000 - Non-Invasive In Vivo Characterization of Breast Tu.pdf:application/pdf}
}

@misc{_dune_????,
	title = {Dune {Medical} {Devices} - {Financial} {Report} {\textbar} {Annual} {Revenue} {\textbar} {Stock}},
	url = {http://www.privco.com.libproxy.tulane.edu:2048/private-company/dune-medical-devices},
	urldate = {2016-07-04},
	file = {Dune Medical Devices - Financial Report | Annual Revenue | Stock:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XPZVTKUQ/dune-medical-devices.html:text/html}
}

@inproceedings{mohanta_agglomerative_2002,
	title = {Agglomerative clustering for image segmentation},
	volume = {1},
	doi = {10.1109/ICPR.2002.1044838},
	abstract = {The paper presents an agglomerative clustering technique for image segmentation. To initiate agglomeration, a set of homogeneous segments is found in the image using level set analysis. A relational matrix is then defined establishing relations between neighbouring segments present in the image. These relations are derived based on the intensity and boundary features of the segments. The agglomeration is performed on this relationship based on asymmetric agglomerative clustering criteria. The performance is demonstrated through results on a number of natural images and through cluster validity criteria.},
	booktitle = {16th {International} {Conference} on {Pattern} {Recognition}, 2002. {Proceedings}},
	author = {Mohanta, P.P. and Mukherjee, D.P. and Acton, S.T.},
	year = {2002},
	keywords = {agglomerative clustering, boundary features, Clustering methods, cluster validity criteria, Estimation theory, homogeneous segments, Image analysis, Image generation, Image segmentation, image segmentation, Information analysis, intensity features, Level set, level set analysis, Marine vehicles, matrix algebra, pattern clustering, Psychology, Q measurement, relational matrix},
	pages = {664--667 vol.1},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BT4DZPMS/Mohanta et al. - 2002 - Agglomerative clustering for image segmentation.html:text/html}
}

@article{bydlon_performance_2010,
	title = {Performance metrics of an optical spectral imaging system for intra-operative assessment of breast tumor margins},
	volume = {18},
	issn = {1094-4087},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939901/},
	doi = {10.1364/OE.18.008058},
	abstract = {As many as 20-70\% of patients undergoing breast conserving surgery require repeat surgeries due to a close or positive surgical margin diagnosed post-operatively [1]. Currently there are no widely accepted tools for intra-operative margin assessment which is a significant unmet clinical need. Our group has developed a first-generation optical visible spectral imaging platform to image the molecular composition of breast tumor margins and has tested it clinically in 48 patients in a previously published study [2]. The goal of this paper is to report on the performance metrics of the system and compare it to clinical criteria for intra-operative tumor margin assessment. The system was found to have an average signal to noise ratio (SNR) {\textgreater}100 and {\textless}15\% error in the extraction of optical properties indicating that there is sufficient SNR to leverage the differences in optical properties between negative and close/positive margins. The probe had a sensing depth of 0.5-2.2 mm over the wavelength range of 450-600 nm which is consistent with the pathologic criterion for clear margins of 0-2 mm. There was {\textless}1\% cross-talk between adjacent channels of the multi-channel probe which shows that multiple sites can be measured simultaneously with negligible cross-talk between adjacent sites. Lastly, the system and measurement procedure were found to be reproducible when evaluated with repeated measures, with a low coefficient of variation ({\textless}0.11). The only aspect of the system not optimized for intra-operative use was the imaging time. The manuscript includes a discussion of how the speed of the system can be improved to work within the time constraints of an intra-operative setting.},
	number = {8},
	urldate = {2016-06-24},
	journal = {Optics Express},
	author = {Bydlon, Torre M. and Kennedy, Stephanie A. and Richards, Lisa M. and Brown, J. Quincy and Yu, Bing and Junker, Marlee K. and Gallagher, Jennifer and Geradts, Joseph and Wilke, Lee G. and Ramanujam, Nimmi},
	month = apr,
	year = {2010},
	pmid = {20588651},
	pmcid = {PMC2939901},
	pages = {8058--8076},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6HCBVTKT/Bydlon et al. - 2010 - Performance metrics of an optical spectral imaging.pdf:application/pdf}
}

@article{shenoy_-arrestin1_2012,
	title = {β-arrestin1 mediates metastatic growth of breast cancer cells by facilitating {HIF}-1-dependent {VEGF} expression},
	volume = {31},
	issn = {0950-9232},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179824/},
	doi = {10.1038/onc.2011.238},
	abstract = {β-arrestins 1 and 2 are multifunctional adaptor proteins originally discovered for their role in desensitizing seven-transmembrane receptor signaling via the heterotrimeric guanine nucleotide binding proteins. Recently identified roles of β-arrestins include regulation of cancer cell chemotaxis and proliferation. Herein we report that β-arrestin1 expression regulates breast tumor colonization in nude mice and cancer cell viability during hypoxia. β-arrestin1 robustly interacts with nuclear hypoxia-induced factor 1α (HIF-1α) that is stabilized during hypoxia and potentiates HIF-1-dependent transcription of the angiogenic factor VEGF-A. Increased expression of β-arrestin1 in human breast cancer (infiltrating ductal carcinoma or IDC and metastatic IDC) correlates with increased levels of VEGF-A. While the anti-angiogenic drug thalidomide inhibits HIF-1-dependent VEGF transcription in breast carcinoma cells, it does not prevent HIF-1α stabilization, but leads to aberrant localization of HIF-1α to the perinuclear compartments and surprisingly stimulates nuclear export of β-arrestin1. Additionally, imatinib mesylate that inhibits release of VEGF induces nuclear export of β-arrestin1-HIF-1α complexes. Our findings suggest that β-arrestin1 regulates nuclear signaling during hypoxia to promote survival of breast cancer cells via VEGF signaling and that drugs that induce its translocation from the nucleus to the cytoplasm could be useful in anti-angiogenic and breast cancer therapies.},
	number = {3},
	urldate = {2016-07-03},
	journal = {Oncogene},
	author = {Shenoy, Sudha K. and Han, Sang-oh and Zhao, Yu Lin and Hara, Makoto R. and Oliver, Timothy and Cao, Yiting and Dewhirst, Mark W.},
	month = jan,
	year = {2012},
	pmid = {21685944},
	pmcid = {PMC3179824},
	pages = {282--292},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QW9W42GV/Shenoy et al. - 2012 - β-arrestin1 mediates metastatic growth of breast c.pdf:application/pdf}
}

@article{giacomelli_virtual_2016,
	title = {Virtual {Hematoxylin} and {Eosin} {Transillumination} {Microscopy} {Using} {Epi}-{Fluorescence} {Imaging}},
	volume = {11},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976978/},
	doi = {10.1371/journal.pone.0159337},
	abstract = {We derive a physically realistic model for the generation of virtual transillumination, white light microscopy images using epi-fluorescence measurements from thick, unsectioned tissue. We demonstrate this technique by generating virtual transillumination H\&E images of unsectioned human breast tissue from epi-fluorescence multiphoton microscopy data. The virtual transillumination algorithm is shown to enable improved contrast and color accuracy compared with previous color mapping methods. Finally, we present an open source implementation of the algorithm in OpenGL, enabling real-time GPU-based generation of virtual transillumination microscopy images using conventional fluorescence microscopy systems.},
	number = {8},
	urldate = {2016-10-04},
	journal = {PLoS ONE},
	author = {Giacomelli, Michael G. and Husvogt, Lennart and Vardeh, Hilde and Faulkner-Jones, Beverly E. and Hornegger, Joachim and Connolly, James L. and Fujimoto, James G.},
	month = aug,
	year = {2016},
	pmid = {27500636},
	pmcid = {PMC4976978},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/D8V3V3QI/Giacomelli et al. - 2016 - Virtual Hematoxylin and Eosin Transillumination Mi.pdf:application/pdf}
}

@article{tryfonidis_management_2015,
	title = {Management of locally advanced breast cancer—perspectives and future directions},
	volume = {12},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1759-4774},
	url = {http://www.nature.com/nrclinonc/journal/v12/n3/full/nrclinonc.2015.13.html},
	doi = {10.1038/nrclinonc.2015.13},
	abstract = {Locally advanced breast cancer (LABC) constitutes a heterogeneous entity that includes advanced-stage primary tumours, cancers with extensive nodal involvement and inflammatory breast carcinomas. Although the definition of LABC can be broadened to include some large operable breast tumours, we use this term to strictly refer to inoperable cancers that are included in the above-mentioned categories. The prognosis of such tumours is often unfavourable; despite aggressive treatment, many patients eventually develop distant metastases and die from the disease. Advances in systemic therapy, including radiation treatment, surgical techniques and the development of new targeted agents have significantly improved clinical outcomes for patients with this disease. Notwithstanding these advances, LABC remains an important clinical problem, particularly in developing countries and those without widely adapted breast cancer awareness programmes. The optimal management of LABC requires a multidisciplinary approach, a well-coordinated treatment schedule and close cooperation between medical, surgical and radiation oncologists. In this Review, we discuss the current state of the art and possible future treatment strategies for patients with LABC.},
	language = {en},
	number = {3},
	urldate = {2016-06-23},
	journal = {Nature Reviews Clinical Oncology},
	author = {Tryfonidis, Konstantinos and Senkus, Elzbieta and Cardoso, Maria J. and Cardoso, Fatima},
	month = mar,
	year = {2015},
	keywords = {BREAST cancer, Chemotherapy, Clinical trials, Combination drug therapy, Targeted therapies},
	pages = {147--162},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F6G3P34P/Tryfonidis et al. - 2015 - Management of locally advanced breast cancer—persp.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/A8U35RXC/nrclinonc.2015.13.html:text/html}
}

@article{campbell_learning_2011,
	title = {Learning with {Support} {Vector} {Machines}},
	volume = {5},
	issn = {1939-4608},
	url = {http://www.morganclaypool.com.libproxy.tulane.edu:2048/doi/abs/10.2200/S00324ED1V01Y201102AIM010},
	doi = {10.2200/S00324ED1V01Y201102AIM010},
	number = {1},
	urldate = {2016-07-04},
	journal = {Synthesis Lectures on Artificial Intelligence and Machine Learning},
	author = {Campbell, Colin and Ying, Yiming},
	month = feb,
	year = {2011},
	pages = {1--95},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7EW9WCDP/Campbell and Ying - 2011 - Learning with Support Vector Machines.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/E5ZDGZNE/S00324ED1V01Y201102AIM010.html:text/html}
}

@article{hickey_evaluation_2014,
	title = {Evaluation of {Genomic} {Selection} {Training} {Population} {Designs} and {Genotyping} {Strategies} in {Plant} {Breeding} {Programs} {Using} {Simulation}},
	volume = {54},
	issn = {0011-183X},
	url = {https://dl.sciencesocieties.org/publications/cs/abstracts/54/4/1476},
	doi = {10.2135/cropsci2013.03.0195},
	language = {en},
	number = {4},
	urldate = {2015-02-10},
	journal = {Crop Science},
	author = {Hickey, John M. and Dreisigacker, Susanne and Crossa, Jose and Hearne, Sarah and Babu, Raman and Prasanna, Boddupalli M. and Grondona, Martin and Zambelli, Andres and Windhausen, Vanessa S. and Mathews, Ky and Gorjanc, Gregor},
	year = {2014},
	pages = {1476},
	file = {Abstract | Digital Library:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XVH4HUJJ/1476.html:text/html;planthickey.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F9P2J67D/planthickey.pdf:application/pdf}
}

@article{sparks_statistical_2013,
	title = {Statistical shape model for manifold regularization: {Gleason} grading of prostate histology},
	volume = {117},
	issn = {1077-3142},
	shorttitle = {Statistical shape model for manifold regularization},
	url = {http://www.sciencedirect.com/science/article/pii/S1077314213000672},
	doi = {10.1016/j.cviu.2012.11.011},
	abstract = {Gleason patterns of prostate cancer histopathology, characterized primarily by morphological and architectural attributes of histological structures (glands and nuclei), have been found to be highly correlated with disease aggressiveness and patient outcome. Gleason patterns 4 and 5 are highly correlated with more aggressive disease and poorer patient outcome, while Gleason patterns 1–3 tend to reflect more favorable patient outcome. Because Gleason grading is done manually by a pathologist visually examining glass (or digital) slides subtle morphologic and architectural differences of histological attributes, in addition to other factors, may result in grading errors and hence cause high inter-observer variability. Recently some researchers have proposed computerized decision support systems to automatically grade Gleason patterns by using features pertaining to nuclear architecture, gland morphology, as well as tissue texture. Automated characterization of gland morphology has been shown to distinguish between intermediate Gleason patterns 3 and 4 with high accuracy. Manifold learning (ML) schemes attempt to generate a low dimensional manifold representation of a higher dimensional feature space while simultaneously preserving nonlinear relationships between object instances. Classification can then be performed in the low dimensional space with high accuracy. However ML is sensitive to the samples contained in the dataset; changes in the dataset may alter the manifold structure. In this paper we present a manifold regularization technique to constrain the low dimensional manifold to a specific range of possible manifold shapes, the range being determined via a statistical shape model of manifolds (SSMM). In this work we demonstrate applications of the SSMM in (1) identifying samples on the manifold which contain noise, defined as those samples which deviate from the SSMM, and (2) accurate out-of-sample extrapolation (OSE) of newly acquired samples onto a manifold constrained by the SSMM. We demonstrate these applications of the SSMM in the context of distinguish between Gleason patterns 3 and 4 using glandular morphologic features in a prostate histopathology dataset of 58 patient studies. Identifying and eliminating noisy samples from the manifold via the SSMM results in a statistically significant improvement in area under the receiver operator characteristic curve (AUC), 0.832 ± 0.048 with removal of noisy samples compared to a AUC of 0.779 ± 0.075 without removal of samples. The use of the SSMM for OSE of newly acquired glands also shows statistically significant improvement in AUC, 0.834 ± 0.051 with the SSMM compared to 0.779 ± 0.054 without the SSMM. Similar results were observed for the synthetic Swiss Roll and Helix datasets.},
	number = {9},
	urldate = {2015-11-30},
	journal = {Computer Vision and Image Understanding},
	author = {Sparks, Rachel and Madabhushi, Anant},
	month = sep,
	year = {2013},
	keywords = {Gleason grading, Manifold learning, Prostate histology, Regularization, Statistical shape models},
	pages = {1138--1146},
	file = {1-s2.0-S1077314213000672-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2S5SXM95/1-s2.0-S1077314213000672-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FRS6QZPQ/S1077314213000672.html:text/html}
}

@article{brown_stuttered_2005,
	title = {Stuttered and fluent speech production: an {ALE} meta-analysis of functional neuroimaging studies},
	volume = {25},
	issn = {1065-9471},
	shorttitle = {Stuttered and fluent speech production},
	doi = {10.1002/hbm.20140},
	abstract = {This study reports an activation likelihood estimation (ALE) meta-analysis of imaging studies of chronic developmental stuttering in adults. Two parallel meta-analyses were carried out: (1) stuttered production in the stutterers; (2) fluent production in the control subjects. The control subjects' data replicated previous analyses of single-word reading, identifying activation in primary motor cortex, premotor cortex, supplementary motor area, Rolandic operculum, lateral cerebellum, and auditory areas, among others. The stuttering subjects' analysis showed that similar brain areas are involved in stuttered speech as in fluent speech, but with some important differences. Motor areas were over-activated in stuttering, including primary motor cortex, supplementary motor area, cingulate motor area, and cerebellar vermis. Frontal operculum, Rolandic operculum, and anterior insula showed anomalous right-laterality in stutterers. Auditory activations, due to hearing one's own speech, were essentially undetectable in stutterers. The phenomenon of efference copy is proposed as a unifying account of the pattern activation revealed within this ALE meta-analysis. This provides the basis for a stuttering system model that is testable and should help to advance the understanding and treatment of this disorder.},
	language = {eng},
	number = {1},
	journal = {Human Brain Mapping},
	author = {Brown, Steven and Ingham, Roger J. and Ingham, Janis C. and Laird, Angela R. and Fox, Peter T.},
	month = may,
	year = {2005},
	pmid = {15846815},
	keywords = {Brain, Brain Mapping, Diagnostic Imaging, Female, Humans, Male, Meta-Analysis as Topic, Speech, Stuttering},
	pages = {105--117}
}

@article{gilday_murine_2014,
	series = {Functional {Tissue} {Engineering}},
	title = {Murine patellar tendon biomechanical properties and regional strain patterns during natural tendon-to-bone healing after acute injury},
	volume = {47},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S0021929013004831},
	doi = {10.1016/j.jbiomech.2013.10.029},
	abstract = {Tendon-to-bone healing following acute injury is generally poor and often fails to restore normal tendon biomechanical properties. In recent years, the murine patellar tendon (PT) has become an important model system for studying tendon healing and repair due to its genetic tractability and accessible location within the knee. However, the mechanical properties of native murine PT, specifically the regional differences in tissue strains during loading, and the biomechanical outcomes of natural PT-to-bone healing have not been well characterized. Thus, in this study, we analyzed the global biomechanical properties and regional strain patterns of both normal and naturally healing murine PT at three time points (2, 5, and 8 weeks) following acute surgical rupture of the tibial enthesis. Normal murine PT exhibited distinct regional variations in tissue strain, with the insertion region experiencing approximately 2.5 times greater strain than the midsubstance at failure (10.80±2.52\% vs. 4.11±1.40\%; mean±SEM). Injured tendons showed reduced structural (ultimate load and linear stiffness) and material (ultimate stress and linear modulus) properties compared to both normal and contralateral sham-operated tendons at all healing time points. Injured tendons also displayed increased local strain in the insertion region compared to contralateral shams at both physiologic and failure load levels. 93.3\% of injured tendons failed at the tibial insertion, compared to only 60\% and 66.7\% of normal and sham tendons, respectively. These results indicate that 8 weeks of natural tendon-to-bone healing does not restore normal biomechanical function to the murine PT following injury.},
	number = {9},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Gilday, Steven D. and Chris Casstevens, E. and Kenter, Keith and Shearn, Jason T. and Butler, David L.},
	month = jun,
	year = {2014},
	keywords = {Insertion site, Patellar tendon, Regional strain, Tendon-to-bone healing},
	pages = {2035--2042},
	file = {murinestressdamage.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5UMZ72WR/murinestressdamage.pdf:application/pdf}
}

@article{curd_construction_2015-1,
	series = {Super-resolution {Light} {Microscopy}},
	title = {Construction of an instant structured illumination microscope},
	volume = {88},
	issn = {1046-2023},
	url = {http://www.sciencedirect.com/science/article/pii/S1046202315300293},
	doi = {10.1016/j.ymeth.2015.07.012},
	abstract = {A challenge in biological imaging is to capture high-resolution images at fast frame rates in live cells. The “instant structured illumination microscope” (iSIM) is a system designed for this purpose. Similarly to standard structured illumination microscopy (SIM), an iSIM provides a twofold improvement over widefield microscopy, in x, y and z, but also allows much faster image acquisition, with real-time display of super-resolution images.

The assembly of an iSIM is reasonably complex, involving the combination and alignment of many optical components, including three micro-optics arrays (two lenslet arrays and an array of pinholes, all with a pitch of 222 μm) and a double-sided scanning mirror. In addition, a number of electronic components must be correctly controlled. Construction of the system is therefore not trivial, but is highly desirable, particularly for live-cell imaging.

We report, and provide instructions for, the construction of an iSIM, including minor modifications to a previous design in both hardware and software. The final instrument allows us to rapidly acquire fluorescence images at rates faster than 100 fps, with approximately twofold improvement in resolution in both x–y and z; sub-diffractive biological features have an apparent size (full width at half maximum) of 145 nm (lateral) and 320 nm (axial), using a 1.49 NA objective and 488 nm excitation.},
	urldate = {2016-06-28},
	journal = {Methods},
	author = {Curd, Alistair and Cleasby, Alexa and Makowska, Katarzyna and York, Andrew and Shroff, Hari and Peckham, Michelle},
	month = oct,
	year = {2015},
	keywords = {Construction, Fluorescence microscopy, Instant structured illumination microscope, Super-resolution},
	pages = {37--47},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UNGHE732/Curd et al. - 2015 - Construction of an instant structured illumination.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/N5EW3HG7/S1046202315300293.html:text/html}
}

@article{lawson_defending_2011,
	title = {Defending the mucosa: adjuvant and carrier formulations for mucosal immunity},
	volume = {23},
	issn = {0952-7915},
	shorttitle = {Defending the mucosa},
	url = {http://www.sciencedirect.com/science/article/pii/S0952791511000343},
	doi = {10.1016/j.coi.2011.03.009},
	abstract = {A majority of infectious microorganisms either colonize or cross mucosal surfaces to enter the host. A major goal in vaccine design is to induce a protective, lasting immune response against potential pathogens at mucosal surfaces. In addition, mucosal vaccines can offer needle-free delivery, thereby improving accessibility, safety, and cost-effectiveness. Challenges to successful mucosal vaccination include poor induction of mucosal immunity, limited understanding of protective mechanisms and crosstalk between mucosal compartments, and the availability of safe, effective mucosal adjuvants and delivery systems. This review focuses on some key advances in the field of mucosal vaccinology within the past 2–3 years, including reports on promising new formulations and investigations into the mechanisms of established mucosal adjuvants and/or particulate carrier systems.},
	number = {3},
	urldate = {2014-11-07},
	journal = {Current Opinion in Immunology},
	author = {Lawson, Louise B and Norton, Elizabeth B and Clements, John D},
	month = jun,
	year = {2011},
	pages = {414--420},
	file = {mucosa.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F8JS7HE6/mucosa.pdf:application/pdf}
}

@article{sharma_auto-fluorescence_2012,
	title = {Auto-fluorescence lifetime and light reflectance spectroscopy for breast cancer diagnosis: potential tools for intraoperative margin detection},
	volume = {3},
	issn = {2156-7085},
	shorttitle = {Auto-fluorescence lifetime and light reflectance spectroscopy for breast cancer diagnosis},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409702/},
	doi = {10.1364/BOE.3.001825},
	abstract = {This study investigates the use of two spectroscopic techniques, auto-fluorescence lifetime measurement (AFLM) and light reflectance spectroscopy (LRS), for detecting invasive ductal carcinoma (IDC) in human ex vivo breast specimens. AFLM used excitation at 447 nm with multiple emission wavelengths (532, 562, 632, and 644 nm), at which auto-fluorescence lifetimes and their weight factors were analyzed using a double exponent model. LRS measured reflectance spectra in the range of 500-840 nm and analyzed the spectral slopes empirically at several distinct spectral regions. Our preliminary results based on 93 measured locations (i.e., 34 IDC, 31 benign fibrous, 28 adipose) from 6 specimens show significant differences in 5 AFLM-derived parameters and 9 LRS-based spectral slopes between benign and malignant breast samples. Multinomial logistic regression with a 10-fold cross validation approach was implemented with selected features to classify IDC from benign fibrous and adipose tissues for the two techniques independently as well as for the combined dual-modality approach. The accuracy for classifying IDC was found to be 96.4 ± 0.8\%, 92.3 ± 0.8\% and 96 ± 1.3\% for LRS, AFLM, and dual-modality, respectively.},
	number = {8},
	urldate = {2016-06-24},
	journal = {Biomedical Optics Express},
	author = {Sharma, Vikrant and Shivalingaiah, Shivaranjani and Peng, Yan and Euhus, David and Gryczynski, Zygmunt and Liu, Hanli},
	month = jul,
	year = {2012},
	pmid = {22876347},
	pmcid = {PMC3409702},
	pages = {1825--1840},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TDQ8IJIN/Sharma et al. - 2012 - Auto-fluorescence lifetime and light reflectance s.pdf:application/pdf}
}

@article{balis_computer_2011,
	title = {Computer aided diagnostic tools aim to empower rather than replace pathologists: {Lessons} learned from computational chess},
	volume = {2},
	issn = {2153-3539},
	shorttitle = {Computer aided diagnostic tools aim to empower rather than replace pathologists},
	url = {http://www.jpathinformatics.org/text.asp?2011/2/1/25/82050},
	doi = {10.4103/2153-3539.82050},
	language = {en},
	number = {1},
	urldate = {2015-03-02},
	journal = {Journal of Pathology Informatics},
	author = {Balis, UlyssesJ and Hipp, Jason and Flotte, Thomas and Monaco, James and Cheng, Jerome and Madabhushi, Anant and Yagi, Yukako and Rodriguez-Canales, Jaime and Emmert-Buck, Michael and Dugan, MichaelC and Hewitt, Stephen and Toner, Mehmet and Tompkins, RonaldG and Lucas, David and Gilbertson, JohnR},
	year = {2011},
	pages = {25},
	file = {Hipp et al J Pathol Inform 2011.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZAN8FUNZ/Hipp et al J Pathol Inform 2011.pdf:application/pdf}
}

@article{kennedy_optical_2010,
	title = {Optical breast cancer margin assessment: an observational study of the effects of tissue heterogeneity on optical contrast},
	volume = {12},
	issn = {1465-5411},
	shorttitle = {Optical breast cancer margin assessment},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046432/},
	doi = {10.1186/bcr2770},
	abstract = {Introduction
Residual cancer following breast conserving surgery increases the risk of local recurrence and mortality. Margin assessment presents an unmet clinical need. Breast tissue is markedly heterogeneous, which makes distinguishing small foci of cancer within the spectrum of normal tissue potentially challenging. This is further complicated by the heterogeneity as a function of menopausal status. Optical spectroscopy can provide surgeons with intra-operative diagnostic tools. Here, we evaluate ex-vivo breast tissue and determine which sources of optical contrast have the potential to detect malignancy at the margins in women of differing breast composition.

Methods
Diffuse reflectance spectra were measured from 595 normal and 38 malignant sites from the margins of 104 partial mastectomy patients. All statistical tests were performed using Wilcoxon Rank-Sum tests. Normal and malignant sites were compared before stratifying the data by tissue type and depth and computing statistical differences. The frequencies of the normal tissue types were separated by menopausal status and compared to the corresponding optical properties.

Results
The mean reduced scattering coefficient, {\textless} μs' {\textgreater}, and concentration of total hemoglobin, [THb]), showed statistical differences between malignant ({\textless} μs' {\textgreater} : 8.96 cm-1 ± 2.24MAD, [THb]: 42.70 μM ± 29.31MAD) compared to normal sites ({\textless} μs' {\textgreater} : 7.29 cm-1 ± 2.15MAD, [THb]: 32.09 μM ± 16.73MAD) (P {\textless} 0.05). The sites stratified according to normal tissue type (fibro-glandular (FG), fibro-adipose (FA), and adipose (A)) or disease type (invasive ductal carcinoma (IDC) and ductal carcinoma in situ (DCIS)) showed that FG exhibited increased {\textless} μs' {\textgreater} and A showed increased [β-carotene] within normal tissues. Scattering differentiated between most malignant sites, DCIS (9.46 cm-1 ± 1.06MAD) and IDC (8.00 cm-1 ± 1.81MAD), versus A (6.50 cm-1 ± 1.95MAD). [β-carotene] showed marginal differences between DCIS (19.00 μM ± 6.93MAD, and FG (15.30 μM ± 5.64MAD). [THb] exhibited statistical differences between positive sites (92.57 μM ± 18.46MAD) and FG (34.12 μM ± 22.77MAD), FA (28.63 μM ± 14.19MAD), and A (30.36 μM ± 14.86MAD). The diagnostic ability of the optical parameters was affected by distance of tumor from the margin as well as menopausal status. Due to decreased fibrous content and increased adipose content, normal sites in post-menopausal patients exhibited lower {\textless} μs' {\textgreater}, but higher [β-carotene] than pre-menopausal patients.

Conclusions
The data indicate that the ability of an optical parameter to differentiate benign from malignant breast tissues may be dictated by patient demographics.  Scattering differentiated between malignant and adipose sites and would be most effective in post-menopausal women.  [β-carotene] or [THb] may be more applicable in pre-menopausal women to differentiate malignant from fibrous sites.  Patient demographics are therefore an important component to incorporate into optical characterization of breast specimens.},
	number = {6},
	urldate = {2016-06-24},
	journal = {Breast Cancer Research : BCR},
	author = {Kennedy, Stephanie and Geradts, Joseph and Bydlon, Torre and Brown, J Quincy and Gallagher, Jennifer and Junker, Marlee and Barry, William and Ramanujam, Nimmi and Wilke, Lee},
	year = {2010},
	pmid = {21054873},
	pmcid = {PMC3046432},
	pages = {R91},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SRCQJU6C/Kennedy et al. - 2010 - Optical breast cancer margin assessment an observ.pdf:application/pdf}
}

@techreport{turk_global_2015,
	address = {Melbourne, Australia},
	type = {{IBISWorld} {Industry} {Report}},
	title = {Global {Pharmaceuticals} \& {Medicine} {Manufacturing}},
	url = {http://clients1.ibisworld.com.libproxy.tulane.edu:2048/reports/gl/industry/default.aspx?entid=720},
	number = {C1933-GL},
	urldate = {2015-11-22},
	institution = {IBISWorld Services},
	author = {Turk, Sarah},
	month = sep,
	year = {2015},
	file = {IBISWorld Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZR9WMM74/login.html:text/html}
}

@article{_1-s2.0-s1053811912011743-main.pdf_????,
	title = {1-s2.0-{S}1053811912011743-main.pdf},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PTCVRSN8/1-s2.0-S1053811912011743-main.pdf:application/pdf}
}

@article{yang_cancer_2015,
	title = {Cancer immunotherapy: harnessing the immune system to battle cancer},
	volume = {125},
	issn = {0021-9738},
	shorttitle = {Cancer immunotherapy},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588312/},
	doi = {10.1172/JCI83871},
	abstract = {The recent clinical successes of immune checkpoint blockade and chimeric antigen receptor T cell therapies represent a turning point in cancer immunotherapy. These successes also underscore the importance of understanding basic tumor immunology for successful clinical translation in treating patients with cancer. The Reviews in this Review Series focus on current developments in cancer immunotherapy, highlight recent advances in our understanding of basic aspects of tumor immunology, and suggest how these insights can lead to the development of new immunotherapeutic strategies.},
	number = {9},
	urldate = {2016-12-06},
	journal = {The Journal of Clinical Investigation},
	author = {Yang, Yiping},
	month = sep,
	year = {2015},
	pmid = {26325031},
	pmcid = {PMC4588312},
	pages = {3335--3337},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RIIP5NJF/Yang - 2015 - Cancer immunotherapy harnessing the immune system.pdf:application/pdf}
}

@article{karadaglic_image_2008,
	title = {Image formation in structured illumination wide-field fluorescence microscopy},
	volume = {39},
	issn = {0968-4328},
	url = {http://www.sciencedirect.com/science/article/pii/S0968432808000267},
	doi = {10.1016/j.micron.2008.01.017},
	abstract = {We present a theoretical analysis of the image formation in structured illumination wide-field fluorescence microscopy (SIWFFM). We show that the optically sectioned images obtained with this approach possess the optical sectioning strengths comparable to those obtained with the confocal microscope. We further show that the transfer function behaviour is directly comparable to that of the true confocal instrument. The theoretical considerations are compared with and confirmed by experimental results.},
	number = {7},
	urldate = {2016-07-08},
	journal = {Micron},
	author = {Karadaglić, Dejan and Wilson, Tony},
	month = oct,
	year = {2008},
	keywords = {Confocal microscopy, Fluorescence microscopy, optical microscopy, Optical sectioning, Structured illumination, Wide-field microscopy},
	pages = {808--818},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/D672J973/S0968432808000267.html:text/html}
}

@article{tummers_real-time_2014,
	title = {Real-time intraoperative detection of breast cancer using near-infrared fluorescence imaging and {Methylene} {Blue}},
	volume = {40},
	issn = {0748-7983},
	url = {http://www.sciencedirect.com/science/article/pii/S0748798314003035},
	doi = {10.1016/j.ejso.2014.02.225},
	abstract = {Background
Despite recent developments in preoperative breast cancer imaging, intraoperative localization of tumor tissue can be challenging, resulting in tumor-positive resection margins during breast conserving surgery. Based on certain physicochemical similarities between Technetium(99mTc)-sestamibi (MIBI), an SPECT radiodiagnostic with a sensitivity of 83–90\% to detect breast cancer preoperatively, and the near-infrared (NIR) fluorophore Methylene Blue (MB), we hypothesized that MB might detect breast cancer intraoperatively using NIR fluorescence imaging.
Methods
Twenty-four patients with breast cancer, planned for surgical resection, were included. Patients were divided in 2 administration groups, which differed with respect to the timing of MB administration. N = 12 patients per group were administered 1.0 mg/kg MB intravenously either immediately or 3 h before surgery. The mini-FLARE imaging system was used to identify the NIR fluorescent signal during surgery and on post-resected specimens transferred to the pathology department. Results were confirmed by NIR fluorescence microscopy.
Results
20/24 (83\%) of breast tumors (carcinoma in N = 21 and ductal carcinoma in situ in N = 3) were identified in the resected specimen using NIR fluorescence imaging. Patients with non-detectable tumors were significantly older. No significant relation to receptor status or tumor grade was seen. Overall tumor-to-background ratio (TBR) was 2.4 ± 0.8. There was no significant difference between TBR and background signal between administration groups. In 2/4 patients with positive resection margins, breast cancer tissue identified in the wound bed during surgery would have changed surgical management. Histology confirmed the concordance of fluorescence signal and tumor tissue.
Conclusions
This feasibility study demonstrated an overall breast cancer identification rate using MB of 83\%, with real-time intraoperative guidance having the potential to alter patient management.},
	number = {7},
	urldate = {2016-06-24},
	journal = {European Journal of Surgical Oncology (EJSO)},
	author = {Tummers, Q. R. J. G. and Verbeek, F. P. R. and Schaafsma, B. E. and Boonstra, M. C. and van der Vorst, J. R. and Liefers, G. -J. and van de Velde, C. J. H. and Frangioni, J. V. and Vahrmeijer, A. L.},
	month = jul,
	year = {2014},
	keywords = {BREAST cancer, Image-guided surgery, Methylene Blue, Near-infrared fluorescence imaging},
	pages = {850--858},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8QIF8H5I/Tummers et al. - 2014 - Real-time intraoperative detection of breast cance.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WNRSPEKU/S0748798314003035.html:text/html}
}

@article{chu_image_2014,
	title = {Image reconstruction for structured-illumination microscopy with low signal level},
	volume = {22},
	issn = {1094-4087},
	url = {https://www.osapublishing.org/abstract.cfm?URI=oe-22-7-8687},
	doi = {10.1364/OE.22.008687},
	language = {en},
	number = {7},
	urldate = {2016-06-27},
	journal = {Optics Express},
	author = {Chu, Kaiqin and McMillan, Paul J. and Smith, Zachary J. and Yin, Jie and Atkins, Jeniffer and Goodwin, Paul and Wachsmann-Hogiu, Sebastian and Lane, Stephen},
	month = apr,
	year = {2014},
	pages = {8687},
	file = {oe-22-7-8687.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JC6UN5XH/oe-22-7-8687.pdf:application/pdf}
}

@article{chang_evidence_2011,
	title = {Evidence of left inferior frontal-premotor structural and functional connectivity deficits in adults who stutter},
	volume = {21},
	issn = {1460-2199},
	doi = {10.1093/cercor/bhr028},
	abstract = {The neurophysiological basis for stuttering may involve deficits that affect dynamic interactions among neural structures supporting fluid speech processing. Here, we examined functional and structural connectivity within corticocortical and thalamocortical loops in adults who stutter. For functional connectivity, we placed seeds in the left and right inferior frontal Brodmann area 44 (BA44) and in the ventral lateral nucleus (VLN) of the thalamus. Subject-specific seeds were based on peak activation voxels captured during speech and nonspeech tasks using functional magnetic resonance imaging. Psychophysiological interaction (PPI) was used to find brain regions with heightened functional connectivity with these cortical and subcortical seeds during speech and nonspeech tasks. Probabilistic tractography was used to track white matter tracts in each hemisphere using the same seeds. Both PPI and tractrography supported connectivity deficits between the left BA44 and the left premotor regions, while connectivity among homologous right hemisphere structures was significantly increased in the stuttering group. No functional connectivity differences between BA44 and auditory regions were found between groups. The functional connectivity results derived from the VLN seeds were less definitive and were not supported by the tractography results. Our data provide strongest support for deficient left hemisphere inferior frontal to premotor connectivity as a neural correlate of stuttering.},
	language = {eng},
	number = {11},
	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
	author = {Chang, Soo-Eun and Horwitz, Barry and Ostuni, John and Reynolds, Richard and Ludlow, Christy L.},
	month = nov,
	year = {2011},
	pmid = {21471556},
	pmcid = {PMC3183422},
	keywords = {Adult, Brain Mapping, Diffusion Tensor Imaging, Female, Frontal Lobe, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Neural Pathways, Stuttering, Ventral Thalamic Nuclei},
	pages = {2507--2518}
}

@article{smith_influence_2002,
	title = {The influence of ageing and exercise on tendon growth and degeneration—hypotheses for the initiation and prevention of strain-induced tendinopathies},
	volume = {133},
	issn = {1095-6433},
	url = {http://www.sciencedirect.com/science/article/pii/S1095643302001484},
	doi = {10.1016/S1095-6433(02)00148-4},
	abstract = {Strain-induced tendinopathy is a common injury in both human and equine athletes, with increasing incidence associated with greater involvement in sport and an increasingly aged population. This paper reviews our studies on the abundant non-collagenous protein, cartilage oligomeric matrix protein (COMP), in equine tendons. Its variation between tendon type and site, age and exercise has provided an insight into how age and exercise influence tendon growth and maturation. Tendons can be broadly divided into two types, reflecting their different matrix composition and function: the energy-storing tendons used for weight-bearing and locomotion, which suffer a high incidence of strain-induced tendinopathy, and positional tendons involved in limb placement or manipulative skills. It would appear that while energy-storing tendon can respond to the mechanical forces applied to it during growth, there is no evidence that it can do so after skeletal maturity. Instead, cumulative fatigue damage causes degeneration at the molecular level, potentially weakening it and increasing the risk of clinical injury. Appropriate exercise regimes early in life may help to improve the quality of growing tendon, thereby reducing the incidence of injury during ageing or subsequent athletic career.},
	number = {4},
	urldate = {2014-11-04},
	journal = {Comparative Biochemistry and Physiology Part A: Molecular \& Integrative Physiology},
	author = {Smith, R. K. W and Birch, H. L and Goodman, S and Heinegård, D and Goodship, A. E},
	month = dec,
	year = {2002},
	keywords = {Ageing, Cartilage oligomeric matrix protein (COMP), Degeneration, Exercise, matrix, Physiology, Tendinopathy, Tendon},
	pages = {1039--1050},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4HUEFSCF/Smith et al. - 2002 - The influence of ageing and exercise on tendon gro.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AAWBI8MI/S1095643302001484.html:text/html}
}

@misc{_what_????,
	title = {What are the key statistics about prostate cancer?},
	url = {http://www.cancer.org/cancer/prostatecancer/detailedguide/prostate-cancer-key-statistics},
	urldate = {2016-07-22},
	file = {What are the key statistics about prostate cancer?:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TRWSAKKC/prostate-cancer-key-statistics.html:text/html}
}

@article{chang_back_2015,
	title = {Back to {Basics}: {Traditional} {Nottingham} {Grade} {Mitotic} {Counts} {Alone} are {Significant} in {Predicting} {Survival} in {Invasive} {Breast} {Carcinoma}},
	volume = {22},
	issn = {1068-9265, 1534-4681},
	shorttitle = {Back to {Basics}},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1245/s10434-015-4616-y},
	doi = {10.1245/s10434-015-4616-y},
	abstract = {Background Newer multigene molecular profiling assays for breast carcinoma rely heavily on the quantification of genes of proliferation, whereas traditional histological grading reports the mitotic count. The mitotic activity of invasive breast carcinomas may be undervalued; therefore, an evaluation of the prognostic significance of mitotic score in predicting prognosis was performed. Methods Retrospective analysis of a single institutional cohort of newly diagnosed estrogen receptor positive (ER+), HER2 negative (HER2−) unilateral invasive breast carcinomas was performed. Mitotic scores from the 3-part Nottingham combined histological grade were compared with clinical parameters. Mitoses were counted on Olympus BX50 microscopes and assigned scores of 1–3 based on observed mitoses. Results A total of 1292 ER+, HER2− invasive breast carcinoma patients were identified, with a median follow-up time of 2.6 years (range 0–14 years). Higher mitotic score was significantly associated with younger age, larger tumor size, angiolymphatic invasion, node-positive disease, higher stage, and the use of hormonal and cytotoxic chemotherapy. Mitotic score was significant in modeling time to local/regional recurrence (p = 0.02), recurrence-free survival/RFS (p {\textless} 0.001), and overall survival/OS (p = 0.01) with higher mitotic scores associated with worse outcomes. Higher mitotic score correlated significantly with intermediate/high risk Oncotype Dx recurrence scores (p = 0.009). Conclusions First-generation molecular profiling assays for estrogen receptor positive invasive breast carcinomas derive much of their predictive power from quantifying genes of proliferation into a single score. Sometimes overlooked in the profusion of molecular data, the time-tested, mitotic count in the Nottingham combined histological grade is a good single-parameter predictor of survival.},
	language = {en},
	number = {3},
	urldate = {2016-06-25},
	journal = {Annals of Surgical Oncology},
	author = {Chang, James M. and McCullough, Ann E. and Dueck, Amylou C. and Kosiorek, Heidi E. and Ocal, Idris T. and Lidner, Thomas K. and Gray, Richard J. and Wasif, Nabil and Northfelt, Donald W. and Anderson, Karen S. and Pockaj, Barbara A.},
	month = may,
	year = {2015},
	pages = {509--515},
	file = {art%3A10.1245%2Fs10434-015-4616-y.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P6Z55S5N/art%3A10.1245%2Fs10434-015-4616-y.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BJMPKWNC/s10434-015-4616-y.html:text/html}
}

@article{moran_society_2014,
	title = {Society of {Surgical} {Oncology}–{American} {Society} for {Radiation} {Oncology} {Consensus} {Guideline} on {Margins} for {Breast}-{Conserving} {Surgery} {With} {Whole}-{Breast} {Irradiation} in {Stages} {I} and {II} {Invasive} {Breast} {Cancer}},
	volume = {88},
	issn = {0360-3016},
	url = {http://www.sciencedirect.com/science/article/pii/S0360301613033154},
	doi = {10.1016/j.ijrobp.2013.11.012},
	abstract = {Purpose
To convene a multidisciplinary panel of breast experts to examine the relationship between margin width and ipsilateral breast tumor recurrence (IBTR) and develop a guideline for defining adequate margins in the setting of breast conserving surgery and adjuvant radiation therapy.
Methods and Materials
A multidisciplinary consensus panel used a meta-analysis of margin width and IBTR from a systematic review of 33 studies including 28,162 patients as the primary evidence base for consensus.
Results
Positive margins (ink on invasive carcinoma or ductal carcinoma in situ) are associated with a 2-fold increase in the risk of IBTR compared with negative margins. This increased risk is not mitigated by favorable biology, endocrine therapy, or a radiation boost. More widely clear margins than no ink on tumor do not significantly decrease the rate of IBTR compared with no ink on tumor. There is no evidence that more widely clear margins reduce IBTR for young patients or for those with unfavorable biology, lobular cancers, or cancers with an extensive intraductal component.
Conclusions
The use of no ink on tumor as the standard for an adequate margin in invasive cancer in the era of multidisciplinary therapy is associated with low rates of IBTR and has the potential to decrease re-excision rates, improve cosmetic outcomes, and decrease health care costs.},
	number = {3},
	urldate = {2016-06-22},
	journal = {International Journal of Radiation Oncology*Biology*Physics},
	author = {Moran, Meena S. and Schnitt, Stuart J. and Giuliano, Armando E. and Harris, Jay R. and Khan, Seema A. and Horton, Janet and Klimberg, Suzanne and Chavez-MacGregor, Mariana and Freedman, Gary and Houssami, Nehmat and Johnson, Peggy L. and Morrow, Monica},
	month = mar,
	year = {2014},
	pages = {553--564},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CV362UIR/Moran et al. - 2014 - Society of Surgical Oncology–American Society for .pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7CGZ57DK/S0360301613033154.html:text/html}
}

@misc{_zotero_????,
	title = {Zotero {\textbar} {Start}},
	url = {https://www.zotero.org/start},
	urldate = {2016-06-22},
	file = {Zotero | Start:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QNMDK86C/start.html:text/html}
}

@article{dong_recovering_2015,
	title = {Recovering higher dimensional image data using multiplexed structured illumination},
	volume = {23},
	issn = {1094-4087},
	url = {https://www.osapublishing.org/abstract.cfm?URI=oe-23-23-30393},
	doi = {10.1364/OE.23.030393},
	language = {en},
	number = {23},
	urldate = {2016-06-25},
	journal = {Optics Express},
	author = {Dong, Siyuan and Guo, Kaikai and Jiang, Shaowei and Zheng, Guoan},
	month = nov,
	year = {2015},
	pages = {30393},
	file = {fds.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/J4AWJFFD/fds.pdf:application/pdf}
}

@article{wang_high-resolution_2015,
	title = {High-{Resolution} {Rapid} {Diagnostic} {Imaging} of {Whole} {Prostate} {Biopsies} {Using} {Video}-{Rate} {Fluorescence} {Structured} {Illumination} {Microscopy}},
	volume = {75},
	copyright = {©2015 American Association for Cancer Research.},
	issn = {0008-5472, 1538-7445},
	url = {http://cancerres.aacrjournals.org/content/75/19/4032},
	doi = {10.1158/0008-5472.CAN-14-3806},
	abstract = {Rapid assessment of prostate core biopsy pathology at the point-of-procedure could provide benefit in a variety of clinical situations. Even with advanced transrectal ultrasound guidance and saturation biopsy protocols, prostate cancer can be missed in up to half of all initial biopsy procedures. In addition, collection of tumor specimens for downstream histologic, molecular, and genetic analysis is hindered by low tumor yield due to inability to identify prostate cancer grossly. However, current point-of-procedure pathology protocols, such as frozen section analysis (FSA), are destructive and too time- and labor-intensive to be practical or economical. Ex vivo microscopy of the excised specimens, stained with fast-acting fluorescent histology dyes, could be an attractive nondestructive alternative to FSA. In this work, we report the first demonstration of video-rate structured illumination microscopy (VR-SIM) for rapid high-resolution diagnostic imaging of prostate biopsies in realistic point-of-procedure timeframes. Large mosaic images of prostate biopsies stained with acridine orange are rendered in seconds and contain excellent contrast and detail, exhibiting close correlation with corresponding hematoxylin and eosin histology. A clinically relevant review of VR-SIM images of 34 unfixed and uncut prostate core biopsies by two independent pathologists resulted in an area under the receiver operative curve (AUC) of 0.82–0.88, with a sensitivity ranging from 63\% to 88\% and a specificity ranging from 78\% to 89\%. When biopsies contained more than 5\% tumor content, the sensitivity improved to 75\% to 92\%. The image quality, speed, minimal complexity, and ease of use of VR-SIM could prove to be features in favor of adoption as an alternative to destructive pathology at the point-of-procedure. Cancer Res; 75(19); 4032–41. ©2015 AACR.},
	language = {en},
	number = {19},
	urldate = {2016-06-22},
	journal = {Cancer Research},
	author = {Wang, Mei and Kimbrell, Hillary Z. and Sholl, Andrew B. and Tulman, David B. and Elfer, Katherine N. and Schlichenmeyer, Tyler C. and Lee, Benjamin R. and Lacey, Michelle and Brown, J. Quincy},
	month = oct,
	year = {2015},
	pmid = {26282168},
	pages = {4032--4041},
	file = {4032.full.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U585DHJQ/4032.full.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RT6DHIJ9/4032.html:text/html}
}

@article{cosma_prediction_2016,
	title = {Prediction of {Pathological} {Stage} in {Patients} with {Prostate} {Cancer}: {A} {Neuro}-{Fuzzy} {Model}},
	volume = {11},
	issn = {1932-6203},
	shorttitle = {Prediction of {Pathological} {Stage} in {Patients} with {Prostate} {Cancer}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892614/},
	doi = {10.1371/journal.pone.0155856},
	abstract = {The prediction of cancer staging in prostate cancer is a process for estimating the likelihood that the cancer has spread before treatment is given to the patient. Although important for determining the most suitable treatment and optimal management strategy for patients, staging continues to present significant challenges to clinicians. Clinical test results such as the pre-treatment Prostate-Specific Antigen (PSA) level, the biopsy most common tumor pattern (Primary Gleason pattern) and the second most common tumor pattern (Secondary Gleason pattern) in tissue biopsies, and the clinical T stage can be used by clinicians to predict the pathological stage of cancer. However, not every patient will return abnormal results in all tests. This significantly influences the capacity to effectively predict the stage of prostate cancer. Herein we have developed a neuro-fuzzy computational intelligence model for classifying and predicting the likelihood of a patient having Organ-Confined Disease (OCD) or Extra-Prostatic Disease (ED) using a prostate cancer patient dataset obtained from The Cancer Genome Atlas (TCGA) Research Network. The system input consisted of the following variables: Primary and Secondary Gleason biopsy patterns, PSA levels, age at diagnosis, and clinical T stage. The performance of the neuro-fuzzy system was compared to other computational intelligence based approaches, namely the Artificial Neural Network, Fuzzy C-Means, Support Vector Machine, the Naive Bayes classifiers, and also the AJCC pTNM Staging Nomogram which is commonly used by clinicians. A comparison of the optimal Receiver Operating Characteristic (ROC) points that were identified using these approaches, revealed that the neuro-fuzzy system, at its optimal point, returns the largest Area Under the ROC Curve (AUC), with a low number of false positives (FPR = 0.274, TPR = 0.789, AUC = 0.812). The proposed approach is also an improvement over the AJCC pTNM Staging Nomogram (FPR = 0.032, TPR = 0.197, AUC = 0.582).},
	number = {6},
	urldate = {2016-11-28},
	journal = {PLoS ONE},
	author = {Cosma, Georgina and Acampora, Giovanni and Brown, David and Rees, Robert C. and Khan, Masood and Pockley, A. Graham},
	month = jun,
	year = {2016},
	pmid = {27258119},
	pmcid = {PMC4892614},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/H37KE7XQ/Cosma et al. - 2016 - Prediction of Pathological Stage in Patients with .pdf:application/pdf}
}

@article{mokhtar_triple_2014,
	title = {Triple assessment of sentinel lymph node metastasis in early breast cancer using preoperative {CTLG}, intraoperative fluorescence navigation and {OSNA}},
	volume = {23},
	issn = {1340-6868, 1880-4233},
	url = {http://link.springer.com/article/10.1007/s12282-014-0551-1},
	doi = {10.1007/s12282-014-0551-1},
	abstract = {Background Sentinel lymph node biopsy (SLNB) became a standard surgical procedure for patients with early breast cancer; however, the optimal method of sentinel lymph node (SLN) identification remains controversial. The current study presents the protocol of our institution for preoperative and intraoperative SLN detection. Methods Fifty female patients with early breast cancer and clinically node-negative axilla were enrolled in this study. All patients underwent preoperative CT lymphography (CTLG), intraoperative SLNB using fluorescence navigation, intraoperative one-step nucleic acid amplification (OSNA) and postoperative hematoxylin and eosin histopathological analysis. Prediction of metastasis by CTLG and detection of metastasis by OSNA were compared to results of histopathology as standard reference. Results SLN were identified by preoperative CTLG and intraoperative SLNB with fluorescence navigation in all patients, the identification rate was 100 \%. SLN metastases were detected as positive by OSNA in 9 patients (18 \%), 4 were (++), 4 were (+) and 1 was (+I). SLN metastases were detected as positive by histopathology in 10 patients (20 \%). The concordance rate between OSNA and permanent sections was 90 \%. The negative predictive value of CTLG was 80 \%. Conclusion Use of CTLG and fluorescence navigation made performing SLNB with high accuracy possible in institutions that cannot use the radioisotope method. OSNA provided accurate intraoperative method, allowing for completion of axillary node dissection during surgery and avoidance of second surgical procedure in patients with positive SLNs, thereby reducing patient distress and, finally, saving hospital costs.},
	language = {en},
	number = {2},
	urldate = {2016-06-24},
	journal = {Breast Cancer},
	author = {Mokhtar, Mohamed and Tadokoro, Yukiko and Nakagawa, Misako and Morimoto, Masami and Takechi, Hirokazu and Kondo, Kazuya and Tangoku, Akira},
	month = jul,
	year = {2014},
	pages = {202--210},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2HFV8T2A/Mokhtar et al. - 2014 - Triple assessment of sentinel lymph node metastasi.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ISC3TDPR/s12282-014-0551-1.html:text/html}
}

@article{quinn_high-resolution_2012,
	title = {High-{Resolution} {Microendoscopy} for the {Detection} of {Cervical} {Neoplasia} in {Low}-{Resource} {Settings}},
	volume = {7},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044924},
	doi = {10.1371/journal.pone.0044924},
	abstract = {Cervical cancer is the second leading cause of cancer death among women in developing countries. Developing countries often lack infrastructure, cytotechnologists, and pathologists necessary to implement current screening tools. Due to their low cost and ease of interpretation at the point-of-care, optical imaging technologies may serve as an appropriate solution for cervical cancer screening in low resource settings. We have developed a high-resolution optical imaging system, the High Resolution Microendoscope (HRME), which can be used to interrogate clinically suspicious areas with subcellular spatial resolution, revealing changes in nuclear to cytoplasmic area ratio. In this pilot study carried out at the women's clinic of Princess Marina Hospital in Botswana, 52 unique sites were imaged in 26 patients, and the results were compared to histopathology as a reference standard. Quantitative high resolution imaging achieved a sensitivity and specificity of 86\% and 87\%, respectively, in differentiating neoplastic (≥CIN 2) tissue from non-neoplastic tissue. These results suggest the potential promise of HRME to assist in the detection of cervical neoplasia in low-resource settings.},
	number = {9},
	urldate = {2016-06-21},
	journal = {PLOS ONE},
	author = {Quinn, Mary K. and Bubi, Tefo C. and Pierce, Mark C. and Kayembe, Mukendi K. and Ramogola-Masire, Doreen and Richards-Kortum, Rebecca},
	month = sep,
	year = {2012},
	keywords = {Biopsy, Cancer detection and diagnosis, Cervical cancer, Cervix, Dysplasia, Epithelium, histopathology, Lesions},
	pages = {e44924},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/25B6B23E/Quinn et al. - 2012 - High-Resolution Microendoscopy for the Detection o.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZGTRFQ5V/article.html:text/html}
}

@article{mari_influence_2010,
	title = {Influence of the live cell {DNA} marker {DRAQ}5 on chromatin-associated processes},
	volume = {9},
	issn = {1568-7864},
	url = {http://www.sciencedirect.com/science/article/pii/S1568786410001291},
	doi = {10.1016/j.dnarep.2010.04.001},
	abstract = {In the last decade, live cell fluorescence microscopy experiments have revolutionized cellular and molecular biology, enabling the localization of proteins within cellular compartments to be analysed and to determine kinetic parameters of enzymatic reactions in living nuclei to be measured. Recently, in vivo DNA labelling by DNA-stains such as DRAQ5, has provided the opportunity to measure kinetic reactions of GFP-fused proteins in targeted areas of the nucleus with different chromatin compaction levels. To verify the suitability of combining DRAQ5-staining with protein dynamic measurements, we have tested the cellular consequences of DRAQ5 DNA intercalation. We show that DRAQ5 intercalation rapidly modifies both the localization and the mobility properties of several DNA-binding proteins such as histones, DNA repair, replication and transcription factors, by stimulating a release of these proteins from their substrate. Most importantly, the effect of DRAQ5 on the mobility of essential cellular enzymes results in a potent inhibition of the corresponding cellular functions. From these observations, we suggest that great caution must be used when interpreting live cell data obtained using DRAQ5.},
	number = {7},
	urldate = {2016-06-25},
	journal = {DNA Repair},
	author = {Mari, Pierre-Olivier and Verbiest, Vincent and Sabbioneda, Simone and Gourdin, Audrey M. and Wijgers, Nils and Dinant, Christoffel and Lehmann, Alan R. and Vermeulen, Wim and Giglia-Mari, Giuseppina},
	month = jul,
	year = {2010},
	keywords = {Histones, NER, PCNA, RPA, TFIIH, TLS polymerases, XPB},
	pages = {848--855},
	file = {1-s2.0-S1568786410001291-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SJRFQCIR/1-s2.0-S1568786410001291-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FTVNABGR/S1568786410001291.html:text/html}
}

@article{jeevan_reoperation_2012,
	title = {Reoperation rates after breast conserving surgery for breast cancer among women in {England}: retrospective study of hospital episode statistics},
	volume = {345},
	copyright = {© Jeevan et al 2012. This is an open-access article distributed under the terms of the Creative Commons Attribution Non-commercial License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited, the use is non commercial and is otherwise in compliance with the license. See: http://creativecommons.org/licenses/by-nc/2.0/  and  http://creativecommons.org/licenses/by-nc/2.0/legalcode.},
	issn = {1756-1833},
	shorttitle = {Reoperation rates after breast conserving surgery for breast cancer among women in {England}},
	url = {http://www.bmj.com.libproxy.tulane.edu:2048/content/345/bmj.e4505},
	doi = {10.1136/bmj.e4505},
	abstract = {Objectives To examine whether rate of reoperation after breast conserving surgery is associated with patients’ characteristics and investigate whether reoperation rates vary among English NHS trusts.
Design Cohort study using patient level data from hospital episode statistics.
Setting English NHS trusts.
Participants Adult women who had breast conserving surgery between 1 April 2005 and 31 March 2008.
Main outcome measure Reoperation rates after primary breast conserving surgery within 3 months, adjusted using logistic regression for tumour type, age, comorbidity, and socioeconomic deprivation. Tumours were grouped by whether a carcinoma in situ component was coded at the time of the primary breast conserving surgery.
Results 55 297 women had primary breast conserving surgery in 156 NHS trusts during the three year period. 11 032 (20.0\%, 95\% confidence interval 19.6\% to 20.3\%) women had at least one reoperation. 10 212 (18.5\%, 18.2\% to 18.8\%) had one reoperation only; of these, 5943 (10.7\%, 10.5\% to 11.0\%) had another breast conserving procedure and 4269 (7.7\%, 7.5\% to 7.9\%) had a mastectomy. Of the 45 793 women with isolated invasive disease, 8229 (18.0\%) had at least one reoperation. In comparison, 2803 (29.5\%) of the 9504 women with carcinoma in situ had at least one reoperation (adjusted odds ratio 1.9, 95\% confidence interval 1.8 to 2.0). Substantial differences were found in the adjusted reoperation rates among the NHS trusts (10th and 90th centiles 12.2\% and 30.2\%).
Conclusion: One in five women who had breast conserving surgery in England had a reoperation. Reoperation was nearly twice as likely when the tumour had a carcinoma in situ component coded. Women should be informed of this reoperation risk when deciding on the type of surgical treatment of their breast cancer.},
	language = {en},
	urldate = {2016-06-30},
	journal = {BMJ},
	author = {Jeevan, R. and Cromwell, D. A. and Trivella, M. and Lawrence, G. and Kearins, O. and Pereira, J. and Sheppard, C. and Caddy, C. M. and Meulen, J. H. P. van der},
	month = jul,
	year = {2012},
	pmid = {22791786},
	pages = {e4505},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/G4EFKT8K/Jeevan et al. - 2012 - Reoperation rates after breast conserving surgery .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/M37FWUG3/bmj.html:text/html}
}

@article{hanahan_hallmarks_2011,
	title = {Hallmarks of {Cancer}: {The} {Next} {Generation}},
	volume = {144},
	issn = {0092-8674},
	shorttitle = {Hallmarks of {Cancer}},
	url = {http://www.sciencedirect.com/science/article/pii/S0092867411001279},
	doi = {10.1016/j.cell.2011.02.013},
	abstract = {The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors. The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease. They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions. Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list—reprogramming of energy metabolism and evading immune destruction. In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the “tumor microenvironment.” Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer.},
	number = {5},
	urldate = {2016-05-22},
	journal = {Cell},
	author = {Hanahan, Douglas and Weinberg, Robert A.},
	month = mar,
	year = {2011},
	pages = {646--674},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7PXZFD34/Hanahan and Weinberg - 2011 - Hallmarks of Cancer The Next Generation.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BZ96FV4K/S0092867411001279.html:text/html}
}

@article{smith_characteristics_2000,
	title = {Characteristics of a novel deep red/infrared fluorescent cell-permeant {DNA} probe, {DRAQ}5, in intact human cells analyzed by flow cytometry, confocal and multiphoton microscopy},
	volume = {40},
	issn = {0196-4763},
	abstract = {BACKGROUND: The multiparameter fluorometric analysis of intact and fixed cells often requires the use of a nuclear DNA discrimination signal with spectral separation from visible range fluorochromes. We have developed a novel deep red fluorescing bisalkylaminoanthraquinone, DRAQ5 (Ex(lambdamax) 646 nm; Em(lambdamax) 681 nm; Em(lambdarange) 665-{\textgreater}800 nm), with high affinity for DNA and a high capacity to enter living cells. We describe here the spectral characteristics and applications of this synthetic compound, particularly in relation to cytometric analysis of the cell cycle.
METHODS: Cultured human tumor cells were examined for the ability to nuclear locate DRAQ5 using single and multiphoton laser scanning microscopy (LSM) and multiparameter flow cytometry.
RESULTS: Multiparameter flow cytometry shows that the dye can rapidly report the cellular DNA content of live and fixed cells at a resolution level adequate for cell cycle analysis and the cycle-specific expression of cellular proteins (e.g., cyclin B1). The preferential excitation of DRAQ5 by laser red lines (633/647 nm) was found to offer a means of fluorescence signal discrimination by selective excitation, with greatly reduced emission overlap with UV-excitable and visible range fluophors as compared with propidium iodide. LSM reveals nuclear architecture and clearly defines chromosomal elements in live cells. DRAQ5 was found to permit multiphoton imaging of nuclei using a 1,047-nm emitting mode-locked YLF laser. The unusual spectral properties of DRAQ5 also permit live cell DNA analysis using conventional 488 nm excitation and the single-photon imaging of nuclear fluorescence using laser excitation between 488 nm and low infrared (IR; 780 nm) wavelengths. Single and multiphoton microscopy studies revealed the ability of DRAQ5 to report three-dimensional nuclear structure and location in live cells expressing endoplasmic reticulum targeted-GFP, MitoTracker-stained mitochondria, or a vital cell probe for free zinc (Zinquin).
CONCLUSION: The fluorescence excitation and emission characteristics of DRAQ5 in living and fixed cells permit the incorporation of the measurement of cellular DNA content into a variety of multiparameter cytometric analyses.},
	language = {eng},
	number = {4},
	journal = {Cytometry},
	author = {Smith, P. J. and Blunt, N. and Wiltshire, M. and Hoy, T. and Teesdale-Spittle, P. and Craven, M. R. and Watson, J. V. and Amos, W. B. and Errington, R. J. and Patterson, L. H.},
	month = aug,
	year = {2000},
	pmid = {10918279},
	keywords = {Anthraquinones, CDC2 Protein Kinase, Cell Cycle, Cyclin B, Cyclin B1, Diagnostic Imaging, DNA, Neoplasm, DNA Probes, Flow cytometry, Fluorescent Antibody Technique, Fluorescent Dyes, Gene Expression, Green Fluorescent Proteins, Humans, Infrared Rays, Luminescent Proteins, Melanoma, Microscopy, Confocal, Microscopy, Fluorescence, Molecular Structure, Nitrogen Oxides, Quinolones, Spectrophotometry, Tosyl Compounds, Tumor Cells, Cultured},
	pages = {280--291},
	file = {Characteristics_of_a_novel_deep_redinfrared_fluore.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/55WWEDXW/Characteristics_of_a_novel_deep_redinfrared_fluore.pdf:application/pdf}
}

@article{neil_method_1997,
	title = {Method of obtaining optical sectioning by using structured light in a conventional microscope},
	volume = {22},
	issn = {0146-9592, 1539-4794},
	url = {https://www.osapublishing.org/abstract.cfm?URI=ol-22-24-1905},
	doi = {10.1364/OL.22.001905},
	language = {en},
	number = {24},
	urldate = {2016-07-01},
	journal = {Optics Letters},
	author = {Neil, M. A. A. and Juškaitis, R. and Wilson, T.},
	month = dec,
	year = {1997},
	pages = {1905}
}

@inproceedings{fink_stray_2013,
	title = {Stray light rejection by structured illumination},
	volume = {2},
	url = {https://www.bmo.uni-luebeck.de/uploads/tx_wapublications/Fink__2013_Stray_light_rejection_by_structured_illumination.pdf},
	urldate = {2016-07-07},
	booktitle = {Student {Conference} {Medical} {Engineering} {Science} 2013: {Proceedings}},
	publisher = {GRIN Verlag},
	author = {Fink, P. K. and Hillmann, D. and Franke, G. L. and Ramm, D. and Koch, P. and Hüttmann, G.},
	year = {2013},
	pages = {71},
	file = {Fink__2013_Stray_light_rejection_by_structured_illumination.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NGK3KIUW/Fink__2013_Stray_light_rejection_by_structured_illumination.pdf:application/pdf}
}

@article{_draq5_2014,
	title = {{DRAQ}5 {DNA} {Stain}},
	volume = {2014},
	issn = {1940-3402, 1559-6095},
	url = {http://cshprotocols.cshlp.org/content/2014/9/pdb.rec081232},
	doi = {10.1101/pdb.rec081232},
	language = {en},
	number = {9},
	urldate = {2016-06-25},
	journal = {Cold Spring Harbor Protocols},
	month = sep,
	year = {2014},
	pages = {pdb.rec081232},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8KFBMS23/pdb.html:text/html}
}

@article{derenzini_nucleolar_2000-1,
	title = {Nucleolar size indicates the rapidity of cell proliferation in cancer tissues},
	volume = {191},
	copyright = {Copyright © 2000 John Wiley \& Sons, Ltd.},
	issn = {1096-9896},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-9896(200006)191:2<181::AID-PATH607>3.0.CO;2-V/abstract},
	doi = {10.1002/(SICI)1096-9896(200006)191:2<181::AID-PATH607>3.0.CO;2-V},
	abstract = {In order to define the importance of the nucleolus in tumour pathology, the relationship between nucleolar size and function and tumour mass growth rate was studied in vivo. Ten established human cancer cell lines from colon carcinomas and neuroblastomas were inoculated subcutaneously in athymic mice and the doubling time (DT) of the xenograft tumour mass was calculated. The tumour DTs ranged from 3.2 to 15.7 days. Nucleolar size was evaluated in sections from formalin-fixed and paraffin-embedded tumour samples after silver staining for AgNOR proteins, using a specific image analysis system. The nucleolar area values were inversely related to the xenograft tumour mass DTs (r=−0.90; p{\textless}0.001). Nucleolar functional activity was also evaluated using rapid, intermediate, and slow growing tumours (one each). The values of RNA polymerase I activity measured in vitro were strongly related to the corresponding tumour DTs (r=−0.99; p=0.03). The labelling indices (LIs) of three proliferation markers, MIB1, PCNA, and bromodeoxyuridine (BrdU), were also evaluated. As revealed by the MIB1 and PCNA LIs, almost all the cells of the xenograft tumours were cycling (86.6±5.6 SD and 95.5±2.0 SD, respectively). Neither the MIB1, PCNA or BrdU LIs were related to the xenograft tumour mass DT, showing that the different growth rates of tumour xenografts were not due to different growth fractions, but were mainly related to different cell proliferation rates. The present data demonstrate that the size and function of the nucleolus are related to the cell proliferation rate of cancer tissue. Evaluation of nucleolar size after silver staining of AgNOR proteins represents a unique parameter for the histological assessment of rapidity of cell proliferation in tumour lesions. Copyright © 2000 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {2},
	urldate = {2016-06-27},
	journal = {The Journal of Pathology},
	author = {Derenzini, Massimo and Trerè, Davide and Pession, Annalisa and Govoni, Marzia and Sirri, Valentina and Chieco, Pasquale},
	month = jun,
	year = {2000},
	keywords = {AgNOR proteins, cancer cells, cell proliferation rate, nucleolus, quantitation, ribosome biogenesis},
	pages = {181--186},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C55HVUC7/abstract.html:text/html;The Journal of Pathology Volume 191 issue 2 2000 [doi 10.1002%2F%28sici%291096-9896%28200006%29191%3A2%3C181%3A%3Aaid-path607%3E3.0.co%3B2-v] Derenzini, Massimo\; Trer�, Davide\; Pession, Annalisa\; Govo.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FPMTRU64/The Journal of Pathology Volume 191 issue 2 2000 [doi 10.1002%2F%28sici%291096-9896%28200006%29191%3A2%3C181%3A%3Aaid-path607%3E3.0.co%3B2-v] De.pdf:application/pdf}
}

@article{bocarsly_minimally_2015,
	title = {Minimally invasive microendoscopy system for in vivo functional imaging of deep nuclei in the mouse brain},
	volume = {6},
	issn = {2156-7085},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646561/},
	doi = {10.1364/BOE.6.004546},
	abstract = {The ability to image neurons anywhere in the mammalian brain is a major goal of optical microscopy. Here we describe a minimally invasive microendoscopy system for studying the morphology and function of neurons at depth. Utilizing a guide cannula with an ultrathin wall, we demonstrated in vivo two-photon fluorescence imaging of deeply buried nuclei such as the striatum (2.5 mm depth), substantia nigra (4.4 mm depth) and lateral hypothalamus (5.0 mm depth) in mouse brain. We reported, for the first time, the observation of neuronal activity with subcellular resolution in the lateral hypothalamus and substantia nigra of head-fixed awake mice.},
	number = {11},
	urldate = {2016-06-22},
	journal = {Biomedical Optics Express},
	author = {Bocarsly, Miriam E. and Jiang, Wan-chen and Wang, Chen and Dudman, Joshua T. and Ji, Na and Aponte, Yeka},
	month = oct,
	year = {2015},
	pmid = {26601017},
	pmcid = {PMC4646561},
	pages = {4546--4556},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IDX5DC33/Bocarsly et al. - 2015 - Minimally invasive microendoscopy system for in vi.pdf:application/pdf}
}

@patent{bryll_edge_2014,
	title = {Edge detection using structured illumination},
	url = {http://www.google.com/patents/US8773526},
	abstract = {A machine vision inspection system (MVIS) and a related light stripe edge feature location method are disclosed. The MVIS comprises a control system, a light stripe projection system, an imaging system, and a user interface. In a region of interest including the edge feature, the light stripe projection system focuses a light stripe transverse to the edge direction and across the edge feature, such that the light stripe has a changing stripe intensity profile along the light stripe. The imaging system acquires an image of the light stripe and the control system analyzes the image to determine the location of the edge feature based on a changing light intensity profile along the stripe. The method may be implemented in an edge detection video tool. The method may be advantageous for inspecting highly textured, beveled, chamfered, rounded or damaged edges, for example.},
	nationality = {United States},
	assignee = {Mitutoyo Corporation},
	number = {US8773526 B2},
	urldate = {2016-07-05},
	author = {Bryll, Robert K.},
	month = jul,
	year = {2014},
	note = {U.S. Classification 348/94; International Classification H04N5/253; Cooperative Classification G06T7/0085, G06T7/0006, G06K9/2036, G06K9/2027, G01N21/8806},
	file = {Google Patents PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QEMJJR6G/Bryll - 2014 - Edge detection using structured illumination.pdf:application/pdf}
}

@article{windhausen_effectiveness_2012,
	title = {Effectiveness of {Genomic} {Prediction} of {Maize} {Hybrid} {Performance} in {Different} {Breeding} {Populations} and {Environments}},
	volume = {2},
	issn = {, 2160-1836},
	url = {http://www.g3journal.org/content/2/11/1427},
	doi = {10.1534/g3.112.003699},
	abstract = {Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25\% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.},
	language = {en},
	number = {11},
	urldate = {2015-02-10},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Windhausen, Vanessa S. and Atlin, Gary N. and Hickey, John M. and Crossa, Jose and Jannink, Jean-Luc and Sorrells, Mark E. and Raman, Babu and Cairns, Jill E. and Tarekegne, Amsal and Semagn, Kassa and Beyene, Yoseph and Grudloyma, Pichet and Technow, Frank and Riedelsheimer, Christian and Melchinger, Albrecht E.},
	month = nov,
	year = {2012},
	pmid = {23173094},
	keywords = {GenPred, grain yield, maize, Shared data resources},
	pages = {1427--1436},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/94MCACUS/Windhausen et al. - 2012 - Effectiveness of Genomic Prediction of Maize Hybri.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RMWWV428/1427.html:text/html}
}

@article{_bci_????,
	title = {{BCI}},
	file = {Speech Preparation in MWS-Proof Brain.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MZU5PENF/Speech Preparation in MWS-Proof Brain.pdf:application/pdf}
}

@article{chang_high-risk_2014,
	title = {High-risk prostate cancer—classification and therapy},
	volume = {11},
	copyright = {© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1759-4774},
	url = {http://www.nature.com/nrclinonc/journal/v11/n6/full/nrclinonc.2014.68.html},
	doi = {10.1038/nrclinonc.2014.68},
	abstract = {Approximately 15\% of patients with prostate cancer are diagnosed with high-risk disease. However, the current definitions of high-risk prostate cancer include a heterogeneous group of patients with a range of prognoses. Some have the potential to progress to a lethal phenotype that can be fatal, while others can be cured with treatment of the primary tumour alone. The optimal management of this patient subgroup is evolving. A refined classification scheme is needed to enable the early and accurate identification of high-risk disease so that more-effective treatment paradigms can be developed. We discuss several principles established from clinical trials, and highlight other questions that remain unanswered. This Review critically evaluates the existing literature focused on defining the high-risk population, the management of patients with high-risk prostate cancer, and future directions to optimize care.},
	language = {en},
	number = {6},
	urldate = {2016-12-12},
	journal = {Nature Reviews Clinical Oncology},
	author = {Chang, Albert J. and Autio, Karen A. and Roach Iii, Mack and Scher, Howard I.},
	month = jun,
	year = {2014},
	keywords = {Hormonal therapies, PROSTATE cancer, Radiotherapy, Surgical oncology},
	pages = {308--323},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/84D9NJRZ/Chang et al. - 2014 - High-risk prostate cancer—classification and thera.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4A5952CR/nrclinonc.2014.68.html:text/html}
}

@article{lim_wide-field_2008,
	title = {Wide-field fluorescence sectioning with hybrid speckle and uniform-illumination microscopy},
	volume = {33},
	issn = {0146-9592, 1539-4794},
	url = {https://www.osapublishing.org/abstract.cfm?URI=ol-33-16-1819},
	doi = {10.1364/OL.33.001819},
	language = {en},
	number = {16},
	urldate = {2016-06-22},
	journal = {Optics Letters},
	author = {Lim, Daryl and Chu, Kengyeh K. and Mertz, Jerome},
	month = aug,
	year = {2008},
	pages = {1819}
}

@book{dixon_breast_2014,
	address = {Edinburgh; New York},
	title = {Breast surgery},
	isbn = {978-0-7020-4967-5},
	url = {http://www.clinicalkey.com/dura/browse/bookChapter/3-s2.0-C2011005737X},
	abstract = {Breast Surgery meets the needs of surgeons in higher training and practising consultants for a contemporary and evidence-based account of this sub-specialty that is relevant to their general surgical practice. It is a practical reference source incorporating the most current information on recent developments, management issues and operative procedures. The text is thoroughly referenced and supported by evidence-based recommendations wherever possible, distinguishing between strong evidence to support a conclusion, and evidence suggesting that a recommendation can be reached on the balance.},
	language = {English},
	urldate = {2016-06-22},
	publisher = {Saunders/Elsevier},
	author = {Dixon, J. M},
	year = {2014},
	note = {OCLC: 828776033},
	file = {3-s2.0-B9780702049590000023.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F6WGUJBC/3-s2.0-B9780702049590000023.pdf:application/pdf;3-s2.0-B9780702049590000047.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F3W72JQM/3-s2.0-B9780702049590000047.pdf:application/pdf}
}

@article{lin_tendon_2005,
	title = {Tendon properties in interleukin-4 and interleukin-6 knockout mice},
	volume = {38},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S002192900400140X},
	doi = {10.1016/j.jbiomech.2004.03.008},
	abstract = {Cytokines are known to play an important role in normal tendon development, function, and maintenance through interactions with fibroblasts and extracellular matrix proteins. However, the role of interleukins on normal tendon activity remains poorly understood. Previous studies that have researched the role of specific cytokines by exogenously applying them have often reported conflicting results. Therefore, a knockout mouse model was used to investigate the role of interleukins 4 and 6 on normal tendon organizational and biomechanical properties. It was hypothesized that interleukin-6 knockout (IL6 -/-) mice will display more organized collagen orientation and greater cross-sectional area and mechanical properties when compared to that of control mice. In addition, interleukin-4 knockout (IL4 -/-) mice will display the most disorganized collagen orientation and lowest cross-sectional area and mechanical properties. As hypothesized, IL6 -/- mice show a trend towards lower angular deviation (more organized) (p\&lt;0.1) when compared to IL4 -/- mice. In addition, the IL6 -/- mice show a trend towards a higher percent relaxation (p\&lt;0.1) and a significantly higher modulus (p\&lt;0.01) when compared to CTL and IL4 -/- mice. Unexpectedly, the IL6 -/- mice exhibited no significant differences in collagen fiber distribution and maximum stress from the other groups and actually had a smaller cross-sectional area than CTL mice (p\&lt;0.1). This study supports transgenic mice as an animal model for investigating how cytokines affect normal tendon properties. In addition, this study demonstrates that interleukins may play an important role in tendon development, function, and maintenance.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Lin, Tony W. and Cardenas, Luis and Soslowsky, Louis J.},
	month = jan,
	year = {2005},
	keywords = {Cytokines, Interleukins, Knockout mice, Tendon, Transgenic mice},
	pages = {99--105},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZCHQWRKT/Lin et al. - 2005 - Tendon properties in interleukin-4 and interleukin.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GVX5D67I/Lin et al. - 2005 - Tendon properties in interleukin-4 and interleukin.html:text/html}
}

@article{lee_co-occurring_2014,
	title = {Co-{Occurring} {Gland} {Angularity} in {Localized} {Subgraphs}: {Predicting} {Biochemical} {Recurrence} in {Intermediate}-{Risk} {Prostate} {Cancer} {Patients}},
	volume = {9},
	shorttitle = {Co-{Occurring} {Gland} {Angularity} in {Localized} {Subgraphs}},
	url = {http://dx.doi.org/10.1371/journal.pone.0097954},
	doi = {10.1371/journal.pone.0097954},
	abstract = {Quantitative histomorphometry (QH) refers to the application of advanced computational image analysis to reproducibly describe disease appearance on digitized histopathology images. QH thus could serve as an important complementary tool for pathologists in interrogating and interpreting cancer morphology and malignancy. In the US, annually, over 60,000 prostate cancer patients undergo radical prostatectomy treatment. Around 10,000 of these men experience biochemical recurrence within 5 years of surgery, a marker for local or distant disease recurrence. The ability to predict the risk of biochemical recurrence soon after surgery could allow for adjuvant therapies to be prescribed as necessary to improve long term treatment outcomes. The underlying hypothesis with our approach, co-occurring gland angularity (CGA), is that in benign or less aggressive prostate cancer, gland orientations within local neighborhoods are similar to each other but are more chaotically arranged in aggressive disease. By modeling the extent of the disorder, we can differentiate surgically removed prostate tissue sections from (a) benign and malignant regions and (b) more and less aggressive prostate cancer. For a cohort of 40 intermediate-risk (mostly Gleason sum 7) surgically cured prostate cancer patients where half suffered biochemical recurrence, the CGA features were able to predict biochemical recurrence with 73\% accuracy. Additionally, for 80 regions of interest chosen from the 40 studies, corresponding to both normal and cancerous cases, the CGA features yielded a 99\% accuracy. CGAs were shown to be statistically signicantly () better at predicting BCR compared to state-of-the-art QH methods and postoperative prostate cancer nomograms.},
	number = {5},
	urldate = {2015-11-30},
	journal = {PLoS ONE},
	author = {Lee, George and Sparks, Rachel and Ali, Sahirzeeshan and Shih, Natalie N. C. and Feldman, Michael D. and Spangler, Elaine and Rebbeck, Timothy and Tomaszewski, John E. and Madabhushi, Anant},
	month = may,
	year = {2014},
	pages = {e97954},
	file = {PLoS Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HQSRR3PN/Lee et al. - 2014 - Co-Occurring Gland Angularity in Localized Subgrap.pdf:application/pdf}
}

@article{haffty_prognostic_1998,
	title = {Prognostic significance of mammographic detection in a cohort of conservatively treated breast cancer patients},
	volume = {4},
	issn = {1081-4442},
	abstract = {PURPOSE: This study aimed to evaluate the prognostic significance of nonpalpable mammographically detected breast cancer in a cohort of conservatively treated breast cancer patients.
METHODS AND MATERIALS: The records of 953 patients with invasive stage I and II breast cancer treated with conservative surgery and radiation therapy prior to January 1990 were reviewed. Mode of presentation with reference to clinical and mammographic findings was recorded. For statistical analysis, patients were divided into two groups: 748 patients presented with clinically palpable masses with or without mammographic abnormalities (PALP), and 205 presented with nonpalpable mammographically detected tumors (MGDET).
RESULTS: Patients in the MGDET group presented with cancers at earlier stages of disease, had tumors of smaller pathological size, were more often hormone-receptor positive, and less frequently required adjuvant systemic therapy. As of December 1995, with a median follow-up of 11.6 years, the MGDET group had a higher 10-year overall survival rate (82\% vs 68\%) and a superior 10-year distant-metastasis-free rate (87\% vs 75\%). The ipsilateral breast tumor relapse rate was similar between the PALP and MGDET groups. When broken down by age ({\textless} 50 years vs {\textgreater} or = 50 years), the benefits of early detection remained apparent with a statistically significant superior distant-metastasis-free rate in women under age 50 in the MGDET group compared with women under age 50 in the PALP group. In a multivariate analysis, mammographic detection remained an independent prognostic factor for distant-metastasis-free survival.
CONCLUSION: Patients presenting with nonpalpable mammographically detected invasive breast cancer have a favorable prognosis compared with their counterparts presenting with clinically palpable masses. Although the issue of lead-time bias cannot be addressed adequately in this retrospective review, the favorable prognosis with respect to disease-free survival and breast conservation is quite evident. The high probability of disease-free survival and breast preservation in these patients should further encourage the widespread using of screening mammography and the increased use of breast-conserving surgery with radiation therapy.},
	language = {eng},
	number = {1},
	journal = {The Cancer Journal from Scientific American},
	author = {Haffty, B. G. and Lee, C. and Philpotts, L. and Horvath, L. and Ward, B. and McKhann, C. and Tocino, I.},
	month = feb,
	year = {1998},
	pmid = {9467044},
	keywords = {Breast neoplasms, Cohort Studies, Combined Modality Therapy, Female, Follow-Up Studies, Humans, mammography, Middle Aged, Multivariate Analysis, Prognosis, Treatment Outcome},
	pages = {35--40}
}

@article{brown_optical_2010,
	title = {Optical assessment of tumor resection margins in the breast},
	volume = {16},
	issn = {1077-260X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085495/},
	abstract = {Breast conserving surgery, in which the breast tumor and surrounding normal tissue are removed, is the primary mode of treatment for invasive and in situ carcinomas of the breast, conditions that affect nearly 200,000 women annually. Of these nearly 200,000 patients who undergo this surgical procedure, between 20–70\% of them may undergo additional surgeries to remove tumor that was left behind in the first surgery, due to the lack of intra-operative tools which can detect whether the boundaries of the excised specimens are free from residual cancer. Optical techniques have many attractive attributes which may make them useful tools for intra-operative assessment of breast tumor resection margins. In this manuscript, we discuss clinical design criteria for intra-operative breast tumor margin assessment, and review optical techniques appied to this problem. In addition, we report on the development and clinical testing of quantitative diffuse reflectance imaging (Q-DRI) as a potential solution to this clinical need. Q-DRI is a spectral imaging tool which has been applied to 56 resection margins in 48 patients at Duke University Medical Center. Clear sources of contrast between cancerous and cancer-free resection margins were identified with the device, and resulted in an overall accuracy of 75\% in detecting positive margins.},
	number = {3},
	urldate = {2016-06-24},
	journal = {IEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society},
	author = {Brown, J. Quincy and Bydlon, Torre M. and Richards, Lisa M. and Yu, Bing and Kennedy, Stephanie A. and Geradts, Joseph and Wilke, Lee G. and Junker, Marlee and Gallagher, Jennifer and Barry, William and Ramanujam, Nimmi},
	month = mar,
	year = {2010},
	pmid = {21544237},
	pmcid = {PMC3085495},
	pages = {530--544},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/46NFANV5/Brown et al. - 2010 - Optical assessment of tumor resection margins in t.pdf:application/pdf}
}

@book{press_numerical_1992,
	address = {Cambridge ; New York},
	edition = {2nd ed},
	title = {Numerical recipes in {C}: the art of scientific computing},
	isbn = {978-0-521-43108-8 978-0-521-43720-2},
	shorttitle = {Numerical recipes in {C}},
	publisher = {Cambridge University Press},
	editor = {Press, William H.},
	year = {1992},
	keywords = {C (Computer program language)},
	file = {c14-1.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZTE38T6W/c14-1.pdf:application/pdf}
}

@article{winter_incoherent_2015,
	title = {Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy},
	volume = {23},
	issn = {1094-4087},
	url = {https://www.osapublishing.org/oe/abstract.cfm?uri=oe-23-4-5327},
	doi = {10.1364/OE.23.005327},
	language = {en},
	number = {4},
	urldate = {2016-07-01},
	journal = {Optics Express},
	author = {Winter, Peter W. and Chandris, Panagiotis and Fischer, Robert S and Wu, Yicong and Waterman, Clare M and Shroff, Hari},
	month = feb,
	year = {2015},
	pages = {5327}
}

@article{jackson_neurophysiological_2014,
	title = {The neurophysiological bases of {EEG} and {EEG} measurement: {A} review for the rest of us},
	volume = {51},
	copyright = {Copyright © 2014 Society for Psychophysiological Research},
	issn = {1469-8986},
	shorttitle = {The neurophysiological bases of {EEG} and {EEG} measurement},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/psyp.12283/abstract},
	doi = {10.1111/psyp.12283},
	abstract = {A thorough understanding of the EEG signal and its measurement is necessary to produce high quality data and to draw accurate conclusions from those data. However, publications that discuss relevant topics are written for divergent audiences with specific levels of expertise: explanations are either at an abstract level that leaves readers with a fuzzy understanding of the electrophysiology involved, or are at a technical level that requires mastery of the relevant physics to understand. A clear, comprehensive review of the origin and measurement of EEG that bridges these high and low levels of explanation fills a critical gap in the literature and is necessary for promoting better research practices and peer review. The present paper addresses the neurophysiological source of EEG, propagation of the EEG signal, technical aspects of EEG measurement, and implications for interpretation of EEG data.},
	language = {en},
	number = {11},
	urldate = {2015-02-18},
	journal = {Psychophysiology},
	author = {Jackson, Alice F. and Bolger, Donald J.},
	month = nov,
	year = {2014},
	keywords = {EEG/ERP, Methods, Signal propagation},
	pages = {1061--1071},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U864U66K/Jackson and Bolger - 2014 - The neurophysiological bases of EEG and EEG measur.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HI8KJ9IP/Jackson and Bolger - 2014 - The neurophysiological bases of EEG and EEG measur.html:text/html}
}

@misc{_recently-approved_????,
	title = {Recently-{Approved} {Devices} {\textgreater} {MarginProbe} {System} – {P}110014},
	url = {http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/DeviceApprovalsandClearances/Recently-ApprovedDevices/ucm335805.htm},
	urldate = {2016-07-04},
	file = {Recently-Approved Devices > MarginProbe System – P110014:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AUWMI82B/ucm335805.html:text/html}
}

@article{meiliana_cancer_2016,
	title = {Cancer {Immunotherapy}: {A} {Review}},
	volume = {8},
	issn = {2355-9179, 2085-3297},
	shorttitle = {Cancer {Immunotherapy}},
	url = {http://inabj.org/index.php/ibj/article/view/189},
	doi = {10.18585/inabj.v8i1.189},
	number = {1},
	urldate = {2016-12-06},
	journal = {The Indonesian Biomedical Journal},
	author = {Meiliana, Anna and Dewi, Nurrani Mustika and Wijaya, Andi},
	month = apr,
	year = {2016},
	pages = {1},
	file = {189-353-2-PB.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FHVPM8JC/189-353-2-PB.pdf:application/pdf}
}

@article{phillips_gentle_2011,
	title = {A {Gentle} {Introduction} to the {Kernel} {Distance}},
	url = {http://arxiv.org/abs/1103.1625},
	abstract = {This document reviews the definition of the kernel distance, providing a gentle introduction tailored to a reader with background in theoretical computer science, but limited exposure to technology more common to machine learning, functional analysis and geometric measure theory. The key aspect of the kernel distance developed here is its interpretation as an L\_2 distance between probability measures or various shapes (e.g. point sets, curves, surfaces) embedded in a vector space (specifically an RKHS). This structure enables several elegant and efficient solutions to data analysis problems. We conclude with a glimpse into the mathematical underpinnings of this measure, highlighting its recent independent evolution in two separate fields.},
	urldate = {2016-11-04},
	journal = {arXiv:1103.1625 [cs]},
	author = {Phillips, Jeff M. and Venkatasubramanian, Suresh},
	month = mar,
	year = {2011},
	note = {arXiv: 1103.1625},
	keywords = {Computer Science - Computational Geometry, Computer Science - Learning}
}

@misc{_100th_????,
	title = {100th {Provider} {Joins} {MarginProbe} {Program} to {Improve} {Breast} {Cancer} {Surgery}},
	url = {http://www.prnewswire.com/news-releases/100th-provider-joins-marginprobe-program-to-improve-breast-cancer-surgery-300195976.html},
	urldate = {2016-07-04},
	file = {100th Provider Joins MarginProbe Program to Improve Breast Cancer Surgery:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3UG3W7UV/100th-provider-joins-marginprobe-program-to-improve-breast-cancer-surgery-300195976.html:text/html}
}

@article{phillips_gentle_2011-1,
	title = {A {Gentle} {Introduction} to the {Kernel} {Distance}},
	url = {http://arxiv.org/abs/1103.1625},
	abstract = {This document reviews the definition of the kernel distance, providing a gentle introduction tailored to a reader with background in theoretical computer science, but limited exposure to technology more common to machine learning, functional analysis and geometric measure theory. The key aspect of the kernel distance developed here is its interpretation as an L\_2 distance between probability measures or various shapes (e.g. point sets, curves, surfaces) embedded in a vector space (specifically an RKHS). This structure enables several elegant and efficient solutions to data analysis problems. We conclude with a glimpse into the mathematical underpinnings of this measure, highlighting its recent independent evolution in two separate fields.},
	urldate = {2016-11-04},
	journal = {arXiv:1103.1625 [cs]},
	author = {Phillips, Jeff M. and Venkatasubramanian, Suresh},
	month = mar,
	year = {2011},
	note = {arXiv: 1103.1625},
	keywords = {Computer Science - Computational Geometry, Computer Science - Learning}
}

@article{mclaughlin_influence_2008,
	title = {Influence of {Frozen}-{Section} {Analysis} of {Sentinel} {Lymph} {Node} and {Lumpectomy} {Margin} {Status} on {Reoperation} {Rates} in {Patients} {Undergoing} {Breast}-{Conservation} {Therapy}},
	volume = {206},
	issn = {1072-7515},
	url = {http://www.sciencedirect.com/science/article/pii/S1072751507013270},
	doi = {10.1016/j.jamcollsurg.2007.07.021},
	abstract = {Background
Frozen-section analysis (FS) of the sentinel lymph node (SLN) is performed to avoid reoperation for axillary lymph node dissection (ALND), but it can miss micrometastatic disease, is labor intensive for the pathologist, and does not alter the number of breast-conservation therapy (BCT) patients needing reoperation for positive margins. The purpose of this study was to determine if eliminating FS would change reoperation rates in BCT patients.
Study Design
Between January 2004 and December 2005, 1,218 patients had simultaneous BCT and SLN biopsy for invasive breast cancer. FS of the SLN was used selectively at the surgeon’s discretion. Clinical and pathologic data were collected.
Results
Overall, 542 of 1,218 (44\%) patients had positive margins. FS of the SLN was performed in 931 of 1,218 (76\%) patients. In those having FS, the SLN positivity rate was 33\% (306 of 931). FS identified the positive SLN in 170 of 306 (56\%) patients with positive nodes, allowing for immediate ALND. But 101 of these 170 patients had positive lumpectomy margins; and FS of the SLN saved 69 of 931 (7\%) patients a second operation. Of patients not having FS, 48 of 287 (17\%) had a positive SLN on final pathology. Only 18 of 48 (those seen on routine hematoxylin and eosin) might have been seen on FS, potentially sparing reoperation. Half of patients not having FS required reexcision for positive margins. FS would have spared reoperation for only 8 of 287 (3\%) patients in this group. Overall, of 354 of 1,218 patients with SLN metastases, 170 had immediate ALND and 98 had delayed ALND. Of those having delayed ALND, 68 of 98 also had positive margins.
Conclusions
Among patients having BCT with SLN biopsy, FS identified the positive SLN in 56\% of patients with positive SLNs, allowing immediate ALND, and was false negative in 44\%. Margin status remains a frequent indication for reoperation in BCT; routine FS analysis of the SLN ultimately saves only a minority of patients a second operation.},
	number = {1},
	urldate = {2016-06-24},
	journal = {Journal of the American College of Surgeons},
	author = {McLaughlin, Sarah A. and Ochoa-Frongia, Lisa M. and Patil, Sujata M. and Cody III, Hiram S. and Sclafani, Lisa M.},
	month = jan,
	year = {2008},
	pages = {76--82},
	file = {1-s2.0-S1072751507013270-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P3VR6TFV/1-s2.0-S1072751507013270-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZT699QDT/abstract.html:text/html}
}

@article{alam_potential_2013,
	title = {Potential {Applications} of {Quantum} {Dots} in {Mapping} {Sentinel} {Lymph} {Node} and {Detection} of {Micrometastases} in {Breast} {Carcinoma}},
	volume = {16},
	issn = {1738-6756},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625755/},
	doi = {10.4048/jbc.2013.16.1.1},
	abstract = {Breast cancer cure aims at complete elimination of malignant cells and essentially requires detection and treatment of any micrometastases. Here, we present a review of the current methods in use and the potential role of the quantum dots (QDs) in detection and visualization of sentinel lymph node and micrometastases in breast cancer patients. The traditional histopathological, immunohistochemical, and reverse transcriptase polymerase chain reaction procedures being used for micrometastases detection had serious drawbacks of high false negativity, specificity variations and false positivity of the results. Photon emission fluorescence multiplexing characteristics of the quantum dots make them potentially ideal probes for studying the dynamics of cellular processes over time such as continuous tracking of cell migration, differentiation, and metastases. In breast cancer, QDs based molecular and genomic detections had an unparallel high sensitivity and specificity.},
	number = {1},
	urldate = {2016-06-25},
	journal = {Journal of Breast Cancer},
	author = {Alam, Feroz and Yadav, Neha},
	month = mar,
	year = {2013},
	pmid = {23593075},
	pmcid = {PMC3625755},
	pages = {1--11},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NKTBKMET/Alam and Yadav - 2013 - Potential Applications of Quantum Dots in Mapping .pdf:application/pdf}
}

@article{miller_computational_2014,
	series = {Functional {Tissue} {Engineering}},
	title = {Computational model of the in vivo development of a tissue engineered vein from an implanted polymeric construct},
	volume = {47},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S0021929013004636},
	doi = {10.1016/j.jbiomech.2013.10.009},
	abstract = {Advances in vascular tissue engineering have been tremendous over the past 15 years, yet there remains a need to optimize current constructs to achieve vessels having true growth potential. Toward this end, it has been suggested that computational models may help hasten this process by enabling time-efficient parametric studies that can reduce the experimental search space. In this paper, we present a first generation computational model for describing the in vivo development of a tissue engineered vein from an implanted polymeric scaffold. The model was motivated by our recent data on the evolution of mechanical properties and microstructural composition over 24 weeks in a mouse inferior vena cava interposition graft. It is shown that these data can be captured well by including both an early inflammatory-mediated and a subsequent mechano-mediated production of extracellular matrix. There remains a pressing need, however, for more data to inform the development of next generation models, particularly the precise transition from the inflammatory to the mechanobiological dominated production of matrix having functional capability.},
	number = {9},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Miller, K. S. and Lee, Y. U. and Naito, Y. and Breuer, C. K. and Humphrey, J. D.},
	month = jun,
	year = {2014},
	keywords = {Constrained mixture theory, Inflammation, Interposition graft, Mechanosensing, Mouse model, Tissue engineering},
	pages = {2080--2087},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/J8467GJ4/Miller et al. - 2014 - Computational model of the in vivo development of .pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S665QKFT/S0021929013004636.html:text/html}
}

@article{bradford_whole_2016,
	title = {Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers},
	volume = {7},
	issn = {1949-2553},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991491/},
	doi = {10.18632/oncotarget.8014},
	abstract = {The tumor microenvironment is emerging as a key regulator of cancer growth and progression, however the exact mechanisms of interaction with the tumor are poorly understood. Whilst the majority of genomic profiling efforts thus far have focused on the tumor, here we investigate RNA-Seq as a hypothesis-free tool to generate independent tumor and stromal biomarkers, and explore tumor-stroma interactions by exploiting the human-murine compartment specificity of patient-derived xenografts (PDX)., Across a pan-cancer cohort of 79 PDX models, we determine that mouse stroma can be separated into distinct clusters, each corresponding to a specific stromal cell type. This implies heterogeneous recruitment of mouse stroma to the xenograft independent of tumor type. We then generate cross-species expression networks to recapitulate a known association between tumor epithelial cells and fibroblast activation, and propose a potentially novel relationship between two hypoxia-associated genes, human MIF and mouse Ddx6. Assessment of disease subtype also reveals MMP12 as a putative stromal marker of triple-negative breast cancer. Finally, we establish that our ability to dissect recruited stroma from trans-differentiated tumor cells is crucial to identifying stem-like poor-prognosis signatures in the tumor compartment., In conclusion, RNA-Seq is a powerful, cost-effective solution to global analysis of human tumor and mouse stroma simultaneously, providing new insights into mouse stromal heterogeneity and compartment-specific disease markers that are otherwise overlooked by alternative technologies. The study represents the first comprehensive analysis of its kind across multiple PDX models, and supports adoption of the approach in pre-clinical drug efficacy studies, and compartment-specific biomarker discovery.},
	number = {15},
	urldate = {2016-11-02},
	journal = {Oncotarget},
	author = {Bradford, James R. and Wappett, Mark and Beran, Garry and Logie, Armelle and Delpuech, Oona and Brown, Henry and Boros, Joanna and Camp, Nicola J. and McEwen, Robert and Mazzola, Anne Marie and D'Cruz, Celina and Barry, Simon T.},
	month = mar,
	year = {2016},
	pmid = {26980748},
	pmcid = {PMC4991491},
	pages = {20773--20787},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SGTFE3BJ/Bradford et al. - 2016 - Whole transcriptome profiling of patient-derived x.pdf:application/pdf}
}

@article{sereysky_structural_2012,
	title = {Structural and mechanical effects of in vivo fatigue damage induction on murine tendon},
	volume = {30},
	copyright = {Copyright © 2011 Orthopaedic Research Society},
	issn = {1554-527X},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/jor.22012/abstract},
	doi = {10.1002/jor.22012},
	abstract = {The purpose of this study was to develop and validate an in vivo mouse model of tendon fatigue and use this model to investigate and quantify the physical manifestations of fatigue damage in mouse tendon. Patellar tendons of C57BL/6J mice were fatigue loaded at 2 Hz to three endpoints (4 N peak force per cycle for 1 h, 6 N for 1 h, and 4 N for 2 h), during which hysteresis, tangent stiffness, and peak strain of each cycle were measured. Damage accumulation was then quantified using in situ histology, and each tendon was loaded monotonically to failure. Histological damage increased significantly in all three groups (≥2-fold), and monotonic stiffness decreased significantly in the 6 N, 1 h and 4 N, 2-h groups (∼25\%), suggesting that damage initially manifests as changes to the collagen structure of the tendon and subsequently as changes to the function. For the fatigue loading protocols used in this study, none of the evaluated real-time parameters from fatigue loading correlated with damage area fraction measured structural damage or monotonic stiffness, suggesting that they are not suited to serve as proxies for damage accumulation. In future studies, this model will be used to compare the biological response of mouse tendon to fatigue damage across genetic strains. © 2011 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 30:965–972, 2012},
	language = {en},
	number = {6},
	urldate = {2014-11-04},
	journal = {Journal of Orthopaedic Research},
	author = {Sereysky, Jedd B. and Andarawis-Puri, Nelly and Jepsen, Karl J. and Flatow, Evan L.},
	month = jun,
	year = {2012},
	keywords = {collagen, Damage, Microstructure, murine, Tendon},
	pages = {965--972},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZHZSQN9E/Sereysky et al. - 2012 - Structural and mechanical effects of in vivo fatig.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UKHF6GU9/abstract.html:text/html}
}

@article{durduran_bulk_2002,
	title = {Bulk optical properties of healthy female breast tissue},
	volume = {47},
	issn = {0031-9155},
	abstract = {We have measured the bulk optical properties of healthy female breast tissues in vivo in the parallel plate, transmission geometry. Fifty-two volunteers were measured. Blood volume and blood oxygen saturation were derived from the optical property data using a novel method that employed a priori spectral information to overcome limitations associated with simple homogeneous tissue models. The measurements provide an estimate of the variation of normal breast tissue optical properties in a fairly large population. The mean blood volume was 34 +/- 9 microM and the mean blood oxygen saturation was 68 +/- 8\%. We also investigated the correlation of these optical properties with demographic factors such as body mass index (BMI) and age. We observed a weak correlation of blood volume and reduced scattering coefficient with BMI: correlation with age, however, was not evident within the statistical error of these experiments. The new information on healthy breast tissue provides insight about the potential contrasts available for diffuse optical tomography of breast tumours.},
	language = {eng},
	number = {16},
	journal = {Physics in Medicine and Biology},
	author = {Durduran, T. and Choe, R. and Culver, J. P. and Zubkov, L. and Holboke, M. J. and Giammarco, J. and Chance, B. and Yodh, A. G.},
	month = aug,
	year = {2002},
	pmid = {12222850},
	keywords = {Adult, Aged, Aging, Blood Volume, Blood Volume Determination, Body Mass Index, Breast, Female, Hemoglobins, Humans, Infrared Rays, Middle Aged, Optics and Photonics, Oxygen, Reference Values, Reproducibility of Results, Scattering, Radiation, Sensitivity and Specificity, Spectroscopy, Near-Infrared, Statistics as Topic, Tomography},
	pages = {2847--2861},
	file = {TDurduran2002PMB47.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MP4R3A67/TDurduran2002PMB47.pdf:application/pdf}
}

@article{lee_flare_2010,
	title = {The {FLARE} {Intraoperative} {Near}-{Infrared} {Fluorescence} {Imaging} {System}: {A} {First}-in-{Human} {Clinical} {Trial} in {Perforator} {Flap} {Breast} {Reconstruction}:},
	volume = {126},
	issn = {0032-1052},
	shorttitle = {The {FLARE} {Intraoperative} {Near}-{Infrared} {Fluorescence} {Imaging} {System}},
	url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage&an=00006534-201011000-00007},
	doi = {10.1097/PRS.0b013e3181f059c7},
	language = {en},
	number = {5},
	urldate = {2016-06-24},
	journal = {Plastic and Reconstructive Surgery},
	author = {Lee, Bernard T. and Hutteman, Merlijn and Gioux, Sylvain and Stockdale, Alan and Lin, Samuel J. and Ngo, Long H. and Frangioni, John V.},
	month = nov,
	year = {2010},
	pages = {1472--1481},
	file = {00006534-201011000-00007.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/E2S5FM45/00006534-201011000-00007.pdf:application/pdf}
}

@misc{_speeding_????,
	title = {Speeding up the {ASI} {Stage} {\textbar} {Kurt}'s {Microscopy} {Blog}},
	url = {http://nic.ucsf.edu/blog/?p=576},
	urldate = {2016-06-28},
	file = {Speeding up the ASI Stage | Kurt's Microscopy Blog:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/EJEVJ58E/blog.html:text/html}
}

@article{arnoczky_loss_2008,
	title = {Loss of {Homeostatic} {Strain} {Alters} {Mechanostat} "{Set} {Point}" of {Tendon} {Cells} {In} {Vitro}},
	volume = {466},
	issn = {0009-921X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2505257/},
	doi = {10.1007/s11999-008-0264-x},
	abstract = {Tendon cells respond to mechanical loads. The character (anabolic or catabolic) and sensitivity of this response is determined by the mechanostat set point of the cell, which is governed by the cytoskeleton and its interaction with the extracellular matrix. To determine if loss of cytoskeletal tension following stress deprivation decreases the mechanoresponsiveness of tendon cells, we cultured rat tail tendons under stress-deprived conditions for 48 hours and then cyclically loaded them for 24 hours at 1\%, 3\%, or 6\% strain at 0.17 Hz. Stress deprivation upregulated MMP-13 mRNA expression and caused progressive loss of cell-matrix contact compared to fresh controls. The application of 1\% strain to fresh tendons for 24 hours inhibited MMP-13 mRNA expression compared to stress-deprived tendons over the same period. However, when tendons were stress-deprived for 48 hours and then subjected to the same loading regime, the inhibition of MMP-13 mRNA expression was decreased. In stress-deprived tendons, it was necessary to increase the strain magnitude to 3\% to achieve the same level of MMP-13 mRNA inhibition seen in fresh tendons exercised at 1\% strain. The data suggest loss of cytoskeletal tension alters the mechanostat set point and decreases the mechanoresponsiveness of tendon cells.},
	number = {7},
	urldate = {2014-11-04},
	journal = {Clinical Orthopaedics and Related Research},
	author = {Arnoczky, Steven P. and Lavagnino, Michael and Egerbacher, Monika and Caballero, Oscar and Gardner, Keri and Shender, Marisa A.},
	month = jul,
	year = {2008},
	pmid = {18459031},
	pmcid = {PMC2505257},
	pages = {1583--1591},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5Z2Z5U3M/Arnoczky et al. - 2008 - Loss of Homeostatic Strain Alters Mechanostat Set.pdf:application/pdf}
}

@article{grimes_uses_2002,
	title = {Uses and abuses of screening tests},
	volume = {359},
	issn = {0140-6736},
	url = {http://www.sciencedirect.com/science/article/pii/S0140673602079485},
	doi = {10.1016/S0140-6736(02)07948-5},
	abstract = {Summary
Screening tests are ubiquitous in contemporary practice, yet the principles of screening are widely misunderstood. Screening is the testing of apparently well people to find those at increased risk of having a disease or disorder. Although an earlier diagnosis generally has intuitive appeal, earlier might not always be better, or worth the cost. Four terms describe the validity of a screening test: sensitivity, specificity, and predictive value of positive and negative results. For tests with continuous variables-eg, blood glucose-sensitivity and specificity are inversely related; where the cutoff for abnormal is placed should indicate the clinical effect of wrong results. The prevalence of disease in a population affects screening test performance: in low-prevalence settings, even very good tests have poor predictive value positives. Hence, knowledge of the approximate prevalence of disease is a prerequisite to interpreting screening test results. Tests are often done in sequence, as is true for syphilis and HIV-1 infection. Lead-time and length biases distort the apparent value of screening programmes; randomised controlled trials are the only way to avoid these biases. Screening can improve health; strong indirect evidence links cervical cytology programmes to declines in cervical cancer mortality. However, inappropriate application or interpretation of screening tests can rob people of their perceived health, initiate harmful diagnostic testing, and squander health-care resources.},
	number = {9309},
	urldate = {2016-07-04},
	journal = {The Lancet},
	author = {Grimes, David A and Schulz, Kenneth F},
	month = mar,
	year = {2002},
	pages = {881--884},
	file = {1-s2.0-S0140673602079485-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AHNISJUR/1-s2.0-S0140673602079485-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SAZE92EM/S0140673602079485.html:text/html}
}

@article{pannu_abstract_2015,
	title = {Abstract {P}5-10-15: {Empowering} the {Nottingham} {Grading} {System}: {An} integrated {Ki}67-mitosis classifier yields a better patient stratification tool},
	volume = {75},
	copyright = {©2015 American Association for Cancer Research.},
	issn = {0008-5472, 1538-7445},
	shorttitle = {Abstract {P}5-10-15},
	url = {http://cancerres.aacrjournals.org/content/75/9_Supplement/P5-10-15},
	doi = {10.1158/1538-7445.SABCS14-P5-10-15},
	abstract = {Therapeutic decision-making for personalized management of breast cancer relies on patient stratification based on the risk conferred by clinicopathologic factors, such as stage, Ki67 Index (KI) and tumor histological grade. The most widely used histologic grading system for breast cancer, the Nottingham Grading System (NGS) provides prognostic information about breast tumor samples by combining analysis of the extent of glandular differentiation, nuclear pleomorphism and mitotic activity present in the tumor sample. In the NGS, the mitotic Index (MI) is defined as the number of mitotic cells per ten high-power fields. KI is a universal prognostic indicator but is not part of the NGS. Although the NGS has been widely used owing to its reproducibility and significant prognostic value, its accuracy in predicting disease prognosis and aggressiveness is limited. Our earlier work has demonstrated that by rationally integrating KI and MI into a new metric called the Ki67-Adjusted Mitotic Score (KAMS), which is a measure of the proportion of mitotic cells amongst Ki67-positive cells, we are able to glean a new layer of prognostic information about metastatic risk. We found that for Nottingham Grade II and III patients, high KAMS values predicted relatively better overall survival (OS) than low KAMS values.
We therefore asked if the incorporation of a KAMS-based classifier subsequent to conventional Nottingham classification, would improve patient stratification to enable their funneling towards more optimal treatment choices. Ideal KAMS thresholds were established by analyzing the KAMS-stratified survival groups and selecting the thresholds which created the widest survival stratification that was additionally confirmed to be statistically significant via a Log-Rank test. For Nottingham Grade II and III patients, an above-threshold KAMS value was deemed as low-risk and a below-threshold KAMS value was deemed as high-risk for the purpose of grade adjustment. Grade adjustments were based solely on the patients’ KAMS values. Thus the adjusted Nottingham Grade I consisted of the original Nottingham Grade I patients along with KAMS determined low-risk original Nottingham Grade II patients. Adjusted Nottingham Grade II patients were composed of KAMS determined high-risk patients originally in Nottingham Grade II along with KAMS determined low-risk original Nottingham Grade III patients. Finally, the adjusted Nottingham Grade III was made up exclusively of high-risk patients from the original Nottingham Grade III.
We found that the adjusted system represents a wider separation between OS curves with adjusted Grade I (n = 774) OS being 95.48\%, adjusted grade II (n = 727) OS at 87.62\%, and adjusted Grade III (n = 110) having an OS of 78.18\%. Overall survival groups between adjusted grade I and II and I and III (p {\textless} 0.001) showed statistical significance. We also found that the hazard ratios for all Nottingham grades are significantly better after adjustment (2.875 versus 2.034 for Grade II and 5.115 versus 3.456 for Grade III) indicating that the KAMS can function as an effective risk-stratification biomarker and that incorporation of a KAMS-based classifier enhances patient stratification.
Citation Format: Vaishali Pannu, Padmashree CG Rida, Sergey Klimov, Nikita Wright, Guilherme Cantuaria, Michelle Reid, Ritu Aneja. Empowering the Nottingham Grading System: An integrated Ki67-mitosis classifier yields a better patient stratification tool [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-10-15.},
	language = {en},
	number = {9 Supplement},
	urldate = {2016-06-26},
	journal = {Cancer Research},
	author = {Pannu, Vaishali and Rida, Padmashree CG and Klimov, Sergey and Wright, Nikita and Cantuaria, Guilherme and Reid, Michelle and Aneja, Ritu},
	month = may,
	year = {2015},
	pages = {P5--10--15--P5--10--15},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QDTAHXXW/P5-10-15.html:text/html}
}

@article{andarawis-puri_relationships_2012,
	title = {The relationships between cyclic fatigue loading, changes in initial mechanical properties, and the in vivo temporal mechanical response of the rat patellar tendon},
	volume = {45},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S0021929011006312},
	doi = {10.1016/j.jbiomech.2011.10.008},
	abstract = {Damage accumulation underlies tendinopathy. Animal models of overuse injuries do not typically control loads applied to the tendon. Our in vivo model in the rat patellar tendon allows direct control of the loading applied to the tendon. Despite this advantage, natural variation among tendons results in different amounts of damage induced by the same loading protocol. Our objectives were to (1) assess changes in the initial mechanical parameters (hysteresis, stiffness of the loading and unloading load-displacement curves, and elongation) after fatigue loading to identify parameters that are indicative of the induced damage, and (2) evaluate the relationships between these identified initial damage indices with the stiffness 7 day after loading. Left patellar tendons of adult, female retired breeder, Sprague-Dawley rats (n=68) were fatigue loaded per our previously published in vivo fatigue loading protocol. To induce a range of damage, fatigue loading consisted of either 5, 100, 500 or 7200 cycles that ranged from 1 N to 40 N. Diagnostic tests were applied before and immediately after fatigue loading, and after 45 min of recovery to deduce recoverable and non-recoverable changes in initial damage indices. Relationships between these initial damage indices and the 7-day stiffness (at sacrifice) were determined. Day-0 hysteresis, loading and unloading stiffness exhibited cycle-dependent changes. Initial hysteresis loss correlated with the 7-day stiffness. k-means cluster analysis demonstrated a relationship between 7-day stiffness and day-0 hysteresis and unloading stiffness. This analysis also separated samples that exhibited low from high damage in response to both high or low number of cycles; a key delineation for interpretation of the biological response in future studies. Identifying initial parameters that reflect the induced damage is critical since the ability of the tendon to repair depends on the damage induced and the number of applied loading cycles.},
	number = {1},
	urldate = {2014-11-03},
	journal = {Journal of Biomechanics},
	author = {Andarawis-Puri, Nelly and Sereysky, Jedd B. and Jepsen, Karl J. and Flatow, Evan L.},
	month = jan,
	year = {2012},
	keywords = {Cluster analysis, Hysteresis, Non-recoverable damage, Stiffness, Tendon fatigue damage},
	pages = {59--65},
	file = {mechanicalresponserat.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XU9HQ9BP/mechanicalresponserat.pdf:application/pdf}
}

@article{tabesh_multifeature_2007,
	title = {Multifeature {Prostate} {Cancer} {Diagnosis} and {Gleason} {Grading} of {Histological} {Images}},
	volume = {26},
	issn = {0278-0062},
	doi = {10.1109/TMI.2007.898536},
	abstract = {We present a study of image features for cancer diagnosis and Gleason grading of the histological images of prostate. In diagnosis, the tissue image is classified into the tumor and nontumor classes. In Gleason grading, which characterizes tumor aggressiveness, the image is classified as containing a low- or high-grade tumor. The image sets used in this paper consisted of 367 and 268 color images for the diagnosis and Gleason grading problems, respectively, and were captured from representative areas of hematoxylin and eosin-stained tissue retrieved from tissue microarray cores or whole sections. The primary contribution of this paper is to aggregate color, texture, and morphometric cues at the global and histological object levels for classification. Features representing different visual cues were combined in a supervised learning framework. We compared the performance of Gaussian, -nearest neighbor, and support vector machine classifiers together with the sequential forward feature selection algorithm. On diagnosis, using a five-fold cross-validation estimate, an accuracy of 96.7\% was obtained. On Gleason grading, the achieved accuracy of classification into low- and high-grade classes was 81.0\%.},
	number = {10},
	journal = {IEEE Transactions on Medical Imaging},
	author = {Tabesh, A. and Teverovskiy, M. and Pang, H. Y. and Kumar, V. P. and Verbel, D. and Kotsianti, A. and Saidi, O.},
	month = oct,
	year = {2007},
	keywords = {Aggregates, Algorithms, Artificial Intelligence, biological tissues, Cancer, Color, Colorimetry, computer-aided diagnosis, eosin-stained tissue, Feature extraction, Glands, Gleason grading, hematoxylin, histological images, Humans, image classification, image classifiers, Image Enhancement, image features, Image Interpretation, Computer-Assisted, Image retrieval, Laboratories, Male, medical image processing, multifeature prostate cancer diagnosis, Neoplasms, nontumor class, Pattern Recognition, Automated, PROSTATE cancer, Prostatic Neoplasms, Reproducibility of Results, Sensitivity and Specificity, sequential forward feature selection algorithm, statistical pattern recognition, Supervised learning, Support vector machines, tissue image, tumor aggressiveness, tumours, visual cues},
	pages = {1366--1378},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DUIKKSV5/4336180.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7IU3KQBC/Tabesh et al. - 2007 - Multifeature Prostate Cancer Diagnosis and Gleason.pdf:application/pdf}
}

@article{narod_ten_2012,
	title = {Ten types of breast cancer?},
	volume = {380},
	issn = {0140-6736},
	url = {http://www.sciencedirect.com/science/article/pii/S0140673612607818},
	doi = {10.1016/S0140-6736(12)60781-8},
	number = {9849},
	urldate = {2016-06-23},
	journal = {The Lancet},
	author = {Narod, Steven A},
	month = oct,
	year = {2012},
	pages = {1212--1213},
	file = {1-s2.0-S0140673612607818-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2MG3ZFSB/1-s2.0-S0140673612607818-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AVAJJ9BC/S0140673612607818.html:text/html}
}

@article{swerts_draq5:_2007,
	title = {{DRAQ}5: {Improved} flow cytometric {DNA} content analysis and minimal residual disease detection in childhood malignancies},
	volume = {379},
	issn = {0009-8981},
	shorttitle = {{DRAQ}5},
	url = {http://www.sciencedirect.com/science/article/pii/S0009898106007960},
	doi = {10.1016/j.cca.2006.12.008},
	abstract = {Background
The majority of flow cytometric DNA content analyses are performed on whole peripheral blood, bone marrow or tumor samples containing significant numbers of non-malignant cells which hamper specific DNA content analysis. Simultaneous analysis of DNA content and immunophenotype greatly improves the specificity of DNA-ploidy measurements. Therefore, a three-color flow cytometric assay using DRAQ5 was developed and validated.
Methods
The results of DNA content analysis using DRAQ5 and propidium iodide were compared using peripheral blood samples of 15 healthy volunteers. The reproducibility of the multiparameter DRAQ5 assay was assayed in 10 analytical runs and the sensitivity was evaluated with addition experiments.
Result
Using DRAQ5, slightly wider CVs of the G0/G1 peak were obtained (average CV = 3.29\%). When DRAQ5 staining and immunophenotyping were combined, the within- and between-run imprecision was 1.98\% and 1.67\%, respectively and the DNA content of 25 DNA-hyperdiploid tumor cells (DNA-index = 1.16) per 4.104 mononuclear cells (0.06\%) could be determined.
Conclusions
The multiparameter DRAQ5 assay has a superior sensitivity and specificity compared to the propidium iodide based method. Since at least 25 DNA-hyperdiploid cells per 104 DNA-diploid mononuclear cells could be detected, multiparameter DRAQ5 DNA content analysis could be used to study minimal residual disease.},
	number = {1–2},
	urldate = {2016-06-25},
	journal = {Clinica Chimica Acta},
	author = {Swerts, Katrien and Van Roy, Nadine and Benoit, Yves and Laureys, Geneviève and Philippé, Jan},
	month = apr,
	year = {2007},
	keywords = {Acute lymphoblastic leukemia, DNA content analysis, DRAQ5, Flow cytometry, Minimal residual disease, Neuroblastoma},
	pages = {154--157},
	file = {1-s2.0-S0009898106007960-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CE3TK8KF/1-s2.0-S0009898106007960-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/D6EVXMZ4/S0009898106007960.html:text/html}
}

@article{derenzini_nucleolar_1998,
	title = {Nucleolar function and size in cancer cells.},
	volume = {152},
	issn = {0002-9440},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1858570/},
	abstract = {We have have studied the relationship between nucleolar function and size and cell doubling time in cancer cells. Seven human cancer cell lines characterized by different proliferation rates were used. Nucleolar functional activity was evaluated by measuring RNA polymerase I activity and expression of RNA polymerase I upstream binding factor (UBF), DNA topoisomerase I, and fibrillarin, three proteins involved in synthesis and processing of rRNA. Transcriptional activity of RNA polymerase I was strictly related to cell doubling time (r = -0.97; P {\textless} 0.001). The quantitative distribution of UBF, DNA topoisomerase I, and fibrillarin was evaluated on Western blots using specific monoclonal antibodies by densitometric analysis of autoradiographic signals. It was found to be directly related to RNA polymerase I transcriptional activity (r = 0.89, P = 0.008 for UBF; r = 0.95, P = 0.001 for DNA topoisomerase I; and r = 0.91, P = 0.004 for fibrillarin) and inversely related to cell doubling time (r = -0.87, P = 0.011 for UBF; r = -0.97, P {\textless} 0.001 for DNA topoisomerase I; and r = -0.91, P = 0.005 for fibrillarin). The nucleolar areas were measured by automated image analysis on toluidine blue-stained cells. The values of the stained nucleolar structures per cell were directly related to RNA polymerase I transcriptional activity (r = 0.94, P = 0.001) and inversely related to cell doubling time (r = -0.98, P {\textless} 0.001). The same area values of the nucleolar structures stained by toluidine blue were also closely related to the amount of UBF (r = 0.92, P = 0.003), DNA topoisomerase I (r = 0.98, P {\textless} 0.001), and fibrillarin (r = 0.95, P = 0.001), and to the in situ quantitative distribution of AgNOR proteins (r = 0.98, P {\textless} 0.001). Our results demonstrated that in cancer cells rRNA transcriptional activity and nucleolar size are inversely related to cell doubling time. Quantitative distribution of nucleolar structures within the cell represents a cytohistological parameter of the rapidity of cell proliferation.},
	number = {5},
	urldate = {2016-06-26},
	journal = {The American Journal of Pathology},
	author = {Derenzini, M. and Trerè, D. and Pession, A. and Montanaro, L. and Sirri, V. and Ochs, R. L.},
	month = may,
	year = {1998},
	pmid = {9588897},
	pmcid = {PMC1858570},
	pages = {1291--1297},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KXBMNS5G/Derenzini et al. - 1998 - Nucleolar function and size in cancer cells..pdf:application/pdf}
}

@article{bitoun_deficiency_2014,
	title = {Deficiency of {BrpB} causes major defects in cell division, stress responses and biofilm formation by {Streptococcus} mutans},
	volume = {160},
	issn = {1350-0872, 1465-2080},
	url = {http://mic.sgmjournals.org.libproxy.tulane.edu:2048/content/160/Pt_1/67},
	doi = {10.1099/mic.0.072884-0},
	language = {en},
	number = {Pt\_1},
	urldate = {2014-11-07},
	journal = {Microbiology},
	author = {Bitoun, J. P. and Liao, S. and Xie, G. G. and Beatty, W. L. and Wen, Z. T.},
	month = jan,
	year = {2014},
	pages = {67--78},
	file = {67.full.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/EUIZMMDG/67.full.pdf:application/pdf;Deficiency of BrpB causes major defects in cell division, stress responses and biofilm formation by Streptococcus mutans:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6VCN39MB/67.html:text/html}
}

@misc{_cycling-centric_????,
	title = {Cycling-{Centric} {Fitness} {App} {Strava} {Raises} \$18.5 {Million} in {Venture} {Capital} {Funding}},
	url = {http://recode.net/2014/10/29/cycling-centric-fitness-app-strava-raises-18-5-million-in-venture-capital-funding/},
	abstract = {Strava plans to grow overseas and become more than just a cycling app.},
	urldate = {2015-03-10},
	journal = {Re/code},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RNUWSQWJ/Cycling-Centric Fitness App Strava Raises \$18.5 Mi.html:text/html}
}

@article{mosquera-lopez_computer-aided_2014,
	title = {Computer-aided {Prostate} {Cancer} {Diagnosis} from {Digitized} {Histopathology}: {A} {Review} on {Texture}-based {Systems}},
	volume = {PP},
	issn = {1937-3333},
	shorttitle = {Computer-aided {Prostate} {Cancer} {Diagnosis} from {Digitized} {Histopathology}},
	doi = {10.1109/RBME.2014.2340401},
	abstract = {Prostate cancer (PCa) is currently diagnosed by microscopic evaluation of biopsy samples. Since tissue assessment heavily relies on the pathologists level of expertise and interpretation criteria, it is still a subjective process with high intra- and interobserver variability. Computer-aided diagnosis (CAD) may have a major impact on detection and grading of PCa by reducing the pathologists reading time, and increasing the accuracy and reproducibility of diagnosis outcomes. However, the complexity of the prostatic tissue and the large volumes of data generated by biopsy procedures make the development of CAD systems for PCa a challenging task. The problem of automated diagnosis of prostatic carcinoma from histopathology has received a lot of attention. As a result, a number of CAD systems, have been proposed for quantitative image analysis and classification. This article aims at providing a detailed description of selected literature in the field of CAD of PCa, emphasizing the role of texture analysis methods in tissue description. It includes a review of image analysis tools for image preprocessing, feature extraction, classification, and validation techniques used in PCa detection and grading, as well as future directions in pursuit of better texture-based CAD systems.},
	number = {99},
	journal = {Biomedical Engineering, IEEE Reviews in},
	author = {Mosquera-Lopez, C. and Agaian, S. and Velez-Hoyos, A. and Thompson, I.},
	year = {2014},
	keywords = {Biopsy, Design automation, Feature extraction, Image color analysis, Principal component analysis, Prostate cancer},
	pages = {1--1},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PSX2PGI6/Mosquera-Lopez et al. - 2014 - Computer-aided Prostate Cancer Diagnosis from Digi.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CAA5F775/Mosquera-Lopez et al. - 2014 - Computer-aided Prostate Cancer Diagnosis from Digi.pdf:application/pdf}
}

@misc{_patent_????,
	title = {Patent {WO}2013126762A1 - {Multi}-focal structured illumination microscopy systems and methods - {Google} {Patents}},
	url = {https://www.google.com/patents/WO2013126762A1?cl=en},
	urldate = {2016-07-05},
	file = {Patent WO2013126762A1 - Multi-focal structured illumination microscopy systems and methods - Google Patents:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/B2MHKFJD/WO2013126762A1.html:text/html}
}

@article{melief_therapeutic_2015,
	title = {Therapeutic cancer vaccines},
	volume = {125},
	issn = {0021-9738},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588240/},
	doi = {10.1172/JCI80009},
	abstract = {The clinical benefit of therapeutic cancer vaccines has been established. Whereas regression of lesions was shown for premalignant lesions caused by HPV, clinical benefit in cancer patients was mostly noted as prolonged survival. Suboptimal vaccine design and an immunosuppressive cancer microenvironment are the root causes of the lack of cancer eradication. Effective cancer vaccines deliver concentrated antigen to both HLA class I and II molecules of DCs, promoting both CD4 and CD8 T cell responses. Optimal vaccine platforms include DNA and RNA vaccines and synthetic long peptides. Antigens of choice include mutant sequences, selected cancer testis antigens, and viral antigens. Drugs or physical treatments can mitigate the immunosuppressive cancer microenvironment and include chemotherapeutics, radiation, indoleamine 2,3-dioxygenase (IDO) inhibitors, inhibitors of T cell checkpoints, agonists of selected TNF receptor family members, and inhibitors of undesirable cytokines. The specificity of therapeutic vaccination combined with such immunomodulation offers an attractive avenue for the development of future cancer therapies.},
	number = {9},
	urldate = {2016-12-06},
	journal = {The Journal of Clinical Investigation},
	author = {Melief, Cornelis J.M. and van Hall, Thorbald and Arens, Ramon and Ossendorp, Ferry and van der Burg, Sjoerd H.},
	month = sep,
	year = {2015},
	pmid = {26214521},
	pmcid = {PMC4588240},
	pages = {3401--3412},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TMC6U25A/Melief et al. - 2015 - Therapeutic cancer vaccines.pdf:application/pdf}
}

@article{mumford_power_2012,
	title = {A power calculation guide for {fMRI} studies},
	issn = {1749-5016, 1749-5024},
	url = {http://scan.oxfordjournals.org/content/early/2012/06/29/scan.nss059},
	doi = {10.1093/scan/nss059},
	abstract = {In the past, power analyses were not that common for fMRI studies, but recent advances in power calculation techniques and software development are making power analyses much more accessible. As a result, power analyses are more commonly expected in grant applications proposing fMRI studies. Even though the software is somewhat automated, there are important decisions to be made when setting up and carrying out a power analysis. This guide provides tips on carrying out power analyses, including obtaining pilot data, defining a region of interest and other choices to help create reliable power calculations. Keywords: Functional Magnetic Resonance Imaging, Classification Analysis, MVPA, Beta Series Estimation, Rapid Event-Related Design},
	language = {en},
	urldate = {2016-06-29},
	journal = {Social Cognitive and Affective Neuroscience},
	author = {Mumford, Jeanette A.},
	month = may,
	year = {2012},
	pmid = {22641837},
	pages = {nss059},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F42HUD9X/Mumford - 2012 - A power calculation guide for fMRI studies.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4ZX8Z6BK/scan.nss059.html:text/html}
}

@article{brown_optical_2013,
	title = {Optical {Spectral} {Surveillance} of {Breast} {Tissue} {Landscapes} for {Detection} of {Residual} {Disease} in {Breast} {Tumor} {Margins}},
	volume = {8},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724737/},
	doi = {10.1371/journal.pone.0069906},
	abstract = {We demonstrate a strategy to “sense” the micro-morphology of a breast tumor margin over a wide field of view by creating quantitative hyperspectral maps of the tissue optical properties (absorption and scattering), where each voxel can be deconstructed to provide information on the underlying histology. Information about the underlying tissue histology is encoded in the quantitative spectral information (in the visible wavelength range), and residual carcinoma is detected as a shift in the histological landscape to one with less fat and higher glandular content. To demonstrate this strategy, fully intact, fresh lumpectomy specimens (n = 88) from 70 patients were imaged intra-operatively. The ability of spectral imaging to sense changes in histology over large imaging areas was determined using inter-patient mammographic breast density (MBD) variation in cancer-free tissues as a model system. We discovered that increased MBD was associated with higher baseline β-carotene concentrations (p = 0.066) and higher scattering coefficients (p = 0.007) as measured by spectral imaging, and a trend toward decreased adipocyte size and increased adipocyte density as measured by histological examination in BMI-matched patients. The ability of spectral imaging to detect cancer intra-operatively was demonstrated when MBD-specific breast characteristics were considered. Specifically, the ratio of β-carotene concentration to the light scattering coefficient can report on the relative amount of fat to glandular density at the tissue surface to determine positive margin status, when baseline differences in these parameters between patients with low and high MBD are taken into account by the appropriate selection of threshold values. When MBD was included as a variable a priori, the device was estimated to have a sensitivity of 74\% and a specificity of 86\% in detecting close or positive margins, regardless of tumor type. Superior performance was demonstrated in high MBD tissue, a population that typically has a higher percentage of involved margins.},
	number = {7},
	urldate = {2016-06-24},
	journal = {PLoS ONE},
	author = {Brown, J. Quincy and Bydlon, Torre M. and Kennedy, Stephanie A. and Caldwell, Matthew L. and Gallagher, Jennifer E. and Junker, Marlee and Wilke, Lee G. and Barry, William T. and Geradts, Joseph and Ramanujam, Nimmi},
	month = jul,
	year = {2013},
	pmid = {23922850},
	pmcid = {PMC3724737},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CQRMQAFI/Brown et al. - 2013 - Optical Spectral Surveillance of Breast Tissue Lan.pdf:application/pdf}
}

@article{sissung_genetic_2014,
	title = {Genetic variation: effect on prostate cancer},
	volume = {1846},
	issn = {0304-419X},
	shorttitle = {Genetic variation},
	url = {http://www.sciencedirect.com/science/article/pii/S0304419X1400081X},
	doi = {10.1016/j.bbcan.2014.08.007},
	abstract = {The crucial role of androgens in the development of prostate cancer is well established. The aim of this review is to examine the role of constitutional (germline) and tumor-specific (somatic) polymorphisms within important regulatory genes of prostate cancer. These include genes encoding enzymes of the androgen biosynthetic pathway, the androgen receptor gene, genes that encode proteins of the signal transduction pathways that may have a role in disease progression and survival, and genes involved in prostate cancer angiogenesis. Characterization of deregulated pathways critical to cancer cell growth have lead to the development of new treatments, including the CYP17 inhibitor abiraterone and clinical trials using novel drugs that are ongoing or recently completed [1]. The pharmacogenetics of the drugs used to treat prostate cancer will also be addressed. This review will define how germline polymorphisms are known affect a multitude of pathways, and therefore phenotypes, in prostate cancer etiology, progression, and treatment.},
	number = {2},
	urldate = {2016-11-28},
	journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
	author = {Sissung, Tristan M. and Price, Douglas K. and Del Re, Marzia and Ley, Ariel M. and Giovannetti, Elisa and Figg, William D. and Danesi, Romano},
	month = dec,
	year = {2014},
	keywords = {Androgen deprivation therapy, Chemotherapy, Pharmacogenomics, PROSTATE cancer, Steroid},
	pages = {446--456},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5PH4J9FT/Sissung et al. - 2014 - Genetic variation effect on prostate cancer.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2E7VAD29/S0304419X1400081X.html:text/html}
}

@misc{_cancer_????,
	title = {Cancer of the {Breast} ({Female}) - {SEER} {Stat} {Fact} {Sheets}},
	url = {http://seer.cancer.gov/statfacts/html/breast.html},
	urldate = {2016-06-23},
	file = {Cancer of the Breast (Female) - SEER Stat Fact Sheets:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T2SRI58H/breast.html:text/html}
}

@article{mueller_quantitative_2013,
	title = {Quantitative {Segmentation} of {Fluorescence} {Microscopy} {Images} of {Heterogeneous} {Tissue}: {Application} to the {Detection} of {Residual} {Disease} in {Tumor} {Margins}},
	volume = {8},
	issn = {1932-6203},
	shorttitle = {Quantitative {Segmentation} of {Fluorescence} {Microscopy} {Images} of {Heterogeneous} {Tissue}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688889/},
	doi = {10.1371/journal.pone.0066198},
	abstract = {Purpose
To develop a robust tool for quantitative in situ pathology that allows visualization of heterogeneous tissue morphology and segmentation and quantification of image features.

Materials and Methods
Tissue excised from a genetically engineered mouse model of sarcoma was imaged using a subcellular resolution microendoscope after topical application of a fluorescent anatomical contrast agent: acriflavine. An algorithm based on sparse component analysis (SCA) and the circle transform (CT) was developed for image segmentation and quantification of distinct tissue types. The accuracy of our approach was quantified through simulations of tumor and muscle images. Specifically, tumor, muscle, and tumor+muscle tissue images were simulated because these tissue types were most commonly observed in sarcoma margins. Simulations were based on tissue characteristics observed in pathology slides. The potential clinical utility of our approach was evaluated by imaging excised margins and the tumor bed in a cohort of mice after surgical resection of sarcoma.

Results
Simulation experiments revealed that SCA+CT achieved the lowest errors for larger nuclear sizes and for higher contrast ratios (nuclei intensity/background intensity). For imaging of tumor margins, SCA+CT effectively isolated nuclei from tumor, muscle, adipose, and tumor+muscle tissue types. Differences in density were correctly identified with SCA+CT in a cohort of ex vivo and in vivo images, thus illustrating the diagnostic potential of our approach.

Conclusion
The combination of a subcellular-resolution microendoscope, acriflavine staining, and SCA+CT can be used to accurately isolate nuclei and quantify their density in anatomical images of heterogeneous tissue.},
	number = {6},
	urldate = {2016-06-24},
	journal = {PLoS ONE},
	author = {Mueller, Jenna L. and Harmany, Zachary T. and Mito, Jeffrey K. and Kennedy, Stephanie A. and Kim, Yongbaek and Dodd, Leslie and Geradts, Joseph and Kirsch, David G. and Willett, Rebecca M. and Brown, J. Quincy and Ramanujam, Nimmi},
	month = jun,
	year = {2013},
	pmid = {23824589},
	pmcid = {PMC3688889},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IEKSC5GR/Mueller et al. - 2013 - Quantitative Segmentation of Fluorescence Microsco.pdf:application/pdf}
}

@misc{_phase_????,
	title = {Phase 3 {Clinical} {Trial} {Costs} {Exceed} \$26,000 per {Patient}},
	url = {http://www.prnewswire.com/news-releases/phase-3-clinical-trial-costs-exceed-26000-per-patient-56447427.html},
	abstract = {RESEARCH TRIANGLE PARK, N.C., Oct. 12 /PRNewswire/ -- The cost per
 patient of running Phase 3 clinical studies of...},
	urldate = {2015-11-23},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7GDHTEVM/phase-3-clinical-trial-costs-exceed-26000-per-patient-56447427.html:text/html}
}

@article{morrow_current_2015,
	title = {Current management of lesions associated with an increased risk of breast cancer},
	volume = {12},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1759-4774},
	url = {http://www.nature.com/nrclinonc/journal/v12/n4/full/nrclinonc.2015.8.html},
	doi = {10.1038/nrclinonc.2015.8},
	abstract = {High-risk breast lesions, which comprise benign lesions and in situ carcinomas (lobular carcinoma in situ and ductal carcinoma in situ), are clinically, morphologically, and biologically heterogeneous and are associated with an increased risk of invasive breast cancer development, albeit to varying degrees. Recognition and proactive management of such lesions can help to prevent progression to invasive disease, and might, therefore, reduce breast cancer incidence, morbidity, and mortality. However, this opportunity comes with the possibility of overdiagnosis and overtreatment, necessitating risk-based intervention. Notably, despite the progress in defining the molecular changes associated with carcinogenesis, alterations identifying the individuals with high-risk lesions that will progress to invasive carcinoma remain to be identified. Thus, until reproducible clinicopathological or molecular features predicting an individual's risk of breast cancer are found, management strategies must be defined by population-level risks as determined by models such as the Gail or IBIS models, as well as patient attitudes toward the risks and benefits of interventions. Herein, we review the contemporary approaches to diagnosis and management of high-risk breast lesions. Progress in this area will ultimately be dependent on the ability to individualize risk prediction through better definition of the key drivers in the carcinogenic process.},
	language = {en},
	number = {4},
	urldate = {2016-06-23},
	journal = {Nature Reviews Clinical Oncology},
	author = {Morrow, Monica and Schnitt, Stuart J. and Norton, Larry},
	month = apr,
	year = {2015},
	keywords = {BREAST cancer, Cancer prevention, Chemoprevention, Preventive medicine},
	pages = {227--238},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MQZQX3DW/Morrow et al. - 2015 - Current management of lesions associated with an i.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MDGZU7GC/nrclinonc.2015.8.html:text/html}
}

@article{moore_radiation-induced_2004,
	title = {Radiation-induced histopathologic changes of the breast: the effects of time},
	volume = {28},
	shorttitle = {Radiation-induced histopathologic changes of the breast},
	url = {http://journals.lww.com/ajsp/Abstract/2004/01000/Radiation_induced_Histopathologic_Changes_of_the.4.aspx},
	number = {1},
	urldate = {2016-07-07},
	journal = {The American journal of surgical pathology},
	author = {Moore, Gene H. and Schiller, John E. and Moore, Geoffrey K.},
	year = {2004},
	pages = {47--53},
	file = {00000478-200401000-00004.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NTUGZDGQ/NTUGZDGQ.pdf:application/pdf}
}

@article{mocellin_ctla-4_2013,
	title = {{CTLA}-4 blockade and the renaissance of cancer immunotherapy},
	volume = {1836},
	issn = {0304-419X},
	url = {http://www.sciencedirect.com/science/article/pii/S0304419X13000358},
	doi = {10.1016/j.bbcan.2013.05.003},
	abstract = {Cytotoxic T-lymphocyte associated antigen 4 (CTLA-4) plays a key role in restraining the adaptive immune response of T-cells towards a variety of antigens including tumor associated antigens (TAAs). The blockade of this immune checkpoint elicits an effective anticancer immune response in a range of preclinical models, suggesting that naturally occurring (or therapeutically induced) TAA specific lymphocytes need to be “unleashed” in order to properly fight against malignant cells. Therefore, investigators have tested this therapeutic hypothesis also in humans: the favorable results obtained with this strategy in patients with advanced cutaneous melanoma are revolutionizing the management of this highly aggressive disease and are fueling new enthusiasm on cancer immunotherapy in general.

Here we summarize the biology of CTLA-4, overview the experimental data supporting the rational for targeting CTLA-4 to treat cancer and review the main clinical findings on this novel anticancer approach. Moreover, we critically discuss the current challenges and potential developments of this promising field of cancer immunotherapy.},
	number = {2},
	urldate = {2016-12-06},
	journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
	author = {Mocellin, Simone and Nitti, Donato},
	month = dec,
	year = {2013},
	keywords = {Cancer, Co-inhibitory molecule, Co-signaling, CTLA-4, Immunotherapy, Tumor immunology},
	pages = {187--196},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9ANWRPTM/Mocellin and Nitti - 2013 - CTLA-4 blockade and the renaissance of cancer immu.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HMTZ8WZH/S0304419X13000358.html:text/html}
}

@article{angarita_perioperative_2014,
	title = {Perioperative measures to optimize margin clearance in breast conserving surgery},
	volume = {23},
	issn = {0960-7404},
	url = {http://www.sciencedirect.com/science/article/pii/S0960740414000115},
	doi = {10.1016/j.suronc.2014.03.002},
	abstract = {Margin status is one of the most important determinants of local recurrence following breast conserving surgery. The fact that up to 60\% of patients undergoing breast conserving surgery require re-excision highlights the importance of optimizing margin clearance. In this review we summarize the following perioperative measures that aim to enhance margin clearance: (1) patient risk stratification, specifically risk factors and nomograms, (2) preoperative imaging, (3) intraoperative techniques including wire-guided localization, radioguided surgery, intraoperative ultrasound-guided resection, intraoperative specimen radiography, standardized cavity shaving, and ink-directed focal re-excision; (4) and intraoperative pathology assessment techniques, namely frozen section analysis and imprint cytology. Novel surgical techniques as well as emerging technologies are also reviewed. Effective treatment requires accurate preoperative planning, developing and implementing a consistent definition of margin clearance, and using tools that provide detailed real-time intraoperative information on margin status.},
	number = {2},
	urldate = {2016-06-22},
	journal = {Surgical Oncology},
	author = {Angarita, Fernando A. and Nadler, Ashlie and Zerhouni, Siham and Escallon, Jaime},
	month = jun,
	year = {2014},
	keywords = {BREAST cancer, Breast conserving surgery, Ductal carcinoma in situ, Invasive ductal carcinoma, Margin, margin clearance, Margin status, Perioperative tools},
	pages = {81--91},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SXWBXIKA/Angarita et al. - 2014 - Perioperative measures to optimize margin clearanc.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WPQMS7QE/S0960740414000115.html:text/html}
}

@article{frkovic-grazio_long_2002,
	title = {Long term prognostic value of {Nottingham} histological grade and its components in early ({pT}1N0M0) breast carcinoma},
	volume = {55},
	issn = {0021-9746},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1769590/},
	abstract = {Aims: To determine the prognostic usefulness of the Nottingham histological grade (NHG) and its components in a series of 270 patients with stage pT1N0M0 breast cancer with a median follow up of 12.5 years., Methods: Microscopic slides were re-examined and the degree of tubule formation, nuclear pleomorphism, and mitotic counts were assessed and scored according to the suggested guidelines. The association with cancer specific survival (CSS) was evaluated by univariate and multivariate analyses., Results: Whereas tumour size, patient age, menopausal status, type of surgery, or adjuvant treatment were not related to prognosis, histological type (p {\textless} 0.01) and NHG (p {\textless} 0.005) were associated with CSS. When evaluating the components of NHG separately, survival was not related to the score for pleomorphism, but was significantly better in tumours with score 1 or 2 for tubule formation (p {\textless} 0.007) and in those with score 1 for mitotic counts (p {\textless} 0.006). The two components retained independent significance in multivariate analysis. When the proposed cut off points for mitotic counts were replaced by lower ones based on tertile values, the mitotic index became the strongest prognostic factor (p = 0.0001) and histological type was the only additional factor of independent prognostic significance., Conclusions: These findings confirm the prognostic value of NHG in pT1N0M0 breast carcinoma, show that the evaluation of tubule formation and mitotic rate provides independent prognostic information, and suggest that the proposed cut off points for mitotic counts may be too high for this particular group of tumours.},
	number = {2},
	urldate = {2016-06-29},
	journal = {Journal of Clinical Pathology},
	author = {Frkovic-Grazio, S and Bracko, M},
	month = feb,
	year = {2002},
	pmid = {11865000},
	pmcid = {PMC1769590},
	pages = {88--92},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MCGSFMEN/Frkovic-Grazio and Bracko - 2002 - Long term prognostic value of Nottingham histologi.pdf:application/pdf}
}

@article{ruidiaz_computerized_2012,
	title = {Computerized {Decision} {Support} {System} for {Intraoperative} {Analysis} of {Margin} {Status} in {Breast} {Conservation} {Therapy}},
	volume = {2012},
	issn = {2090-5785},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505663/},
	doi = {10.5402/2012/546721},
	abstract = {Background. Breast conservation therapy (BCT) is the standard treatment for breast cancer; however, 32–63\% of procedures have a positive margin leading to secondary procedures. The standard of care to evaluate surgical margins is based on permanent section. Imprint cytology (IC) has been used to evaluate surgical samples but is limited by excessive cauterization thus requiring experienced cytopathologist for interpretation. An automated image screening process has been developed to detect cancerous cells from IC on cauterized margins. Methods. IC was prospectively performed on margins during lumpectomy operations for breast cancer in addition to permanent section on 127 patients. An 8-slide training subset and 8-slide testing subset were culled. H\&E IC automated analysis, based on linear discriminant analysis, was compared to manual pathologist interpretation. Results. The most important descriptors, from highest to lowest performance, are nucleus color (23\%), cytoplasm color (15\%), shape (12\%), grey intensity (9\%), and local area (5\%). There was 100\% agreement between automated and manual interpretation of IC slides. Conclusion. Although limited by IC sampling variability, an automated system for accurate IC cancer cell identification system is demonstrated, with high correlation to manual analysis, even in the face of cauterization effects which supplement permanent section analysis.},
	urldate = {2016-06-24},
	journal = {ISRN Surgery},
	author = {Ruidíaz, Manuel E. and Blair, Sarah L. and Kummel, Andrew C. and Wang-Rodriguez, Jessica},
	month = nov,
	year = {2012},
	pmid = {23213570},
	pmcid = {PMC3505663},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/G885KD8K/Ruidíaz et al. - 2012 - Computerized Decision Support System for Intraoper.pdf:application/pdf}
}

@misc{_purchases_????,
	title = {Purchases of recreational transport products in the {U}.{S}. 2002-2012 {\textbar} {Statistic}},
	url = {http://www.statista.com/statistics/200800/recreational-transport-product-purchases-in-the-us-since-2004/},
	abstract = {This time line depicts the consumer purchases of recreational transport products in the U.S. from 2002 to 2012. In 2004, recreational transport products with a total value of 36.53 billion U.S. dollars were purchased in the U.S.},
	urldate = {2015-03-10},
	journal = {Statista},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7ZN3T9P3/Purchases of recreational transport products in th.html:text/html}
}

@article{verkooijen_interobserver_2003,
	title = {Interobserver variability between general and expert pathologists during the histopathological assessment of large-core needle and open biopsies of non-palpable breast lesions},
	volume = {39},
	issn = {0959-8049},
	url = {http://www.sciencedirect.com/science/article/pii/S0959804903005409},
	doi = {10.1016/S0959-8049(03)00540-9},
	abstract = {The purpose of this study was to assess whether general pathologists are able to make as accurate and reproducible a diagnosis on large-core needle biopsies as on open breast biopsy specimens. A total of 688 patients underwent a stereotactic large-core (14G) needle biopsy and subsequent surgical excision of 718 non-palpable breast lesions. Forty-two pathologists from 10 departments of pathology (generalists) made a diagnosis on both the needle and open biopsy specimens. Afterwards, three pathologists and two radiologists with extensive experience in breast pathology (experts) diagnosed all of the biopsy specimens. The general pathologists made a similar histological diagnosis as the experts in 632 (88\%) of the needle biopsies and 649 (90\%) of the open biopsy specimens. Accordingly, the interobserver agreement for the diagnosis of large-core needle biopsies between the general and experts pathologists was excellent (kappa 0.83) and not significantly different from the interobserver agreement for the diagnosis of open breast biopsies (kappa 0.86). However, many inconsistencies were observed in the category of borderline lesions: only 24\% of the large-core needle biopsies and 43\% of the open biopsies with an expert diagnosis of ‘borderline’ were diagnosed similarly by the general pathologists. Additionally, the risk of benign/malignant inconsistencies between general pathologists and experts was approximately 1 in 55 for both needle and open biopsies.},
	number = {15},
	urldate = {2015-09-01},
	journal = {European Journal of Cancer},
	author = {Verkooijen, H. M. and Peterse, J. L. and Schipper, M. E. I. and Buskens, E. and Hendriks, J. H. C. L. and Pijnappel, R. M. and Peeters, P. H. M. and Borel Rinkes, I. H. M. and Mali, W. P. Th. M. and Holland, R.},
	month = oct,
	year = {2003},
	keywords = {Biopsy, Breast biopsy, Breast diseases, Breast neoplasms, Diagnosis, Interobserver variability, Needle},
	pages = {2187--2191},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9HABPR4T/Verkooijen et al. - 2003 - Interobserver variability between general and expe.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W7G87VFR/Verkooijen et al. - 2003 - Interobserver variability between general and expe.html:text/html}
}

@misc{williams_under_????,
	title = {Under {Armour} {Has} {Acquired} {MyFitnessPal} and {Endomondo}},
	url = {http://thenextweb.com/apps/2015/02/04/armour-acquired-myfitnesspal-endomondo/},
	abstract = {Under Armour just announced it has acquired both Endomondo and MyFitnessPal today. The company said the acquisition establishes ownership of the “largest digital health and fitness community” now reaching more…},
	urldate = {2015-03-10},
	journal = {The Next Web},
	author = {Williams, Owen},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2MAP3RXE/Williams - Under Armour Has Acquired MyFitnessPal and Endomon.html:text/html}
}

@article{foundas_aberrant_2004,
	title = {Aberrant auditory processing and atypical planum temporale in developmental stuttering},
	volume = {63},
	issn = {1526-632X},
	abstract = {OBJECTIVE: To learn if people with persistent developmental stuttering and atypical anatomy of their auditory temporal cortex have, when compared to control subjects, changes in fluency induced with delayed auditory feedback (DAF).
BACKGROUND: DAF improves fluency in many individuals who stutter, and induces dysfluency in some normal people. The planum temporale (PT), a portion of auditory temporal cortex, is anatomically atypical in some adults who stutter and atypical anatomy might induce aberrant function. Thus, the people who demonstrate the paradoxical response to DAF might be those who have atypical anatomy.
METHODS: Experimental subjects were adults with developmental stuttering (n = 14) and control subjects (n = 14) matched for age, sex, education, and handedness. Volumetric MRI scans of all subjects were obtained and the PT was measured in the right and left hemispheres. Based on these scans, subjects were classified as typical (leftward PT asymmetry) or atypical (rightward PT asymmetry). Prose passages were read at baseline, with non-altered feedback (NAF), and with DAF, and fluency was measured in these three conditions.
RESULTS: At baseline the adults with developmental stuttering were significantly more dysfluent than controls (p {\textless} 0.0005). Controls' fluency did not significantly change with DAF, but DAF improved fluency in adults with developmental stuttering (p {\textless} 0.0005). In the stutter group enhanced fluency was associated with atypical (rightward) PT asymmetry, and the presence of typical (leftward) PT asymmetry was not associated with any significant change in fluency. The individuals with atypical PT asymmetry also had more severe stuttering at baseline compared to the experimental subjects with typical PT anatomy.
CONCLUSIONS: In adults with persistent developmental stuttering and atypical PT anatomy, fluency is improved with DAF. These experimental subjects who showed improvement had more severe stuttering at baseline. Anomalous PT anatomy may be a neural risk for developmental stuttering in some individuals. Although a number of explanations are tenable, it may be that atypical rightward PT asymmetry may alter speech feedback, and treatment with DAF might allow these people to compensate.},
	language = {eng},
	number = {9},
	journal = {Neurology},
	author = {Foundas, A. L. and Bollich, A. M. and Feldman, J. and Corey, D. M. and Hurley, M. and Lemen, L. C. and Heilman, K. M.},
	month = nov,
	year = {2004},
	pmid = {15534249},
	keywords = {Adult, Auditory Cortex, Auditory Perceptual Disorders, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Reading, Stuttering},
	pages = {1640--1646}
}

@article{biglia_clinical-pathologic_2013,
	title = {Clinical-pathologic features, long term-outcome and surgical treatment in a large series of patients with invasive lobular carcinoma ({ILC}) and invasive ductal carcinoma ({IDC})},
	volume = {39},
	issn = {0748-7983},
	url = {http://www.sciencedirect.com/science/article/pii/S0748798313002515},
	doi = {10.1016/j.ejso.2013.02.007},
	abstract = {Purpose of the study
A retrospective analysis on 1407 patients with invasive ductal carcinoma (IDC) and 243 invasive lobular carcinoma (ILC) was performed in order to compare the histological features, the immunohistochemical characteristics, the surgical treatment and the clinical outcome in the two groups.
Results
ILC seems to be more likely multifocal, estrogen receptor positive, HER-2 negative and to have a lower proliferative index compared to IDC. ILC, when treated with conservative surgery, required more frequently re-excision and/or mastectomy because of positive resection margins. No difference was observed in terms of 5-year disease free survival and local relapse free survival between the two groups, in the whole series and in the subgroup of patients treated with breast-conserving treatment.
Conclusion
ILC can be safely treated with conservative surgery but a more accurate preoperative evaluation of tumor size and multifocality could be advocated, in order to reduce the re-excision rate.},
	number = {5},
	urldate = {2016-06-25},
	journal = {European Journal of Surgical Oncology (EJSO)},
	author = {Biglia, N. and Maggiorotto, F. and Liberale, V. and Bounous, V. E. and Sgro, L. G. and Pecchio, S. and D'Alonzo, M. and Ponzone, R.},
	month = may,
	year = {2013},
	keywords = {BREAST cancer, Breast cancer prognosis, Breast conserving treatment, Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Surgical treatment},
	pages = {455--460},
	file = {1-s2.0-S0748798313002515-main copy.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U834T7FV/1-s2.0-S0748798313002515-main copy.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W474Z5A3/S0748798313002515.html:text/html}
}

@article{schlichenmeyer_video-rate_2014,
	title = {Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas},
	volume = {5},
	issn = {2156-7085},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920869/},
	doi = {10.1364/BOE.5.000366},
	abstract = {We report the development of a structured illumination microscopy instrument specifically designed for the requirements for high-area-throughput, optically-sectioned imaging of large, fluorescently-stained tissue specimens. The system achieves optical sectioning frame-rates of up to 33 Hz (and pixel sampling rates of up to 138.4 MHz), by combining a fast, ferroelectric spatial light modulator for pattern generation with the latest large-format, high frame-rate scientific CMOS camera technology. Using a 10X 0.45 NA objective and a 7 mm/sec scan stage, we demonstrate 4.4 cm2/min area-throughput rates in bright tissue-simulating phantoms, and 2 cm2/min area-throughput rates in thick, highly-absorbing, fluorescently-stained muscle tissue, with 1.3 μm lateral resolution. We demonstrate high-contrast, high-resolution imaging of a fluorescently-stained 30.4 cm2 bovine muscle specimen in 15 minutes comprising 7.55 gigapixels, demonstrating the feasibility of the approach for gigapixel imaging of large tissues in short timeframes, such as would be needed for intraoperative imaging of tumor resection specimens.},
	number = {2},
	urldate = {2016-06-22},
	journal = {Biomedical Optics Express},
	author = {Schlichenmeyer, Tyler C. and Wang, Mei and Elfer, Katherine N. and Brown, J. Quincy},
	month = jan,
	year = {2014},
	pmid = {24575333},
	pmcid = {PMC3920869},
	pages = {366--377},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9DPFCDEK/Schlichenmeyer et al. - 2014 - Video-rate structured illumination microscopy for .pdf:application/pdf}
}

@article{shaw_high_2015,
	series = {Super-resolution {Light} {Microscopy}},
	title = {High speed structured illumination microscopy in optically thick samples},
	volume = {88},
	issn = {1046-2023},
	url = {http://www.sciencedirect.com/science/article/pii/S1046202315001371},
	doi = {10.1016/j.ymeth.2015.03.020},
	abstract = {Structured illumination microscopy (SIM) allows imaging of fluorescently labelled biological samples with a spatial resolution improved by a factor of approximately two compared to traditional optical microscopy techniques. The cost of this resolution improvement is the need to capture a number of raw images of the sample to reconstruct a single SIM image, increasing sample light exposure and limiting the ability of the technique to capture dynamic processes. In this paper we describe image acquisition and reconstruction techniques that allow fast super-resolution imaging within optically thick specimens. By exploiting overlaps between SIM information passbands we are able to generate optically sectioned, super-resolution images from an image sequence acquired in a single focal plane. We consider how single plane super-resolution images may be obtained using 2D and 3D SIM illumination patterns, and compare the resulting images to those obtained using conventional 2D SIM reconstruction methods. By combining a single plane reconstruction algorithm with hardware for high-speed switching between illumination patterns and rapid acquisition of fluorescence images, we demonstrate high speed super-resolution imaging inside biological organisms.},
	urldate = {2016-06-22},
	journal = {Methods},
	author = {Shaw, Michael and Zajiczek, Lydia and O’Holleran, Kevin},
	month = oct,
	year = {2015},
	keywords = {Fluorescence microscopy, Optical sectioning, Structured illumination microscopy, Super-resolution microscopy},
	pages = {11--19},
	file = {1-s2.0-S1046202315001371-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T63PRX3U/1-s2.0-S1046202315001371-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/N336C5N8/S1046202315001371.html:text/html}
}

@article{brown_pd15-01_2015,
	series = {2015 {Annual} {Meeting} {Program} {AbstractsAUA} {Annual} {Meeting}},
	title = {{PD}15-01 {VIDEO}-{RATE} {STRUCTURED} {ILLUMINATION} {MICROSCOPY} {FOR} {RAPID} {ASSESSMENT} {OF} {SURGICAL} {MARGINS} {DURING} {RADICAL} {PROSTATECTOMY}},
	volume = {193},
	issn = {0022-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S0022534715016298},
	doi = {10.1016/j.juro.2015.02.1318},
	number = {4, Supplement},
	urldate = {2016-06-22},
	journal = {The Journal of Urology},
	author = {Brown, J. Quincy and Maddox, Michael and Wang, Mei and Kimbrell, Hillary and Tulman, David and Schlichenmeyer, Tyler and Mandava, Sree and Lee, Benjamin},
	month = apr,
	year = {2015},
	pages = {e323--e324},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/55KJ3J8C/S0022534715016298.html:text/html;sim.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FNRN7IM5/sim.pdf:application/pdf}
}

@misc{_cancer/tumor_????,
	title = {Cancer/{Tumor} {Profiling} {Market} worth \$35.03 {Billion} by 2018},
	url = {http://www.marketsandmarkets.com/PressReleases/cancer-tumor-profiling.asp},
	urldate = {2016-07-04},
	file = {Cancer/Tumor Profiling Market worth \$35.03 Billion by 2018:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/73P8MG8N/cancer-tumor-profiling.html:text/html}
}

@article{wang_network_2012,
	title = {Network {Meta}-analysis of {Margin} {Threshold} for {Women} {With} {Ductal} {Carcinoma} {In} {Situ}},
	volume = {104},
	issn = {0027-8874, 1460-2105},
	url = {http://jnci.oxfordjournals.org/content/104/7/507},
	doi = {10.1093/jnci/djs142},
	abstract = {Background Negative margins are associated with reduced risk of ipsilateral breast tumor recurrence (IBTR) for women with ductal carcinoma in situ (DCIS) treated with breast-conserving surgery (BCS). However, there is no consensus about the best minimum margin width.
Methods We searched the PubMed database for studies of DCIS published in English between January 1970 and July 2010 and examined the relationship between IBTR and margin status after BCS for DCIS. Women with DCIS were stratified into two groups, BCS with or without radiotherapy. We used frequentist and Bayesian approaches to estimate the odds ratios (OR) of IBTR for groups with negative margins and positive margins. We further examined specific margin thresholds using mixed treatment comparisons and meta-regression techniques. All statistical tests were two-sided.
Results We identified 21 studies published in 24 articles. A total of 1066 IBTR events occurred in 7564 patients, including BCS alone (565 IBTR events in 3098 patients) and BCS with radiotherapy (501 IBTR events in 4466 patients). Compared with positive margins, negative margins were associated with reduced risk of IBTR in patients with radiotherapy (OR = 0.46, 95\% credible interval [CrI] = 0.35 to 0.59), and in patients without radiotherapy (OR = 0.34, 95\% CrI = 0.24 to 0.47). Compared with patients with positive margins, the risk of IBTR for patients with negative margins was smaller (negative margin {\textgreater}0 mm, OR = 0.45, 95\% CrI = 0.38 to 0.53; {\textgreater}2 mm, OR = 0.38, 95\% CrI = 0.28 to 0.51; {\textgreater}5 mm, OR = 0.55, 95\% CrI = 0.15 to 1.30; and {\textgreater}10 mm, OR = 0.17, 95\% CrI = 0.12 to 0.24). Compared with a negative margin greater than 2 mm, a negative margin of at least 10 mm was associated with a lower risk of IBTR (OR = 0.46, 95\% CrI = 0.29 to 0.69). We found a probability of .96 that a negative margin threshold greater than 10 mm is the best option compared with other margin thresholds.
Conclusions Negative surgical margins should be obtained for DCIS patients after BCS regardless of radiotherapy. Within cosmetic constraint, surgeons should attempt to achieve negative margins as wide as possible in their first attempt. More studies are needed to understand whether margin thresholds greater than 10 mm are warranted.},
	language = {en},
	number = {7},
	urldate = {2016-06-22},
	journal = {Journal of the National Cancer Institute},
	author = {Wang, Shi-Yi and Chu, Haitao and Shamliyan, Tatyana and Jalal, Hawre and Kuntz, Karen M. and Kane, Robert L. and Virnig, Beth A.},
	month = apr,
	year = {2012},
	pmid = {22440677},
	pages = {507--516},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8F34CEQR/Wang et al. - 2012 - Network Meta-analysis of Margin Threshold for Wome.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FXNST3WM/507.html:text/html}
}

@article{champion_breast_1971,
	title = {Breast {Cancer} {Grading}},
	volume = {25},
	copyright = {© 1971 Nature Publishing Group},
	issn = {0007-0920},
	url = {http://www.nature.com/bjc/journal/v25/n3/abs/bjc197156a.html},
	doi = {10.1038/bjc.1971.56},
	abstract = {Histological sections of the primary tumour from 496 women with operable breast cancer have been examined for purposes of histological grading by two observers working independently. Each found a similar distribution of grade through the series, and a virtually identical influence of grade on prognosis. This close agreement occurred despite a 30\% disagreement as to grade in individual cases. It is suggested therefore, that this technique while of relevance to analysis of groups of cases is of very limited reliability in individual patient prognosis.},
	language = {en},
	number = {3},
	urldate = {2016-06-25},
	journal = {British Journal of Cancer},
	author = {Champion, H. R. and Wallace, I. W. J.},
	month = sep,
	year = {1971},
	pages = {441--448},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C362ET4X/Champion and Wallace - 1971 - Breast Cancer Grading.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AJSQSDDH/bjc197156a.html:text/html}
}

@article{fu_optimization_2013,
	title = {Optimization of a {Widefield} {Structured} {Illumination} {Microscope} for {Non}-{Destructive} {Assessment} and {Quantification} of {Nuclear} {Features} in {Tumor} {Margins} of a {Primary} {Mouse} {Model} of {Sarcoma}},
	volume = {8},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720887/},
	doi = {10.1371/journal.pone.0068868},
	abstract = {Cancer is associated with specific cellular morphological changes, such as increased nuclear size and crowding from rapidly proliferating cells. In situ tissue imaging using fluorescent stains may be useful for intraoperative detection of residual cancer in surgical tumor margins. We developed a widefield fluorescence structured illumination microscope (SIM) system with a single-shot FOV of 2.1×1.6 mm (3.4 mm2) and sub-cellular resolution (4.4 µm). The objectives of this work were to measure the relationship between illumination pattern frequency and optical sectioning strength and signal-to-noise ratio in turbid (i.e. thick) samples for selection of the optimum frequency, and to determine feasibility for detecting residual cancer on tumor resection margins, using a genetically engineered primary mouse model of sarcoma. The SIM system was tested in tissue mimicking solid phantoms with various scattering levels to determine impact of both turbidity and illumination frequency on two SIM metrics, optical section thickness and modulation depth. To demonstrate preclinical feasibility, ex vivo 50 µm frozen sections and fresh intact thick tissue samples excised from a primary mouse model of sarcoma were stained with acridine orange, which stains cell nuclei, skeletal muscle, and collagenous stroma. The cell nuclei were segmented using a high-pass filter algorithm, which allowed quantification of nuclear density. The results showed that the optimal illumination frequency was 31.7 µm−1 used in conjunction with a 4×0.1 NA objective ( = 0.165). This yielded an optical section thickness of 128 µm and an 8.9×contrast enhancement over uniform illumination. We successfully demonstrated the ability to resolve cell nuclei in situ achieved via SIM, which allowed segmentation of nuclei from heterogeneous tissues in the presence of considerable background fluorescence. Specifically, we demonstrate that optical sectioning of fresh intact thick tissues performed equivalently in regards to nuclear density quantification, to physical frozen sectioning and standard microscopy.},
	number = {7},
	urldate = {2016-06-24},
	journal = {PLoS ONE},
	author = {Fu, Henry L. and Mueller, Jenna L. and Javid, Melodi P. and Mito, Jeffrey K. and Kirsch, David G. and Ramanujam, Nimmi and Brown, J. Quincy},
	month = jul,
	year = {2013},
	pmid = {23894357},
	pmcid = {PMC3720887},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T9R9Z2NI/Fu et al. - 2013 - Optimization of a Widefield Structured Illuminatio.pdf:application/pdf}
}

@article{george_automated_2013,
	series = {Signal and {Image} {Processing} {Techniques} for {Detection} of {Breast} {Diseases}},
	title = {Automated cell nuclei segmentation for breast fine needle aspiration cytology},
	volume = {93},
	issn = {0165-1684},
	url = {http://www.sciencedirect.com/science/article/pii/S0165168412002642},
	doi = {10.1016/j.sigpro.2012.07.034},
	abstract = {Breast cancer detection and segmentation of cytological images is the standard clinical practice for the diagnosis and prognosis of breast cancer. This paper presents a fully automated method for cell nuclei detection and segmentation in breast cytological images. The images are enhanced with histogram stretching and contrast-limited adaptive histogram equalization (CLAHE). The locations of the cell nuclei in the image are detected with circular Hough transform (CHT) and local maximum filtering. The elimination of false positive findings (noisy circles and blood cells) is achieved using Otsu’s thresholding method and fuzzy C-means clustering technique. The segmentation of the nuclei boundaries is accomplished with the application of the marker controlled watershed transform in the gradient image, using the nuclei markers extracted in the detection step. The proposed method is evaluated using 92 breast cytological images containing 11,502 cell nuclei. Experimental evidence shows that the proposed method has very effective results even in the case of images with high degree of blood cells, noisy circles.},
	number = {10},
	urldate = {2016-06-30},
	journal = {Signal Processing},
	author = {George, Yasmeen M. and Bagoury, Bassant M. and Zayed, Hala H. and Roushdy, Mohamed I.},
	month = oct,
	year = {2013},
	keywords = {Circular Hough transform (CHT), Contrast limited adaptive histogram equalization (CLAHE), Cytological image segmentation, Fine needle aspiration cytology (FNAC), Fuzzy c-means clustering (FCM), Marker controlled watershed transform, Otsu’s thresholding method},
	pages = {2804--2816},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6ATC8XE4/George et al. - 2013 - Automated cell nuclei segmentation for breast fine.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WCP3K7D4/S0165168412002642.html:text/html}
}

@article{howard_parametric_2014,
	title = {Parametric and {Nonparametric} {Statistical} {Methods} for {Genomic} {Selection} of {Traits} with {Additive} and {Epistatic} {Genetic} {Architectures}},
	volume = {4},
	issn = {, 2160-1836},
	url = {http://www.g3journal.org/content/4/6/1027},
	doi = {10.1534/g3.114.010298},
	abstract = {Parametric and nonparametric methods have been developed for purposes of predicting phenotypes. These methods are based on retrospective analyses of empirical data consisting of genotypic and phenotypic scores. Recent reports have indicated that parametric methods are unable to predict phenotypes of traits with known epistatic genetic architectures. Herein, we review parametric methods including least squares regression, ridge regression, Bayesian ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian LASSO, best linear unbiased prediction (BLUP), Bayes A, Bayes B, Bayes C, and Bayes Cπ. We also review nonparametric methods including Nadaraya-Watson estimator, reproducing kernel Hilbert space, support vector machine regression, and neural networks. We assess the relative merits of these 14 methods in terms of accuracy and mean squared error (MSE) using simulated genetic architectures consisting of completely additive or two-way epistatic interactions in an F2 population derived from crosses of inbred lines. Each simulated genetic architecture explained either 30\% or 70\% of the phenotypic variability. The greatest impact on estimates of accuracy and MSE was due to genetic architecture. Parametric methods were unable to predict phenotypic values when the underlying genetic architecture was based entirely on epistasis. Parametric methods were slightly better than nonparametric methods for additive genetic architectures. Distinctions among parametric methods for additive genetic architectures were incremental. Heritability, i.e., proportion of phenotypic variability, had the second greatest impact on estimates of accuracy and MSE.},
	language = {en},
	number = {6},
	urldate = {2015-02-10},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Howard, Réka and Carriquiry, Alicia L. and Beavis, William D.},
	month = jun,
	year = {2014},
	pmid = {24727289},
	keywords = {epistasis, genomic selection, GenPred, nonparametric, parametric, prediction, Shared data resources},
	pages = {1027--1046},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BFHF4BC3/Howard et al. - 2014 - Parametric and Nonparametric Statistical Methods f.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SHC72AH8/Howard et al. - 2014 - Parametric and Nonparametric Statistical Methods f.html:text/html}
}

@article{risbridger_breast_2010,
	title = {Breast and prostate cancer: more similar than different},
	volume = {10},
	issn = {1474175X},
	shorttitle = {Breast and prostate cancer},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=48245056&site=ehost-live&scope=site},
	doi = {10.1038/nrc2795},
	abstract = {Breast cancer and prostate cancer are the two most common invasive cancers in women and men, respectively. Although these cancers arise in organs that are different in terms of anatomy and physiological function both organs require gonadal steroids for their development, and tumours that arise from them are typically hormone-dependent and have remarkable underlying biological similarities. Many of the recent advances in understanding the pathophysiology of breast and prostate cancers have paved the way for new treatment strategies. In this Opinion article we discuss some key issues common to breast and prostate cancer and how new insights into these cancers could improve patient outcomes.},
	number = {3},
	urldate = {2015-08-31},
	journal = {Nature Reviews Cancer},
	author = {Risbridger, Gail P. and Davis, Ian D. and Birrell, Stephen N. and Tilley, Wayne D.},
	month = mar,
	year = {2010},
	keywords = {BREAST cancer, LIPIDS, PATHOLOGICAL physiology, PROSTATE cancer, STEROIDS},
	pages = {205--212},
	file = {EBSCO Full Text:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8ZZFVR8H/Risbridger et al. - 2010 - Breast and prostate cancer more similar than diff.pdf:application/pdf}
}

@article{guo_image_2014-1,
	title = {An image processing pipeline to detect and segment nuclei in muscle fiber microscopic images},
	volume = {77},
	copyright = {© 2014 Wiley Periodicals, Inc.},
	issn = {1097-0029},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/jemt.22373/abstract},
	doi = {10.1002/jemt.22373},
	abstract = {Muscle fiber images play an important role in the medical diagnosis and treatment of many muscular diseases. The number of nuclei in skeletal muscle fiber images is a key bio-marker of the diagnosis of muscular dystrophy. In nuclei segmentation one primary challenge is to correctly separate the clustered nuclei. In this article, we developed an image processing pipeline to automatically detect, segment, and analyze nuclei in microscopic image of muscle fibers. The pipeline consists of image pre-processing, identification of isolated nuclei, identification and segmentation of clustered nuclei, and quantitative analysis. Nuclei are initially extracted from background by using local Otsu's threshold. Based on analysis of morphological features of the isolated nuclei, including their areas, compactness, and major axis lengths, a Bayesian network is trained and applied to identify isolated nuclei from clustered nuclei and artifacts in all the images. Then a two-step refined watershed algorithm is applied to segment clustered nuclei. After segmentation, the nuclei can be quantified for statistical analysis. Comparing the segmented results with those of manual analysis and an existing technique, we find that our proposed image processing pipeline achieves good performance with high accuracy and precision. The presented image processing pipeline can therefore help biologists increase their throughput and objectivity in analyzing large numbers of nuclei in muscle fiber images. Microsc. Res. Tech. 77:547–559, 2014. © 2014 Wiley Periodicals, Inc.},
	language = {en},
	number = {8},
	urldate = {2016-07-04},
	journal = {Microscopy Research and Technique},
	author = {Guo, Yanen and Xu, Xiaoyin and Wang, Yuanyuan and Wang, Yaming and Xia, Shunren and Yang, Zhong},
	month = aug,
	year = {2014},
	keywords = {Bayesian network, clustered nuclei, identification, muscle fiber images, watershed},
	pages = {547--559},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HQ64KP4N/Guo et al. - 2014 - An image processing pipeline to detect and segment.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/V4GCRIIT/abstract.html:text/html}
}

@article{searle_theory_2013,
	title = {Theory of mind and {Darwin}'s legacy},
	volume = {110},
	issn = {0027-8424},
	url = {http://www.jstor.org/stable/42706665},
	abstract = {We do not have an adequate theory of consciousness. Both dualism and materialism are mistaken because they deny consciousness is part of the physical world. False claims include (i) behaviorism, (ii) computationalism, (iii) epiphenomenalism, (iv) the readiness potential, (v) subjectivity, and (vi) materialism. Ontological subjectivity does not preclude epistemic objectivity. Observer relative phenomena are created by consciousness, but consciousness is not itself observer relative. Consciousness consists of feeling, sentience, or awareness with (i) qualitativeness, (ii) ontological subjectivity, (iii) unified conscious field, (iv) intentionality, and (v) intentional causation. All conscious states are caused by lower level neurobiological processes in the brain, and they are realized in the brain as higher level features. Efforts to get a detailed scientific account of how brain processes cause consciousness are disappointing. The Darwinian revolution gave us a new form of explanation; two levels were substituted: a causal level, where we specify the mechanism by which the phenotype functions, and a functional level, where we specify the selectional advantage that the phenotype provides. Sociobiology attempted to explain general features of human society, ethics, etc. It failed. For the incest taboo, it confuses inhibition with prohibition. It did not explain the moral force of the taboo. To explain the function of consciousness we cannot ask, "What would be subtracted if we subtracted consciousness but left everything else the same?" We cannot leave everything else the same because consciousness is necessary for higher functions of human and animal life. The unified conscious field gives the organism vastly increased power.},
	urldate = {2016-12-05},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Searle, John},
	year = {2013},
	pages = {10343--10348}
}

@article{dourte_influence_2012,
	title = {Influence of {Decorin} on the {Mechanical}, {Compositional}, and {Structural} {Properties} of the {Mouse} {Patellar} {Tendon}},
	volume = {134},
	issn = {0148-0731},
	url = {http://dx.doi.org/10.1115/1.4006200},
	doi = {10.1115/1.4006200},
	abstract = {The interactions of small leucine-rich proteoglycans (SLRPs) with collagen fibrils, their association with water, and their role in fibrillogenesis suggests that SLRPs may play an important role in tendon mechanics. Some studies have assessed the role of SLRPs in the mechanical response of the tendon, but the relationships between sophisticated mechanics, assembly of collagen, and SLRPs have not been well characterized. Decorin content was varied in a dose dependent manner using decorin null, decorin heterozygote, and wild type mice. Quantitative measures of mechanical (tension and compression), compositional, and structural changes of the mouse patellar tendon were evaluated. Viscoelastic, tensile dynamic modulus was increased in the decorin heterozygous tendons compared to wild type. These tendons also had a significant decrease in total collagen and no structural changes compared to wild type. Decorin null tendons did not have any mechanical changes; however, a significant decrease in the average fibril diameter was found. No differences were seen between genotypes in elastic or compressive properties, and all tendons demonstrated viscoelastic mechanical dependence on strain rate and frequency. These results suggest that decorin, a member of the SLRP family, plays a role in tendon viscoelasticity that cannot be completely explained by its role in collagen fibrillogenesis. In addition, reductions in decorin do not cause large changes in indentation compressive properties, suggesting that other factors contribute to these properties. Understanding these relationships may ultimately help guide development of tissue engineered constructs or treatment modalities.},
	number = {3},
	urldate = {2014-11-03},
	journal = {Journal of Biomechanical Engineering},
	author = {Dourte, LeAnn M. and Pathmanathan, Lydia and Jawad, Abbas F. and Iozzo, Renato V. and Mienaltowski, Michael J. and Birk, David E. and Soslowsky, Louis J.},
	month = mar,
	year = {2012},
	pages = {031005--031005},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZQRIR4SX/Dourte et al. - 2012 - Influence of Decorin on the Mechanical, Compositio.pdf:application/pdf}
}

@article{humphrey_gleason_2004,
	title = {Gleason grading and prognostic factors in carcinoma of the prostate},
	volume = {17},
	copyright = {© 2004 Nature Publishing Group},
	issn = {0893-3952},
	url = {http://www.nature.com.libproxy.tulane.edu:2048/modpathol/journal/v17/n3/full/3800054a.html},
	doi = {10.1038/modpathol.3800054},
	abstract = {Gleason grade of adenocarcinoma of the prostate is an established prognostic indicator that has stood the test of time. The Gleason grading method was devised in the 1960s and 1970s by Dr Donald F Gleason and members of the Veterans Administration Cooperative Urological Research Group. This grading system is based entirely on the histologic pattern of arrangement of carcinoma cells in H\&E-stained sections. Five basic grade patterns are used to generate a histologic score, which can range from 2 to 10. These patterns are illustrated in a standard drawing that can be employed as a guide for recognition of the specific Gleason grades. Increasing Gleason grade is directly related to a number of histopathologic end points, including tumor size, margin status, and pathologic stage. Indeed, models have been developed that allow for pretreatment prediction of pathologic stage based upon needle biopsy Gleason grade, total serum prostate-specific antigen level, and clinical stage. Gleason grade has been linked to a number of clinical end points, including clinical stage, progression to metastatic disease, and survival. Gleason grade is often incorporated into nomograms used to predict response to a specific therapy, such as radiotherapy or surgery. Needle biopsy Gleason grade is routinely used to plan patient management and is also often one of the criteria for eligibility for clinical trials testing new therapies. Gleason grade should be routinely reported for adenocarcinoma of the prostate in all types of tissue samples. Experimental approaches that could be of importance in the future include determination of percentage of high-grade Gleason pattern 4 or 5, and utilization of markers discovered by gene expression profiling or by genetic testing for DNA abnormalities. Such markers would be of prognostic usefulness if they provided added value beyond the established indicators of Gleason grade, serum prostate-specific antigen, and stage. Currently, established prognostic factors for prostatic carcinoma recommended for routine reporting are TNM stage, surgical margin status, serum prostate-specific antigen, and Gleason grade.},
	number = {3},
	urldate = {2015-08-30},
	journal = {Modern Pathology},
	author = {Humphrey, Peter A.},
	month = feb,
	year = {2004},
	keywords = {cancer, Gleason grade, prognosis, prostate},
	pages = {292--306},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/I7XZ6C9C/Humphrey - 2004 - Gleason grading and prognostic factors in carcinom.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2SF8WBW5/Humphrey - 2004 - Gleason grading and prognostic factors in carcinom.html:text/html}
}

@article{montironi_nuclear_2000,
	title = {Nuclear changes in the normal-looking columnar epithelium adjacent to and distant from prostatic intraepithelial neoplasia and prostate cancer},
	volume = {437},
	issn = {0945-6317, 1432-2307},
	url = {http://link.springer.com/article/10.1007/s004280000290},
	doi = {10.1007/s004280000290},
	abstract = {. Subtle morphological changes and molecular alterations have been reported in normal-appearing tissue in prostates with high-grade prostatic intraepithelial neoplasia (PIN) and prostate cancer (PCa). The severity and the distribution of these changes and alterations within the prostate gland have not been addressed in previous publications. The aim of this study was to investigate morphometrically the nuclear changes of the normal-looking columnar epithelium adjacent to and distant from high-grade PIN and PCa. Karyometry was performed on the whole-mount histological sections of three radical prostatectomy (RP) specimens. Two concentrical lines, one corresponding to the outer surface (or capsule) of the prostate and the other corresponding to one centimeter towards the center, were drawn with a black pen on each whole-mount section. The part of the prostate tissue between these two boundaries was then divided into twelve equal sectors or regions. The part within the inner line was divided into two regions. The analysis was also performed on the slides of the apex and base of the prostate. One prostate contained normal-looking epithelium only (case no. 1). Another contained both high-grade PIN and PCa, the former occupying larger areas than the latter (case no. 2). Both high-grade PIN and PCa were present in the third sample, in which PCa was more widely distributed than PIN (case no. 3). The lesion measured in each region was always the most severe, e.g., either high-grade PIN or PCa. When neither were identifiable, then the normal-looking columnar epithelium was analyzed. For each sector, the mean and standard deviation of the nuclear area, maximum nuclear diameter, nuclear roundness factor, and nucleolar area were calculated. In normal-looking columnar epithelium, the mean of the mean nuclear area of the sectors of case no. 1 was 35.19 µm2 (SD 4.14). The mean nuclear areas in cases no. 2 and no. 3 were 37.94 µm2 (SD 4.65) and 37.31 µm2 (SD 4.36), respectively. The mean of the mean nuclear area of the sectors with high-grade PIN of case no. 2 was 49.85 µm2 (SD 8.44), whereas it was 54.26 µm2 (SD 2.91) in case no. 3. The mean of the nuclear area values obtained in the sectors of cases no. 2 and no. 3 with PCa was 56.74 µm2 (SD 6.56) and 61.17 µm2 (SD 8.13), respectively. When considering the normal-looking tissue of the second and third case, 79\% and 90\%, respectively, of the regions showed nuclear area values greater than 34.94 µm2 (e.g., the 50th percentile of the mean nuclear area values of the regions of the first case). Sectors with normal-looking epithelium, whose nuclear area was above this threshold, were both adjacent to and at a distance of more than 1 cm from those with PIN or PCa. The other nuclear features showed a similar trend of value changes. This study demonstrates that the normal-looking ducts and acini from prostate harboring preneoplastic and neoplastic lesions show morphological nuclear abnormalities that are not seen by the human eyes but that can be detected with image analysis. Such changes may be of diagnostic importance, especially in cases where clinical suspicion for cancer prevails after a negative biopsy.},
	language = {en},
	number = {6},
	urldate = {2016-04-21},
	journal = {Virchows Archiv},
	author = {Montironi, Rodolfo and Filho, Adhemar Longatto and Santinelli, Alfredo and Mazzucchelli, Roberta and Pomante, Roberto and Colanzi, Paola and Scarpelli, Marina},
	month = dec,
	year = {2000},
	keywords = {Prostate Normal prostate Prostatic intraepithelial neoplasia PIN Prostate cancer malignancy-associated changes Karyometry Quantitative analysis Morphometry},
	pages = {625--634},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CND2PMC7/Montironi et al. - 2000 - Nuclear changes in the normal-looking columnar epi.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VS7PRXQQ/s004280000290.html:text/html}
}

@article{lafortune_directorate_2012,
	title = {Directorate for {Employment}, {Labour} and {Social} {Affairs}},
	url = {http://www.oecd.org/els/health-systems/Comparing-activities-and-performance-of-the-hospital-sector-in-Europe_Inpatient-and-day-cases-surgical-procedures.pdf},
	urldate = {2016-07-10},
	author = {Lafortune, Gaetan and Balestat, Gaelle and Durand, Anne and {others}},
	year = {2012},
	file = {oecd.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MCR6MNHW/oecd.pdf:application/pdf}
}

@article{au_assessing_2012,
	title = {Assessing {Breast} {Cancer} {Margins} {Ex} {Vivo} {Using} {Aqueous} {Quantum}-{Dot}-{Molecular} {Probes}, {Assessing} {Breast} {Cancer} {Margins} {Ex} {Vivo} {Using} {Aqueous} {Quantum}-{Dot}-{Molecular} {Probes}},
	volume = {2012, 2012},
	issn = {2090-1402, 2090-1402},
	url = {http://www.hindawi.com/journals/ijso/2012/861257/abs/, http://www.hindawi.com/journals/ijso/2012/861257/abs/},
	doi = {10.1155/2012/861257, 10.1155/2012/861257},
	abstract = {Positive margins have been a critical issue that hinders the success of breast- conserving surgery. The incidence of positive margins is estimated to range from 20\&\#x25; to as high as 60\&\#x25;. Currently, there is no effective intraoperative method for margin assessment. It would be desirable if there is a rapid and reliable breast cancer margin assessment tool in the operating room so that further surgery can be continued if necessary to reduce re-excision rate. In this study, we seek to develop a sensitive and specific molecular probe to help surgeons assess if the surgical margin is clean. The molecular probe consists of the unique aqueous quantum dots developed in our laboratory conjugated with antibodies specific to breast cancer markers such as Tn-antigen. Excised tumors from tumor-bearing nude mice were used to demonstrate the method. AQD-Tn mAb probe proved to be sensitive and specific to identify cancer area quantitatively without being affected by the heterogeneity of the tissue. The integrity of the surgical specimen was not affected by the AQD treatment. Furthermore, AQD-Tn mAb method could determine margin status within 30 minutes of tumor excision, indicating its potential as an accurate intraoperative margin assessment method., Positive margins have been a critical issue that hinders the success of breast- conserving surgery. The incidence of positive margins is estimated to range from 20\&\#x25; to as high as 60\&\#x25;. Currently, there is no effective intraoperative method for margin assessment. It would be desirable if there is a rapid and reliable breast cancer margin assessment tool in the operating room so that further surgery can be continued if necessary to reduce re-excision rate. In this study, we seek to develop a sensitive and specific molecular probe to help surgeons assess if the surgical margin is clean. The molecular probe consists of the unique aqueous quantum dots developed in our laboratory conjugated with antibodies specific to breast cancer markers such as Tn-antigen. Excised tumors from tumor-bearing nude mice were used to demonstrate the method. AQD-Tn mAb probe proved to be sensitive and specific to identify cancer area quantitatively without being affected by the heterogeneity of the tissue. The integrity of the surgical specimen was not affected by the AQD treatment. Furthermore, AQD-Tn mAb method could determine margin status within 30 minutes of tumor excision, indicating its potential as an accurate intraoperative margin assessment method.},
	language = {en},
	urldate = {2016-06-22},
	journal = {International Journal of Surgical Oncology, International Journal of Surgical Oncology},
	author = {Au, Giang H. T. and Shih, Wan Y. and Shih, Wei-Heng and Mejias, Linette and Swami, Vanlila K. and Wasko, Kimberly and Brooks, Ari D. and Au, Giang H. T. and Shih, Wan Y. and Shih, Wei-Heng and Mejias, Linette and Swami, Vanlila K. and Wasko, Kimberly and Brooks, Ari D.},
	month = dec,
	year = {2012},
	pages = {e861257},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VXU7MSPJ/Au et al. - 2012 - Assessing Breast Cancer Margins Ex Vivo Using Aque.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TJHQJISD/861257.html:application/xhtml+xml}
}

@article{pilewskie_effect_2014,
	title = {Effect of {Margin} {Width} on {Local} {Recurrence} in {Triple} {Negative} {Breast} {Cancer} {Patients} {Treated} with {Breast}-{Conserving} {Therapy}},
	volume = {21},
	issn = {1068-9265},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349354/},
	doi = {10.1245/s10434-013-3416-5},
	abstract = {Background
The effect of increasing negative margin width following breast conserving therapy (BCT) on local recurrence (LR) is controversial. LR rates vary by subtype, with the highest rates seen in triple negative breast cancer (TNBC). This study examined LR rates in relationship to margin width in TNBC treated with BCT.

Methods
Women with TNBC who underwent BCT between 1999-2009 were identified. Margins were defined as positive (ink on tumor), 0.1-2.0, and 2 mm. Patients with positive margins were excluded. Statistical comparisons were by t tests, Fishers exact test and Wilcoxon rank sum test. Cumulative incidence of LR was compared using competing-risks methodology.

Results
Of 535 cancers, 71 had margins ≤2mm and 464 had margins {\textgreater}2mm. At median follow-up of 84 months (range 8-165 months) there were 37 local, 18 regional, and 77 distant recurrences or deaths as first events. 10 patients had a locoregional recurrence prior to planned radiation therapy and were excluded from cumulative incidence analyses. The cumulative incidence of LR at 60 months for margins ≤2mm was 4.7\% (95\% CI 0, 10.0), and for {\textgreater}2mm 3.7\% (1.8, 5.5), p=0.11. After controlling for chemotherapy and tumor size, there was no difference in LR between the two margin groups (p=.06). A difference in the risk of distant recurrence or death was not observed (p=.53).

Conclusions
Margin width greater than 2mm was not associated with reduced LR rates. This data supports a negative margin definition of no ink on tumor, even in this high risk TNBC cohort.},
	number = {4},
	urldate = {2016-06-22},
	journal = {Annals of surgical oncology},
	author = {Pilewskie, Melissa and Ho, Alice and Orell, Emily and Stempel, Michelle and Chen, Yu and Eaton, Anne and Patil, Sujata and Morrow, Monica},
	month = apr,
	year = {2014},
	pmid = {24327132},
	pmcid = {PMC4349354},
	pages = {1209--1214},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZNC4HQ89/Pilewskie et al. - 2014 - Effect of Margin Width on Local Recurrence in Trip.pdf:application/pdf}
}

@misc{health_overview_????,
	type = {{WebContent}},
	title = {Overview of {Device} {Regulation}},
	url = {http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/Overview/},
	abstract = {Device Advice. Overview of regulations for medical devices: premarket notifications (510(k)), establishment registration, device listing, quality systems, labeling and reporting requirements.},
	language = {en},
	urldate = {2015-11-22},
	author = {Health, Center for Devices {and} Radiological},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PNC595V3/Overview.html:text/html}
}

@article{li_assessing_2015,
	title = {Assessing breast tumor margin by multispectral photoacoustic tomography},
	volume = {6},
	issn = {2156-7085},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399666/},
	doi = {10.1364/BOE.6.001273},
	abstract = {An unmet need exists in high-speed and highly-sensitive intraoperative assessment of breast cancer margin during conservation surgical procedures. Here, we demonstrate a multispectral photoacoustic tomography system for breast tumor margin assessment using fat and hemoglobin as contrasts. This system provides {\textasciitilde}3 mm tissue depth and {\textasciitilde}125 μm axial resolution. The results agreed with the histological findings. A high sensitivity in margin assessment was accomplished, which opens a compelling way to intraoperative margin assessment.},
	number = {4},
	urldate = {2016-07-03},
	journal = {Biomedical Optics Express},
	author = {Li, Rui and Wang, Pu and Lan, Lu and Lloyd, Frank P. and Goergen, Craig J. and Chen, Shaoxiong and Cheng, Ji-Xin},
	month = mar,
	year = {2015},
	pmid = {25909011},
	pmcid = {PMC4399666},
	pages = {1273--1281},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HME3QUNR/Li et al. - 2015 - Assessing breast tumor margin by multispectral pho.pdf:application/pdf}
}

@article{bansal_comparative_2012,
	title = {Comparative evaluation of the modified {Scarff}-{Bloom}-{Richardson} grading system on breast carcinoma aspirates and histopathology},
	volume = {9},
	issn = {1742-6413},
	url = {http://www.cytojournal.com/text.asp?2012/9/1/4/92550},
	doi = {10.4103/1742-6413.92550},
	language = {en},
	number = {1},
	urldate = {2016-06-25},
	journal = {CytoJournal},
	author = {Bansal, Cherry and Misra, Sanjeev and Tiwari, Vandana and Singh, Us and Sharma, KiranLata and Srivastava, An},
	year = {2012},
	pages = {4}
}

@article{attard_prostate_????,
	title = {Prostate cancer},
	issn = {0140-6736},
	url = {http://www.sciencedirect.com/science/article/pii/S0140673614619474},
	doi = {10.1016/S0140-6736(14)61947-4},
	abstract = {Summary
Much progress has been made in research for prostate cancer in the past decade. There is now greater understanding for the genetic basis of familial prostate cancer with identification of rare but high-risk mutations (eg, BRCA2, HOXB13) and low-risk but common alleles (77 identified so far by genome-wide association studies) that could lead to targeted screening of patients at risk. This is especially important because screening for prostate cancer based on prostate-specific antigen remains controversial due to the high rate of overdiagnosis and unnecessary prostate biopsies, despite evidence that it reduces mortality. Classification of prostate cancer into distinct molecular subtypes, including mutually exclusive ETS-gene-fusion-positive and SPINK1-overexpressing, CHD1-loss cancers, could allow stratification of patients for different management strategies. Presently, men with localised disease can have very different prognoses and treatment options, ranging from observation alone through to radical surgery, with few good-quality randomised trials to inform on the best approach for an individual patient. The survival of patients with metastatic prostate cancer progressing on androgen-deprivation therapy (castration-resistant prostate cancer) has improved substantially. In addition to docetaxel, which has been used for more than a decade, in the past 4 years five new drugs have shown efficacy with improvements in overall survival leading to licensing for the treatment of metastatic castration-resistant prostate cancer. Because of this rapid change in the therapeutic landscape, no robust data exist to inform on the selection of patients for a specific treatment for castration-resistant prostate cancer or the best sequence of administration. Moreover, the high cost of the newer drugs limits their widespread use in several countries. Data from continuing clinical and translational research are urgently needed to improve, and, crucially, to personalise management.},
	urldate = {2015-08-30},
	journal = {The Lancet},
	author = {Attard, Gerhardt and Parker, Chris and Eeles, Ros A and Schröder, Fritz and Tomlins, Scott A and Tannock, Ian and Drake, Charles G and de Bono, Johann S},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/H58AHUUM/Attard et al. - Prostate cancer.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7KVRFRRQ/Attard et al. - Prostate cancer.html:text/html}
}

@article{wilson_abstract_2012,
	title = {Abstract {P}4-03-04: {The} potential use of {Optical} {Coherence} {Tomography} for intraoperative breast tumour margin width estimation},
	volume = {72},
	copyright = {© 2012},
	issn = {0008-5472, 1538-7445},
	shorttitle = {Abstract {P}4-03-04},
	url = {http://cancerres.aacrjournals.org/content/72/24_Supplement/P4-03-04},
	doi = {10.1158/0008-5472.SABCS12-P4-03-04},
	abstract = {Total mastectomy and lumpectomy with radiation have been shown to have equivalent patient outcomes, which has likely contributed to the more widespread adoption of breast conserving surgery (BCS) procedures. Assessment of breast lumpectomy margin widths in both an accurate and timely manner is essential to successful breast conservation procedures. Current BCS methodologies have been reported to result in reoperation rates of up to 20–60\%, which represents a significant and unmet need for improved margin assessment. High reoperation rates present both increased treatment risk to patients and increased burden on healthcare systems. In the USA alone, over 150,000 lumpectomies are performed per year at an average cost between \$11,000 and \$19,000 USD per procedure. Assuming a relatively modest average repeat operation rate of 25\%, potentially preventable repeat surgeries represent an approximate cost to the US healthcare system of \$500M (USD) annually.
Reducing the prevalence of repeat surgeries may be accomplished by providing faster and more accurate intraoperative tools for assessing margin widths during the time of the first surgery. One such potential technique involves the use of Optical Coherence Tomography (OCT) imaging, which uses light to produce images in much the same way that ultrasound produces images with sound. Compared to ultrasound, OCT provides decreased depth of penetration, but increased resolution capabilities. The increased resolution that OCT provides allows for the visualization of the internal cellular structure within a tissue sample and therefore, provides the potential ability to differentiate cancerous from normal or benign cells. We propose the use of an intraoperative OCT imaging system to provide near real-time imaging information about the internal structure of tissue samples excised during BCS procedures. Our hypothesis is that the overall rate of repeat operations can be reduced by providing a tool to assist surgeons with the task of margin width estimation during the time of surgery.
We have developed an early stage prototype OCT imaging system that has completed laboratory phantom and preclinical studies. This paper will present the capabilities of an OCT imaging system to provide margin assessment information in biological breast tissue mimicking phantoms. The phantoms were designed to encompass imaging characteristics across a wide range of human breast densities. The paper will go on to describe preclinical imaging that was done in tumor specimens excised from human breast cancer rat models. The results obtained in the phantom and preclinical studies suggest the potential for OCT as a near-real time, intraoperative imaging tool to aid surgeons with breast lumpectomy margin width estimation. To help realize this potential, further research is required in to the use of OCT during BCS.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-03-04.},
	language = {en},
	number = {24 Supplement},
	urldate = {2016-06-24},
	journal = {Cancer Research},
	author = {Wilson, B. C. and Akens, M. K. and Niu, C. J.},
	month = dec,
	year = {2012},
	pages = {P4--03--04--P4--03--04},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GIC7VT8Z/P4-03-04.html:text/html}
}

@article{khan_intraoperative_2013,
	title = {Intraoperative margin re-resection for colorectal cancer liver metastases},
	volume = {2},
	issn = {2304-3881},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924657/},
	doi = {10.3978/j.issn.2304-3881.2012.10.16},
	abstract = {One of the basic tenets of surgical oncology is the achievement of margin-negative resection. The importance of surgical margins in hepatic resection for colorectal cancer liver metastases (CRCLM) is reflected in the abundance of literature written about this topic. However, the definition of the ideal surgical margin has evolved in parallel with advances in systemic chemotherapy, biologic therapy and surgical technology. A better understanding of the biology of liver metastasis is of critical importance in the context of surgical strategy for CRCLM. The value of intraoperative margin re-resection to achieve R0 status for CRCLM is addressed, taking into consideration current understandings of cancer biology.},
	number = {2},
	urldate = {2016-07-05},
	journal = {Hepatobiliary Surgery and Nutrition},
	author = {Khan, Sajid A. and Matthews, Jeffrey B.},
	month = apr,
	year = {2013},
	pmid = {24570924},
	pmcid = {PMC3924657},
	pages = {108--112},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5RQJ2NM8/Khan and Matthews - 2013 - Intraoperative margin re-resection for colorectal .pdf:application/pdf}
}

@article{ough_comparative_2011,
	title = {A comparative analysis of core needle biopsy and final excision for breast cancer: histology and marker expression},
	volume = {201},
	issn = {0002-9610},
	shorttitle = {A comparative analysis of core needle biopsy and final excision for breast cancer},
	url = {http://www.sciencedirect.com/science/article/pii/S0002961010002710},
	doi = {10.1016/j.amjsurg.2010.02.015},
	abstract = {Background
Core needle biopsy (CNB) is used increasingly not only to diagnose breast cancer, but to determine tumor histology, grade and marker expression, select neoadjuvant therapy, and predict sentinel lymph node status. Thus, we undertook this study to evaluate the accuracy of CNB as a predictor of breast cancer histology and marker expression.
Methods
We identified 209 Breast Cancer Registry cases with a preoperative CNB and reviewed all clinicopathologic data for accuracy. Statistical analysis was performed with statistical software.
Results
CNB unequivocally showed cancer in 93\%. Exact tumor histology concordance was 86\%. Ductal carcinoma in situ on CNB was upgraded to invasive cancer in 23\%. Concordance was substantial for estrogen receptor expression (88\%, κ = .71), but kappa values were less than .6 for tumor grade, mitotic rate, progesterone receptor (PR), Ki-67, HER-2/neu, and p53 expression.
Conclusions
Reliance on CNB grade and marker expression for critical decision making may be inadvisable. Further study is warranted to optimize breast cancer patient care.},
	number = {5},
	urldate = {2016-06-25},
	journal = {The American Journal of Surgery},
	author = {Ough, Matthew and Velasco, Jose and Hieken, Tina J.},
	month = may,
	year = {2011},
	keywords = {BREAST cancer, Core needle biopsy, Her-2/neu, Histology, p53, Tumor markers},
	pages = {692--694},
	file = {1-s2.0-S0002961010002710-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PXUPGW33/1-s2.0-S0002961010002710-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VBGXNZUC/S0002961010002710.html:text/html}
}

@article{key_optical_1991,
	title = {Optical attenuation characteristics of breast tissues at visible and near-infrared wavelengths},
	volume = {36},
	issn = {0031-9155},
	url = {http://stacks.iop.org/0031-9155/36/i=5/a=002},
	doi = {10.1088/0031-9155/36/5/002},
	abstract = {Optical experiments are described for measuring the attenuation characteristics of breast tissues at visible and near-infrared wavelengths. Total attenuation coefficients post mortem were measured directly in thin tissue sections. They are usually within the range from 10 to 30 mm -1 , are rather higher in fat than in fibroglandular specimens and decrease with increasing wavelength. The scattering phase function is strongly forward-peaked with the mean cosine of scattering in the range from 0.85 to 0.97 and appearing more forward-peaked in fat than in fibroglandular tissue. The reduced scattering coefficient is of the order of 1 mm -1 in all tissues. Absorption coefficients were measured indirectly in optically thick sections. They are typically between 0.1 and 0.5 mm -1 at wavelengths around 580 nm and an order of magnitude lower at 580 nm. At 850 nm and shorter wavelengths the absorption in carcinoma is significantly higher than in adjacent uninvolved tissue.},
	language = {en},
	number = {5},
	urldate = {2016-06-28},
	journal = {Physics in Medicine and Biology},
	author = {Key, H. and Davies, E. R. and Jackson, P. C. and Wells, P. N. T.},
	year = {1991},
	pages = {579},
	file = {IOP Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UNNPWTS2/Key et al. - 1991 - Optical attenuation characteristics of breast tiss.pdf:application/pdf}
}

@article{agner_spectral_2013,
	title = {Spectral embedding based active contour ({SEAC}) for lesion segmentation on breast dynamic contrast enhanced magnetic resonance imaging},
	volume = {40},
	issn = {0094-2405},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598842/},
	doi = {10.1118/1.4790466},
	abstract = {Purpose: Segmentation of breast lesions on dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) is the first step in lesion diagnosis in a computer-aided diagnosis framework. Because manual segmentation of such lesions is both time consuming and highly susceptible to human error and issues of reproducibility, an automated lesion segmentation method is highly desirable. Traditional automated image segmentation methods such as boundary-based active contour (AC) models require a strong gradient at the lesion boundary. Even when region-based terms are introduced to an AC model, grayscale image intensities often do not allow for clear definition of foreground and background region statistics. Thus, there is a need to find alternative image representations that might provide (1) strong gradients at the margin of the object of interest (OOI); and (2) larger separation between intensity distributions and region statistics for the foreground and background, which are necessary to halt evolution of the AC model upon reaching the border of the OOI., Methods: In this paper, the authors introduce a spectral embedding (SE) based AC (SEAC) for lesion segmentation on breast DCE-MRI. SE, a nonlinear dimensionality reduction scheme, is applied to the DCE time series in a voxelwise fashion to reduce several time point images to a single parametric image where every voxel is characterized by the three dominant eigenvectors. This parametric eigenvector image (PrEIm) representation allows for better capture of image region statistics and stronger gradients for use with a hybrid AC model, which is driven by both boundary and region information. They compare SEAC to ACs that employ fuzzy c-means (FCM) and principal component analysis (PCA) as alternative image representations. Segmentation performance was evaluated by boundary and region metrics as well as comparing lesion classification using morphological features from SEAC, PCA+AC, and FCM+AC., Results: On a cohort of 50 breast DCE-MRI studies, PrEIm yielded overall better region and boundary-based statistics compared to the original DCE-MR image, FCM, and PCA based image representations. Additionally, SEAC outperformed a hybrid AC applied to both PCA and FCM image representations. Mean dice similarity coefficient (DSC) for SEAC was significantly better (DSC = 0.74 ± 0.21) than FCM+AC (DSC = 0.50 ± 0.32) and similar to PCA+AC (DSC = 0.73 ± 0.22). Boundary-based metrics of mean absolute difference and Hausdorff distance followed the same trends. Of the automated segmentation methods, breast lesion classification based on morphologic features derived from SEAC segmentation using a support vector machine classifier also performed better (AUC = 0.67 ± 0.05; p {\textless} 0.05) than FCM+AC (AUC = 0.50 ± 0.07), and PCA+AC (AUC = 0.49 ± 0.07)., Conclusions: In this work, we presented SEAC, an accurate, general purpose AC segmentation tool that could be applied to any imaging domain that employs time series data. SE allows for projection of time series data into a PrEIm representation so that every voxel is characterized by the dominant eigenvectors, capturing the global and local time-intensity curve similarities in the data. This PrEIm allows for the calculation of strong tensor gradients and better region statistics than the original image intensities or alternative image representations such as PCA and FCM. The PrEIm also allows for building a more accurate hybrid AC scheme.},
	number = {3},
	urldate = {2016-07-03},
	journal = {Medical Physics},
	author = {Agner, Shannon C. and Xu, Jun and Madabhushi, Anant},
	month = mar,
	year = {2013},
	pmid = {23464337},
	pmcid = {PMC3598842},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8IS8KS8T/Agner et al. - 2013 - Spectral embedding based active contour (SEAC) for.pdf:application/pdf}
}

@article{masilamani_parallelism_2013,
	title = {A parallelism between spectral grading and {Gleason} grading of malignant prostate tissues},
	volume = {10},
	issn = {1572-1000},
	url = {http://www.sciencedirect.com/science/article/pii/S1572100012001342},
	doi = {10.1016/j.pdpdt.2012.12.002},
	abstract = {Summary
Gleason score is the most common method of grading the virulence of prostate malignancy and is based on the pathological assessment of morphology of cellular matrix. Since this involves the excision of the tissue, we are working on a new, minimally invasive, non-contact, procedure of spectral diagnosis of prostate malignancy. In this preliminary in vitro study reported here, we have analyzed 27 tissue samples (normal control = 7: benign = 8: malignant = 12) by Stokes’ shift spectra (SSS) to establish a one-to-one correspondence between spectral grading and Gleason grading.},
	number = {2},
	urldate = {2016-12-12},
	journal = {Photodiagnosis and Photodynamic Therapy},
	author = {Masilamani, V. and AlSalhi, M. S. and Devanesan, S. and Atif, M. and Rabah, D. and Farhat, K. and Pu, Y. and Alfano, R. R.},
	month = may,
	year = {2013},
	keywords = {Malignant prostate tissue, Spectral grading and Gleason grading, Stokes’ shift spectra},
	pages = {168--172},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FXFJGKR8/Masilamani et al. - 2013 - A parallelism between spectral grading and Gleason.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W8ZP23RP/S1572100012001342.html:text/html}
}

@article{searle_theory_2013-1,
	title = {Theory of mind and {Darwin}’s legacy},
	volume = {110},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/110/Supplement_2/10343},
	doi = {10.1073/pnas.1301214110},
	abstract = {We do not have an adequate theory of consciousness. Both dualism and materialism are mistaken because they deny consciousness is part of the physical world. False claims include (i) behaviorism, (ii) computationalism, (iii) epiphenomenalism, (iv) the readiness potential, (v) subjectivity, and (vi) materialism. Ontological subjectivity does not preclude epistemic objectivity. Observer relative phenomena are created by consciousness, but consciousness is not itself observer relative. Consciousness consists of feeling, sentience, or awareness with (i) qualitativeness, (ii) ontological subjectivity, (iii) unified conscious field, (iv) intentionality, and (v) intentional causation. All conscious states are caused by lower level neurobiological processes in the brain, and they are realized in the brain as higher level features. Efforts to get a detailed scientific account of how brain processes cause consciousness are disappointing. The Darwinian revolution gave us a new form of explanation; two levels were substituted: a causal level, where we specify the mechanism by which the phenotype functions, and a functional level, where we specify the selectional advantage that the phenotype provides. Sociobiology attempted to explain general features of human society, ethics, etc. It failed. For the incest taboo, it confuses inhibition with prohibition. It did not explain the moral force of the taboo. To explain the function of consciousness we cannot ask, “What would be subtracted if we subtracted consciousness but left everything else the same?” We cannot leave everything else the same because consciousness is necessary for higher functions of human and animal life. The unified conscious field gives the organism vastly increased power.},
	language = {en},
	number = {Supplement 2},
	urldate = {2016-12-05},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Searle, John},
	month = jun,
	year = {2013},
	pmid = {23754416},
	keywords = {objective/subjective, unconscious},
	pages = {10343--10348},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TX3X6H73/Searle - 2013 - Theory of mind and Darwin’s legacy.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2ZTRVDMI/10343.html:text/html}
}

@article{bianchini_triple-negative_2016,
	title = {Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease},
	volume = {advance online publication},
	copyright = {© 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1759-4774},
	shorttitle = {Triple-negative breast cancer},
	url = {http://www.nature.com/nrclinonc/journal/vaop/ncurrent/full/nrclinonc.2016.66.html},
	doi = {10.1038/nrclinonc.2016.66},
	abstract = {Chemotherapy is the primary established systemic treatment for patients with triple-negative breast cancer (TNBC) in both the early and advanced-stages of the disease. The lack of targeted therapies and the poor prognosis of patients with TNBC have fostered a major effort to discover actionable molecular targets to treat patients with these tumours. Massively parallel sequencing and other 'omics' technologies have revealed an unexpected level of heterogeneity of TNBCs and have led to the identification of potentially actionable molecular features in some TNBCs, such as germline BRCA1/2 mutations or 'BRCAness', the presence of the androgen receptor, and several rare genomic alterations. Whether these alterations are molecular 'drivers', however, has not been clearly established. A subgroup of TNBCs shows a high degree of tumour-infiltrating lymphocytes that also correlates with a lower risk of disease relapse and a higher likelihood of benefit from chemotherapy. Proof-of-principle studies with immune-checkpoint inhibitors in advanced-stage TNBC have yielded promising results, indicating the potential benefit of immunotherapy for patients with TNBC. In this Review, we discuss the most relevant molecular findings in TNBC from the past decade and the most promising therapeutic opportunities derived from these data.},
	language = {en},
	urldate = {2016-06-23},
	journal = {Nature Reviews Clinical Oncology},
	author = {Bianchini, Giampaolo and Balko, Justin M. and Mayer, Ingrid A. and Sanders, Melinda E. and Gianni, Luca},
	month = may,
	year = {2016},
	keywords = {BREAST cancer, Cancer immunotherapy, Chemotherapy, Targeted therapies, Tumour biomarkers},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RHKGIUAF/Bianchini et al. - 2016 - Triple-negative breast cancer challenges and oppo.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F26HCQBX/nrclinonc.2016.66.html:text/html}
}

@inproceedings{lynch_determination_2002,
	title = {Determination of modulus and {Poisson}'s ratio in two dimensions for evaluation of tendon equilibrium behavior},
	doi = {10.1109/NEBC.2002.999464},
	abstract = {In this study uniaxial tensile testing of rabbit patellar tendon was used to determine whether constant strain rate ramp testing approximates equilibrium tendon behavior. Modulus and Poisson's ratio calculated from constant strain-rate ramp tests were compared with modulus and Poisson's ratio calculated from incremental stress-relaxation tests, which allow viscoelastic behaviors to dissipate. Samples were tested along the fiber direction and perpendicular to the fiber direction},
	booktitle = {Bioengineering {Conference}, 2002. {Proceedings} of the {IEEE} 28th {Annual} {Northeast}},
	author = {Lynch, H.A. and Wu, J.P. and Jawa, A. and Elliott, D.M.},
	year = {2002},
	keywords = {biological tissues, biorheology, Capacitive sensors, constant strain rate ramp testing, Elasticity, fiber direction, fibres, Laboratories, Mathematical model, Optical fiber testing, Orthopedic surgery, Poisson ratio, rabbit patellar tendon, Rabbits, Stress measurement, stress relaxation, Tendons, tensile testing, tissue mechanics, uniaxial tensile testing, viscoelastic behaviors dissipation, viscoelasticity, Viscosity},
	pages = {59--60},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NK2C45BG/abs_all.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GGA534QI/Lynch et al. - 2002 - Determination of modulus and Poisson's ratio in tw.pdf:application/pdf}
}

@article{fuchs_computational_2011,
	series = {Whole {Slide} {Image} {Process}},
	title = {Computational pathology: {Challenges} and promises for tissue analysis},
	volume = {35},
	issn = {0895-6111},
	shorttitle = {Computational pathology},
	url = {http://www.sciencedirect.com/science/article/pii/S0895611111000383},
	doi = {10.1016/j.compmedimag.2011.02.006},
	abstract = {The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data provide a detailed overview of the health status of a patient. Medical doctors need to assess these information sources and they rely on data driven automatic analysis tools. Methods for classification, grouping and segmentation of heterogeneous data sources as well as regression of noisy dependencies and estimation of survival probabilities enter the processing workflow of a pathology diagnosis system at various stages. This paper reports on state-of-the-art of the design and effectiveness of computational pathology workflows and it discusses future research directions in this emergent field of medical informatics and diagnostic machine learning.},
	number = {7–8},
	urldate = {2016-11-30},
	journal = {Computerized Medical Imaging and Graphics},
	author = {Fuchs, Thomas J. and Buhmann, Joachim M.},
	month = oct,
	year = {2011},
	keywords = {Cancer Research, Computational pathology, Machine learning, Medical imaging, Survival statistics, whole slide imaging},
	pages = {515--530},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S7V5XKIX/S7V5XKIX.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NJMBDHGI/S0895611111000383.html:text/html}
}

@article{massague_tgf_2008,
	title = {{TGFβ} in {Cancer}},
	volume = {134},
	issn = {0092-8674},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512574/},
	doi = {10.1016/j.cell.2008.07.001},
	abstract = {The transforming growth factor β (TGFβ) signaling pathway is a key player in metazoan biology, and its misregulation can result in tumor development. The regulatory cytokine TGFβ exerts tumor-suppressive effects that cancer cells must elude for malignant evolution. Yet, paradoxically, TGFβ also modulates processes such as cell invasion, immune regulation, and microenvironment modification that cancer cells may exploit to their advantage. Consequently, the output of a TGFβ response is highly contextual throughout development, across different tissues, and also in cancer. The mechanistic basis and clinical relevance of TGFβ’s role in cancer is becoming increasingly clear, paving the way for a better understanding of the complexity and therapeutic potential of this pathway.},
	number = {2},
	urldate = {2016-12-06},
	journal = {Cell},
	author = {Massagué, Joan},
	month = jul,
	year = {2008},
	pmid = {18662538},
	pmcid = {PMC3512574},
	pages = {215--230},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S4ZTJMM5/Massagué - 2008 - TGFβ in Cancer.pdf:application/pdf}
}

@article{christens-barry_william_a_quantitative_1997,
	series = {{JOHN} {HOPKINS} {UNIV} {APPLIED} {PHYSICS} {LABORATORY}},
	title = {Quantitative grading of tissue and nuclei in prostate cancer for prognosis prediction},
	volume = {18},
	number = {2},
	journal = {Johns Hopkins Apl Technical Digest},
	author = {Christens-Barry, William A, Alan W, Partin},
	year = {1997},
	pages = {227},
	file = {chris.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/J8RX6E62/chris.pdf:application/pdf}
}

@article{robinson_strain-rate_2004,
	title = {Strain-{Rate} {Sensitive} {Mechanical} {Properties} of {Tendon} {Fascicles} {From} {Mice} {With} {Genetically} {Engineered} {Alterations} in {Collagen} and {Decorin}},
	volume = {126},
	issn = {0148-0731},
	url = {http://dx.doi.org/10.1115/1.1695570},
	doi = {10.1115/1.1695570},
	abstract = {Tendons have complex mechanical behaviors that are nonlinear and time dependent. It is widely held that these behaviors are provided by the tissue’s composition and structure. It is generally thought that type I collagen provides the primary elastic strength to tendon while proteoglycans, such as decorin, play a role in failure and viscoelastic properties. This study sought to quantify such structure-function relationships by comparing tendon mechanical properties between normal mice and mice genetically engineered for altered type I collagen content and absence of decorin. Uniaxial tensile ramp to failure experiments were performed on tail tendon fascicles at two strain rates, 0.5\%/s and 50\%/s. Mutations in type I collagen led to reduced failure load and stiffness with no changes in failure stress, modulus or strain rate sensitivity. Fascicles without decorin had similar elastic properties to normal fascicles, but reduced strain rate sensitivity. Fascicles from immature mice, with increased decorin content compared to adult fascicles, had inferior elastic properties but higher strain rate sensitivity. These results showed that tendon viscoelasticity is affected by decorin content but not by collagen alterations. This study provides quantitative evidence for structure-function relationships in tendon, including the role of proteoglycan in viscoelasticity.},
	number = {2},
	urldate = {2014-11-03},
	journal = {Journal of Biomechanical Engineering},
	author = {Robinson, Paul S. and Lin, Tony W. and Reynolds, Paul R. and Derwin, Kathleen A. and Iozzo, Renato V. and Soslowsky, Louis J.},
	month = may,
	year = {2004},
	pages = {252--257},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NPZRGXEN/Robinson et al. - 2004 - Strain-Rate Sensitive Mechanical Properties of Ten.pdf:application/pdf}
}

@article{buckley_validation_2013,
	title = {Validation of an {Empirical} {Damage} {Model} for {Aging} and in {Vivo} {Injury} of the {Murine} {Patellar} {Tendon}},
	volume = {135},
	issn = {0148-0731},
	url = {http://dx.doi.org/10.1115/1.4023700},
	doi = {10.1115/1.4023700},
	abstract = {While useful models have been proposed to predict the mechanical impact of damage in tendon and other soft tissues, the applicability of these models for describing in vivo injury and age-related degeneration has not been investigated. Therefore, the objective of this study was to develop and validate a simple damage model to predict mechanical alterations in mouse patellar tendons after aging, injury, or healing. To characterize baseline properties, uninjured controls at age 150 days were cyclically loaded across three strain levels and five frequencies. For comparison, damage was induced in mature (120 day-old) mice through either injury or aging. Injured mice were sacrificed at three or six weeks after surgery, while aged mice were sacrificed at either 300 or 570 days old. Changes in mechanical properties (relative to baseline) in the three week post-injury group were assessed and used to develop an empirical damage model based on a simple damage parameter related to the equilibrium stress at a prescribed strain (6\%). From the derived model, the viscoelastic properties of the 300 day-old, 570 day-old, and six week post-injury groups were accurately predicted. Across testing conditions, nearly all correlations between predicted and measured parameters were statistically significant and coefficients of determination ranged from R2 = 0.25 to 0.97. Results suggest that the proposed damage model could exploit simple in vivo mechanical measurements to predict how an injured or aged tendon will respond to complex physiological loading regimens.},
	number = {4},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanical Engineering},
	author = {Buckley, Mark R. and Dunkman, Andrew A. and Reuther, Katherine E. and Kumar, Akash and Pathmanathan, Lydia and Beason, David P. and Birk, David E. and Soslowsky, Louis J.},
	month = apr,
	year = {2013},
	pages = {041005--041005},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NGPV4H27/Buckley et al. - 2013 - Validation of an Empirical Damage Model for Aging .pdf:application/pdf}
}

@article{lal_structured_2016,
	title = {Structured illumination microscopy image reconstruction algorithm},
	issn = {1077-260X, 1558-4542},
	url = {http://arxiv.org/abs/1602.06904},
	doi = {10.1109/JSTQE.2016.2521542},
	abstract = {Structured illumination microscopy (SIM) is a very important super-resolution microscopy technique, which provides high speed super-resolution with about two-fold spatial resolution enhancement. Several attempts aimed at improving the performance of SIM reconstruction algorithm have been reported. However, most of these highlight only one specific aspect of the SIM reconstruction -- such as the determination of the illumination pattern phase shift accurately -- whereas other key elements -- such as determination of modulation factor, estimation of object power spectrum, Wiener filtering frequency components with inclusion of object power spectrum information, translocating and the merging of the overlapping frequency components -- are usually glossed over superficially. In addition, most of the work reported lie scattered throughout the literature and a comprehensive review of the theoretical background is found lacking. The purpose of the present work is two-fold: 1) to collect the essential theoretical details of SIM algorithm at one place, thereby making them readily accessible to readers for the first time; and 2) to provide an open source SIM reconstruction code (named OpenSIM), which enables users to interactively vary the code parameters and study it's effect on reconstructed SIM image.},
	urldate = {2016-06-27},
	journal = {IEEE Journal of Selected Topics in Quantum Electronics},
	author = {Lal, Amit and Shan, Chunyan and Xi, Peng},
	year = {2016},
	note = {arXiv: 1602.06904},
	keywords = {Computer Science - Computer Vision and Pattern Recognition},
	pages = {1--1},
	file = {arXiv\:1602.06904 PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S9WX9VFF/Lal et al. - 2016 - Structured illumination microscopy image reconstru.pdf:application/pdf;arXiv.org Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/56WK8WUR/1602.html:text/html}
}

@article{zhao_feature_2015,
	title = {Feature {Quantification} and {Abnormal} {Detection} on {Cervical} {Squamous} {Epithelial} {Cells}, {Feature} {Quantification} and {Abnormal} {Detection} on {Cervical} {Squamous} {Epithelial} {Cells}},
	volume = {2015, 2015},
	issn = {1748-670X, 1748-670X},
	url = {http://www.hindawi.com/journals/cmmm/2015/941680/abs/, http://www.hindawi.com/journals/cmmm/2015/941680/abs/},
	doi = {10.1155/2015/941680, 10.1155/2015/941680},
	abstract = {Feature analysis and classification detection of abnormal cells from images for pathological analysis are an important issue for the realization of computer assisted disease diagnosis. This paper studies a method for cervical squamous epithelial cells. Based on cervical cytological classification standard and expert diagnostic experience, expressive descriptors are extracted according to morphology, color, and texture features of cervical scales epithelial cells. Further, quantificational descriptors related to cytopathology are derived as well, including morphological difference degree, cell hyperkeratosis, and deeply stained degree. The relationship between quantified value and pathological feature can be established by these descriptors. Finally, an effective method is proposed for detecting abnormal cells based on feature quantification. Integrated with clinical experience, the method can realize fast abnormal cell detection and preliminary cell classification., Feature analysis and classification detection of abnormal cells from images for pathological analysis are an important issue for the realization of computer assisted disease diagnosis. This paper studies a method for cervical squamous epithelial cells. Based on cervical cytological classification standard and expert diagnostic experience, expressive descriptors are extracted according to morphology, color, and texture features of cervical scales epithelial cells. Further, quantificational descriptors related to cytopathology are derived as well, including morphological difference degree, cell hyperkeratosis, and deeply stained degree. The relationship between quantified value and pathological feature can be established by these descriptors. Finally, an effective method is proposed for detecting abnormal cells based on feature quantification. Integrated with clinical experience, the method can realize fast abnormal cell detection and preliminary cell classification.},
	language = {en},
	urldate = {2016-07-02},
	journal = {Computational and Mathematical Methods in Medicine, Computational and Mathematical Methods in Medicine},
	author = {Zhao, Mingzhu and Chen, Lei and Bian, Linjie and Zhang, Jianhua and Yao, Chunyan and Zhang, Jianwei and Zhao, Mingzhu and Chen, Lei and Bian, Linjie and Zhang, Jianhua and Yao, Chunyan and Zhang, Jianwei},
	month = mar,
	year = {2015},
	pages = {e941680},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VIVSNVXD/Zhao et al. - 2015 - Feature Quantification and Abnormal Detection on C.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/35FWD8ZP/941680.html:application/xhtml+xml}
}

@article{schnitt_classification_2010-1,
	title = {Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy},
	volume = {23},
	copyright = {© 2010 Nature Publishing Group},
	issn = {0893-3952},
	shorttitle = {Classification and prognosis of invasive breast cancer},
	url = {http://www.nature.com.libproxy.tulane.edu:2048/modpathol/journal/v23/n2s/full/modpathol201033a.html},
	doi = {10.1038/modpathol.2010.33},
	abstract = {For many years, patient age, axillary lymph node status, tumor size, histological features (especially histological grade and lymphovascular invasion), hormone receptor status, and HER2 status have been the major factors used to categorize patients with breast cancer in order to assess prognosis and determine the appropriate therapy. These factors are most often viewed in combination to group patients into various risk categories. Although these risk categories are useful for assessing prognosis and risk in groups of patients with breast cancer, their role in determining prognosis and evaluating risk in an individual patient is more limited. Therefore, better methods are required to help assess prognosis and determine the most appropriate treatment for patients on an individual basis. Recently, various molecular techniques, particular gene expression profiling, have been increasingly used to help refine breast cancer classification and to assess prognosis and response to therapy. Although the precise role of these newer techniques in the daily management of patients with breast cancer continues to evolve, it is clear that they have the potential to provide value above and beyond that provided by the traditional clinical and pathological prognostic and predictive factors.},
	number = {S2},
	urldate = {2016-06-25},
	journal = {Modern Pathology},
	author = {Schnitt, Stuart J.},
	month = may,
	year = {2010},
	keywords = {BREAST cancer, classification, gene expression profiling, molecular, Prognosis},
	pages = {S60--S64},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JST32BPA/Schnitt - 2010 - Classification and prognosis of invasive breast ca.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UMRZEUAK/modpathol201033a.html:text/html}
}

@article{mora_tumor_2012,
	title = {Tumor architecture exerts no bias on nuclear grading in breast cancer diagnosis},
	volume = {461},
	issn = {0945-6317, 1432-2307},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1007/s00428-012-1304-1},
	doi = {10.1007/s00428-012-1304-1},
	abstract = {We recently reported that nuclear grading in prostate cancer is subject to a strong confirmation bias induced by the tumor architecture. We now wondered whether a similar bias governs nuclear grading in breast carcinoma. An unannounced test was performed at a pathology conference. Pathologists were asked to grade nuclei in a PowerPoint presentation. Circular high power fields of 27 invasive ductal carcinomas were shown, superimposed over low power background images of either tubule-rich or tubule-poor carcinomas. We found (a) that diagnostic reproducibility of nuclear grades was poor to moderate (weighed kappa values between 0.07 and 0.54, 27 cases, 44 graders), but (b) that nuclear grades were not affected by the tumor architecture. We speculate that the categorized grading in breast cancer, separating tubule formation, nuclear pleomorphism, and mitotic figure counts in a combined three tier score, prevents the bias that architecture exerts on nuclear grades in less well-controlled situations.},
	language = {en},
	number = {4},
	urldate = {2016-06-25},
	journal = {Virchows Archiv},
	author = {Mora, Braulio and Bombari, Dario and Schaefer, Stephan C. and Schmidt, Marcus and Delaloye, Jean-Francois and Mast, Fred and Lehr, Hans-Anton},
	month = aug,
	year = {2012},
	pages = {399--403},
	file = {art%3A10.1007%2Fs00428-012-1304-1.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BAC9DMEX/art%3A10.1007%2Fs00428-012-1304-1.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RFZDPN6P/s00428-012-1304-1.html:text/html}
}

@article{shinden_rapid_2016,
	title = {Rapid diagnosis of lymph node metastasis in breast cancer using a new fluorescent method with γ-glutamyl hydroxymethyl rhodamine green},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899706/},
	doi = {10.1038/srep27525},
	abstract = {Sentinel lymph node biopsy is performed as a standard procedure in breast cancer surgery, and the development of quick and simple methods to detect metastatic lesions is in high demand. Here, we validated a new fluorescent method using γ-glutamyl hydroxymethyl rhodamine green to diagnose metastatic lymph nodes in breast cancer. One hundred and forty-nine lymph nodes from 38 breast cancer patients were evaluated in this study. Comparison of fluorescent and pathological images showed that this fluorescent method was successful for visualizing breast cancer cells in lymph nodes. This method had a sufficiently high sensitivity (97\%), specificity (79\%) and negative predictive value (99\%) to render it useful for an intraoperative diagnosis of cancer. These preliminary findings suggest that this novel method is useful for distinguishing non-cancerous specimens from those in need of careful examination and could help save time and cost for surgeons and pathologists.},
	urldate = {2016-06-24},
	journal = {Scientific Reports},
	author = {Shinden, Yoshiaki and Ueo, Hiroki and Tobo, Taro and Gamachi, Ayako and Utou, Mitsuaki and Komatsu, Hisateru and Nambara, Sho and Saito, Tomoko and Ueda, Masami and Hirata, Hidenari and Sakimura, Shotaro and Takano, Yuki and Uchi, Ryutaro and Kurashige, Junji and Akiyoshi, Sayuri and Iguchi, Tomohiro and Eguchi, Hidetoshi and Sugimachi, Keishi and Kubota, Yoko and Kai, Yuichiro and Shibuta, Kenji and Kijima, Yuko and Yoshinaka, Heiji and Natsugoe, Shoji and Mori, Masaki and Maehara, Yoshihiko and Sakabe, Masayo and Kamiya, Mako and Kakareka, John W. and Pohida, Thomas J. and Choyke, Peter L. and Kobayashi, Hisataka and Ueo, Hiroaki and Urano, Yasuteru and Mimori, Koshi},
	month = jun,
	year = {2016},
	pmid = {27277343},
	pmcid = {PMC4899706},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XC984M26/Shinden et al. - 2016 - Rapid diagnosis of lymph node metastasis in breast.pdf:application/pdf}
}

@article{bitoun_psr_2013,
	title = {Psr is involved in regulation of glucan production, and double deficiency of {BrpA} and {Psr} is lethal in {Streptococcus} mutans},
	volume = {159},
	issn = {1350-0872, 1465-2080},
	url = {http://mic.sgmjournals.org.libproxy.tulane.edu:2048/content/159/Pt_3/493},
	doi = {10.1099/mic.0.063032-0},
	language = {en},
	number = {Pt\_3},
	urldate = {2014-11-07},
	journal = {Microbiology},
	author = {Bitoun, J. P. and Liao, S. and McKey, B. A. and Yao, X. and Fan, Y. and Abranches, J. and Beatty, W. L. and Wen, Z. T.},
	month = mar,
	year = {2013},
	pages = {493--506},
	file = {493.full.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IRH3SXZ9/493.full.pdf:application/pdf;Psr is involved in regulation of glucan production, and double deficiency of BrpA and Psr is lethal in Streptococcus mutans:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/922GGHXM/493.html:text/html}
}

@article{janowczyk_quantifying_2013,
	title = {Quantifying local heterogeneity via morphologic scale: {Distinguishing} tumoral from stromal regions},
	volume = {4},
	issn = {2229-5089},
	shorttitle = {Quantifying local heterogeneity via morphologic scale},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678744/},
	doi = {10.4103/2153-3539.109865},
	abstract = {Introduction:
The notion of local scale was introduced to characterize varying levels of image detail so that localized image processing tasks could be performed while simultaneously yielding a globally optimal result. In this paper, we have presented the methodological framework for a novel locally adaptive scale definition, morphologic scale (MS), which is different from extant local scale definitions in that it attempts to characterize local heterogeneity as opposed to local homogeneity.

Methods:
At every point of interest, the MS is determined as a series of radial paths extending outward in the direction of least resistance, navigating around obstructions. Each pixel can then be directly compared to other points of interest via a rotationally invariant quantitative feature descriptor, determined by the application of Fourier descriptors to the collection of these paths.

Results:
Our goal is to distinguish tumor and stromal tissue classes in the context of four different digitized pathology datasets: prostate tissue microarrays (TMAs) stained with hematoxylin and eosin (HE) (44 images) and TMAs stained with only hematoxylin (H) (44 images), slide mounts of ovarian H (60 images), and HE breast cancer (51 images) histology images. Classification performance over 50 cross-validation runs using a Bayesian classifier produced mean areas under the curve of 0.88 ± 0.01 (prostate HE), 0.87 ± 0.02 (prostate H), 0.88 ± 0.01 (ovarian H), and 0.80 ± 0.01 (breast HE).

Conclusion:
For each dataset listed in Table 3, we randomly selected 100 points per image, and using the procedure described in Experiment 1, we attempted to separate them as belonging to stroma or epithelium.},
	number = {Suppl},
	urldate = {2015-11-30},
	journal = {Journal of Pathology Informatics},
	author = {Janowczyk, Andrew and Chandran, Sharat and Madabhushi, Anant},
	month = mar,
	year = {2013},
	pmid = {23766944},
	pmcid = {PMC3678744},
	file = {JPatholInform428-3960048_110000.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HEJQ6287/JPatholInform428-3960048_110000.pdf:application/pdf}
}

@misc{_modulation_????,
	title = {Modulation {Transfer} {Function} - what is it and why does it matter? - photo.net},
	url = {http://photo.net/learn/optics/mtf/},
	urldate = {2016-07-11},
	file = {Modulation Transfer Function - what is it and why does it matter? - photo.net:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/X983KBE5/mtf.html:text/html}
}

@article{zhang_exogenous_2011,
	title = {Exogenous near-infrared fluorophores and their applications in cancer diagnosis: biological and clinical perspectives},
	volume = {5},
	issn = {1753-0059},
	shorttitle = {Exogenous near-infrared fluorophores and their applications in cancer diagnosis},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090156/},
	abstract = {Introduction
Near-infrared fluorescent (NIRF) imaging is a rapidly growing research field which has the potential to be an important imaging modality in cancer diagnosis. Various exogenous NIR fluorophores have been developed for the technique, including small molecule fluorophores and nanoparticles. NIRF imaging has been used in animal models for the detection of cancer overthe last twenty years and has in recent years been used in human clinical trials.

Areas covered
This article describes the types and characteristics of exogenous fluorophores available for in vivo fluorescent cancer imaging. The article also discusses the progression of NIRF cancer imaging over recent years and its future challenges, from both a biological and clinical perspective. in The review also looks at its application for lymph node mapping, tumor targeting and characterization, and tumor margin definition for surgical guidance.

Expert Opinion
NIRF imaging is not in routine clinical cancer practice; yet, the authors predict that techniques using NIR fluorophores for tumor margin definition and lymph node mapping will enter clinical practice in the near future. The authors also anticipate that NIRF imaging research will lead to the development of flurophores with ‘high brightness’ that will overcome the limited penetration of this modality and be better suited for non invasive tumor targeting},
	number = {3},
	urldate = {2016-06-25},
	journal = {Expert opinion on medical diagnostics},
	author = {Zhang, Hua and Uselman, Ryan R. and Yee, Douglas},
	month = may,
	year = {2011},
	pmid = {21566703},
	pmcid = {PMC3090156},
	pages = {241--251},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WQSCBH89/Zhang et al. - 2011 - Exogenous near-infrared fluorophores and their app.pdf:application/pdf}
}

@article{coffey_similarities_2001,
	series = {New {Clinical} {Trial} {Strategies} for {Prostate} {Cancer} {Prevention}},
	title = {Similarities of prostate and breast cancer: {Evolution}, diet, and estrogens},
	volume = {57},
	issn = {0090-4295},
	shorttitle = {Similarities of prostate and breast cancer},
	url = {http://www.sciencedirect.com/science/article/pii/S0090429500009389},
	doi = {10.1016/S0090-4295(00)00938-9},
	abstract = {Environment determines the risk of both prostate and breast cancer, and this risk can vary \&gt;10-fold. In contrast, no risk exists for human seminal vesicle cancer demonstrating tissue specificity. There is also species specificity, because there is no risk for prostate cancer in any other aging mammal except the dog. A study of evolution indicates that the prostate and breast appeared at the same time 65 million years ago with the development of mammals. All male mammals have a prostate; however, the seminal vesicles are variable and are determined by the diet so that species primarily eating meat do not have seminal vesicles. The exception is the human, who has seminal vesicles and consumes meat, although this is a recent dietary change. Human lineage departed from other higher primates 8 million years ago. The closest existing primate to humans is the bonobo (pigmy chimpanzee), which does not eat meat but exists primarily on a high fruit and fresh vegetable diet. Homo sapiens evolved only about 150,000 years ago, and only in the last 10\% of that time (10 to 15 thousand years ago) did humans and dogs dramatically alter their diets. This is the time when humans domesticated the dog, bred animals, grew crops, and cooked, processed, and stored meats and vegetables. All current epidemiologic evidence and suggestions for preventing prostate and breast cancer in humans indicates that we should return to the original diets under which our ancestors evolved. The recent development of the Western-type diet is associated with breast and prostate cancer throughout the world. It is believed that the exposure to and metabolism of estrogens, and the dietary intake of phytoestrogens, combined with fat intake, obesity, and burned food processing may all be related to hormonal carcinogenesis and oxidative DNA damage. An explanatory model is proposed.},
	number = {4, Supplement 1},
	urldate = {2015-08-30},
	journal = {Urology},
	author = {Coffey, Donald S},
	month = apr,
	year = {2001},
	pages = {31--38},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TAHEXIT7/Coffey - 2001 - Similarities of prostate and breast cancer Evolut.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DQQZ4QUG/Coffey - 2001 - Similarities of prostate and breast cancer Evolut.html:text/html}
}

@misc{_breast_????,
	title = {Breast {Cancer} {Facts} \& {Figures} {\textbar} {American} {Cancer} {Society}},
	url = {http://www.cancer.org/research/cancerfactsstatistics/breast-cancer-facts-figures},
	urldate = {2016-07-04},
	file = {Breast Cancer Facts & Figures | American Cancer Society:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GG5G9IJA/breast-cancer-facts-figures.html:text/html}
}

@article{russo_hospital_2006,
	title = {Hospital stays for breast cancer, 2004},
	url = {http://www.ncbi.nlm.nih.gov/books/NBK63483/},
	urldate = {2016-07-04},
	author = {Russo, C. Allison and Milenkovic, Mirjana and Steiner, Claudia},
	year = {2006},
	file = {sb15.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3639SGC4/sb15.pdf:application/pdf}
}

@article{humphrey_constrained_2002,
	title = {A {Constrained} {Mixture} {Model} for {Growth} and {Remodeling} of {Soft} {Tissues}},
	volume = {12},
	issn = {02182025},
	url = {http://libproxy.tulane.edu:2048/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=7229809&site=ehost-live&scope=site},
	abstract = {Not long ago it was thought that the most important characteristics of the mechanics of soft tissues were their complex mechanical properties: they often exhibit nonlinear, anisotropic, nearly incompressible, viscoelastic behavior over finite strains. Indeed, these properties endow soft tissues with unique structural capabilities that continue to be extremely challenging to quantify via constitutive relations. More recently, however, we have come to appreciate an even more important characteristic of soft tissues, their homeostatic tendency to adapt in response to changes in their mechanical environment. Thus, to understand well the biomechanical properties of a soft tissue, we must not only quantify their structure and function at a given time, we must also quantify how their structure and function change in response to altered stimuli. In this paper, we introduce a new constrained mixture theory model for studying growth and remodeling of soft tissues. The model melds ideas from classical mixture and homogenization theories so as to exploit advantages of each while avoiding particular difficulties. Salient features include the kinetics of the production and removal of individual constituents and recognition that the neighborhood of a material point of each constituent can have a different, evolving natural (i.e. stress-free) configuration.},
	number = {3},
	urldate = {2014-11-04},
	journal = {Mathematical Models \& Methods in Applied Sciences},
	author = {Humphrey, J. D. and Rajagopal, K. R. and Bellomo, N.},
	month = mar,
	year = {2002},
	keywords = {MATHEMATICAL models, tissue mechanics},
	pages = {407},
	file = {EBSCO Full Text:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GJSI9JSZ/Humphrey et al. - 2002 - A Constrained Mixture Model for Growth and Remodel.pdf:application/pdf}
}

@article{dobbs_porters_2012,
	title = {Porter's {Five} {Forces} in {Practice}: {Templates} for {Firm} and {Case} {Analysis}},
	volume = {10},
	copyright = {Copyright American Society for Competitiveness 2012},
	issn = {15452581},
	shorttitle = {Porter's {Five} {Forces} in {Practice}},
	url = {http://search.proquest.com/docview/1189673886/abstract/945495367A9349ABPQ/1},
	abstract = {Michael Porter's (1980) five forces framework is a rich, in-depth assessment of the underpinnings of competition and profitability in an industry and is neither easily nor quickly conducted, perhaps leading to its misunderstanding and even misuse. To aid students and managers, I developed a set of templates that systematically guides an analyst through a comprehensive assessment of the five forces using graphics, visual cues, a uniform structure, and straightforward descriptions of concepts. In this paper, I provide a copy of the templates, describe their structure and use, provide an example of a completed template, and discuss possible modifications and extensions. [PUBLICATION ABSTRACT]},
	language = {English},
	number = {1},
	urldate = {2016-02-04},
	journal = {Competition Forum},
	author = {Dobbs, Michael E.},
	year = {2012},
	keywords = {Business And Economics, Competition, Industry analysis, Management theory, Profitability, Studies},
	pages = {22--33},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Q6D4J45B/Dobbs - 2012 - Porter's Five Forces in Practice Templates for Fi.pdf:application/pdf}
}

@article{guo_image_2014-2,
	title = {An image processing pipeline to detect and segment nuclei in muscle fiber microscopic images},
	volume = {77},
	copyright = {© 2014 Wiley Periodicals, Inc.},
	issn = {1097-0029},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/jemt.22373/abstract},
	doi = {10.1002/jemt.22373},
	abstract = {Muscle fiber images play an important role in the medical diagnosis and treatment of many muscular diseases. The number of nuclei in skeletal muscle fiber images is a key bio-marker of the diagnosis of muscular dystrophy. In nuclei segmentation one primary challenge is to correctly separate the clustered nuclei. In this article, we developed an image processing pipeline to automatically detect, segment, and analyze nuclei in microscopic image of muscle fibers. The pipeline consists of image pre-processing, identification of isolated nuclei, identification and segmentation of clustered nuclei, and quantitative analysis. Nuclei are initially extracted from background by using local Otsu's threshold. Based on analysis of morphological features of the isolated nuclei, including their areas, compactness, and major axis lengths, a Bayesian network is trained and applied to identify isolated nuclei from clustered nuclei and artifacts in all the images. Then a two-step refined watershed algorithm is applied to segment clustered nuclei. After segmentation, the nuclei can be quantified for statistical analysis. Comparing the segmented results with those of manual analysis and an existing technique, we find that our proposed image processing pipeline achieves good performance with high accuracy and precision. The presented image processing pipeline can therefore help biologists increase their throughput and objectivity in analyzing large numbers of nuclei in muscle fiber images. Microsc. Res. Tech. 77:547–559, 2014. © 2014 Wiley Periodicals, Inc.},
	language = {en},
	number = {8},
	urldate = {2016-07-04},
	journal = {Microscopy Research and Technique},
	author = {Guo, Yanen and Xu, Xiaoyin and Wang, Yuanyuan and Wang, Yaming and Xia, Shunren and Yang, Zhong},
	month = aug,
	year = {2014},
	keywords = {Bayesian network, clustered nuclei, identification, muscle fiber images, watershed},
	pages = {547--559},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ERSZ3J4Z/Guo et al. - 2014 - An image processing pipeline to detect and segment.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9GRHJIFN/abstract.html:text/html}
}

@article{saha_comparative_2013,
	title = {Comparative evaluation of six cytological grading systems in breast carcinoma},
	volume = {30},
	issn = {0970-9371},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701344/},
	doi = {10.4103/0970-9371.112647},
	abstract = {Background:
Cytological grading is a useful tool for selection of therapy and prognosis in breast carcinoma. Despite having many cytological grading systems, there is still no agreement among pathologists to accept one of them as a gold standard.

Aim:
This study was undertaken to evaluate six such three-tier cytological grading systems to determine which system corresponds best to histological grading done by Nottingham modification of Scarff Bloom Richardson (SBR)'s method.

Materials and Methods:
In a double-blind study, preoperative cytological grades obtained by six systems on fine-needle aspiration cytology (FNAC) smears were compared by testing concordance, association and correlation with histological grade derived postoperatively by the SBR's method in 57 patients of breast carcinoma. Bivariate correlation studies and multiple linear regressions were done to assess the significance of the different cytological parameters to predict final cytological grades.

Results:
Robinson's system demonstrated the best correlation (ρ = 0.799; P = 0.000 and τ = 0.765; P = 0.000), maximum percent agreement (77.19\%) and a substantial kappa value of agreement (κ = 0.62) with the SBR's grading system. All the six cytological grading systems correlated with histological grading strongly and positively. In multiple regression analysis, all of the cytological parameters of Robinson's system except cell size and nucleoli had significance in predicting the final cytological grade.

Conclusions:
Robinson's grading system is simple, more objective and reproducible, and demonstrated the best concordance with histological grading. So, Robinson's system should be used routinely for breast carcinoma aspirates.},
	number = {2},
	urldate = {2016-07-10},
	journal = {Journal of Cytology / Indian Academy of Cytologists},
	author = {Saha, Kaushik and Raychaudhuri, Gargi and Chattopadhyay, Bitan Kuamr and Das, Indranil},
	year = {2013},
	pmid = {23833396},
	pmcid = {PMC3701344},
	pages = {87--93}
}

@incollection{john_wiley_&_sons_ltd_nucleolus_2005,
	address = {Chichester, UK},
	title = {Nucleolus},
	isbn = {978-0-470-01617-6 978-0-470-01590-2},
	url = {http://doi.wiley.com/10.1038/npg.els.0003958},
	language = {en},
	urldate = {2016-06-27},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Shaw, Peter J},
	editor = {{John Wiley \& Sons, Ltd}},
	month = sep,
	year = {2005},
	file = {nucleolus.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KJT4CGKT/nucleolus.pdf:application/pdf}
}

@article{wang_high-resolution_2015-1,
	title = {High-{Resolution} {Rapid} {Diagnostic} {Imaging} of {Whole} {Prostate} {Biopsies} {Using} {Video}-{Rate} {Fluorescence} {Structured} {Illumination} {Microscopy}},
	volume = {75},
	issn = {0008-5472, 1538-7445},
	url = {http://cancerres.aacrjournals.org/content/75/19/4032},
	doi = {10.1158/0008-5472.CAN-14-3806},
	abstract = {Rapid assessment of prostate core biopsy pathology at the point-of-procedure could provide benefit in a variety of clinical situations. Even with advanced transrectal ultrasound guidance and saturation biopsy protocols, prostate cancer can be missed in up to half of all initial biopsy procedures. In addition, collection of tumor specimens for downstream histologic, molecular, and genetic analysis is hindered by low tumor yield due to inability to identify prostate cancer grossly. However, current point-of-procedure pathology protocols, such as frozen section analysis (FSA), are destructive and too time- and labor-intensive to be practical or economical. Ex vivo microscopy of the excised specimens, stained with fast-acting fluorescent histology dyes, could be an attractive nondestructive alternative to FSA. In this work, we report the first demonstration of video-rate structured illumination microscopy (VR-SIM) for rapid high-resolution diagnostic imaging of prostate biopsies in realistic point-of-procedure timeframes. Large mosaic images of prostate biopsies stained with acridine orange are rendered in seconds and contain excellent contrast and detail, exhibiting close correlation with corresponding hematoxylin and eosin histology. A clinically relevant review of VR-SIM images of 34 unfixed and uncut prostate core biopsies by two independent pathologists resulted in an area under the receiver operative curve (AUC) of 0.82–0.88, with a sensitivity ranging from 63\% to 88\% and a specificity ranging from 78\% to 89\%. When biopsies contained more than 5\% tumor content, the sensitivity improved to 75\% to 92\%. The image quality, speed, minimal complexity, and ease of use of VR-SIM could prove to be features in favor of adoption as an alternative to destructive pathology at the point-of-procedure. Cancer Res; 75(19); 4032–41. ©2015 AACR.},
	language = {en},
	number = {19},
	urldate = {2016-05-06},
	journal = {Cancer Research},
	author = {Wang, Mei and Kimbrell, Hillary Z. and Sholl, Andrew B. and Tulman, David B. and Elfer, Katherine N. and Schlichenmeyer, Tyler C. and Lee, Benjamin R. and Lacey, Michelle and Brown, J. Quincy},
	month = oct,
	year = {2015},
	pmid = {26282168},
	pages = {4032--4041},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MVS4AUAE/Wang et al. - 2015 - High-Resolution Rapid Diagnostic Imaging of Whole .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TB3DQ444/4032.html:text/html}
}

@article{tashk_automatic_2015,
	title = {Automatic detection of breast cancer mitotic cells based on the combination of textural, statistical and innovative mathematical features},
	volume = {39},
	issn = {0307-904X},
	url = {http://www.sciencedirect.com/science/article/pii/S0307904X15000542},
	doi = {10.1016/j.apm.2015.01.051},
	abstract = {Automatic grading systems based on histopathological slide images are applied to various types of cancers. To date, cancer scientists and researchers have conducted many experiments to find and evaluate new and innovative automatic cancer grading systems to accelerate their therapeutic diagnoses and ultimately to enable more efficient prognoses. The previously proposed automatic or computer-aided systems for breast cancer grading, including specializing mitosis counting, suffer from various shortcomings. The most important one is their low efficiency along with high complexity due to the huge amount of features. In this paper, three types of features with more flexibility and less complexity are employed. These features are: completed local binary pattern (CLBP) as textural features, statistical moment entropy (SME) and stiffness matrix (SM) as a mathematical model which includes geometric, morphometric and shape-based features. In the proposed automatic mitosis detection method, these three types of features are fused with each other. The SM feature comprises of characteristics which are to be extracted for reliable discrimination of mitosis objects from non-mitosis ones. The evaluations are applied over histology datasets A and H provided by the Mitos-ICPR2012 contest sponsors. Employing both a nonlinear radial basis function (RBF) kernel for support vector machine (SVM) and also random forest classifiers, leads to the best efficiencies among the other competitive methods which have been proposed in the past. The results are in the form of F-measure criterion which is a basis for bioinformatics assessments and evaluation.},
	number = {20},
	urldate = {2016-06-30},
	journal = {Applied Mathematical Modelling},
	author = {Tashk, Ashkan and Helfroush, Mohammad Sadegh and Danyali, Habibollah and Akbarzadeh-jahromi, Mojgan},
	month = oct,
	year = {2015},
	keywords = {Completed local binary pattern (CLBP), Histology slide images, Mitosis counting, Random forest (RF), Statistical moments entropy (SME), Stiffness matrix (SM)},
	pages = {6165--6182},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XQJ85WVA/Tashk et al. - 2015 - Automatic detection of breast cancer mitotic cells.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6QXSFN7C/S0307904X15000542.html:text/html}
}

@article{arnoczky_mechanobiological_2007,
	title = {The mechanobiological aetiopathogenesis of tendinopathy: is it the over-stimulation or the under-stimulation of tendon cells?},
	volume = {88},
	issn = {0959-9673},
	shorttitle = {The mechanobiological aetiopathogenesis of tendinopathy},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517314/},
	doi = {10.1111/j.1365-2613.2007.00548.x},
	abstract = {While there is a significant amount of information available on the clinical presentation(s) and pathological changes associated with tendinopathy, the precise aetiopathogenesis of this condition remains a topic of debate. Classically, the aetiology of tendinopathy has been linked to the performance of repetitive activities (so-called overuse injuries). This has led many investigators to suggest that it is the mechanobiologic over-stimulation of tendon cells that is the initial stimulus for the degradative processes which have been shown to accompany tendinopathy. Although several studies have been able to demonstrate that the in vitro over-stimulation of tendon cells in monolayer can result in a pattern(s) of gene expression seen in clinical cases of tendinopathy, the strain magnitudes and durations used in these in vitro studies, as well as the model systems, may not be clinically relevant. Using a rat tail tendon model, we have studied the in vitro mechanobiologic response of tendon cells in situ to various tensile loading regimes. These studies have led to the hypothesis that the aetiopathogenic stimulus for the degenerative cascade which precedes the overt pathologic development of tendinopathy is the catabolic response of tendon cells to mechanobiologic under-stimulation as a result of microscopic damage to the collagen fibres of the tendon. In this review, we examine the rationale for this hypothesis and provide evidence in support of this theory.},
	number = {4},
	urldate = {2014-11-04},
	journal = {International Journal of Experimental Pathology},
	author = {Arnoczky, Steven P and Lavagnino, Michael and Egerbacher, Monika},
	month = aug,
	year = {2007},
	pmid = {17696902},
	pmcid = {PMC2517314},
	pages = {217--226},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/K8TZZH84/Arnoczky et al. - 2007 - The mechanobiological aetiopathogenesis of tendino.pdf:application/pdf}
}

@misc{_number_????,
	title = {Number of cyclists/bike riders in the {USA}, 2014},
	url = {http://www.statista.com/statistics/227415/number-of-cyclists-and-bike-riders-usa/},
	abstract = {This statistic illustrates the number of cyclists and bike riders within the last 12 months in the United States (USA) from spring 2008 to spring 2014. In spring 2008, the number of people who have been cycling within the last 12 months amounted to 47.16 million.},
	urldate = {2015-03-10},
	journal = {Statista},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SIVNU6BN/Number of cyclistsbike riders in the USA, 2014.html:text/html}
}

@article{bansal_comparative_2012-1,
	title = {Comparative evaluation of the modified {Scarff}-{Bloom}-{Richardson} grading system on breast carcinoma aspirates and histopathology},
	volume = {9},
	issn = {0974-5963},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280007/},
	doi = {10.4103/1742-6413.92550},
	abstract = {Background:
Fine needle aspiration (FNA) is a quick, minimally invasive procedure for evaluation of breast tumors. The Scarff-Bloom-Richardson (SBR) grade on histological sections is a well-established tool to guide selection of adjuvant systemic therapy. Grade evaluation is possible on cytology smears to avoid and minimize the morbidity associated with overtreatment of lower grade tumors.

Aim:
The aim was to test the hypothesis whether breast FNA from the peripheral portion of the lesion is representative of Scarff-Bloom-Richardson grade on histopathology as compared to FNA from the central portion.

Materials and Methods:
Fine-needle aspirates and subsequent tissue specimens from 45 women with ductal carcinoma (not otherwise specified) were studied. FNAs were performed under ultrasound guidance from the central as well as the peripheral third of the lesion for each case avoiding areas of necrosis/calcification. The SBR grading was compared on alcohol fixed aspirates and tissue sections for each case.

Results:
Comparative analysis of SBR grade on aspirates from the peripheral portion and histopathology by the Pearson chi-square test (χ2 =78.00) showed that it was statistically significant (P{\textless}0.001) with 93\% concordance. Lower mitotic score on aspirates from the peripheral portion was observed in only 4 out of 45 (9\%) cases. The results of the Pearson chi-square test (χ2 = 75.824) with statistically significant (P=0.000).

Conclusion:
This prospective study shows that FNA smears from the peripheral portion of the lesion are representative of the grading performed on the corresponding histopathological sections. It is possible to score and grade by SBR system on FNA smears.},
	urldate = {2016-06-25},
	journal = {CytoJournal},
	author = {Bansal, Cherry and Singh, U. S. and Misra, Sanjeev and Sharma, Kiran Lata and Tiwari, Vandana and Srivastava, A. N.},
	month = jan,
	year = {2012},
	pmid = {22363393},
	pmcid = {PMC3280007}
}

@article{down_oncological_2013-1,
	title = {Oncological {Advantages} of {Oncoplastic} {Breast}-{Conserving} {Surgery} in {Treatment} of {Early} {Breast} {Cancer}},
	volume = {19},
	copyright = {© 2013 Wiley Periodicals, Inc.},
	issn = {1524-4741},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1111/tbj.12047/abstract},
	doi = {10.1111/tbj.12047},
	abstract = {The standard approach to breast-conserving surgery is wide local excision of the tumor and radiotherapy. However, a significant number of patients require further surgery to obtain oncologically clear margins, and may obtain a poor cosmetic result following adjuvant radiotherapy. Oncoplastic techniques may result in improved cosmesis, but few studies have investigated the oncological advantage of this approach. The aim of this retrospective study was to compare tumor clearance and the need for further margin excision following standard wide local excision (group A, 121 patients), and oncoplastic breast-conserving surgery (group B, 37 patients). These techniques included therapeutic mammoplasty, sub-axillary fat pad rotation mammoplasty, thoraco-epigastric flap, and central flap. Compared to standard surgery (group A), oncoplastic techniques (group B) can be employed for significantly larger tumors (17.6 mm versus 23.9 mm, p = 0.002). Oncoplastic breast-conserving surgery results in higher mean specimen weights (58.1 g versus 231.1 g, p {\textless} 0.0001), higher specimen volumes (112.3 cm3 versus 484.5 cm3, p {\textless} 0.0001), and wider clear margins (6.1 mm versus 14.3 mm, p {\textless} 0.0001), resulting in lower rates of further surgery (28.9\% versus 5.4\%, p = 0.002). There was no statistical increase in complication rates following oncoplastic surgery. Oncoplastic breast-conserving surgery is more successful than standard wide local excision in treating larger tumors and obtaining wider radial margins, thus reducing the need for further margin excision, which delays adjuvant therapy. There was no increase in postoperative complication rate using an oncoplastic approach.},
	language = {en},
	number = {1},
	urldate = {2016-06-23},
	journal = {The Breast Journal},
	author = {Down, Sue K. and Jha, Pankaj K., MBBS MS MSc and Burger, Amy and Hussien, Maged I.},
	month = jan,
	year = {2013},
	keywords = {breast-conserving surgery, breast reconstruction, mammoplasty},
	pages = {56--63},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZKNTN6DZ/Down et al. - 2013 - Oncological Advantages of Oncoplastic Breast-Conse.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/G5EQ6NP4/abstract.html:text/html}
}

@article{rahman_breast_2011,
	title = {Breast {Conserving} {Therapy}: {A} surgical {Technique} where {Little} can {Mean} {More}},
	volume = {3},
	issn = {2006-8808},
	shorttitle = {Breast {Conserving} {Therapy}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192521/},
	doi = {10.4103/2006-8808.78459},
	number = {1},
	urldate = {2016-07-07},
	journal = {Journal of Surgical Technique and Case Report},
	author = {Rahman, Ganiyu A.},
	year = {2011},
	pmid = {22022642},
	pmcid = {PMC3192521},
	pages = {1--4}
}

@article{marudanayagam_effect_2008,
	title = {Effect of {Cavity} {Shaving} on {Reoperation} {Rate} {Following} {Breast}-{Conserving} {Surgery}},
	volume = {14},
	copyright = {© 2008 Wiley Periodicals, Inc.},
	issn = {1524-4741},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1111/j.1524-4741.2008.00649.x/abstract},
	doi = {10.1111/j.1524-4741.2008.00649.x},
	abstract = {Abstract:  Breast-conserving surgery (BCS) without adequate margin clearance carries a high risk of local recurrence. We introduced cavity shaving at primary surgery 31 months ago, to assess tumor margin involvement. The aim of this study was to determine how cavity shaving affects the re-excision rate. We compared a group of 394 patients who underwent BCS with cavity shaving of macroscopically clear margins at primary operation, from March 2003 to September 2005 with a group of 392 patients who underwent BCS only from January 2000 to February 2003. Cavity shaves and re-excision specimens were measured and oriented with reference to the primary cancer. Pathological results of all the specimens were analyzed and re-excision rates in both groups were recorded. Compared with BCS alone where 49 of 392 patients (12.5\%) required reoperation for margin clearance, only 22 of 394 patients (5.58\%) of the group who had concurrent cavity shaves required further surgery (p {\textless} 0.01). Analysis of re-excised specimens suggests that reoperation could have been avoided in 44 of 49 patients, if they had standard sized cavity shave at primary operation. We conclude that cavity shavings during primary BCS significantly reduce the re-excision rate to ensure microscopic clearance.},
	language = {en},
	number = {6},
	urldate = {2016-06-30},
	journal = {The Breast Journal},
	author = {Marudanayagam, Ravi and Singhal, Rishi and Tanchel, Bruce and O’Connor, Brendan and Balasubramanian, Balapathiran and Paterson, Ian},
	month = nov,
	year = {2008},
	keywords = {breast-conserving surgery, cavity shave},
	pages = {570--573},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GN688VDU/Marudanayagam et al. - 2008 - Effect of Cavity Shaving on Reoperation Rate Follo.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JGK3F53I/abstract.html:text/html}
}

@misc{_world_????,
	title = {The {World} {Market} for {Cancer} {Diagnostics}, 6th {Edition} ({Histology} [{ISH}, {IHC}, {HPV}, {Pap}], {Flow} {Cytometry}, {PSA}, {CEA}, {Liquid} {Biopsy}, {FOB} and {Other} {Rapid}, {Image} {Cytometry}, {Sequencing}, {Digital} {Pathology}, {Molecular} {Assays}) : {Market} {Research} {Report}},
	url = {http://www.kaloramainformation.com/Cancer-Diagnostics-Edition-9292184/},
	urldate = {2016-07-04},
	file = {The World Market for Cancer Diagnostics, 6th Edition (Histology [ISH, IHC, HPV, Pap], Flow Cytometry, PSA, CEA, Liquid Biopsy, FOB and Other Rapid, Image Cytometry, Sequencing, Digital Pathology, Molecular Assays) \: Market Research Report:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NSKW3BDI/Cancer-Diagnostics-Edition-9292184.html:text/html}
}

@article{kim_optical_2013,
	title = {Optical {Molecular} {Imaging} for {Diagnosing} {Intestinal} {Diseases}},
	volume = {46},
	issn = {2234-2400},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856262/},
	doi = {10.5946/ce.2013.46.6.620},
	abstract = {Real-time visualization of the molecular signature of cells can be achieved with advanced targeted imaging techniques using molecular probes and fluorescence endoscopy. This molecular optical imaging in gastrointestinal endoscopy is promising for improving the detection of neoplastic lesions, their characterization for patient stratification, and the assessment of their response to molecular targeted therapy and radiotherapy. In inflammatory bowel disease, this method can be used to detect dysplasia in the presence of background inflammation and to visualize inflammatory molecular targets for assessing disease severity and prognosis. Several preclinical and clinical trials have applied this method in endoscopy; however, this field has just started to evolve. Hence, many problems have yet to be solved to enable the clinical application of this novel method.},
	number = {6},
	urldate = {2016-06-25},
	journal = {Clinical Endoscopy},
	author = {Kim, Sang-Yeob and Myung, Seung-Jae},
	month = nov,
	year = {2013},
	pmid = {24340254},
	pmcid = {PMC3856262},
	pages = {620--626},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7GPVHSKQ/Kim and Myung - 2013 - Optical Molecular Imaging for Diagnosing Intestina.pdf:application/pdf}
}

@article{siegel_cancer_2016,
	title = {Cancer statistics, 2016},
	volume = {66},
	copyright = {© 2016 American Cancer Society},
	issn = {1542-4863},
	url = {http://onlinelibrary.wiley.com/doi/10.3322/caac.21332/abstract},
	doi = {10.3322/caac.21332},
	abstract = {Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data were collected by the National Cancer Institute (Surveillance, Epidemiology, and End Results [SEER] Program), the Centers for Disease Control and Prevention (National Program of Cancer Registries), and the North American Association of Central Cancer Registries. Mortality data were collected by the National Center for Health Statistics. In 2016, 1,685,210 new cancer cases and 595,690 cancer deaths are projected to occur in the United States. Overall cancer incidence trends (13 oldest SEER registries) are stable in women, but declining by 3.1\% per year in men (from 2009-2012), much of which is because of recent rapid declines in prostate cancer diagnoses. The cancer death rate has dropped by 23\% since 1991, translating to more than 1.7 million deaths averted through 2012. Despite this progress, death rates are increasing for cancers of the liver, pancreas, and uterine corpus, and cancer is now the leading cause of death in 21 states, primarily due to exceptionally large reductions in death from heart disease. Among children and adolescents (aged birth-19 years), brain cancer has surpassed leukemia as the leading cause of cancer death because of the dramatic therapeutic advances against leukemia. Accelerating progress against cancer requires both increased national investment in cancer research and the application of existing cancer control knowledge across all segments of the population. CA Cancer J Clin 2016;7–30. © 2015 American Cancer Society.},
	language = {en},
	number = {1},
	urldate = {2016-06-23},
	journal = {CA: A Cancer Journal for Clinicians},
	author = {Siegel, Rebecca L. and Miller, Kimberly D. and Jemal, Ahmedin},
	month = jan,
	year = {2016},
	keywords = {cancer cases, cancer statistics, death rates, incidence, mortality, survival, trends},
	pages = {7--30},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/B9ZZ9UZM/Siegel et al. - 2016 - Cancer statistics, 2016.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MTQSPW4E/abstract.html:text/html}
}

@article{ponnusamy_vitro_2012,
	title = {In vitro degradation and release characteristics of spin coated thin films of {PLGA} with a “breath figure” morphology},
	volume = {2},
	issn = {2159-2527},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549860/},
	doi = {10.4161/biom.20390},
	abstract = {Poly (lactic-co-glycolic acid) (PLGA) coatings on implant materials are widely used in controlled drug delivery applications. Typically, such coatings are made with non-porous films. Here, we have synthesized a thin PLGA film coating with a highly ordered microporous structure using a simple and inexpensive water templating “breath figure” technique. A single stage process combining spin coating and breath figure process was used to obtain drug incorporated porous thin films. The films were characterized by scanning electron microscope (SEM) to observe the surface and bulk features of porosity and also, degradation pattern of the films. Moreover, the effect of addition of small amount of poly (ethylene glycol) (PEG) into PLGA was characterized. SEM analysis revealed an ordered array of {\textasciitilde}2 µm sized pores on the surface with the average film thickness measured to be 20 µm. The incorporation of hydrophilic poly (ethylene glycol) (PEG) enhances pore structure uniformity and facilitates ingress of water into the structure. A five week in vitro degradation study showed a gradual deterioration of the breath figure pores. During the course of degradation, the surface pore structure deteriorates to initially flatten the surface. This is followed by the formation of new pinprick pores that eventually grow into a macroporous film prior to film breakup. Salicylic acid (highly water soluble) and Ibuprofen (sparingly water soluble) were chosen as model drug compounds to characterize release rates, which are higher in films of the breath figure morphology rather than in non-porous films. The results are of significance in the design of biodegradable films used as coatings to modulate delivery.},
	number = {2},
	urldate = {2015-11-22},
	journal = {Biomatter},
	author = {Ponnusamy, Thiruselvam and Lawson, Louise B. and Freytag, Lucy C. and Blake, Diane A. and Ayyala, Ramesh S. and John, Vijay T.},
	month = apr,
	year = {2012},
	pmid = {23507805},
	pmcid = {PMC3549860},
	pages = {77--86},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TDEIBB8Z/Ponnusamy et al. - 2012 - In vitro degradation and release characteristics o.pdf:application/pdf}
}

@article{wang_automatic_2016,
	title = {Automatic cell nuclei segmentation and classification of breast cancer histopathology images},
	volume = {122},
	issn = {0165-1684},
	url = {http://www.sciencedirect.com/science/article/pii/S0165168415003916},
	doi = {10.1016/j.sigpro.2015.11.011},
	abstract = {Breast cancer is the leading type of malignant tumor observed in women and the effective treatment depends on its early diagnosis. Diagnosis from histopathological images remains the "gold standard" for breast cancer. The complexity of breast cell histopathology (BCH) images makes reliable segmentation and classification hard. In this paper, an automatic quantitative image analysis technique of BCH images is proposed. For the nuclei segmentation, top-bottom hat transform is applied to enhance image quality. Wavelet decomposition and multi-scale region-growing (WDMR) are combined to obtain regions of interest (ROIs) thereby realizing precise location. A double-strategy splitting model (DSSM) containing adaptive mathematical morphology and Curvature Scale Space (CSS) corner detection method is applied to split overlapped cells for better accuracy and robustness. For the classification of cell nuclei, 4 shape-based features and 138 textural features based on color spaces are extracted. Optimal feature set is obtained by support vector machine (SVM) with chain-like agent genetic algorithm (CAGA). The proposed method was tested on 68 BCH images containing more than 3600 cells. Experimental results show that the mean segmentation sensitivity was 91.53\% (±4.05\%) and specificity was 91.64\% (±4.07\%). The classification performance of normal and malignant cell images can achieve 96.19\% (±0.31\%) for accuracy, 99.05\% (±0.27\%) for sensitivity and 93.33\% (±0.81\%) for specificity.},
	urldate = {2016-06-30},
	journal = {Signal Processing},
	author = {Wang, Pin and Hu, Xianling and Li, Yongming and Liu, Qianqian and Zhu, Xinjian},
	month = may,
	year = {2016},
	keywords = {BREAST cancer, Chain-like agent genetic algorithm, Curvature scale space corner detection, nuclei segmentation, Support vector machine classification, Wavelet decomposition},
	pages = {1--13},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GJJ6VPCM/Wang et al. - 2016 - Automatic cell nuclei segmentation and classificat.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P3J8AI87/S0165168415003916.html:text/html}
}

@article{bitoun_brpa_2012,
	title = {{BrpA} {Is} {Involved} in {Regulation} of {Cell} {Envelope} {Stress} {Responses} in {Streptococcus} mutans},
	volume = {78},
	issn = {0099-2240},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318800/},
	doi = {10.1128/AEM.07823-11},
	abstract = {Previous studies have shown that BrpA plays a major role in acid and oxidative stress tolerance and biofilm formation by Streptococcus mutans. Mutant strains lacking BrpA also display increased autolysis and decreased viability, suggesting a role for BrpA in cell envelope integrity. In this study, we examined the impact of BrpA deficiency on cell envelope stresses induced by envelope-active antimicrobials. Compared to the wild-type strain UA159, the BrpA-deficient mutant (TW14D) was significantly more susceptible to antimicrobial agents, especially lipid II inhibitors. Several genes involved in peptidoglycan synthesis were identified by DNA microarray analysis as downregulated in TW14D. Luciferase reporter gene fusion assays also revealed that expression of brpA is regulated in response to environmental conditions and stresses induced by exposure to subinhibitory concentrations of cell envelope antimicrobials. In a Galleria mellonella (wax worm) model, BrpA deficiency was shown to diminish the virulence of S. mutans OMZ175, which, unlike S. mutans UA159, efficiently kills the worms. Collectively, these results suggest that BrpA plays a role in the regulation of cell envelope integrity and that deficiency of BrpA adversely affects the fitness and diminishes the virulence of OMZ175, a highly invasive strain of S. mutans.},
	number = {8},
	urldate = {2014-11-07},
	journal = {Applied and Environmental Microbiology},
	author = {Bitoun, J. P. and Liao, S. and Yao, X. and Ahn, S.-J. and Isoda, R. and Nguyen, A. H. and Brady, L. J. and Burne, R. A. and Abranches, J. and Wen, Z. T.},
	month = apr,
	year = {2012},
	pmid = {22327589},
	pmcid = {PMC3318800},
	pages = {2914--2922},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VB88JGX8/Bitoun et al. - 2012 - BrpA Is Involved in Regulation of Cell Envelope St.pdf:application/pdf}
}

@article{leze_advantages_2014,
	title = {Advantages of {Evaluating} {Mean} {Nuclear} {Volume} as an {Adjunct} {Parameter} in {Prostate} {Cancer}},
	volume = {9},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102156},
	doi = {10.1371/journal.pone.0102156},
	abstract = {Background   Efforts to improve the diagnosis, prognosis and surveillance of prostate cancer (PCa) are relevant. Gleason score (GSc) overestimation may subject individuals to unnecessary aggressive treatment. We aimed to use stereology in PCa evaluations and investigate whether mean nuclear volume (MNV) correlates with the Gleason primary pattern (Gpp) and to improve the subjective GSc to obtain an objective and reliable method without inter-observer dissension.      Methods   We identified 74 radical prostatectomy specimens that were divided into six groups based on Gpp, from 3 to 5. Controls (C) were designed in paired non-tumor regions of the same specimens. MNV was estimated using the “point-sampled intercepts” method. Differences in MNV among the C groups and the Gpp groups were tested with the Kruskall-Wallis test and Dunn post-hoc test. Differences between each Gpp group and its control counterpart were tested with the Wilcoxon test. Correlations were evaluated with the Spearman rank correlation (R [Spearman] ).      Results   The correlations between prostate-specific antigen (PSA) and GSc (R [Spearman]  of 0.76) and between PSA and MNV (R [Spearman]  of 0.78) were moderately strong and highly significant, and the correlation between MNV and Gpp (R [Spearman]  of 0.53) was moderate and highly significant. MNV was significantly greater in cancerous regions than in paired-control regions. Limitations included sample size.      Conclusions   Proper planning of a study, as well as the availability of equipment and software for morphological quantification, can provide incentive to quickly and accurately estimate MNV as an adjunct parameter in the assessment of PCa. Current data are in favor of the use of MNV associated with GSc and PSA in the assessment of PCa.},
	number = {7},
	urldate = {2016-04-22},
	journal = {PLOS ONE},
	author = {Leze, Eduardo and Maciel-Osorio, Clarice F. E. and Mandarim-de-Lacerda, Carlos A.},
	month = jul,
	year = {2014},
	keywords = {Biopsy, Brazil, Cancer detection and diagnosis, Histology, Pathologists, Prognosis, PROSTATE cancer, Radical prostatectomy},
	pages = {e102156},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/433SSSJW/Leze et al. - 2014 - Advantages of Evaluating Mean Nuclear Volume as an.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UP9GAB36/article.html:text/html}
}

@article{sood_comparative_2013,
	title = {Comparative {Study} of {Cytomorphological} {Robinson}'s {Grading} for {Breast} {Carcinoma} with {Modified} {Bloom}-{Richardson} {Histopathological} {Grading}},
	volume = {2013},
	issn = {2090-8091},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800647/},
	doi = {10.1155/2013/146542},
	abstract = {Objective. To study the correlation of cytomorphological Robinson's grading for breast cancers with a modified Bloom-Richardson histopathological grading. Materials and Methods. One hundred sixteen cytologically malignant breast tumour cases were included in this study and correlated with paraffin embedded sections. Breast lumps were varied from less than 1 cm to 11 cm in greatest dimension. FNA was performed from different sites of the breast lump, and smears were stained with Giemsa and H\&E stain and evaluated for cytological grading according to Robinson's grading system. Paraffin embedded tissue sections were stained with hematoxylin and eosin stain and graded according to modified Bloom-Richardson grading system. Comparison between these two grading systems was done. Results. Cytologically grade I, grade II, and grade III cases were 13.8\%, 64.65\%, and 21.55\%, respectively. Histologically 25\%, 54.31\%, and 20.69\% cases were grade I, grade II, and grade III, respectively. Concordance rate between cytology and histology of grade I, grade II, and grade III tumors was 75\%, 70.67\%, and 60\% respectively. The absolute concordance rate was 68.97\%. Conclusion. In the era of multiple treatment modalities and neoadjuvant therapy, cytological grading can be used as a prognostic factor for better management of patients.},
	urldate = {2016-06-25},
	journal = {Pathology Research International},
	author = {Sood, Neelam and Nigam, Jitendra Singh and Yadav, Poonam and Rewri, Shivani and Sharma, Ankit and Omhare, Anita and Malhotra, Jaya},
	year = {2013},
	pmid = {24187646},
	pmcid = {PMC3800647},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C7NQ3DKK/Sood et al. - 2013 - Comparative Study of Cytomorphological Robinson's .pdf:application/pdf}
}

@article{shamir_pattern_2010,
	title = {Pattern {Recognition} {Software} and {Techniques} for {Biological} {Image} {Analysis}},
	volume = {6},
	issn = {1553-734X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991255/},
	doi = {10.1371/journal.pcbi.1000974},
	abstract = {The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.},
	number = {11},
	urldate = {2016-07-04},
	journal = {PLoS Computational Biology},
	author = {Shamir, Lior and Delaney, John D. and Orlov, Nikita and Eckley, D. Mark and Goldberg, Ilya G.},
	month = nov,
	year = {2010},
	pmid = {21124870},
	pmcid = {PMC2991255},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WDDNVBB8/Shamir et al. - 2010 - Pattern Recognition Software and Techniques for Bi.pdf:application/pdf}
}

@article{arenas_morphometric_2001,
	title = {Morphometric evaluation of the human prostate},
	volume = {24},
	issn = {1365-2605},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2605.2001.00267.x/abstract},
	doi = {10.1046/j.1365-2605.2001.00267.x},
	abstract = {In order to clarify the ageing-related histological changes in the human prostate, a quantitative morphometric analysis was performed. Complete prostates were obtained at autopsy from 281 men (aged 20–84 years) who died in traffic accidents and presented no clinical symptoms of prostatic disease. The prostates were classified as: histologically normal (n=182), with nodular hyperplasia (n=42), with intraepithelial neoplasia (n=40) and carcinomatous with low Gleason grade (n=20). Each prostate was divided into three regions (periurethral, central and peripheral) and the volume of each region, as well as the average volume occupied by stroma and epithelium in each region were quantified. For each parameter, the average values for each age group were compared. In the histologically normal prostates, an increase with ageing in the total volume and the volume occupied by the central region were observed; these increases were mainly caused by an increase in the stromal volume of the central region in men after 30 years of age. No histologically normal prostates were found in men older than 70 years of age. Nodular prostatic hyperplasia was found in men over 30 years of age and a fluctuation in the total volume throughout ageing was observed. Prostates with intraepithelial neoplasia (PIN) and carcinoma were observed in men aged {\textgreater}20 years and the total volume and those of each prostatic region showed multiple variations, except for the eighth decade where a marked increase with regard to that of the previous decades was observed.},
	language = {en},
	number = {1},
	urldate = {2016-04-21},
	journal = {International Journal of Andrology},
	author = {Arenas, María I and Romo, Eva and Royuela, Mar and Ruiz, Antonio and Fraile, Benito and Sánchez-Chapado, Manuel and Paniagua, Ricardo},
	month = feb,
	year = {2001},
	keywords = {Ageing, morphometry, normal prostate},
	pages = {37--47},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZD865AH5/Arenas et al. - 2001 - Morphometric evaluation of the human prostate.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/J3CQ3FCH/abstract.html:text/html}
}

@article{wilke_rapid_2009,
	title = {Rapid {Non}-invasive {Optical} {Imaging} of {Tissue} {Composition} in {Breast} {Tumor} {Margins}},
	volume = {198},
	issn = {0002-9610},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764289/},
	doi = {10.1016/j.amjsurg.2009.06.018},
	abstract = {Optical spectral imaging has the ability to identify differences between benign and malignant tissue in breast tumor margins. The use of this rapid, non-destructive technology could help reduce the need for second operations in women desiring breast conservation therapy (BCT).},
	number = {4},
	urldate = {2016-06-22},
	journal = {American journal of surgery},
	author = {Wilke, Lee G. and Brown, J. Quincy and Bydlon, Torre M. and Kennedy, Stephanie A. and Richards, Lisa M. and Junker, Marlee K. and Gallagher, Jennifer and Barry, William T. and Geradts, Joseph and Ramanujam, Nimmi},
	month = oct,
	year = {2009},
	pmid = {19800470},
	pmcid = {PMC2764289},
	pages = {566--574},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PQ9ZCS92/Wilke et al. - 2009 - Rapid Non-invasive Optical Imaging of Tissue Compo.pdf:application/pdf}
}

@article{chan_extent_2001,
	title = {Extent of excision margin width required in breast conserving surgery for ductal carcinoma in situ},
	volume = {91},
	copyright = {Copyright © 2001 American Cancer Society},
	issn = {1097-0142},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/1097-0142(20010101)91:1<9::AID-CNCR2>3.0.CO;2-E/abstract},
	doi = {10.1002/1097-0142(20010101)91:1<9::AID-CNCR2>3.0.CO;2-E},
	abstract = {BACKGROUND
Breast conserving surgery (BCS) is common practice for unifocal ductal carcinoma in situ (DCIS) less than 4 cm in size, but the extent of tumor free margin width around DCIS necessary to minimize recurrence is unclear.
METHODS
Clinical and pathologic details were recorded from all patients with pure DCIS {\textless} 4 cm in size, treated with BCS between 1978 and 1997. Histologic margins were measured by using an ocular micrometer. Patients with clear margins ({\textgreater} 1 mm) were divided up into 3 groups for analysis based on margin of normal tissue excised: 1.1–5 mm, 5.1–10 mm, and 10.1–40 mm.
RESULTS
There were 66 patients with close margins (≤ 1 mm), of which 25 cases (37.9\%) recurred. The recurrence rates for the 3 clear margin groups ranged from 4.5–7.1\%. Median followup was 47 months (range 12–197 mos). Risk of recurrence in the group with close margins was greater than the subgroups with clear margins (P {\textless} 0.001); no differences in recurrence was seen between the individual subgroups with clear margins. Nuclear Grade 3 was predictive of recurrence (P = 0.03). Following excision alone, the recurrence rate was 18.6\%, compared with 11.1\% when radiotherapy was given as adjuvant therapy. Women with clear margins following excision had a recurrence rate of only 8.1\%.
CONCLUSION
After BCS for DCIS, close margins were associated with a high risk of local recurrence. Radiotherapy did not compensate for inadequate surgical clearance. Cancer 2001;91:9–16. © 2001 American Cancer Society.},
	language = {en},
	number = {1},
	urldate = {2016-06-22},
	journal = {Cancer},
	author = {Chan, Kai C. and Knox, W. Fiona and Sinha, Guria and Gandhi, Ashu and Barr, Lester and Baildam, Andrew D. and Bundred, Nigel J.},
	month = jan,
	year = {2001},
	keywords = {adjuvant therapy, breast-conserving surgery (BCS), ductal carcinoma in situ (DCIS), margin clearance},
	pages = {9--16},
	file = {2_ftp.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8AMK8ZXZ/2_ftp.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/777EZZWZ/abstract.html:text/html}
}

@book{scholkopf_advances_1999,
	address = {Cambridge, Mass},
	title = {Advances in kernel methods: support vector learning},
	isbn = {978-0-262-19416-7},
	shorttitle = {Advances in kernel methods},
	publisher = {MIT Press},
	editor = {Schölkopf, Bernhard and Burges, Christopher J. C. and Smola, Alexander J.},
	year = {1999},
	keywords = {Algorithms, Kernel functions, Machine learning},
	file = {cuSVMDesc.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/R938256A/cuSVMDesc.pdf:application/pdf}
}

@article{ford_fast_2012,
	title = {Fast optically sectioned fluorescence {HiLo} endomicroscopy},
	volume = {17},
	issn = {1083-3668},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382350/},
	doi = {10.1117/1.JBO.17.2.021105},
	abstract = {We describe a nonscanning, fiber bundle endomicroscope that performs optically sectioned fluorescence imaging with fast frame rates and real-time processing. Our sectioning technique is based on HiLo imaging, wherein two widefield images are acquired under uniform and structured illumination and numerically processed to reject out-of-focus background. This work is an improvement upon an earlier demonstration of widefield optical sectioning through a flexible fiber bundle. The improved device features lateral and axial resolutions of 2.6 and 17 μm, respectively, a net frame rate of 9.5 Hz obtained by real-time image processing with a graphics processing unit (GPU) and significantly reduced motion artifacts obtained by the use of a double-shutter camera. We demonstrate the performance of our system with optically sectioned images and videos of a fluorescently labeled chorioallantoic membrane (CAM) in the developing G. gallus embryo. HiLo endomicroscopy is a candidate technique for low-cost, high-speed clinical optical biopsies.},
	number = {2},
	urldate = {2016-06-22},
	journal = {Journal of Biomedical Optics},
	author = {Ford, Tim N. and Lim, Daryl and Mertz, Jerome},
	month = feb,
	year = {2012},
	pmid = {22463023},
	pmcid = {PMC3382350},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9FPNHJS8/Ford et al. - 2012 - Fast optically sectioned fluorescence HiLo endomic.pdf:application/pdf}
}

@article{schlichenmeyer_video-rate_2014-1,
	title = {Video-rate structured illumination microscopy for high-throughput imaging of large tissue areas},
	volume = {5},
	issn = {2156-7085},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920869/},
	doi = {10.1364/BOE.5.000366},
	abstract = {We report the development of a structured illumination microscopy instrument specifically designed for the requirements for high-area-throughput, optically-sectioned imaging of large, fluorescently-stained tissue specimens. The system achieves optical sectioning frame-rates of up to 33 Hz (and pixel sampling rates of up to 138.4 MHz), by combining a fast, ferroelectric spatial light modulator for pattern generation with the latest large-format, high frame-rate scientific CMOS camera technology. Using a 10X 0.45 NA objective and a 7 mm/sec scan stage, we demonstrate 4.4 cm2/min area-throughput rates in bright tissue-simulating phantoms, and 2 cm2/min area-throughput rates in thick, highly-absorbing, fluorescently-stained muscle tissue, with 1.3 μm lateral resolution. We demonstrate high-contrast, high-resolution imaging of a fluorescently-stained 30.4 cm2 bovine muscle specimen in 15 minutes comprising 7.55 gigapixels, demonstrating the feasibility of the approach for gigapixel imaging of large tissues in short timeframes, such as would be needed for intraoperative imaging of tumor resection specimens.},
	number = {2},
	urldate = {2016-05-06},
	journal = {Biomedical Optics Express},
	author = {Schlichenmeyer, Tyler C. and Wang, Mei and Elfer, Katherine N. and Brown, J. Quincy},
	month = jan,
	year = {2014},
	pmid = {24575333},
	pmcid = {PMC3920869},
	pages = {366--377},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FEBZ29E9/Schlichenmeyer et al. - 2014 - Video-rate structured illumination microscopy for .pdf:application/pdf}
}

@misc{_grade_????,
	title = {Grade of {Breast} {Cancer}},
	url = {http://pathology.jhu.edu/breast/grade.php},
	urldate = {2016-06-25},
	file = {Grade of Breast Cancer:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/P7ETRZGS/grade.html:text/html}
}

@article{hickey_simulated_2012,
	title = {Simulated {Data} for {Genomic} {Selection} and {Genome}-{Wide} {Association} {Studies} {Using} a {Combination} of {Coalescent} and {Gene} {Drop} {Methods}},
	volume = {2},
	issn = {, 2160-1836},
	url = {http://www.g3journal.org/content/2/4/425},
	doi = {10.1534/g3.111.001297},
	abstract = {An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quantitative trait loci effects, and with sequence and single nucleotide polymorphism-phased alleles and genotypes. Ten replicates of a representative scenario used to study genomic selection in livestock were generated and have been made publically available. The simulated data sets were structured to encompass a spectrum of additive quantitative trait loci effect distributions, relationship structures, and single nucleotide polymorphism chip densities.},
	language = {en},
	number = {4},
	urldate = {2015-02-10},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Hickey, John M. and Gorjanc, Gregor},
	month = apr,
	year = {2012},
	pmid = {22540033},
	keywords = {genome-wide association studies (GWAS), GenPred, pedigrees, quantitative trait loci (QTL), shared data resources, simulation method},
	pages = {425--427},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2JX2EN4S/Hickey and Gorjanc - 2012 - Simulated Data for Genomic Selection and Genome-Wi.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZX2VX8BI/Hickey and Gorjanc - 2012 - Simulated Data for Genomic Selection and Genome-Wi.html:text/html}
}

@article{shah_pathogenesis_2014,
	title = {Pathogenesis, prevention, diagnosis and treatment of breast cancer},
	volume = {5},
	issn = {2218-4333},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127601/},
	doi = {10.5306/wjco.v5.i3.283},
	abstract = {Breast cancer is the most common cancer affecting women worldwide. Prediction models stratify a woman’s risk for developing cancer and can guide screening recommendations based on the presence of known and quantifiable hormonal, environmental, personal, or genetic risk factors. Mammography remains the mainstay breast cancer screening and detection but magnetic resonance imaging and ultrasound have become useful diagnostic adjuncts in select patient populations. The management of breast cancer has seen much refinement with increased specialization and collaboration with multidisciplinary teams that include surgeons, oncologists, radiation oncologists, nurses, geneticist, reconstructive surgeons and patients. Evidence supports a less invasive surgical approach to the staging and management of the axilla in select patients. In the era of patient/tumor specific management, the advent of molecular and genomic profiling is a paradigm shift in the treatment of a biologically heterogenous disease.},
	number = {3},
	urldate = {2016-06-23},
	journal = {World Journal of Clinical Oncology},
	author = {Shah, Rupen and Rosso, Kelly and Nathanson, S David},
	month = aug,
	year = {2014},
	pmid = {25114845},
	pmcid = {PMC4127601},
	pages = {283--298},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5M34KN5I/5M34KN5I.pdf:application/pdf}
}

@article{doyle_cascaded_2012,
	title = {Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: {Gleason} grading of prostate cancer},
	volume = {13},
	copyright = {2012 Doyle et al.; licensee BioMed Central Ltd.},
	issn = {1471-2105},
	shorttitle = {Cascaded discrimination of normal, abnormal, and confounder classes in histopathology},
	url = {http://www.biomedcentral.com/1471-2105/13/282/abstract},
	doi = {10.1186/1471-2105-13-282},
	abstract = {Automated classification of histopathology involves identification of multiple classes, including benign, cancerous, and confounder categories. The confounder tissue classes can often mimic and share attributes with both the diseased and normal tissue classes, and can be particularly difficult to identify, both manually and by automated classifiers. In the case of prostate cancer, they may be several confounding tissue types present in a biopsy sample, posing as major sources of diagnostic error for pathologists. Two common multi-class approaches are one-shot classification (OSC), where all classes are identified simultaneously, and one-versus-all (OVA), where a “target” class is distinguished from all “non-target” classes. OSC is typically unable to handle discrimination of classes of varying similarity (e.g. with images of prostate atrophy and high grade cancer), while OVA forces several heterogeneous classes into a single “non-target” class. In this work, we present a cascaded (CAS) approach to classifying prostate biopsy tissue samples, where images from different classes are grouped to maximize intra-group homogeneity while maximizing inter-group heterogeneity.},
	language = {en},
	number = {1},
	urldate = {2015-11-30},
	journal = {BMC Bioinformatics},
	author = {Doyle, Scott and Feldman, Michael D. and Shih, Natalie and Tomaszewski, John and Madabhushi, Anant},
	month = oct,
	year = {2012},
	pmid = {23110677},
	pages = {282},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UJIU8U7S/Doyle et al. - 2012 - Cascaded discrimination of normal, abnormal, and c.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/VE9FMWDT/282.html:text/html}
}

@article{price_cancer_2012,
	title = {Cancer hospitalizations for adults, 2009},
	url = {http://www.ncbi.nlm.nih.gov/books/NBK92614/?report=printable},
	urldate = {2016-07-04},
	author = {Price, Rebecca Anhang and Stranges, Elizabeth and Elixhauser, Anne},
	year = {2012},
	file = {sb125.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/D77HQQEN/sb125.pdf:application/pdf}
}

@article{nguyen_prostate_2012,
	series = {Special {Issue} on {Awards} from {ICPR} 2010},
	title = {Prostate cancer grading: {Gland} segmentation and structural features},
	volume = {33},
	issn = {0167-8655},
	shorttitle = {Prostate cancer grading},
	url = {http://www.sciencedirect.com/science/article/pii/S0167865511003230},
	doi = {10.1016/j.patrec.2011.10.001},
	abstract = {In this paper, we introduce a novel approach to grade prostate malignancy using digitized histopathological specimens of the prostate tissue. Most of the approaches proposed in the literature to address this problem utilize various textural features computed from the prostate tissue image. Our approach differs in that we only focus on the tissue structure and the well-known Gleason grading system specification. The color space representing the tissue image is investigated and basic components of the prostate tissue are detected. The components and their structural relationship constitute a complete gland region. Tissue structural features extracted from gland morphology are used to classify a tissue pattern into three major categories: benign, grade 3 carcinoma and grade 4 carcinoma. Our experiments show that the proposed method outperforms a texture-based method in the three-class classification problem and most of the two-class classification problems except for the grade 3 vs grade 4 classification. Based on these results, we propose a hierarchical (binary) classification scheme which utilizes the two methods and obtains 85.6\% accuracy in classifying an input tissue pattern into one of the three classes.},
	number = {7},
	urldate = {2016-04-21},
	journal = {Pattern Recognition Letters},
	author = {Nguyen, Kien and Sabata, Bikash and Jain, Anil K.},
	month = may,
	year = {2012},
	keywords = {Benign, Carcinoma, Gland segmentation, Gleason grading system, Nuclei, PROSTATE cancer},
	pages = {951--961},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KCZQFQUQ/Nguyen et al. - 2012 - Prostate cancer grading Gland segmentation and st.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5DW8VAFU/S0167865511003230.html:text/html}
}

@article{van_zee_relationship_2015,
	title = {Relationship {Between} {Margin} {Width} and {Recurrence} of {Ductal} {Carcinoma} {In} {Situ}: {Analysis} of 2996 {Women} {Treated} {With} {Breast}-conserving {Surgery} for 30 {Years}},
	issn = {0003-4932},
	shorttitle = {Relationship {Between} {Margin} {Width} and {Recurrence} of {Ductal} {Carcinoma} {In} {Situ}},
	url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage&an=00000658-900000000-97242},
	doi = {10.1097/SLA.0000000000001454},
	language = {en},
	urldate = {2016-06-22},
	journal = {Annals of Surgery},
	author = {Van Zee, Kimberly J. and Subhedar, Preeti and Olcese, Cristina and Patil, Sujata and Morrow, Monica},
	month = oct,
	year = {2015},
	pages = {1},
	file = {00000658-201510000-00008.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PWBQQE74/00000658-201510000-00008.pdf:application/pdf}
}

@article{choi_comparison_2016,
	title = {Comparison of ipsilateral breast tumor recurrence after breast-conserving surgery between ductal carcinoma in situ and invasive breast cancer},
	volume = {14},
	issn = {1477-7819},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848787/},
	doi = {10.1186/s12957-016-0885-6},
	abstract = {Background
We aimed to evaluate the differences in the rates and predictive factors for ipsilateral breast tumor recurrence (IBTR) after breast-conserving surgery (BCS) between ductal carcinoma in situ (DCIS) and invasive breast cancer. And, we evaluated the impact of IBTR on overall survival and distant metastasis.

Methods
We retrospectively reviewed 322 consecutive patients with DCIS or invasive breast cancer who underwent BCS between 2004 and 2010. We evaluated the rates of IBTR of DCIS and invasive breast cancer. Univariate and multivariate analyses were performed to determine the predictive factors for IBTR, and survival rates were analyzed with Kaplan-Meier estimates.

Results
With a median follow-up period of 57 months, 5 (10 \%) out of 50 DCIS patients and 14 (5.1 \%) out of 272 invasive cancer patients had developed IBTR. Factors associated with IBTR on univariate and multivariate analyses were positive resection margin status in DCIS and omission of radiotherapy in invasive cancer, respectively. The hormone receptor negativity was strong independent predictive factors for IBTR in both DCIS and invasive breast cancer. Although the differences of survival curve did not reach statistical significance, the 5-year overall survival and distant metastasis-free survival of invasive cancer patients who suffered IBTR were inferior to those without (84 vs. 98 \% and 63.3 vs. 96.5 \%, respectively). Advanced initial stage, lymph node metastasis and experience of IBTR were associated with poor overall survival and distant metastasis on univariate and multivariate analyses.

Conclusions
The hormone receptor negativity was revealed as independent predictive factor for IBTR after BCS in both DCIS and invasive cancer. Experience of IBTR was independent prognostic factor for poor overall outcome in patients with invasive breast cancer. Aggressive local control and adjuvant therapy should be made in hormone receptor-negative patients who receive treatment with BCS.},
	urldate = {2016-06-22},
	journal = {World Journal of Surgical Oncology},
	author = {Choi, Young Jin and Shin, Young Duck and Song, Young Jin},
	month = apr,
	year = {2016},
	pmid = {27122132},
	pmcid = {PMC4848787},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9MTXZAHN/Choi et al. - 2016 - Comparison of ipsilateral breast tumor recurrence .pdf:application/pdf}
}

@book{groves_biomarkers_????,
	title = {From {Biomarkers} to {Diagnostics}–{The} {Road} to {Success}},
	url = {http://www.quintiles.com/~/media/library/white%20papers/biomarkers-diagnostics.pdf},
	urldate = {2016-07-04},
	author = {Groves, Eric},
	file = {biomarkers-diagnostics.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2DKMAFUS/biomarkers-diagnostics.pdf:application/pdf}
}

@article{taber_towards_2009-1,
	title = {Towards a unified theory for morphomechanics},
	volume = {367},
	issn = {1364-503X, 1471-2962},
	url = {http://rsta.royalsocietypublishing.org/content/367/1902/3555},
	doi = {10.1098/rsta.2009.0100},
	abstract = {Mechanical forces are closely involved in the construction of an embryo. Experiments have suggested that mechanical feedback plays a role in regulating these forces, but the nature of this feedback is poorly understood. Here, we propose a general principle for the mechanics of morphogenesis, as governed by a pair of evolution equations based on feedback from tissue stress. In one equation, the rate of growth (or contraction) depends on the difference between the current tissue stress and a target (homeostatic) stress. In the other equation, the target stress changes at a rate that depends on the same stress difference. The parameters in these morphomechanical laws are assumed to depend on stress rate. Computational models are used to illustrate how these equations can capture a relatively wide range of behaviours observed in developing embryos, as well as show the limitations of this theory. Specific applications include growth of pressure vessels (e.g. the heart, arteries and brain), wound healing and sea urchin gastrulation. Understanding the fundamental principles of tissue construction can help engineers design new strategies for creating replacement tissues and organs in vitro.},
	language = {en},
	number = {1902},
	urldate = {2014-11-10},
	journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
	author = {Taber, Larry A.},
	month = sep,
	year = {2009},
	pmid = {19657011},
	keywords = {Biomechanics, computational models, development, growth, Mechanobiology, morphogenesis},
	pages = {3555--3583},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NACV4PIV/Taber - 2009 - Towards a unified theory for morphomechanics.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IKMW4FG5/3555.html:text/html}
}

@book{md_cancer_2016,
	address = {Philadelphia},
	edition = {10th ed. edition},
	title = {Cancer of the {Breast}: {From} {Cancer}: {Principles} \& {Practice} of {Oncology}, 10th edition},
	isbn = {978-1-4963-3398-8},
	shorttitle = {Cancer of the {Breast}},
	abstract = {Selected from the world’s leading comprehensive cancer textbook, this tightly focused resource provides you with the practical, cutting-edge information you need to provide the best cancer care to each patient.  Cancer of the Breast: Cancer: Principles \& Practice of Oncology, 10th Edition, offers a comprehensive and balanced view of this rapidly changing field, meeting the needs of oncology practitioners, fellows, and others who need an in-depth understanding of breast cancer. The print reference gives you the solid, dependable guidance you’ve come to expect from this outstanding title, and the Inkling version features new quarterly updates written by a team of experts selected by the authors.Key Features:Delivers focused, comprehensive information on cancer of the breast drawn from the world’s leading cancer textbook, DeVita, Hellman, and Rosenberg’s Cancer:  Principles \& Practice of Oncology.Covers the molecular biology of breast cancer, malignant tumors of the breast, and genetic testing in breast cancer.Discusses in detail the growing importance of prevention and screening, giving you the understanding you need to improve your patients’ chances for a healthier, cancer-free life.Explains how the latest developments in biologic therapy applies to cancer of the breast.Provides exhaustive coverage of combined modality cancer treatment, helping you determine when and how to integrate modalities in patient treatment.Ensures that you’re fully up to date thanks to easy, mobile access to quarterly updates.Now with the print edition, enjoy the bundled interactive eBook edition, which can be downloaded to your tablet and smartphone or accessed online and includes features like:Complete content with enhanced navigationPowerful search tools and smart navigation cross-links that pull results from content in the book, your notes, and even the webCross-linked pages, references, and more for easy navigationHighlighting tool for easier reference of key content throughout the textAbility to take and share notes with friends and colleaguesQuick reference tabbing to save your favorite content for future use},
	language = {English},
	publisher = {Wolters Kluwer},
	editor = {MD, Vincent T. DeVita Jr and PhD, Theodore S. Lawrence MD and PhD, Steven A. Rosenberg MD},
	month = may,
	year = {2016}
}

@article{venthur_pyff_2010,
	title = {Pyff – {A} {Pythonic} {Framework} for {Feedback} {Applications} and {Stimulus} {Presentation} in {Neuroscience}},
	volume = {4},
	issn = {1662-4548},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001756/},
	doi = {10.3389/fnins.2010.00179},
	abstract = {This paper introduces Pyff, the Pythonic feedback framework for feedback applications and stimulus presentation. Pyff provides a platform-independent framework that allows users to develop and run neuroscientific experiments in the programming language Python. Existing solutions have mostly been implemented in C++, which makes for a rather tedious programming task for non-computer-scientists, or in Matlab, which is not well suited for more advanced visual or auditory applications. Pyff was designed to make experimental paradigms (i.e., feedback and stimulus applications) easily programmable. It includes base classes for various types of common feedbacks and stimuli as well as useful libraries for external hardware such as eyetrackers. Pyff is also equipped with a steadily growing set of ready-to-use feedbacks and stimuli. It can be used as a standalone application, for instance providing stimulus presentation in psychophysics experiments, or within a closed loop such as in biofeedback or brain–computer interfacing experiments. Pyff communicates with other systems via a standardized communication protocol and is therefore suitable to be used with any system that may be adapted to send its data in the specified format. Having such a general, open-source framework will help foster a fruitful exchange of experimental paradigms between research groups. In particular, it will decrease the need of reprogramming standard paradigms, ease the reproducibility of published results, and naturally entail some standardization of stimulus presentation.},
	urldate = {2015-02-18},
	journal = {Frontiers in Neuroscience},
	author = {Venthur, Bastian and Scholler, Simon and Williamson, John and Dähne, Sven and Treder, Matthias S. and Kramarek, Maria T. and Müller, Klaus-Robert and Blankertz, Benjamin},
	month = dec,
	year = {2010},
	pmid = {21160550},
	pmcid = {PMC3001756}
}

@article{skala_vivo_2007,
	title = {In vivo multiphoton microscopy of {NADH} and {FAD} redox states, fluorescence lifetimes, and cellular morphology in precancerous epithelia},
	volume = {104},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/104/49/19494},
	doi = {10.1073/pnas.0708425104},
	abstract = {Metabolic imaging of the relative amounts of reduced NADH and FAD and the microenvironment of these metabolic electron carriers can be used to noninvasively monitor changes in metabolism, which is one of the hallmarks of carcinogenesis. This study combines cellular redox ratio, NADH and FAD lifetime, and subcellular morphology imaging in three dimensions to identify intrinsic sources of metabolic and structural contrast in vivo at the earliest stages of cancer development. There was a significant (P {\textless} 0.05) increase in the nuclear to cytoplasmic ratio (NCR) with depth within the epithelium in normal tissues; however, there was no significant change in NCR with depth in precancerous tissues. The redox ratio significantly decreased in the less differentiated basal epithelial cells compared with the more mature cells in the superficial layer of the normal stratified squamous epithelium, indicating an increase in metabolic activity in cells with increased NCR. However, the redox ratio was not significantly different between the superficial and basal cells in precancerous tissues. A significant decrease was observed in the contribution and lifetime of protein-bound NADH (averaged over the entire epithelium) in both low- and high-grade epithelial precancers compared with normal epithelial tissues. In addition, a significant increase in the protein-bound FAD lifetime and a decrease in the contribution of protein-bound FAD are observed in high-grade precancers only. Increased intracellular variability in the redox ratio, NADH, and FAD fluorescence lifetimes were observed in precancerous cells compared with normal cells.},
	language = {en},
	number = {49},
	urldate = {2015-03-06},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Skala, Melissa C. and Riching, Kristin M. and Gendron-Fitzpatrick, Annette and Eickhoff, Jens and Eliceiri, Kevin W. and White, John G. and Ramanujam, Nirmala},
	month = dec,
	year = {2007},
	pmid = {18042710},
	keywords = {diagnosis, imaging, mitochondria, oral cancer},
	pages = {19494--19499},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/S8JKWHNN/Skala et al. - 2007 - In vivo multiphoton microscopy of NADH and FAD red.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HES6E2X5/Skala et al. - 2007 - In vivo multiphoton microscopy of NADH and FAD red.html:text/html}
}

@article{chang_imaging_2015,
	title = {Imaging breast cancer morphology using probe-based confocal laser endomicroscopy: towards a real-time intraoperative imaging tool for cavity scanning},
	volume = {153},
	issn = {0167-6806, 1573-7217},
	shorttitle = {Imaging breast cancer morphology using probe-based confocal laser endomicroscopy},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1007/s10549-015-3543-8},
	doi = {10.1007/s10549-015-3543-8},
	abstract = {Current techniques for assessing the adequacy of tumour excision during breast conserving surgery do not provide real-time direct cytopathological assessment of the internal cavity walls within the breast. This study investigates the ability of probe-based confocal laser endomicroscopy (pCLE), an emerging imaging tool, to image the morphology of neoplastic and non-neoplastic breast tissues, and determines the ability of histopathologists and surgeons to differentiate these images. Freshly excised tumour samples and adjacent non-diseased sections from 50 consenting patients were stained with 0.01 \% acriflavine hydrochloride and imaged using pCLE. All discernible pCLE features were cross-examined with conventional histopathology. Following pattern recognition training, 17 histopathologists and surgeons with no pCLE experience interpreted 50 pCLE images independently whilst blinded to histopathology results. Three-hundred and fifty pCLE image mosaics were analysed. Consistent with histopathology findings, the glandular structures, adipocytes and collagen fibres of normal breast were readily visible on pCLE images. These were distinguishable from the morphological architecture exhibited by invasive and non-invasive carcinoma. The mean accuracy of pCLE image interpretation for histopathologists and surgeons was 94 and 92 \%, respectively. Overall, inter-observer agreement for histopathologists was ‘almost perfect’, κ = 0.82; and ‘substantial’ for surgeons, κ = 0.74. pCLE morphological features of neoplastic and non-neoplastic breast tissues are readily visualized and distinguishable with high accuracy by both histopathologists and surgeons. Further research is required to investigate a potential role for the use of pCLE intraoperatively for in situ detection of residual cancerous foci, thereby guiding operating decision-making based on real-time breast cavity scanning.},
	language = {en},
	number = {2},
	urldate = {2016-06-25},
	journal = {Breast Cancer Research and Treatment},
	author = {Chang, Tou Pin and Leff, Daniel R. and Shousha, Sami and Hadjiminas, Dimitri J. and Ramakrishnan, Rathi and Hughes, Michael R. and Yang, Guang-Zhong and Darzi, Ara},
	month = aug,
	year = {2015},
	pages = {299--310},
	file = {art%3A10.1007%2Fs10549-015-3543-8.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NHCJNSFA/art%3A10.1007%2Fs10549-015-3543-8.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3CAJGH84/s10549-015-3543-8.html:text/html}
}

@book{_frozen_????,
	title = {Frozen {Section} {Library}},
	url = {http://www.springer.com/series/7869},
	abstract = {The Frozen Section Library series provides convenient, user-friendly handbooks for each organ system to expedite use in the hurried frozen section situation. These books are small and light-weight, copiously color illustrated with ...},
	urldate = {2016-06-22},
	file = {9781461407171-c1-2.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T7KVI85K/9781461407171-c1-2.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4U9G4BR2/7869.html:text/html}
}

@article{pleijhuis_tissue-simulating_2014,
	title = {Tissue-simulating {Phantoms} for {Assessing} {Potential} {Near}-infrared {Fluorescence} {Imaging} {Applications} in {Breast} {Cancer} {Surgery}},
	issn = {1940-087X},
	url = {http://www.jove.com/video/51776/tissue-simulating-phantoms-for-assessing-potential-near-infrared},
	doi = {10.3791/51776},
	language = {en},
	number = {91},
	urldate = {2016-06-28},
	journal = {Journal of Visualized Experiments},
	author = {Pleijhuis, Rick and Timmermans, Arwin and De Jong, Johannes and De Boer, Esther and Ntziachristos, Vasilis and Van Dam, Gooitzen},
	month = sep,
	year = {2014}
}

@article{knottnerus_evidence_2002,
	title = {Evidence {Base} {Of} {Clinical} {Diagnosis}: {Evaluation} {Of} {Diagnostic} {Procedures}},
	volume = {324},
	issn = {0959-8138},
	shorttitle = {Evidence {Base} {Of} {Clinical} {Diagnosis}},
	url = {http://www.jstor.org/stable/25227552},
	number = {7335},
	urldate = {2016-07-04},
	journal = {BMJ: British Medical Journal},
	author = {Knottnerus, J. André and van Weel, Chris and Muris, Jean W. M.},
	year = {2002},
	pages = {477--480},
	file = {JSTOR Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/DM4EHTU6/Knottnerus et al. - 2002 - Evidence Base Of Clinical Diagnosis Evaluation Of.pdf:application/pdf}
}

@article{lin_tendon_2005-1,
	title = {Tendon properties in interleukin-4 and interleukin-6 knockout mice},
	volume = {38},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S002192900400140X},
	doi = {10.1016/j.jbiomech.2004.03.008},
	abstract = {Cytokines are known to play an important role in normal tendon development, function, and maintenance through interactions with fibroblasts and extracellular matrix proteins. However, the role of interleukins on normal tendon activity remains poorly understood. Previous studies that have researched the role of specific cytokines by exogenously applying them have often reported conflicting results. Therefore, a knockout mouse model was used to investigate the role of interleukins 4 and 6 on normal tendon organizational and biomechanical properties. It was hypothesized that interleukin-6 knockout (IL6 -/-) mice will display more organized collagen orientation and greater cross-sectional area and mechanical properties when compared to that of control mice. In addition, interleukin-4 knockout (IL4 -/-) mice will display the most disorganized collagen orientation and lowest cross-sectional area and mechanical properties. As hypothesized, IL6 -/- mice show a trend towards lower angular deviation (more organized) (p\&lt;0.1) when compared to IL4 -/- mice. In addition, the IL6 -/- mice show a trend towards a higher percent relaxation (p\&lt;0.1) and a significantly higher modulus (p\&lt;0.01) when compared to CTL and IL4 -/- mice. Unexpectedly, the IL6 -/- mice exhibited no significant differences in collagen fiber distribution and maximum stress from the other groups and actually had a smaller cross-sectional area than CTL mice (p\&lt;0.1). This study supports transgenic mice as an animal model for investigating how cytokines affect normal tendon properties. In addition, this study demonstrates that interleukins may play an important role in tendon development, function, and maintenance.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Lin, Tony W. and Cardenas, Luis and Soslowsky, Louis J.},
	month = jan,
	year = {2005},
	keywords = {Cytokines, Interleukins, Knockout mice, Tendon, Transgenic mice},
	pages = {99--105},
	file = {tendonprop.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/A3GQM3HH/tendonprop.pdf:application/pdf}
}

@article{mueller_rapid_2016,
	title = {Rapid staining and imaging of subnuclear features to differentiate between malignant and benign breast tissues at a point-of-care setting},
	volume = {142},
	issn = {0171-5216, 1432-1335},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1007/s00432-016-2165-9},
	doi = {10.1007/s00432-016-2165-9},
	abstract = {Purpose Histopathology is the clinical standard for tissue diagnosis; however, it requires tissue processing, laboratory personnel and infrastructure, and a highly trained pathologist to diagnose the tissue. Optical microscopy can provide real-time diagnosis, which could be used to inform the management of breast cancer. The goal of this work is to obtain images of tissue morphology through fluorescence microscopy and vital fluorescent stains and to develop a strategy to segment and quantify breast tissue features in order to enable automated tissue diagnosis. Methods We combined acriflavine staining, fluorescence microscopy, and a technique called sparse component analysis to segment nuclei and nucleoli, which are collectively referred to as acriflavine positive features (APFs). A series of variables, which included the density, area fraction, diameter, and spacing of APFs, were quantified from images taken from clinical core needle breast biopsies and used to create a multivariate classification model. The model was developed using a training data set and validated using an independent testing data set. Results The top performing classification model included the density and area fraction of smaller APFs (those less than 7 µm in diameter, which likely correspond to stained nucleoli).When applied to the independent testing set composed of 25 biopsy panels, the model achieved a sensitivity of 82 \%, a specificity of 79 \%, and an overall accuracy of 80 \%. Conclusions These results indicate that our quantitative microscopy toolbox is a potentially viable approach for detecting the presence of malignancy in clinical core needle breast biopsies.},
	language = {en},
	number = {7},
	urldate = {2016-07-07},
	journal = {Journal of Cancer Research and Clinical Oncology},
	author = {Mueller, Jenna L. and Gallagher, Jennifer E. and Chitalia, Rhea and Krieger, Marlee and Erkanli, Alaattin and Willett, Rebecca M. and Geradts, Joseph and Ramanujam, Nimmi},
	month = apr,
	year = {2016},
	pages = {1475--1486},
	file = {art%3A10.1007%2Fs00432-016-2165-9.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GNNZB22I/art%3A10.1007%2Fs00432-016-2165-9.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/94U9UBX6/s00432-016-2165-9.html:text/html}
}

@article{rodriguez_stress-dependent_1994,
	title = {Stress-dependent finite growth in soft elastic tissues},
	volume = {27},
	issn = {0021-9290},
	abstract = {Growth and remodeling in tissues may be modulated by mechanical factors such as stress. For example, in cardiac hypertrophy, alterations in wall stress arising from changes in mechanical loading lead to cardiac growth and remodeling. A general continuum formulation for finite volumetric growth in soft elastic tissues is therefore proposed. The shape change of an unloaded tissue during growth is described by a mapping analogous to the deformation gradient tensor. This mapping is decomposed into a transformation of the local zero-stress reference state and an accompanying elastic deformation that ensures the compatibility of the total growth deformation. Residual stress arises from this elastic deformation. Hence, a complete kinematic formulation for growth in general requires a knowledge of the constitutive law for stress in the tissue. Since growth may in turn be affected by stress in the tissue, a general form for the stress-dependent growth law is proposed as a relation between the symmetric growth-rate tensor and the stress tensor. With a thick-walled hollow cylinder of incompressible, isotropic hyperelastic material as an example, the mechanics of left ventricular hypertrophy are investigated. The results show that transmurally uniform pure circumferential growth, which may be similar to eccentric ventricular hypertrophy, changes the state of residual stress in the heart wall. A model of axially loaded bone is used to test a simple stress-dependent growth law in which growth rate depends on the difference between the stress due to loading and a predetermined growth equilibrium stress.},
	language = {eng},
	number = {4},
	journal = {Journal of Biomechanics},
	author = {Rodriguez, E. K. and Hoger, A. and McCulloch, A. D.},
	month = apr,
	year = {1994},
	pmid = {8188726},
	keywords = {Bone and Bones, Bone Development, Elasticity, Elastic Tissue, Heart, Humans, Hypertrophy, Hypertrophy, Left Ventricular, Mathematics, Models, Biological, Stress, Mechanical},
	pages = {455--467},
	file = {rod.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CRCGMQN2/rod.pdf:application/pdf}
}

@article{figueroa_predicting_2012,
	title = {Predicting sample size required for classification performance},
	volume = {12},
	issn = {1472-6947},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307431/},
	doi = {10.1186/1472-6947-12-8},
	abstract = {Background
Supervised learning methods need annotated data in order to generate efficient models. Annotated data, however, is a relatively scarce resource and can be expensive to obtain. For both passive and active learning methods, there is a need to estimate the size of the annotated sample required to reach a performance target.

Methods
We designed and implemented a method that fits an inverse power law model to points of a given learning curve created using a small annotated training set. Fitting is carried out using nonlinear weighted least squares optimization. The fitted model is then used to predict the classifier's performance and confidence interval for larger sample sizes. For evaluation, the nonlinear weighted curve fitting method was applied to a set of learning curves generated using clinical text and waveform classification tasks with active and passive sampling methods, and predictions were validated using standard goodness of fit measures. As control we used an un-weighted fitting method.

Results
A total of 568 models were fitted and the model predictions were compared with the observed performances. Depending on the data set and sampling method, it took between 80 to 560 annotated samples to achieve mean average and root mean squared error below 0.01. Results also show that our weighted fitting method outperformed the baseline un-weighted method (p {\textless} 0.05).

Conclusions
This paper describes a simple and effective sample size prediction algorithm that conducts weighted fitting of learning curves. The algorithm outperformed an un-weighted algorithm described in previous literature. It can help researchers determine annotation sample size for supervised machine learning.},
	urldate = {2016-07-03},
	journal = {BMC Medical Informatics and Decision Making},
	author = {Figueroa, Rosa L and Zeng-Treitler, Qing and Kandula, Sasikiran and Ngo, Long H},
	month = feb,
	year = {2012},
	pmid = {22336388},
	pmcid = {PMC3307431},
	pages = {8},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZKK2FXBG/Figueroa et al. - 2012 - Predicting sample size required for classification.pdf:application/pdf}
}

@article{okser_regularized_2014,
	title = {Regularized {Machine} {Learning} in the {Genetic} {Prediction} of {Complex} {Traits}},
	volume = {10},
	url = {http://dx.doi.org/10.1371/journal.pgen.1004754},
	doi = {10.1371/journal.pgen.1004754},
	number = {11},
	urldate = {2015-02-18},
	journal = {PLoS Genet},
	author = {Okser, Sebastian and Pahikkala, Tapio and Airola, Antti and Salakoski, Tapio and Ripatti, Samuli and Aittokallio, Tero},
	month = nov,
	year = {2014},
	pages = {e1004754},
	file = {PLoS Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/PW5CWRJ9/Okser et al. - 2014 - Regularized Machine Learning in the Genetic Predic.pdf:application/pdf}
}

@article{veltri_nuclear_2012,
	title = {Nuclear morphometry, nucleomics and prostate cancer progression},
	volume = {14},
	issn = {1745-7262},
	doi = {10.1038/aja.2011.148},
	abstract = {Prostate cancer (PCa) results from a multistep process. This process includes initiation, which occurs through various aging events and multiple insults (such as chronic infection, inflammation and genetic instability through reactive oxygen species causing DNA double-strand breaks), followed by a multistep process of progression. These steps include several genetic and epigenetic alterations, as well as alterations to the chromatin structure, which occur in response to the carcinogenic stress-related events that sustain proliferative signaling. Events such as evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis are readily observed. In addition, in conjunction with these critical drivers of carcinogenesis, other factors related to the etiopathogenesis of PCa, involving energy metabolism and evasion of the immune surveillance system, appear to be involved. In addition, when cancer spread and metastasis occur, the 'tumor microenvironment' in the bone of PCa patients may provide a way to sustain dormancy or senescence and eventually establish a 'seed and soil' site where PCa proliferation and growth may occur over time. When PCa is initiated and progression ensues, significant alterations in nuclear size, shape and heterochromatin (DNA transcription) organization are found, and key nuclear transcriptional and structural proteins, as well as multiple nuclear bodies can lead to precancerous and malignant changes. These series of cellular and tissue-related malignancy-associated events can be quantified to assess disease progression and management.},
	language = {eng},
	number = {3},
	journal = {Asian Journal of Andrology},
	author = {Veltri, Robert W. and Christudass, Christhunesa S. and Isharwal, Sumit},
	month = may,
	year = {2012},
	pmid = {22504875},
	pmcid = {PMC3720156},
	keywords = {Cell Nucleus, Disease Progression, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic, Heterochromatin, Humans, Image Processing, Computer-Assisted, Immunologic Surveillance, Male, Prognosis, Prostate, Prostatic Neoplasms, Tumor Markers, Biological, Watchful Waiting},
	pages = {375--384},
	file = {Veltri et al Asian J Androl 2012.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C7WUSN5F/C7WUSN5F.pdf:application/pdf}
}

@article{patel_ocular_2013,
	title = {Ocular drug delivery systems: {An} overview},
	volume = {2},
	issn = {2220-3192},
	shorttitle = {Ocular drug delivery systems},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289909/},
	doi = {10.5497/wjp.v2.i2.47},
	abstract = {The major challenge faced by today’s pharmacologist and formulation scientist is ocular drug delivery. Topical eye drop is the most convenient and patient compliant route of drug administration, especially for the treatment of anterior segment diseases. Delivery of drugs to the targeted ocular tissues is restricted by various precorneal, dynamic and static ocular barriers. Also, therapeutic drug levels are not maintained for longer duration in target tissues. In the past two decades, ocular drug delivery research acceleratedly advanced towards developing a novel, safe and patient compliant formulation and drug delivery devices/techniques, which may surpass these barriers and maintain drug levels in tissues. Anterior segment drug delivery advances are witnessed by modulation of conventional topical solutions with permeation and viscosity enhancers. Also, it includes development of conventional topical formulations such as suspensions, emulsions and ointments. Various nanoformulations have also been introduced for anterior segment ocular drug delivery. On the other hand, for posterior ocular delivery, research has been immensely focused towards development of drug releasing devices and nanoformulations for treating chronic vitreoretinal diseases. These novel devices and/or formulations may help to surpass ocular barriers and associated side effects with conventional topical drops. Also, these novel devices and/or formulations are easy to formulate, no/negligibly irritating, possess high precorneal residence time, sustain the drug release, and enhance ocular bioavailability of therapeutics. An update of current research advancement in ocular drug delivery necessitates and helps drug delivery scientists to modulate their think process and develop novel and safe drug delivery strategies. Current review intends to summarize the existing conventional formulations for ocular delivery and their advancements followed by current nanotechnology based formulation developments. Also, recent developments with other ocular drug delivery strategies employing in situ gels, implants, contact lens and microneedles have been discussed.},
	number = {2},
	urldate = {2015-11-22},
	journal = {World journal of pharmacology},
	author = {Patel, Ashaben and Cholkar, Kishore and Agrahari, Vibhuti and Mitra, Ashim K},
	year = {2013},
	pmid = {25590022},
	pmcid = {PMC4289909},
	pages = {47--64},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JATU9FBB/Patel et al. - 2013 - Ocular drug delivery systems An overview.pdf:application/pdf}
}

@article{_surgery_2014,
	title = {Surgery},
	volume = {50},
	issn = {0959-8049},
	url = {http://www.sciencedirect.com/science/article/pii/S0959804914700942},
	doi = {10.1016/S0959-8049(14)70094-2},
	urldate = {2016-06-22},
	journal = {European Journal of Cancer},
	month = mar,
	year = {2014},
	pages = {S123--S159},
	file = {marg.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/QFPMP7G7/marg.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RQVDF7UH/S0959804914700942.html:text/html}
}

@article{ueo_rapid_2015,
	title = {Rapid intraoperative visualization of breast lesions with γ-glutamyl hydroxymethyl rhodamine green},
	volume = {5},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep12080},
	doi = {10.1038/srep12080},
	urldate = {2016-06-22},
	journal = {Scientific Reports},
	author = {Ueo, Hiroki and Shinden, Yoshiaki and Tobo, Taro and Gamachi, Ayako and Udo, Mitsuaki and Komatsu, Hisateru and Nambara, Sho and Saito, Tomoko and Ueda, Masami and Hirata, Hidenari and Sakimura, Shotaro and Takano, Yuki and Uchi, Ryutaro and Kurashige, Junji and Akiyoshi, Sayuri and Iguchi, Tomohiro and Eguchi, Hidetoshi and Sugimachi, Keishi and Kubota, Yoko and Kai, Yuichiro and Shibuta, Kenji and Kijima, Yuko and Yoshinaka, Heiji and Natsugoe, Shoji and Mori, Masaki and Maehara, Yoshihiko and Sakabe, Masayo and Kamiya, Mako and Kakareka, John W. and Pohida, Thomas J. and Choyke, Peter L. and Kobayashi, Hisataka and Ueo, Hiroaki and Urano, Yasuteru and Mimori, Koshi},
	month = jul,
	year = {2015},
	pages = {12080},
	file = {srep12080.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/I4469XW2/srep12080.pdf:application/pdf}
}

@article{hsieh_design_2011,
	title = {Design {Ensemble} {Machine} {Learning} {Model} for {Breast} {Cancer} {Diagnosis}},
	volume = {36},
	issn = {0148-5598, 1573-689X},
	url = {http://link.springer.com/article/10.1007/s10916-011-9762-6},
	doi = {10.1007/s10916-011-9762-6},
	abstract = {In this paper, we classify the breast cancer of medical diagnostic data. Information gain has been adapted for feature selections. Neural fuzzy (NF), k-nearest neighbor (KNN), quadratic classifier (QC), each single model scheme as well as their associated, ensemble ones have been developed for classifications. In addition, a combined ensemble model with these three schemes has been constructed for further validations. The experimental results indicate that the ensemble learning performs better than individual single ones. Moreover, the combined ensemble model illustrates the highest accuracy of classifications for the breast cancer among all models.},
	language = {en},
	number = {5},
	urldate = {2016-06-30},
	journal = {Journal of Medical Systems},
	author = {Hsieh, Sheau-Ling and Hsieh, Sung-Huai and Cheng, Po-Hsun and Chen, Chi-Huang and Hsu, Kai-Ping and Lee, I.-Shun and Wang, Zhenyu and Lai, Feipei},
	month = aug,
	year = {2011},
	pages = {2841--2847},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NKSZCCTV/Hsieh et al. - 2011 - Design Ensemble Machine Learning Model for Breast .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/CH6UQKQT/s10916-011-9762-6.html:text/html}
}

@article{singh_parallel_2011,
	title = {Parallel implementation of {Otsu}’s binarization approach on {GPU}},
	url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.259.1845&rep=rep1&type=pdf},
	urldate = {2016-07-04},
	journal = {Int. J. of Computer Applications},
	author = {Singh, Brij Mohan and Sharma, Rahul and Mittal, Ankush and Ghosh, Debashish},
	year = {2011},
	file = {10.1.1.259.1845.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JAGRV6RG/10.1.1.259.1845.pdf:application/pdf}
}

@article{loeffler_classifying_2012,
	title = {Classifying {Prostate} {Cancer} {Malignancy} by {Quantitative} {Histomorphometry}},
	volume = {187},
	issn = {00225347},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0022534711060010},
	doi = {10.1016/j.juro.2011.12.054},
	language = {en},
	number = {5},
	urldate = {2016-07-02},
	journal = {The Journal of Urology},
	author = {Loeffler, Markus and Greulich, Lars and Scheibe, Patrick and Kahl, Philip and Shaikhibrahim, Zaki and Braumann, Ulf-Dietrich and Kuska, Jens-Peer and Wernert, Nicolas},
	month = may,
	year = {2012},
	pages = {1867--1875},
	file = {quanthistoProstate.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/338HNJDJ/quanthistoProstate.pdf:application/pdf}
}

@article{ateshian_continuum_2012,
	title = {Continuum {Mixture} {Models} of {Biological} {Growth} and {Remodeling}: {Past} {Successes} and {Future} {Opportunities}},
	volume = {14},
	shorttitle = {Continuum {Mixture} {Models} of {Biological} {Growth} and {Remodeling}},
	url = {http://dx.doi.org/10.1146/annurev-bioeng-071910-124726},
	doi = {10.1146/annurev-bioeng-071910-124726},
	abstract = {Biological growth processes involve mass exchanges that increase, decrease, or replace material that constitutes cells, tissues, and organs. In most cases, such exchanges alter the structural makeup of the material and consequently affect associated mechanobiological responses to applied loads. Given that the type and extent of changes in structural integrity depend on the different constituents involved (e.g., particular cytoskeletal or extracellular matrix proteins), the continuum theory of mixtures is ideally suited to model the mechanics of growth and remodeling. The goal of this review is twofold: first, to highlight a few illustrative examples that show diverse applications of mixture theory to describe biological growth and/or remodeling; second, to identify some open problems in the fields of modeling soft-tissue growth and remodeling.},
	number = {1},
	urldate = {2014-11-04},
	journal = {Annual Review of Biomedical Engineering},
	author = {Ateshian, G.A. and Humphrey, J.D.},
	year = {2012},
	pmid = {22809138},
	keywords = {adaptations, constitutive relations, mass exchange, stress response},
	pages = {97--111},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8PMKINCK/Ateshian and Humphrey - 2012 - Continuum Mixture Models of Biological Growth and .pdf:application/pdf}
}

@article{_tomorrows_2014,
	title = {Tomorrow's {Practice} {Changing} {Abstracts}},
	volume = {50},
	issn = {0959-8049},
	url = {http://www.sciencedirect.com/science/article/pii/S0959804914700814},
	doi = {10.1016/S0959-8049(14)70081-4},
	urldate = {2016-06-22},
	journal = {European Journal of Cancer},
	month = mar,
	year = {2014},
	pages = {S97--S98},
	file = {clinab.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZSVC9IEH/clinab.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NBJXFTUU/S0959804914700814.html:text/html}
}

@misc{_fluorescein_2014,
	title = {Fluorescein isothiocyanate},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {http://en.wikipedia.org/w/index.php?title=Fluorescein_isothiocyanate&oldid=635980511},
	abstract = {Fluorescein isothiocyanate (FITC) is a derivative of fluorescein used in wide-ranging applications including flow cytometry. FITC is the original fluorescein molecule functionalized with an isothiocyanate reactive group (-N=C=S), replacing a hydrogen atom on the bottom ring of the structure. This derivative is reactive towards nucleophiles including amine and sulfhydryl groups on proteins.
A succinimidyl-ester functional group attached to the fluorescein core, creating "NHS-fluorescein", forms another common amine reactive derivative that has much greater specificity toward primary amines in the presence of other nucleophiles.
FITC has excitation and emission spectrum peak wavelengths of approximately 495 nm/519 nm. Like most fluorochromes, it is prone to photobleaching. Because of the problem with photobleaching, derivatives of fluorescein such as Alexa 488 and DyLight 488 have been tailored for various chemical and biological applications where greater photostability, higher fluorescence intensity, or different attachment groups are needed.},
	language = {en},
	urldate = {2015-03-08},
	journal = {Wikipedia, the free encyclopedia},
	month = nov,
	year = {2014},
	note = {Page Version ID: 635980511},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/H28TU8X7/2014 - Fluorescein isothiocyanate.html:text/html}
}

@article{pallas_ductal_2013,
	title = {Ductal carcinoma in-situ discovered post-operatively affects the reoperation rate following breast conserving surgery},
	volume = {11},
	issn = {1743-9191},
	url = {http://www.sciencedirect.com/science/article/pii/S174391911300280X},
	doi = {10.1016/j.ijsu.2013.06.118},
	number = {8},
	urldate = {2016-06-30},
	journal = {International Journal of Surgery},
	author = {Pallas, Robert and Elhassan, Mohammed and Lloyd-Evans, Jonathan and Gateley, Chris},
	month = oct,
	year = {2013},
	pages = {608--609},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2ZS34GMT/S174391911300280X.html:text/html}
}

@article{mueller_quantitative_2013-1,
	title = {Quantitative {Segmentation} of {Fluorescence} {Microscopy} {Images} of {Heterogeneous} {Tissue}: {Application} to the {Detection} of {Residual} {Disease} in {Tumor} {Margins}},
	volume = {8},
	shorttitle = {Quantitative {Segmentation} of {Fluorescence} {Microscopy} {Images} of {Heterogeneous} {Tissue}},
	url = {http://dx.doi.org/10.1371/journal.pone.0066198},
	doi = {10.1371/journal.pone.0066198},
	abstract = {PurposeTo develop a robust tool for quantitative in situ pathology that allows visualization of heterogeneous tissue morphology and segmentation and quantification of image features.Materials and MethodsTissue excised from a genetically engineered mouse model of sarcoma was imaged using a subcellular resolution microendoscope after topical application of a fluorescent anatomical contrast agent: acriflavine. An algorithm based on sparse component analysis (SCA) and the circle transform (CT) was developed for image segmentation and quantification of distinct tissue types. The accuracy of our approach was quantified through simulations of tumor and muscle images. Specifically, tumor, muscle, and tumor+muscle tissue images were simulated because these tissue types were most commonly observed in sarcoma margins. Simulations were based on tissue characteristics observed in pathology slides. The potential clinical utility of our approach was evaluated by imaging excised margins and the tumor bed in a cohort of mice after surgical resection of sarcoma.ResultsSimulation experiments revealed that SCA+CT achieved the lowest errors for larger nuclear sizes and for higher contrast ratios (nuclei intensity/background intensity). For imaging of tumor margins, SCA+CT effectively isolated nuclei from tumor, muscle, adipose, and tumor+muscle tissue types. Differences in density were correctly identified with SCA+CT in a cohort of ex vivo and in vivo images, thus illustrating the diagnostic potential of our approach.ConclusionThe combination of a subcellular-resolution microendoscope, acriflavine staining, and SCA+CT can be used to accurately isolate nuclei and quantify their density in anatomical images of heterogeneous tissue.},
	number = {6},
	urldate = {2015-08-31},
	journal = {PLoS ONE},
	author = {Mueller, Jenna L. and Harmany, Zachary T. and Mito, Jeffrey K. and Kennedy, Stephanie A. and Kim, Yongbaek and Dodd, Leslie and Geradts, Joseph and Kirsch, David G. and Willett, Rebecca M. and Brown, J. Quincy and Ramanujam, Nimmi},
	month = jun,
	year = {2013},
	pages = {e66198},
	file = {PLoS Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/45SHJM68/Mueller et al. - 2013 - Quantitative Segmentation of Fluorescence Microsco.pdf:application/pdf}
}

@article{kothe_bcilab:_2013,
	title = {{BCILAB}: a platform for brain–computer interface development},
	volume = {10},
	issn = {1741-2552},
	shorttitle = {{BCILAB}},
	url = {http://iopscience.iop.org/1741-2552/10/5/056014},
	doi = {10.1088/1741-2560/10/5/056014},
	abstract = {Objective. The past two decades have seen dramatic progress in our ability to model brain signals recorded by electroencephalography, functional near-infrared spectroscopy, etc., and to derive real-time estimates of user cognitive state, response, or intent for a variety of purposes: to restore communication by the severely disabled, to effect brain-actuated control and, more recently, to augment human–computer interaction. Continuing these advances, largely achieved through increases in computational power and methods, requires software tools to streamline the creation, testing, evaluation and deployment of new data analysis methods. Approach. Here we present BCILAB, an open-source MATLAB-based toolbox built to address the need for the development and testing of brain-computer interface (BCI) methods by providing an organized collection of over 100 pre-implemented methods and method variants, an easily extensible framework for the rapid prototyping of new methods, and a highly automated framework for systematic testing and evaluation of new implementations. Main results. To validate and illustrate the use of the framework, we present two sample analyses of publicly available data sets from recent BCI competitions and from a rapid serial visual presentation task. We demonstrate the straightforward use of BCILAB to obtain results compatible with the current BCI literature. Significance. The aim of the BCILAB toolbox is to provide the BCI community a powerful toolkit for methods research and evaluation, thereby helping to accelerate the pace of innovation in the field, while complementing the existing spectrum of tools for real-time BCI experimentation, deployment and use.},
	language = {en},
	number = {5},
	urldate = {2015-02-18},
	journal = {Journal of Neural Engineering},
	author = {Kothe, Christian Andreas and Makeig, Scott},
	month = oct,
	year = {2013},
	pages = {056014},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8IESR9NW/Kothe and Makeig - 2013 - BCILAB a platform for braincomputer interface de.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/47R355GV/Kothe and Makeig - 2013 - BCILAB a platform for braincomputer interface de.html:text/html}
}

@book{schwarcz_right_2012,
	title = {The {Right} {Chemistry}: 108 {Enlightening}, {Nutritious}, {Health}-{Conscious} and {Occasionally} {Bizarre} {Inquiries} into the {Science} of {Daily} {Life}},
	isbn = {978-0-385-67160-6},
	shorttitle = {The {Right} {Chemistry}},
	abstract = {A big part of Dr. Joe's job as director of McGill University's Office of Science and Society is persuading people that the pursuit of science knowledge is a potential source of wonder, enlightenment and well-being for everyone. And as a chemist, he's particularly keen to rescue chemistry from the bad rep it's developed over recent decades. There is more to chemistry than toxins, pollution, and "Don't drink that soda--it's full of chemicals." The evangelic zeal Dr. Joe brings to his day job is of course also the driving force behind his work as an author. Once again, here he is to tell that everything is full of chemicals, and that chemistry means health, nutrition, beauty products, cleaning products, DNA, and the means by which Lady Gaga's meat dress was held together. In the style established with the bestselling Brain Fuel, each section here is themed and contains a mixture of short, pithy items and slightly longer mini-essays. And as before--but never with such energy and relish--Dr. Joe goes on the attack against charlatans in the alternative health trade, naming and shaming them in a particularly entertaining and edifying section of the book called "Claptrap."You will learn whether to put broccoli on a pizza before or after baking, whether beauty pills are worth taking, and whether the baby shampoo you're using is poisonous. You will discover but not use, please, the recipe for a Molotov cocktail. You will be enabled to enthrall fellow dinner guests with the derivation of the name Persil, and the definition of a kangarian (it's someone who only eats kangaroo meat).As ever, this torrent of entertainment is delivered in Dr. Joe's unmistakably warm, lively and authorative voice.},
	language = {en},
	publisher = {Doubleday Canada},
	author = {Schwarcz, Joe},
	month = nov,
	year = {2012},
	keywords = {Science / General}
}

@article{tacket_immunogenicity_1998,
	title = {Immunogenicity in humans of a recombinant bacterial antigen delivered in a transgenic potato},
	volume = {4},
	issn = {1078-8956},
	abstract = {Compared with vaccine delivery by injection, oral vaccines offer the hope of more convenient immunization strategies and a more practical means of implementing universal vaccination programs throughout the world. Oral vaccines act by stimulating the immune system at effector sites (lymphoid tissue) located in the gut. Genetic engineering has been used with variable success to design living and non-living systems as a means to deliver antigens to these sites and to stimulate a desired immune response. More recently, plant biotechnology techniques have been used to create plants which contain a gene derived from a human pathogen; the resultant plant tissues will accumulate an antigenic protein encoded by the foreign DNA. In pre-clinical trials, we found that antigenic proteins produced in transgenic plants retained immunogenic properties when purified; if injected into mice the antigen caused production of protein-specific antibodies. Moreover, in some experiments, if the plant tissues were simply fed to mice, a mucosal immune response occurred. The present study was conducted as a proof of principle to determine if humans would also develop a serum and/or mucosal immune response to an antigen delivered in an uncooked foodstuff.},
	language = {eng},
	number = {5},
	journal = {Nature Medicine},
	author = {Tacket, C. O. and Mason, H. S. and Losonsky, G. and Clements, J. D. and Levine, M. M. and Arntzen, C. J.},
	month = may,
	year = {1998},
	pmid = {9585236},
	keywords = {Adolescent, Adult, Antibodies, Bacterial, Antigens, Bacterial, Bacterial Toxins, Bacterial Vaccines, Eating, Enterotoxins, Escherichia coli, Escherichia coli Proteins, Feces, Humans, Middle Aged, Neutralization Tests, Plants, Genetically Modified, Solanum tuberosum, Time Factors, Vaccines, Synthetic},
	pages = {607--609}
}

@article{polyak_heterogeneity_2011,
	title = {Heterogeneity in breast cancer},
	volume = {121},
	issn = {0021-9738},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195489/},
	doi = {10.1172/JCI60534},
	abstract = {Breast cancer is a heterogeneous disease. There is a high degree of diversity between and within tumors as well as among cancer-bearing individuals, and all of these factors together determine the risk of disease progression and therapeutic resistance. Advances in technologies such as whole-genome sequencing and functional viability screens now allow us to analyze tumors at unprecedented depths. However, translating this increasing knowledge into clinical practice remains a challenge in part due to tumor evolution driven by the diversity of cancer cell populations and their microenvironment. The articles in this Review series discuss recent advances in our understanding of breast tumor heterogeneity, therapies tailored based on this knowledge, and future ways of assessing and treating heterogeneous tumors.},
	number = {10},
	urldate = {2016-06-23},
	journal = {The Journal of Clinical Investigation},
	author = {Polyak, Kornelia},
	month = oct,
	year = {2011},
	pmid = {21965334},
	pmcid = {PMC3195489},
	pages = {3786--3788},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/UHH66BI7/Polyak - 2011 - Heterogeneity in breast cancer.pdf:application/pdf}
}

@article{krontiras_what_2014,
	title = {What {Is} a {Clear} {Margin} in {Breast} {Conserving} {Cancer} {Surgery}?},
	volume = {15},
	issn = {1527-2729, 1534-6277},
	url = {http://link.springer.com/article/10.1007/s11864-013-0270-4},
	doi = {10.1007/s11864-013-0270-4},
	abstract = {Opinion statement Team work is the key to successful breast conservation therapy. Patient education and the informed consent process should include a discussion about the importance of margin status. Specimen management is critically important to obtain the highest quality information about margins. Operating technique should avoid trauma to or disruption of the specimen surface. The specimen should be oriented for the pathologist using standard techniques including sutures, clips, or colored inks. Specimen radiography is mandatory to confirm complete resection of the target tissues and can be used to direct additional margin resections during the initial procedure. With a well-designed and oriented specimen, the pathologist can give an accurate description of the margin distance for both the invasive and in situ components of the cancer. In most cases, decision-making about margins will be straightforward. Positive margins should be re-excised or the treatment is converted to mastectomy. Clear margins ({\textgreater}5 mm) require no further surgical therapy. “Close” margins (1–4 mm) will remain a point of controversy because of conflicting reports from clinical series. At UAB, decision for re-excision is made on a case-by-case basis. Routinely 2 mm is considered adequate, however, volume of disease and intraductal component are important considerations when making recommendations.},
	language = {en},
	number = {1},
	urldate = {2016-06-22},
	journal = {Current Treatment Options in Oncology},
	author = {Krontiras, Helen and Lancaster, Rachael B. and Urist, Marshall M.},
	month = jan,
	year = {2014},
	keywords = {BCT, Breast conservation therapy, DCIS, Early stage breast cancer, Local recurrence, Lumpectom, Margin, Oncology, Radiation therapy, Specimen management, Surgery},
	pages = {79--85},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/U8G457K9/Krontiras et al. - 2014 - What Is a Clear Margin in Breast Conserving Cancer.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8NAZPAAC/s11864-013-0270-4.html:text/html}
}

@article{birch_tendon_2007,
	title = {Tendon matrix composition and turnover in relation to functional requirements},
	volume = {88},
	issn = {1365-2613},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2613.2007.00552.x/abstract},
	doi = {10.1111/j.1365-2613.2007.00552.x},
	abstract = {Tendons are dense regular connective tissue structures that are defined based on their anatomical position of connecting muscle to bone. Despite these obvious commons features tendons from different locations within the body show remarkable variation in terms of their morphological, molecular and mechanical properties which relates to their specialized function. An appreciation of these differences is necessary to understand all aspects of tendon biology in health and disease. In our work, we have used a combination of mechanical assessment, histological measurements and molecular analysis of matrix in functionally distinct tendons to determine relationships between function and structure. We have found significant differences in material and molecular properties between spring-like tendons that are subjected to high strains during locomotion and positional tendons which are subjected to much lower strains. Furthermore, we have data to suggest that not only is the matrix composition different but also the ability of cells to synthesize and degrade the matrix (matrix turnover) varies between tendon types. We propose that these differences relate to the magnitude of strain that the tendon experiences during normal activities in life. Tendon cells may be preprogrammed during embryological development for the strain they will encounter in life or may simply respond to the particular strain environment they are subjected to. The elucidation of controlling mechanisms resulting in tendon cell specialization will have important consequences for cell based therapies and engineering strategies to repair damaged tendons.},
	language = {en},
	number = {4},
	urldate = {2014-11-03},
	journal = {International Journal of Experimental Pathology},
	author = {Birch, Helen L.},
	month = aug,
	year = {2007},
	keywords = {collagen, function, matrix, mechanics, Metabolism, Tendon},
	pages = {241--248},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/C9TIVGXJ/Birch - 2007 - Tendon matrix composition and turnover in relation.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4WPVJ78F/full.html:text/html}
}

@article{borisova_endogenous_2014,
	title = {Endogenous and {Exogenous} {Fluorescence} {Skin} {Cancer} {Diagnostics} for {Clinical} {Applications}},
	volume = {20},
	issn = {1077-260X},
	doi = {10.1109/JSTQE.2013.2280503},
	abstract = {A short review will be presented of the recent clinical achievements in the field of skin autofluorescence and exogenous fluorescence tumor detection. Photosensitizers used for exogenous photodetection of cutaneous lesions will be discussed from the point of view of their photodynamic diagnostic properties and their advantages and drawbacks associated with clinical applications. A survey on various results of detection and differentiation of the fluorescent data observed from malignant cutaneous lesions will be summarized and an optimization of the skin cancer detection techniques based on fluorescence diagnostics will be analyzed and discussed. A short presentation will be given of own experimental results and clinical experience acquired in the past decade in the autofluorescence diagnostics of different benign, dysplastic, and malignant skin neoplasia. The origins of the fluorescence spectra, their peculiarities, the feasibility of clinical tumor detection, and differentiation needs will also be discussed.},
	number = {2},
	journal = {IEEE Journal of Selected Topics in Quantum Electronics},
	author = {Borisova, E. G. and Angelova, L. P. and Pavlova, E. P.},
	month = mar,
	year = {2014},
	keywords = {benign skin neoplasia, Cancer, clinical tumor detection, clinical tumor differentiation, Compounds, Drugs, dysplastic skin neoplasia, endogenous fluorescence skin cancer diagnostics, exogenous fluorescence skin cancer diagnostics, exogenous fluorescence tumor photodetection, fluorescence, fluorescence spectroscopy, Lesions, malignant cutaneous lesions, malignant skin neoplasia, medical disorders, optimisation, patient diagnosis, photochemistry, photodiagnosis, photodynamic diagnostic properties, photosensitizers, skin, skin autofluorescence, skin autofluorescence diagnostics, skin cancer detection, skin cancer detection techniques, tumours},
	pages = {211--222},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2FGFIWVU/abs_all.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7KIM9HUJ/Borisova et al. - 2014 - Endogenous and Exogenous Fluorescence Skin Cancer .pdf:application/pdf}
}

@article{sun_cycle-dependent_2010,
	title = {Cycle-dependent matrix remodeling gene expression response in fatigue-loaded rat patellar tendons},
	volume = {28},
	copyright = {Copyright © 2010 Orthopaedic Research Society},
	issn = {1554-527X},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/jor.21132/abstract},
	doi = {10.1002/jor.21132},
	abstract = {Expression profiling of selected matrix remodeling genes was conducted to evaluate differences in molecular response to low-cycle (100) and high-cycle (7,200) sub-failure-fatigue loading of patellar tendons. Using our previously developed in vivo patellar tendon model, tendons were loaded for 100 or 7,200 cycles and expression of selected metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), and collagens were quantified by real-time RT-PCR at 1- and 7-day post-loading. Expression profiles were also obtained from lacerated tendons as an acute injury model. The high-cycle group showed upregulation of TIMP-1, -2, Col3a1, and Col5a1, and downregulation TIMP-4 at both time points, upregulation of MMP-2 at 7-day post-loading and downregulation of MMP-13 and -14 at 1-day post-loading, suggesting overall repair/remodeling. In contrast, the low-cycle loaded group showed upregulation of MMP-2, -3, -13, and Col12a1 at both time points, upregulation of TIMP-1, -2, -3, Col3a1, and integrin β1 and downregulation of integrin α11 at 1-day post-loading and upregulation of Col1a1 at 7-day post-loading, consistent with a hypertrophic (adaptive) pattern. Lacerated tendons showed a typical acute wound response with upregulation of all examined remodeling genes. Differences found in tendon response to high- and low-cycle loading are suggestive of the underlying mechanisms associated with a healthy or damaging response. Published by Wiley Periodicals, Inc. J Orthop Res 28:1380–1386, 2010},
	language = {en},
	number = {10},
	urldate = {2014-11-04},
	journal = {Journal of Orthopaedic Research},
	author = {Sun, Hui B. and Andarawis-Puri, Nelly and Li, Yonghui and Fung, David T. and Lee, Jonathan Y. and Wang, Vincent M. and Basta-Pljakic, Jelena and Leong, Daniel J. and Sereysky, Jedd B. and Ros, Stephen J. and Klug, Raymond A. and Braman, Jonathan and Schaffler, Mitch B. and Jepsen, Karl J. and Flatow, Evan L.},
	month = oct,
	year = {2010},
	keywords = {collagen, fatigue loading, MMP, Patellar tendon, TIMP},
	pages = {1380--1386},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KAKPJB93/Sun et al. - 2010 - Cycle-dependent matrix remodeling gene expression .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NEHJUZT7/abstract.html:text/html}
}

@misc{_premarket_????,
	title = {Premarket {Approval} ({PMA}) {\textgreater} {PMA} {Review} {Process}},
	url = {http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/HowtoMarketYourDevice/PremarketSubmissions/PremarketApprovalPMA/ucm047991.htm},
	urldate = {2016-07-05},
	file = {Premarket Approval (PMA) > PMA Review Process:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GTU3FEJF/ucm047991.html:text/html}
}

@misc{_ubuntu_????,
	title = {Ubuntu {Start} {Page}},
	url = {about:startpage},
	urldate = {2016-06-24},
	file = {Ubuntu Start Page:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9DS8XXRR/startpage.html:text/html}
}

@article{korhonen_impact_2013,
	title = {The impact of lobular and ductal breast cancer histology on the metastatic behavior and long term survival of breast cancer patients},
	volume = {22},
	issn = {0960-9776},
	url = {http://www.sciencedirect.com/science/article/pii/S0960977613001306},
	doi = {10.1016/j.breast.2013.06.001},
	abstract = {The aim of the study was to evaluate the long-term survival of patients with invasive lobular carcinomas (ILC) and invasive ductal carcinomas (IDC) and the metastatic behavior of these two disease entities. Originally, all consecutive patients with pure lobular invasive breast cancers diagnosed between 1990 and 1999 in the area served by the Tampere University Hospital and their matched IDC controls were identified and re-evaluated histopathologically in this follow-up study, resulting in a total of 243 ILCs and 243 IDCs. Data on recurrences and survival were collected until the end of year 2009. Statistical analyses including Kaplan–Meier method, log-rank test, Fisher's exact test and Cox regression analysis were performed with the PASW Statistics 18.0 computer program. P-values of \&lt;0.05 were considered statistically significant.

Within the mean follow-up time of 10.04 years, locoregional recurrences were significantly more common among the ILCs than IDCs (35 vs. 20, p = 0.04), but no differences in the total number of distant recurrences or bilaterality were observed. However, when the first distant recurrence sites were studied, ILC patients had significantly less lung metastases (p = 0.04), but more skin metastases (p = 0.04). During the whole follow-up period IDCs metastasized significantly more frequently to the lungs (p = 0.002), whereas gastrointestinal metastases were more common among ILCs (p = 0.02). Although the known favorable prognostic factors (hormone receptor positivity, low grade, low s-phase) were more common for the ILCs, the disease-free survival, the overall survival and the survival after recurrence did not differ between the groups. However, the Cox-regression model showed significantly worse survival for ILCs after adjusting for age, TNM-status, grade and ER-positivity (p = 0.004).

In conclusion, ILC and IDC differ in respect for visceral metastases. Despite the known favorable prognostic factors and originally favorable survival, patients with lobular histology appear to have a worse survival in the multivariate analysis after a prolonged follow-up.},
	number = {6},
	urldate = {2016-06-25},
	journal = {The Breast},
	author = {Korhonen, T. and Kuukasjärvi, T. and Huhtala, H. and Alarmo, E. -L. and Holli, K. and Kallioniemi, A. and Pylkkänen, L.},
	month = dec,
	year = {2013},
	keywords = {Biology, BREAST cancer, Cox-regression analysis, Ductal, Lobular, Recurrence},
	pages = {1119--1124},
	file = {1-s2.0-S0960977613001306-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/FHH9DPIS/1-s2.0-S0960977613001306-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/435GFSUN/S0960977613001306.html:text/html}
}

@misc{_can_????,
	title = {Can someone explain {Kernel} {Trick} intuitively? : {MachineLearning}},
	url = {https://www.reddit.com/r/MachineLearning/comments/1joh9v/can_someone_explain_kernel_trick_intuitively/},
	urldate = {2016-07-11},
	file = {Can someone explain Kernel Trick intuitively? \: MachineLearning:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MZK6KNBC/can_someone_explain_kernel_trick_intuitively.html:text/html}
}

@article{pannu_abstract_2015-1,
	title = {Abstract {P}5-10-15: {Empowering} the {Nottingham} {Grading} {System}: {An} integrated {Ki}67-mitosis classifier yields a better patient stratification tool},
	volume = {75},
	issn = {0008-5472, 1538-7445},
	shorttitle = {Abstract {P}5-10-15},
	url = {http://cancerres.aacrjournals.org/content/75/9_Supplement/P5-10-15},
	doi = {10.1158/1538-7445.SABCS14-P5-10-15},
	abstract = {Therapeutic decision-making for personalized management of breast cancer relies on patient stratification based on the risk conferred by clinicopathologic factors, such as stage, Ki67 Index (KI) and tumor histological grade. The most widely used histologic grading system for breast cancer, the Nottingham Grading System (NGS) provides prognostic information about breast tumor samples by combining analysis of the extent of glandular differentiation, nuclear pleomorphism and mitotic activity present in the tumor sample. In the NGS, the mitotic Index (MI) is defined as the number of mitotic cells per ten high-power fields. KI is a universal prognostic indicator but is not part of the NGS. Although the NGS has been widely used owing to its reproducibility and significant prognostic value, its accuracy in predicting disease prognosis and aggressiveness is limited. Our earlier work has demonstrated that by rationally integrating KI and MI into a new metric called the Ki67-Adjusted Mitotic Score (KAMS), which is a measure of the proportion of mitotic cells amongst Ki67-positive cells, we are able to glean a new layer of prognostic information about metastatic risk. We found that for Nottingham Grade II and III patients, high KAMS values predicted relatively better overall survival (OS) than low KAMS values. We therefore asked if the incorporation of a KAMS-based classifier subsequent to conventional Nottingham classification, would improve patient stratification to enable their funneling towards more optimal treatment choices. Ideal KAMS thresholds were established by analyzing the KAMS-stratified survival groups and selecting the thresholds which created the widest survival stratification that was additionally confirmed to be statistically significant via a Log-Rank test. For Nottingham Grade II and III patients, an above-threshold KAMS value was deemed as low-risk and a below-threshold KAMS value was deemed as high-risk for the purpose of grade adjustment. Grade adjustments were based solely on the patients’ KAMS values. Thus the adjusted Nottingham Grade I consisted of the original Nottingham Grade I patients along with KAMS determined low-risk original Nottingham Grade II patients. Adjusted Nottingham Grade II patients were composed of KAMS determined high-risk patients originally in Nottingham Grade II along with KAMS determined low-risk original Nottingham Grade III patients. Finally, the adjusted Nottingham Grade III was made up exclusively of high-risk patients from the original Nottingham Grade III. We found that the adjusted system represents a wider separation between OS curves with adjusted Grade I (n = 774) OS being 95.48\%, adjusted grade II (n = 727) OS at 87.62\%, and adjusted Grade III (n = 110) having an OS of 78.18\%. Overall survival groups between adjusted grade I and II and I and III (p {\textbackslash}textless 0.001) showed statistical significance. We also found that the hazard ratios for all Nottingham grades are significantly better after adjustment (2.875 versus 2.034 for Grade II and 5.115 versus 3.456 for Grade III) indicating that the KAMS can function as an effective risk-stratification biomarker and that incorporation of a KAMS-based classifier enhances patient stratification. Citation Format: Vaishali Pannu, Padmashree CG Rida, Sergey Klimov, Nikita Wright, Guilherme Cantuaria, Michelle Reid, Ritu Aneja. Empowering the Nottingham Grading System: An integrated Ki67-mitosis classifier yields a better patient stratification tool [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-10-15.},
	number = {9},
	urldate = {2016-06-26},
	author = {Pannu, Vaishali and Rida, Padmashree CG and Klimov, Sergey and Wright, Nikita and Cantuaria, Guilherme and Reid, Michelle and Aneja, Ritu},
	month = may,
	year = {2015},
	pages = {P5--10--15--P5--10--15},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/5U6E2WJT/P5-10-15.html:text/html}
}

@article{rojas_methodology_2015,
	title = {Methodology to study the three-dimensional spatial distribution of prostate cancer and their dependence on clinical parameters},
	volume = {2},
	issn = {2329-4302},
	url = {http://dx.doi.org/10.1117/1.JMI.2.3.037502},
	doi = {10.1117/1.JMI.2.3.037502},
	abstract = {Abstract. 
A methodology to study the relationship between clinical variables [e.g., prostate specific antigen (PSA) or Gleason score] and cancer spatial distribution is described. Three-dimensional (3-D) models of 216 glands are reconstructed from digital images of whole mount histopathological slices. The models are deformed into one prostate model selected as an atlas using a combination of rigid, affine, and B-spline deformable registration techniques. Spatial cancer distribution is assessed by counting the number of tumor occurrences among all glands in a given position of the 3-D registered atlas. Finally, a difference between proportions is used to compare different spatial distributions. As a proof of concept, we compare spatial distributions from patients with PSA greater and less than 5  ng/ml and from patients older and younger than 60 years. Results suggest that prostate cancer has a significant difference in the right zone of the prostate between populations with PSA greater and less than 5  ng/ml. Age does not have any impact in the spatial distribution of the disease. The proposed methodology can help to comprehend prostate cancer by understanding its spatial distribution and how it changes according to clinical parameters. Finally, this methodology can be easily adapted to other organs and pathologies.},
	number = {3},
	urldate = {2016-02-12},
	journal = {Journal of Medical Imaging},
	author = {Rojas, Kristians Diaz and Montero, Maria L. and Yao, Jorge and Messing, Edward and Fazili, Anees and Joseph, Jean and Ou, Yangming and Rubens, Deborah J. and Parker, Kevin J. and Davatzikos, Christos and Castaneda, Benjamin},
	year = {2015},
	pages = {037502--037502}
}

@article{jacob_slow_2001,
	series = {Opthalmic {Special} {Issue}},
	title = {Slow release of the antimetabolite 5-fluorouracil (5-{FU}) from modified {Baerveldt} glaucoma drains to prolong drain function},
	volume = {22},
	issn = {0142-9612},
	url = {http://www.sciencedirect.com/science/article/pii/S0142961201001703},
	doi = {10.1016/S0142-9612(01)00170-3},
	abstract = {Drainage devices are routinely placed in the eyes of patients with glaucoma to reduce intraocular pressure (IOP) by providing controlled outflow of fluid (aqueous humor) via a filtering bleb. However, the natural wound healing response often interferes with fluid outflow by thickening the walls of the bleb over time, so that these devices rarely remain functional for more than 5 years. We investigated the use of controlled release of an antimetabolite, 5-fluorouracil (5-FU), within glaucoma drains to determine if the wound healing response could be reduced and the useful life span of the device increased. Collagen plugs containing 1.125 mg of 5-FU were placed in the silicone tubes of modified Baerveldt glaucoma drains. Eight drains with 5-FU and eight drains without 5-FU were implanted in one eye each of 16 New Zealand white rabbits; the contralateral eyes served as unoperated controls. Results were evaluated in terms of IOP, fibrous capsule thickness, macrophage density, and presence of type III collagen surrounding the drain plate, 3 and 6 months after implantation. In general, eyes implanted with antimetabolite-containing drains demonstrated significantly lower values for all evaluated parameters at 3 months and lower or equal values at 6 months, compared with the eyes not receiving 5-FU and the unoperated controls, indicating improved IOP-lowering function, reduced bleb wall thickness, and earlier achievement of a steady-state wound healing response. All eyes remained healthy throughout the 6-month duration of the study with no cytotoxicity complications in any of the eyes. Thus, biodegradable plugs placed within the silicone tubes of glaucoma drains can safely deliver 5-FU to filtering blebs over time, which could prolong the functional life of the bleb by decreasing the thickness of the anterior fibrous capsule and permitting sufficient fluid outflow to reduce IOP to physiological levels.},
	number = {24},
	urldate = {2015-11-22},
	journal = {Biomaterials},
	author = {Jacob, Jean T and LaCour, Owen J and Burgoyne, Claude F},
	month = dec,
	year = {2001},
	keywords = {Antimetabolite, Biocompatibility, Glaucoma drains, Wound healing},
	pages = {3329--3335},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KSATHIPE/S0142961201001703.html:text/html}
}

@article{beason_development_2012,
	title = {Development and evaluation of multiple tendon injury models in the mouse},
	volume = {45},
	issn = {0021-9290},
	url = {http://www.sciencedirect.com/science/article/pii/S0021929012001443},
	doi = {10.1016/j.jbiomech.2012.02.022},
	abstract = {The mouse has proven to be an advantageous animal model system in basic science research focused on aiding in development and evaluation of potential treatments; however, the small size of mouse tendons makes consistent and reproducible injury models and subsequent biomechanical evaluation challenging for studying tendon healing. In this study, we investigated the feasibility and reproducibility of multiple mouse tendon injury models. Our hypothesis was that incisional (using a blade) and excisional (using a biopsy punch) injuries would result in consistent differences in tendon material properties. At 16 weeks of age, 17 C57BL/6 mice underwent surgery to create defects in the flexor digitorum longus, Achilles, or patellar tendon. Each animal received 1–2 full-thickness, central-width incisional or excisional injuries per limb; at least one tendon per limb remained uninjured. The injuries were distributed such that each tendon type had comparable numbers of uninjured, incisionally injured, and excisionally injured specimens. Three weeks after injury, all animals were euthanized and tendons were harvested for mechanical testing. As hypothesized, differences were detected for all three different tendon types at three weeks post-injury. While all models created injuries that produced predictable outcomes, the patellar tendon model was the most consistent in terms of number and size of significant differences in injured tendons compared to native properties, as well as in the overall variance in the data. This finding provides support for its use in fundamental tendon healing studies; however, future work may use any of these models, based on their appropriateness for the specific question under study.},
	number = {8},
	urldate = {2014-11-04},
	journal = {Journal of Biomechanics},
	author = {Beason, David P. and Kuntz, Andrew F. and Hsu, Jason E. and Miller, Kristin S. and Soslowsky, Louis J.},
	month = may,
	year = {2012},
	keywords = {Animal model, Biomechanics, Injury, Mouse, Tendon},
	pages = {1550--1553},
	file = {1-s2.0-S0021929012001443-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XPQP9ZJ6/1-s2.0-S0021929012001443-main.pdf:application/pdf}
}

@misc{_what_????-1,
	title = {What is the kernel trick? - {Quora}},
	url = {https://www.quora.com/What-is-the-kernel-trick},
	urldate = {2016-07-11},
	file = {What is the kernel trick? - Quora:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TJUKQR6H/What-is-the-kernel-trick.html:text/html}
}

@article{agner_spectral_2013-1,
	title = {Spectral embedding based active contour ({SEAC}) for lesion segmentation on breast dynamic contrast enhanced magnetic resonance imaging},
	volume = {40},
	issn = {0094-2405},
	doi = {10.1118/1.4790466},
	abstract = {PURPOSE: Segmentation of breast lesions on dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) is the first step in lesion diagnosis in a computer-aided diagnosis framework. Because manual segmentation of such lesions is both time consuming and highly susceptible to human error and issues of reproducibility, an automated lesion segmentation method is highly desirable. Traditional automated image segmentation methods such as boundary-based active contour (AC) models require a strong gradient at the lesion boundary. Even when region-based terms are introduced to an AC model, grayscale image intensities often do not allow for clear definition of foreground and background region statistics. Thus, there is a need to find alternative image representations that might provide (1) strong gradients at the margin of the object of interest (OOI); and (2) larger separation between intensity distributions and region statistics for the foreground and background, which are necessary to halt evolution of the AC model upon reaching the border of the OOI.
METHODS: In this paper, the authors introduce a spectral embedding (SE) based AC (SEAC) for lesion segmentation on breast DCE-MRI. SE, a nonlinear dimensionality reduction scheme, is applied to the DCE time series in a voxelwise fashion to reduce several time point images to a single parametric image where every voxel is characterized by the three dominant eigenvectors. This parametric eigenvector image (PrEIm) representation allows for better capture of image region statistics and stronger gradients for use with a hybrid AC model, which is driven by both boundary and region information. They compare SEAC to ACs that employ fuzzy c-means (FCM) and principal component analysis (PCA) as alternative image representations. Segmentation performance was evaluated by boundary and region metrics as well as comparing lesion classification using morphological features from SEAC, PCA+AC, and FCM+AC.
RESULTS: On a cohort of 50 breast DCE-MRI studies, PrEIm yielded overall better region and boundary-based statistics compared to the original DCE-MR image, FCM, and PCA based image representations. Additionally, SEAC outperformed a hybrid AC applied to both PCA and FCM image representations. Mean dice similarity coefficient (DSC) for SEAC was significantly better (DSC = 0.74 ± 0.21) than FCM+AC (DSC = 0.50 ± 0.32) and similar to PCA+AC (DSC = 0.73 ± 0.22). Boundary-based metrics of mean absolute difference and Hausdorff distance followed the same trends. Of the automated segmentation methods, breast lesion classification based on morphologic features derived from SEAC segmentation using a support vector machine classifier also performed better (AUC = 0.67 ± 0.05; p {\textless} 0.05) than FCM+AC (AUC = 0.50 ± 0.07), and PCA+AC (AUC = 0.49 ± 0.07).
CONCLUSIONS: In this work, we presented SEAC, an accurate, general purpose AC segmentation tool that could be applied to any imaging domain that employs time series data. SE allows for projection of time series data into a PrEIm representation so that every voxel is characterized by the dominant eigenvectors, capturing the global and local time-intensity curve similarities in the data. This PrEIm allows for the calculation of strong tensor gradients and better region statistics than the original image intensities or alternative image representations such as PCA and FCM. The PrEIm also allows for building a more accurate hybrid AC scheme.},
	language = {eng},
	number = {3},
	journal = {Medical Physics},
	author = {Agner, Shannon C. and Xu, Jun and Madabhushi, Anant},
	month = mar,
	year = {2013},
	pmid = {23464337},
	pmcid = {PMC3598842},
	keywords = {Algorithms, Breast neoplasms, Contrast Media, Fuzzy Logic, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Principal component analysis},
	pages = {032305}
}

@article{konofagou_ultrasound-induced_2012,
	title = {Ultrasound-induced blood-brain barrier opening},
	volume = {13},
	issn = {1873-4316},
	abstract = {Over 4 million U.S. men and women suffer from Alzheimer's disease; 1 million from Parkinson's disease; 350,000 from multiple sclerosis (MS); and 20,000 from amyotrophic lateral sclerosis (ALS). Worldwide, these four diseases account for more than 20 million patients. In addition, aging greatly increases the risk of neurodegenerative disease. Although great progress has been made in recent years toward understanding of these diseases, few effective treatments and no cures are currently available. This is mainly due to the impermeability of the blood-brain barrier (BBB) that allows only 5\% of the 7000 small-molecule drugs available to treat only a tiny fraction of these diseases. On the other hand, safe and localized opening of the BBB has been proven to present a significant challenge. Of the methods used for BBB disruption shown to be effective, Focused Ultrasound (FUS), in conjunction with microbubbles, is the only technique that can induce localized BBB opening noninvasively and regionally. FUS may thus have a huge impact in trans-BBB brain drug delivery. The primary objective in this paper is to elucidate the interactions between ultrasound, microbubbles and the local microenvironment during BBB opening with FUS, which are responsible for inducing the BBB disruption. The mechanism of the BBB opening in vivo is monitored through the MRI and passive cavitation detection (PCD), and the safety of BBB disruption is assessed using H\&E histology at distinct pressures, pulse lengths and microbubble diameters. It is hereby shown that the BBB can be disrupted safely and transiently under specific acoustic pressures (under 0.45 MPa) and microbubble (diameter under 8 μm) conditions.},
	language = {eng},
	number = {7},
	journal = {Current Pharmaceutical Biotechnology},
	author = {Konofagou, Elisa E. and Tung, Yao-Sheng and Choi, James and Deffieux, Thomas and Baseri, Babak and Vlachos, Fotios},
	month = jun,
	year = {2012},
	pmid = {22201586},
	pmcid = {PMC4038976},
	keywords = {Animals, Blood-Brain Barrier, Brain, Drug Delivery Systems, Humans, Microbubbles, Ultrasonics},
	pages = {1332--1345}
}

@article{kummerow_nationwide_2015,
	title = {Nationwide {Trends} in {Mastectomy} for {Early}-{Stage} {Breast} {Cancer}},
	volume = {150},
	issn = {2168-6254},
	url = {http://archsurg.jamanetwork.com/article.aspx?doi=10.1001/jamasurg.2014.2895},
	doi = {10.1001/jamasurg.2014.2895},
	language = {en},
	number = {1},
	urldate = {2016-07-10},
	journal = {JAMA Surgery},
	author = {Kummerow, Kristy L. and Du, Liping and Penson, David F. and Shyr, Yu and Hooks, Mary A.},
	month = jan,
	year = {2015},
	pages = {9},
	file = {Nationwide Trends in Mastectomy for Early-Stage Breast Cancer.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NGDX8REV/Nationwide Trends in Mastectomy for Early-Stage Breast Cancer.pdf:application/pdf}
}

@article{connizzo_diabetes_2014,
	title = {Diabetes {Alters} {Mechanical} {Properties} and {Collagen} {Fiber} {Re}-{Alignment} in {Multiple} {Mouse} {Tendons}},
	volume = {42},
	issn = {0090-6964, 1573-9686},
	url = {http://link.springer.com/article/10.1007/s10439-014-1031-7},
	doi = {10.1007/s10439-014-1031-7},
	abstract = {Tendons function to transfer load from muscle to bone through their complex composition and hierarchical structure, consisting mainly of type I collagen. Recent evidence suggests that type II diabetes may cause alterations in collagen structure, such as irregular fibril morphology and density, which could play a role in the mechanical function of tendons. Using the db/db mouse model of type II diabetes, the diabetic skin was found to have impaired biomechanical properties when compared to the non-diabetic group. The purpose of this study was to assess the effect of diabetes on biomechanics, collagen fiber re-alignment, and biochemistry in three functionally different tendons (Achilles, supraspinatus, patellar) using the db/db mouse model. Results showed that cross-sectional area and stiffness, but not modulus, were significantly reduced in all three tendons. However, the tendon response to load (transition strain, collagen fiber re-alignment) occurred earlier in the mechanical test, contrary to expectations. In addition, the patellar tendon had an altered response to diabetes when compared to the other two tendons, with no changes in fiber re-alignment and decreased collagen content at the midsubstance of the tendon. Overall, type II diabetes alters tendon mechanical properties and the dynamic response to load.},
	language = {en},
	number = {9},
	urldate = {2014-11-04},
	journal = {Annals of Biomedical Engineering},
	author = {Connizzo, Brianne K. and Bhatt, Pankti R. and Liechty, Kenneth W. and Soslowsky, Louis J.},
	month = sep,
	year = {2014},
	keywords = {Achilles, Biochemistry, general, Biomedical Engineering, Biomedicine general, Biophysics and Biological Physics, db/db mouse, mechanics, Patellar, Realignment, Supraspinatus, Tendon mechanics, Type II diabetes},
	pages = {1880--1888},
	file = {diabetestendon.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/KG2R74BM/diabetestendon.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8KNQ7JQZ/s10439-014-1031-7.html:text/html}
}

@inproceedings{litjens_distinguishing_2014,
	title = {Distinguishing prostate cancer from benign confounders via a cascaded classifier on multi-parametric {MRI}},
	volume = {9035},
	url = {http://dx.doi.org/10.1117/12.2043751},
	doi = {10.1117/12.2043751},
	abstract = {Learning how to separate benign confounders from prostate cancer is important because the imaging characteristics of these confounders are poorly understood. Furthermore, the typical representations of the MRI parameters might not be enough to allow discrimination. The diagnostic uncertainty this causes leads to a lower diagnostic accuracy. In this paper a new cascaded classifier is introduced to separate prostate cancer and benign confounders on MRI in conjunction with specific computer-extracted features to distinguish each of the benign classes (benign prostatic hyperplasia (BPH), inflammation, atrophy or prostatic intra-epithelial neoplasia (PIN). In this study we tried to (1) calculate different mathematical representations of the MRI parameters which more clearly express subtle differences between different classes, (2) learn which of the MRI image features will allow to distinguish specific benign confounders from prostate cancer, and (2) find the combination of computer-extracted MRI features to best discriminate cancer from the confounding classes using a cascaded classifier. One of the most important requirements for identifying MRI signatures for adenocarcinoma, BPH, atrophy, inflammation, and PIN is accurate mapping of the location and spatial extent of the confounder and cancer categories from ex vivo histopathology to MRI. Towards this end we employed an annotated prostatectomy data set of 31 patients, all of whom underwent a multi-parametric 3 Tesla MRI prior to radical prostatectomy. The prostatectomy slides were carefully co-registered to the corresponding MRI slices using an elastic registration technique. We extracted texture features from the T2-weighted imaging, pharmacokinetic features from the dynamic contrast enhanced imaging and diffusion features from the diffusion-weighted imaging for each of the confounder classes and prostate cancer. These features were selected because they form the mainstay of clinical diagnosis. Relevant features for each of the classes were selected using maximum relevance minimum redundancy feature selection, allowing us to perform classifier independent feature selection. The selected features were then incorporated in a cascading classifier, which can focus on easier sub-tasks at each stage, leaving the more difficult classification tasks for later stages. Results show that distinct features are relevant for each of the benign classes, for example the fraction of extra-vascular, extra-cellular space in a voxel is a clear discriminator for inflammation. Furthermore, the cascaded classifier outperforms both multi-class and one-shot classifiers in overall accuracy for discriminating confounders from cancer: 0.76 versus 0.71 and 0.62.},
	urldate = {2015-11-30},
	author = {Litjens, G.J.S. and Elliott, R. and Shih, N. and Feldman, M. and Barentsz, J. O. and Hulsbergen - van de Kaa, C. A. and Kovacs, I. and Huisman, H. J. and Madabhushi, A.},
	year = {2014},
	pages = {903512--903512--14},
	file = {DIstinguishing_PCa_from_Benign_Confounders.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8H4CUW4W/DIstinguishing_PCa_from_Benign_Confounders.pdf:application/pdf}
}

@misc{health_premarket_????,
	type = {{WebContent}},
	title = {Premarket {Approval} ({PMA})},
	url = {http://www.fda.gov/Medicaldevices/Deviceregulationandguidance/Howtomarketyourdevice/Premarketsubmissions/Premarketapprovalpma/Default.Htm},
	abstract = {Device Advice - Overview of premarket approval process, including definitions from regulations, and other information necessary to submission of an application for a PMA.},
	language = {en},
	urldate = {2015-11-22},
	author = {Health, Center for Devices {and} Radiological},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/WIGHQ7BB/Default.html:text/html}
}

@misc{health_medical_????,
	type = {{WebContent}},
	title = {Medical {Device} {User} {Fee} and {Modernization} {Act} ({MDUFMA})},
	url = {http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/Overview/MedicalDeviceUserFeeandModernizationActMDUFMA/},
	abstract = {Information on the Medical Device User Fee and Modernization Act of 2002},
	language = {en},
	urldate = {2015-11-22},
	author = {Health, Center for Devices {and} Radiological},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6E9BKZW2/MedicalDeviceUserFeeandModernizationActMDUFMA.html:text/html}
}

@article{pleijhuis_near-infrared_2011,
	title = {Near-infrared fluorescence ({NIRF}) imaging in breast-conserving surgery: {Assessing} intraoperative techniques in tissue-simulating breast phantoms},
	volume = {37},
	issn = {0748-7983},
	shorttitle = {Near-infrared fluorescence ({NIRF}) imaging in breast-conserving surgery},
	url = {http://www.sciencedirect.com/science/article/pii/S0748798310005482},
	doi = {10.1016/j.ejso.2010.10.006},
	abstract = {Purpose
Breast-conserving surgery (BCS) results in tumour-positive surgical margins in up to 40\% of the patients. Therefore, new imaging techniques are needed that support the surgeon with real-time feedback on tumour location and margin status. In this study, the potential of near-infrared fluorescence (NIRF) imaging in BCS for pre- and intraoperative tumour localization, margin status assessment and detection of residual disease was assessed in tissue-simulating breast phantoms.
Methods
Breast-shaped phantoms were produced with optical properties that closely match those of normal breast tissue. Fluorescent tumour-like inclusions containing indocyanine green (ICG) were positioned at predefined locations in the phantoms to allow for simulation of (i) preoperative tumour localization, (ii) real-time NIRF-guided tumour resection, and (iii) intraoperative margin assessment. Optical imaging was performed using a custom-made clinical prototype NIRF intraoperative camera.
Results
Tumour-like inclusions in breast phantoms could be detected up to a depth of 21 mm using a NIRF intraoperative camera system. Real-time NIRF-guided resection of tumour-like inclusions proved feasible. Moreover, intraoperative NIRF imaging reliably detected residual disease in case of inadequate resection.
Conclusion
We evaluated the potential of NIRF imaging applications for BCS. The clinical setting was simulated by exploiting tissue-like breast phantoms with fluorescent tumour-like agarose inclusions. From this evaluation, we conclude that intraoperative NIRF imaging is feasible and may improve BCS by providing the surgeon with imaging information on tumour location, margin status, and presence of residual disease in real-time. Clinical studies are needed to further validate these results.},
	number = {1},
	urldate = {2016-06-24},
	journal = {European Journal of Surgical Oncology (EJSO)},
	author = {Pleijhuis, R. G. and Langhout, G. C. and Helfrich, W. and Themelis, G. and Sarantopoulos, A. and Crane, L. M. A. and Harlaar, N. J. and de Jong, J. S. and Ntziachristos, V. and van Dam, G. M.},
	month = jan,
	year = {2011},
	keywords = {Human breast cancer, Intraoperative imaging, Near-infrared fluorescence, Tissue-simulating phantoms},
	pages = {32--39},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/XQ9ARGA3/Pleijhuis et al. - 2011 - Near-infrared fluorescence (NIRF) imaging in breas.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/R4UGSEHR/S0748798310005482.html:text/html}
}

@article{venkataraju_assembling_????,
	title = {{ASSEMBLING} {LARGE} {MOSAICS} {OF} {ELECTRON} {MICROSCOPE} {IMAGES} {USING} {GPU}},
	url = {http://citeseerx.ist.psu.edu/viewdoc/citations?doi=10.1.1.163.213},
	abstract = {CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Abstract—Understanding the neural circuitry of the retina requires us to map the connectivity of individual neurons in large neuronal tissue sections and analyze signal communication across processes from the electron microscopy images. One of the major bottlenecks in the critical path is the image mosaicing process where 2D slices are assembled from scanned microscopy image tiles. The problem of assembling the tiles is computationally non-trivial because of distortion of the specimen in the electron microscope due to heat and overlap between the scanned tiles. The complexity of the calculation arises from the massive size of the dataset and mathematical calculations required to calculate value of each pixel of the mosaic. We propose to use texture memory lookups to speedup the access to image tiles and data parallel computing enabled by the GPUs to accelerate this process. The proposed method results in noticeable improvements in speed of computation compared to other methods. Index Terms—Serial-section TEM, image mosaicing, GPGPU, CUDA, texture},
	urldate = {2016-07-01},
	author = {Venkataraju, Kannan Umadevi and Kim, Mark and Gerszewski, Dan and Anderson, James R. and Hall, Mary},
	file = {saahpc09.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RP3SXCX9/saahpc09.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/AAVSPP3V/citations.html:text/html}
}

@article{xu_stacked_2015,
	title = {Stacked {Sparse} {Autoencoder} ({SSAE}) for {Nuclei} {Detection} on {Breast} {Cancer} {Histopathology} images},
	issn = {1558-254X},
	doi = {10.1109/TMI.2015.2458702},
	abstract = {Automated nuclear detection is a critical step for a number of computer assisted pathology related image analysis algorithms such as for automated grading of breast cancer tissue specimens. The Nottingham Histologic Score system is highly correlated with the shape and appearance of breast cancer nuclei in histopathological images. However, automated nucleus detection is complicated by (1) the large number of nuclei and the size of high resolution digitized pathology images, and (2) the variability in size, shape, appearance, and texture of the individual nuclei. Recently there has been interest in the application of "Deep Learning" strategies for classification and analysis of big image data. Histopathology, given its size and complexity, represents an excellent use case for application of deep learning strategies. In this paper, a Stacked Sparse Autoencoder (SSAE), an instance of a deep learning strategy, is presented for efficient nuclei detection on high-resolution histopathological images of breast cancer. The SSAE learns high-level features from just pixel intensities alone in order to identify distinguishing features of nuclei. A sliding window operation is applied to each image in order to represent image patches via high-level features obtained via the autoencoder, which are then subsequently fed to a classifier which categorizes each image patch as nuclear or nonnuclear. Across a cohort of 500 histopathological images (2200×2200) and approximately 3500 manually segmented individual nuclei serving as the groundtruth, SSAE was shown to have an improved F-measure 84:49\% and an average area under Precision-Recall curve (AveP) 78:83\%. The SSAE approach also out-performed 9 other state of the art nuclear detection strategies.},
	language = {ENG},
	journal = {IEEE transactions on medical imaging},
	author = {Xu, Jun and Xiang, Lei and Liu, Qinshan and Gilmore, Hannah and Wu, Jianzhong and Tang, Jinghai and Madabhushi, Anant},
	month = jul,
	year = {2015},
	pmid = {26208307}
}

@article{walsh_ex_2012,
	title = {Ex vivo optical metabolic measurements from cultured tissue reflect in vivo tissue status},
	volume = {17},
	issn = {1560-2281},
	doi = {10.1117/1.JBO.17.11.116015},
	abstract = {Optical measurements of metabolism are ideally acquired in vivo; however, intravital measurements are often impractical. Accurate ex vivo assessments would greatly broaden the applicability of optical measurements of metabolism. We investigate the use of live tissue culture experiments to serve as a surrogate for in vivo metabolic measurements. To validate this approach, NADH and FAD fluorescence intensity and lifetime images were acquired with a two-photon microscope from hamster cheek pouch epithelia in vivo, from biopsies maintained in live tissue culture up to 48 h, and from flash-frozen and thawed biopsies. We found that the optical redox ratio (fluorescence intensity of NADH/FAD) of the cultured biopsy was statistically identical to the in vivo measurement until 24 h, while the redox ratio of the frozen-thawed samples decreased by 15\% (p{\textless}0.01). The NADH mean fluorescence lifetime (τm) remained unchanged (p{\textgreater}0.05) during the first 8 h of tissue culture, while the NADH τm of frozen-thawed samples increased by 13\% (p{\textless}0.001). Cellular morphology did not significantly change between in vivo, cultured, and frozen-thawed tissues (p{\textgreater}0.05). All results were consistent across multiple depth layers in this stratified squamous epithelial tissue. Histological markers for proliferation and apoptosis also confirm the viability of tissues maintained in culture. This study suggests that short-term ex vivo tissue culture may be more appropriate than frozen-thawed tissue for optical metabolic and morphologic measurements that approximate in vivo status.},
	language = {eng},
	number = {11},
	journal = {Journal of Biomedical Optics},
	author = {Walsh, Alex J. and Poole, Kristin M. and Duvall, Craig L. and Skala, Melissa C.},
	month = nov,
	year = {2012},
	pmid = {23117810},
	pmcid = {PMC3484268},
	keywords = {Animals, Cheek, Cricetinae, Flavin-Adenine Dinucleotide, Mesocricetus, Metabolism, Microscopy, Fluorescence, Multiphoton, Mouth Mucosa, NAD, Optical Phenomena, Oxidation-Reduction, Tissue Culture Techniques},
	pages = {116015}
}

@article{nakamura_dynamic_2016,
	title = {Dynamic fluorescent imaging with the activatable probe, γ-glutamyl hydroxymethyl rhodamine green in the detection of peritoneal cancer metastases: {Overcoming} the problem of dilution when using a sprayable optical probe},
	issn = {1949-2553},
	shorttitle = {Dynamic fluorescent imaging with the activatable probe, γ-glutamyl hydroxymethyl rhodamine green in the detection of peritoneal cancer metastases},
	doi = {10.18632/oncotarget.9898},
	abstract = {Optical fluorescence-guided imaging is increasingly used to guide surgery and endoscopic procedures. Activatable probes are particularly useful because of high target-to-background ratios that increase sensitivity for tiny cancer foci. However, green fluorescent activatable probes suffer from interference from autofluorescence found in biological tissue. The purpose of this study was to determine if dynamic imaging can be used to differentiate specific fluorescence arising from an activated probe in a tumor from autofluorescence in background tissues especially when low concentrations of the dye are applied. Serial fluorescence imaging was performed using various concentrations of γ-glutamyl hydroxymethyl rhodamine green (gGlu-HMRG) which was sprayed on the peritoneal surface with tiny implants of SHIN3-DsRed ovarian cancer tumors. Temporal differences in signal between specific green fluorescence in cancer foci and non-specific autofluorescence in background tissue were measured at 5, 10, 20 and 30 min after application of gGlu-HMRG and were processed into three kinetic maps reflecting maximum fluorescence signal (MF), wash-in rate (WIR), and area under the curve (AUC), respectively. Using concentrations up to 10 μM of gGlu-HMRG, the fluorescence intensity of cancer foci was significantly higher than that of small intestine but only at 30 min. However, on kinetic maps derived from dynamic fluorescence imaging, the signal of cancer foci was significantly higher than that of small intestine after only 5 min even at concentrations as low as 2.5 μM of gGlu-HMRG (p {\textless} 0.01). At lower concentrations, kinetic maps derived from dynamic fluorescence imaging were superior to unprocessed images for cancer detection.},
	language = {ENG},
	journal = {Oncotarget},
	author = {Nakamura, Yuko and Harada, Toshiko and Nagaya, Tadanobu and Sato, Kazuhide and Okuyama, Shuhei and Choyke, Peter L. and Kobayashi, Hisataka},
	month = jun,
	year = {2016},
	pmid = {27286461},
	keywords = {autofluorescence, green emitting probe, kinetic map, peritoneal cancer metastases, γ-glutamyltranspeptidase},
	file = {9898-150775-1-PB.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6WMK2K7A/9898-150775-1-PB.pdf:application/pdf}
}

@incollection{tot_new_2011,
	title = {A {New} {Approach} to {Early} {Breast} {Cancer}},
	copyright = {©2011 Springer Science+Business Media B.V.},
	isbn = {978-94-007-0488-6 978-94-007-0489-3},
	url = {http://link.springer.com/chapter/10.1007/978-94-007-0489-3_1},
	abstract = {In the era of population-based organized mammographic screening, breast carcinoma is detected at an early stage of its natural history and corresponds to pure in situ carcinomas and/or invasive carcinomas {\textless} 15 mm in size in more than half of the cases. These tumours are characterized in general by less aggressive biological phenotypic parameters as compared with their more advanced counterparts, and they have an excellent long-term prognosis. Nevertheless, breast cancer in these early stages is already heterogeneous, and neither the first-generation prognostic factors (the tumour size, the extent of the in situ component, the lymph node status and the histology grade), nor the usual additional parameters (the receptor status and proliferation markers) are reliable enough to allow an estimate of the outcome. Newer approaches to a classification of early breast cancer include a consideration of the mammographic appearance, the extent of the disease instead of just the largest dimension of the main invasive focus, and the mode of detection or the use of molecular tests. Early breast cancers may occupy a relatively large area as they are multifocal and extensive in a considerable number of cases. Detailed preoperative characterization of the tumours with modern imaging methods and careful selection of the cases for individualized treatment ensure fewer complications and a long disease-free survival. Guidelines developed for the adjuvant therapy of operable breast cancers should not be implemented automatically for cancers in the very early stages. Most cancers in the very early stages do not need adjuvant systemic therapy; aggressive therapy should be reserved for high-risk cases. A further reduction of therapy-related risks may be achieved by the implementation of individualized radiotherapy or its avoidance in selected cases.},
	language = {en},
	urldate = {2016-06-23},
	booktitle = {Breast {Cancer}, a {Heterogeneous} {Disease} {Entity}},
	publisher = {Springer Netherlands},
	author = {Tot, Tibor and Kahán, Zsuzsanna},
	editor = {Kahán, Zsuzsanna},
	year = {2011},
	note = {DOI: 10.1007/978-94-007-0489-3\_1},
	keywords = {Cancer Research, Early breast cancer, Human Physiology, Individualized therapy, Mammographic screening, Pharmacology/Toxicology, Prognosis, Prognostic factors},
	pages = {1--22},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TMNEFSNM/Tot and Kahán - 2011 - A New Approach to Early Breast Cancer.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/BXU6GJMB/978-94-007-0489-3_1.html:text/html}
}

@article{dyment_relationships_2012,
	title = {The relationships among spatiotemporal collagen gene expression, histology, and biomechanics following full-length injury in the murine patellar tendon},
	volume = {30},
	copyright = {Copyright © 2011 Orthopaedic Research Society},
	issn = {1554-527X},
	url = {http://onlinelibrary.wiley.com.libproxy.tulane.edu:2048/doi/10.1002/jor.21484/abstract},
	doi = {10.1002/jor.21484},
	abstract = {Tendon injuries are major orthopedic problems that worsen as the population ages. Type-I (Col1) and type-II (Col2) collagens play important roles in tendon midsubstance and tendon-to-bone insertion healing, respectively. Using double transgenic mice, this study aims to spatiotemporally monitor Col1 and Col2 gene expression, histology, and biomechanics up to 8 weeks following a full-length patellar tendon injury. Gene expression and histology were analyzed weekly for up to 5 weeks while mechanical properties were measured at 1, 2, 5, and 8 weeks. At week 1, the healing region displayed loose granulation tissue with little Col1 expression. Col1 expression peaked at 2 weeks, but the ECM was highly disorganized and hypercellular. By 3 weeks, Col1 expression had reduced and by 5 weeks, the ECM was generally aligned along the tendon axis. Col2 expression was not seen in the healing midsubstance or insertion at any time point. The biomechanics of the healing tissue was inadequate at all time points, achieving ultimate loads and stiffnesses of 48\% and 63\% of normal values by 8 weeks. Future studies will further characterize the cells within the healing midsubstance and insertion using tenogenic markers and compare these results to those of tendon cells during normal development. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:28–36, 2012},
	language = {en},
	number = {1},
	urldate = {2014-11-03},
	journal = {Journal of Orthopaedic Research},
	author = {Dyment, Nathaniel A. and Kazemi, Namdar and Aschbacher-Smith, Lindsey E. and Barthelery, Nicolas J. and Kenter, Keith and Gooch, Cynthia and Shearn, Jason T. and Wylie, Christopher and Butler, David L.},
	month = jan,
	year = {2012},
	keywords = {collagen, healing, murine, Tendon, transgenic},
	pages = {28--36},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3N7TKHBW/Dyment et al. - 2012 - The relationships among spatiotemporal collagen ge.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/E6Q3P8JK/abstract.html:text/html}
}

@article{wu_emerging_2016,
	title = {The emerging roles of orphan nuclear receptors in prostate cancer},
	volume = {1866},
	issn = {0304-419X},
	url = {http://www.sciencedirect.com/science/article/pii/S0304419X16300415},
	doi = {10.1016/j.bbcan.2016.06.001},
	abstract = {Orphan nuclear receptors are members of the nuclear receptor (NR) superfamily and are so named because their endogenous physiological ligands are either unknown or may not exist. Because of their important regulatory roles in many key physiological processes, dysregulation of signalings controlled by these receptors is associated with many diseases including cancer. Over years, studies of orphan NRs have become an area of great interest because their specific physiological and pathological roles have not been well-defined, and some of them are promising drug targets for diseases. The recently identified synthetic small molecule ligands, acting as agonists or antagonists, to these orphan NRs not only help to understand better their functional roles but also highlight that the signalings mediated by these ligand-independent NRs in diseases could be therapeutically intervened. This review is a summary of the recent advances in elucidating the emerging functional roles of orphan NRs in cancers, especially prostate cancer. In particular, some orphan NRs, RORγ, TR2, TR4, COUP-IFII, ERRα, DAX1 and SHP, exhibit crosstalk or interference with androgen receptor (AR) signaling in either normal or malignant prostatic cells, highlighting their involvement in prostate cancer progression as androgen and AR signaling pathway play critical roles in this process. We also propose that a better understanding of the mechanism of actions of these orphan NRs in prostate gland or prostate cancer could help to evaluate their potential value as therapeutic targets for prostate cancer.},
	number = {1},
	urldate = {2016-11-28},
	journal = {Biochimica et Biophysica Acta (BBA) - Reviews on Cancer},
	author = {Wu, Dinglan and Cheung, Alyson and Wang, Yuliang and Yu, Shan and Chan, Franky L.},
	month = aug,
	year = {2016},
	keywords = {Androgen receptor signaling, Castration resistance, Metabolism, Orphan nuclear receptors, PROSTATE cancer},
	pages = {23--36},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MAACQIHI/Wu et al. - 2016 - The emerging roles of orphan nuclear receptors in .pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7WWKEMVJ/S0304419X16300415.html:text/html}
}

@patent{shroff_multi-focal_2013,
	title = {Multi-focal structured illumination microscopy systems and methods},
	url = {http://www.google.com/patents/WO2013126762A1},
	abstract = {A multi-focal selective illumination microscopy (SIM) system for generating multi-focal patterns of a sample is disclosed. The multi-focal SIM system performs a focusing, scaling and summing operation on each multi-focal pattern in a sequence of multi-focal patterns that completely scan the sample to produce a high resolution composite image.},
	assignee = {The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Office Of Technology Transfer, National Institutes Of Health},
	number = {WO2013126762 A1},
	urldate = {2016-07-05},
	author = {Shroff, Hari and YORK, Andrew},
	month = aug,
	year = {2013},
	note = {International Classification G02B21/00; Cooperative Classification G02B21/0076, G02B21/0036, G02B21/004, G02B21/0032}
}

@inproceedings{blattner_hybrid_2014,
	title = {A {Hybrid} {CPU}-{GPU} {System} for {Stitching} {Large} {Scale} {Optical} {Microscopy} {Images}},
	doi = {10.1109/ICPP.2014.9},
	abstract = {Researchers in various fields are using optical microscopy to acquire very large images, 10000 - 200000 of pixels per side. Optical microscopes acquire these images as grids of overlapping partial images (thousands of pixels per side) that are then stitched together via software. Composing such large images is a compute and data intensive task even for modern machines. Researchers compound this difficulty further by obtaining time-series, volumetric, or multiple channel images with the resulting data sets now having or approaching terabyte sizes. We present a scalable hybrid CPU-GPU implementation of image stitching that processes large image sets at near interactive rates. Our implementation scales well with both image sizes and the number of CPU cores and GPU cards in a machine. It processes a grid of 42 × 59 tiles into a 17 k × 22 k pixels image in 43 s (end-to-end execution times) when using one NVIDIA Tesla C2070 card and two Intel Xeon E-5620 quad-core CPUs, and in 29 s when using two Tesla C2070 cards and the same two CPUs. It also composes and renders the composite image without saving it in 15 s. In comparison, ImageJ/Fiji, which is widely used by biologists, has an image stitching plugin that takes {\textgreater} 3.6 h for the same workload despite being multithreaded and executing the same mathematical operators, it composes and saves the large image in an additional 1.5 h. This implementation takes advantage of coarse-grain parallelism. It organizes the computation into a pipeline architecture that spans CPU and GPU resources and overlaps computation with data motion. The implementation achieves a nearly 10× performance improvement over our optimized non-pipeline GPU implementation and demonstrates near-linear speedup when increasing CPU thread count and increasing number of GPUs.},
	booktitle = {2014 43rd {International} {Conference} on {Parallel} {Processing}},
	author = {Blattner, T. and Keyrouz, W. and Chalfoun, J. and Stivalet, B. and Brady, M. and Zhou, S.},
	month = sep,
	year = {2014},
	keywords = {coarse-grain parallelism, Correlation, graphics processing units, Heterogeneous (hybrid) systems, hybrid CPU-GPU implementation, Hybrid systems, Image processing, image stitching plugin, Intel Xeon E-5620 quad-core CPU, Kernel, large scale optical microscopy image, Microscopy, NVIDIA Tesla C2070 card, optical images, optical microscopy, Parallel Architectures, pipeline architecture, pipeline processing, Random access memory, Scheduling and task partitioning, Transforms},
	pages = {1--9},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/GRDWIAA8/freeabs_all.html:text/html}
}

@article{frangioni_new_2008,
	title = {New {Technologies} for {Human} {Cancer} {Imaging}},
	volume = {26},
	issn = {0732-183X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654310/},
	doi = {10.1200/JCO.2007.14.3065},
	abstract = {Despite technical advances in many areas of diagnostic radiology, the detection and imaging of human cancer remains poor. A meaningful impact on cancer screening, staging, and treatment is unlikely to occur until the tumor-to-background ratio improves by three to four orders of magnitude (ie, 103- to 104-fold), which in turn will require proportional improvements in sensitivity and contrast agent targeting. This review analyzes the physics and chemistry of cancer imaging and highlights the fundamental principles underlying the detection of malignant cells within a background of normal cells. The use of various contrast agents and radiotracers for cancer imaging is reviewed, as are the current limitations of ultrasound, x-ray imaging, magnetic resonance imaging (MRI), single-photon emission computed tomography, positron emission tomography (PET), and optical imaging. Innovative technologies are emerging that hold great promise for patients, such as positron emission mammography of the breast and spectroscopy-enhanced colonoscopy for cancer screening, hyperpolarization MRI and time-of-flight PET for staging, and ion beam-induced PET scanning and near-infrared fluorescence-guided surgery for cancer treatment. This review explores these emerging technologies and considers their potential impact on clinical care. Finally, those cancers that are currently difficult to image and quantify, such as ovarian cancer and acute leukemia, are discussed.},
	number = {24},
	urldate = {2016-06-22},
	journal = {Journal of Clinical Oncology},
	author = {Frangioni, John V.},
	month = aug,
	year = {2008},
	pmid = {18711192},
	pmcid = {PMC2654310},
	pages = {4012--4021},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3527SIVD/Frangioni - 2008 - New Technologies for Human Cancer Imaging.pdf:application/pdf}
}

@article{meyer_breast_2005,
	title = {Breast carcinoma malignancy grading by {Bloom}–{Richardson} system vs proliferation index: reproducibility of grade and advantages of proliferation index},
	volume = {18},
	copyright = {© 2005 Nature Publishing Group},
	issn = {0893-3952},
	shorttitle = {Breast carcinoma malignancy grading by {Bloom}–{Richardson} system vs proliferation index},
	url = {http://www.nature.com/modpathol/journal/v18/n8/full/3800388a.html},
	doi = {10.1038/modpathol.3800388},
	abstract = {Questions of reproducibility and efficacy of histologic malignancy grading relative to alternative proliferation index measurements for outcome prediction remain unanswered. Microsections of specimens from the Cooperative Breast Cancer Tissue Resource (CBCTR) were evaluated by seven pathologists for reproducibility of grade and classification. Nuclear figure classification was assessed using photographs. Grade was assigned by the Bloom–Richardson method, Nottingham modification. Proliferation index was evaluated prospectively by deoxyribose nucleic acid precursor uptake with thymidine (autoradiographic) or bromodeoxyuridine (immunohistochemical) labeling index using fresh tissue from 631 node-negative breast cancer patients accessioned at St Luke's Hospital. A modified Nottingham–Bloom–Richardson grade was derived from histopathologic data. Median post-treatment observation was 6.4 years. Agreement on classification of nuclear figures (N=43) was less than good by kappa statistic (=0.38). Grade was moderately reproducible in four trials (N=10,10,19, 10) with CBCTR specimens (=0.50–0.59). Of components of Bloom–Richardson grade, agreement was least for nuclear pleomorphism (=0.37–0.50), best for tubularity (=0.57–0.83), and intermediate for mitotic count (=0.45–0.64). Bloom–Richardson grade was a univariate predictor of prognosis in node-negative St Luke's patients, and was improved when mitotic count was replaced by labeling index (low, mid, or high). When labeling index was added to a multivariate model containing tumor size and vessel invasion, grade was no longer a significant predictor of tumor-specific relapse-free or overall survival. Mitotic index predicted best when intervals were lowered to 0–2, 3–10, and {\textgreater}10 mitotic figures per ten 0.18 mm2 high-power fields. We conclude that Nottingham–Bloom–Richardson grades remain only modestly reproducible. Prognostically useful components of grade are mitotic index and tubularity. The Nottingham–Bloom–Richardson system can be improved by lowering cutoffs for mitotic index and by counting 20–30 rather than 10 high-power fields. Measurement of proliferation index by immunohistochemically detectable markers will probably give superior prognostic results in comparison to grade.},
	language = {en},
	number = {8},
	urldate = {2015-09-01},
	journal = {Modern Pathology},
	author = {Meyer, John S. and Alvarez, Consuelo and Milikowski, Clara and Olson, Neal and Russo, Irma and Russo, Jose and Glass, Andrew and Zehnbauer, Barbara A. and Lister, Karen and Parwaresch, Reza},
	month = may,
	year = {2005},
	keywords = {Bloom–Richardson, breast neoplasms, bromodeoxyuridine, cell kinetics, grade, proliferation, reproducibility},
	pages = {1067--1078},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/TRFGXNVW/Meyer et al. - 2005 - Breast carcinoma malignancy grading by Bloom–Richa.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/Q4N8QASV/Meyer et al. - 2005 - Breast carcinoma malignancy grading by Bloom–Richa.html:text/html}
}

@misc{_histological_????,
	title = {Histological {Grading} of {Breast} {Cancer}},
	url = {http://tvmouse.ucdavis.edu/bcancercd/311/grading_diagram.html},
	urldate = {2016-06-25},
	file = {Histological Grading of Breast Cancer:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W4D9ZSVP/grading_diagram.html:text/html}
}

@article{keating_advances_2016,
	title = {Advances in {Intraoperative} {Margin} {Assessment} for {Breast} {Cancer}},
	volume = {4},
	issn = {2167-4817},
	url = {http://link.springer.com.libproxy.tulane.edu:2048/article/10.1007/s40137-016-0136-3},
	doi = {10.1007/s40137-016-0136-3},
	abstract = {Breast-conserving therapy including partial mastectomy and radiation is commonly performed for patients who are surgical candidates for breast cancer. Although it is as effective as mastectomy for the treatment of early breast cancer, re-excision for positive or close margins is common. This is costly, inconvenient for patients and delays initiation of adjuvant therapies. Commonly used methods for breast tumor localization and optimization of margin assessment include preoperative wire or seed localization, precise specimen orientation, specimen radiography, and cavity shaving. Unfortunately, these techniques do not assess margins on a microscopic scale in real time. Our report reviews the current and experimental techniques of intraoperative microscopic margin assessment including frozen section, cytologic imprint analysis, ultrasound, micro-CT, MarginProbe ® , near-infrared imaging, and spectroscopy.},
	language = {en},
	number = {4},
	urldate = {2016-06-30},
	journal = {Current Surgery Reports},
	author = {Keating, Jane J. and Fisher, Carla and Batiste, Rebecca and Singhal, Sunil},
	month = mar,
	year = {2016},
	pages = {1--8},
	file = {art%3A10.1007%2Fs40137-016-0136-3.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/ZXWMA46G/art%3A10.1007%2Fs40137-016-0136-3.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/HDTNFP2B/s40137-016-0136-3.html:text/html}
}

@inproceedings{kohavi_study_1995,
	title = {A study of cross-validation and bootstrap for accuracy estimation and model selection},
	volume = {14},
	url = {https://pdfs.semanticscholar.org/0be0/d781305750b37acb35fa187febd8db67bfcc.pdf},
	urldate = {2016-07-03},
	booktitle = {Ijcai},
	author = {Kohavi, Ron and {others}},
	year = {1995},
	pages = {1137--1145},
	file = {accEst.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/MPN3TU8A/accEst.pdf:application/pdf}
}

@article{schnitt_should_2012-1,
	title = {Should {Intraoperative} {Frozen} {Section} {Evaluation} of {Breast} {Lumpectomy} {Margins} {Become} {Routine} {Practice}?},
	volume = {138},
	copyright = {© American Society for Clinical Pathology},
	issn = {0002-9173, 1943-7722},
	url = {http://ajcp.oxfordjournals.org/content/138/5/635},
	doi = {10.1309/AJCPPQ1JGV0GJIAB},
	abstract = {In this issue of the Journal , Jorns et al1 report that intraoperative frozen section examination of breast lumpectomy margins was associated with a substantial reduction in the rate of reexcision. In their retrospective study, at some time after the initial lumpectomy a reexcision was performed in 48.9\% of patients who did not have frozen section margin evaluation compared with only 14.9\% of those in whom frozen section evaluation of the margins was performed. Further, these investigators developed a technique to overcome the methodological difficulties of attempting to cut frozen sections of fatty tissue such as margins of breast specimens. So if it is now technically feasible to obtain adequate frozen sections from lumpectomy margins and if intraoperative frozen section evaluations of these margins can reduce the need for a subsequent reexcision by almost 70\%, should pathologists the world over be gearing up to routinely freeze margins of breast lumpectomy specimens? To answer this question, we must first review some fundamental data on lumpectomy margins and their association with local recurrence, and put these data into current clinical context.

Various patient factors, treatment factors, and pathologic factors have been reported to be associated with an increased risk of recurrence in the ipsilateral breast (local recurrence) after breast-conserving treatment for invasive breast cancer and ductal carcinoma in situ (DCIS). Arguably the most important of these is the status of the microscopic margins of excision of the resected breast specimen. Positive margins (ie, invasive carcinoma or DCIS at an inked tissue edge) have consistently been associated with a higher risk of local recurrence than negative margins.2 Therefore, obtaining negative margins is the primary goal of breast-conserving surgery. Unfortunately, there is far from universal agreement as to what constitutes an adequate negative margin. In fact, results of surveys of surgeons and …},
	language = {en},
	number = {5},
	urldate = {2016-06-22},
	journal = {American Journal of Clinical Pathology},
	author = {Schnitt, Stuart J. and Morrow, Monica},
	month = nov,
	year = {2012},
	pmid = {23086762},
	pages = {635--638},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/35TAIFPG/Schnitt and Morrow - 2012 - Should Intraoperative Frozen Section Evaluation of.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/K2II2FM9/635.html:text/html}
}

@article{fajdic_criteria_2013,
	title = {Criteria and {Procedures} for {Breast} {Conserving} {Surgery}},
	volume = {21},
	issn = {0353-8109},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610577/},
	doi = {10.5455/AIM.2013.21.16-19},
	abstract = {Aim
Emphasizing circumstances that determine increasingly popular surgical approach of breast conserving surgery (BCS), used in lower grade breast tumors, while maintaining survival that is found when more radical procedures are used.

Patients and methods
Several leading oncological protocols in the world are compared, using PubMed database, and our own experience. Data gathered are compared to conclusions of Consensus Conference on Breast Conservation (Milan, 2005). Furthermore, surgical contraindications found in our everyday work are considered, having in mind satisfactory cosmetic outcome, as well as keeping the 1 cm border of “clear” edges. Such more practical problems of edge detection can compromise BCS results.

Results
After observing several relevant protocols, we found very high frequency of mastectomy vs. BCS, despite the fact that stage of disease was low. We also found only 20\% of absolute contraindications for BCS. Most frequent contraindication for BCS was multicentricity of the tumor (with micro calcifications), especially in ductal in situ carcinoma.

Conclusion
BCS followed by radiation therapy with tumor-free edges is standard procedure in treatment of T1 and small T2 breast cancers. This approach implies higher risk of local recurrence (LR), although local recurrence is low (1\% per year), with rates of survival similar to radical procedures.},
	number = {1},
	urldate = {2016-06-22},
	journal = {Acta Informatica Medica},
	author = {Fajdic, Josip and Djurovic, Drazen and Gotovac, Nikola and Hrgovic, Zlatko},
	month = mar,
	year = {2013},
	pmid = {23572855},
	pmcid = {PMC3610577},
	pages = {16--19},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/4QEQQD37/Fajdic et al. - 2013 - Criteria and Procedures for Breast Conserving Surg.pdf:application/pdf}
}

@article{lopez-abente_breast_2014,
	title = {Breast and prostate cancer: an analysis of common epidemiological features in mortality trends in {Spain}},
	volume = {14},
	copyright = {2014 López-Abente et al.; licensee BioMed Central Ltd.},
	issn = {1471-2407},
	shorttitle = {Breast and prostate cancer},
	url = {http://www.biomedcentral.com/1471-2407/14/874/abstract},
	doi = {10.1186/1471-2407-14-874},
	abstract = {PMID: 25421124},
	language = {en},
	number = {1},
	urldate = {2015-08-31},
	journal = {BMC Cancer},
	author = {López-Abente, Gonzalo and Mispireta, Sergio and Pollán, Marina},
	month = nov,
	year = {2014},
	pmid = {25421124},
	keywords = {Age-period-cohort, Breast cancer, Epidemiology, Prostate cancer, Spain},
	pages = {874},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/W6CRA9FJ/López-Abente et al. - 2014 - Breast and prostate cancer an analysis of common .pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3VQ3B2TV/López-Abente et al. - 2014 - Breast and prostate cancer an analysis of common .html:text/html}
}

@book{cooper_cell_2000,
	edition = {2nd},
	title = {The {Cell}},
	isbn = {978-0-87893-106-4},
	abstract = {ExcerptAs in the first edition, The Cell is focused on the molecular biology of cells as a unifying theme, with specialized topics discussed throughout the book as examples of more general principles. Aspects of developmental biology, the immune system, the nervous system, and plant biology are thus discussed in their broader biological context in chapters covering areas such as genome structure, gene expression, DNA rearrangements, the plasma membrane, cell signaling, and the cell cycle. Relationships between cell biology and medicine are similarly discussed throughout the text, as well as being highlighted in the Molecular Medicine essays that are included as a special feature in each chapter. These discussions illustrate the striking impact of molecular and cellular biology on human health, and are intended to stimulate as well as inform those students interested in medicine.},
	publisher = {Sinauer Associates},
	author = {Cooper, Geoffrey M.},
	year = {2000}
}

@article{dinardo_accuracy_2000,
	title = {Accuracy, {Utility}, and {Cost} of {Frozen} {Section} {Margins} in {Head} and {Neck} {Cancer} {Surgery}},
	volume = {110},
	copyright = {Copyright © 2000 The Triological Society},
	issn = {1531-4995},
	url = {http://onlinelibrary.wiley.com/doi/10.1097/00005537-200010000-00039/abstract},
	doi = {10.1097/00005537-200010000-00039},
	abstract = {Objectives Intraoperative frozen section analysis of surgical margins is widely used in head and neck cancer surgery. This study evaluates frozen section accuracy relative to permanent controls and final margins from the entire specimen, the rate at which frozen sections impact intraoperative management, and the resultant cost. Study Design Retrospective. Methods From 1997 to 1999 the frozen section results, permanent controls, and final tumor margins from 80 consecutive patients undergoing 420 intraoperative frozen section margins for head and neck malignancy were reviewed. Results A 98.3\% accuracy rate (sensitivity, 88.8\%; specificity, 98.9\%) was found compared with permanent sections of the same tissue. However, 40\% (8 of 20) of patients with positive final margins on the resection specimen, and 100\% (15 of 15) with close ({\textless}5 mm) margins were not detected by frozen section analysis. The overall accuracy of frozen section in the evaluation of close or positive final margins was 71.3\% (sensitivity, 34.3\%; specificity, 100\%). In addition, 5\% (4 of 80) of patients potentially benefited from intraoperative frozen section by virtue of immediate margin revision. The estimated cost of intraoperative frozen section averaged as much as \$3123 per patient, with a cost-benefit ratio of 20:1. Conclusions Intraoperative frozen section margins are accurate, but they are costly and cannot reliably eradicate positive final margins. Patients with early-stage lesions and those undergoing re-resection for recurrence or salvage surgery after radiation failure derived the greatest potential benefit from frozen section margins.},
	language = {en},
	number = {10},
	urldate = {2016-07-05},
	journal = {The Laryngoscope},
	author = {DiNardo, Laurence J. and Lin, James and Karageorge, Lampros S. and Powers, Celeste N.},
	month = oct,
	year = {2000},
	keywords = {Frozen section, head and neck cancer, tumor margins.},
	pages = {1773--1776},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NHKITHVJ/DiNardo et al. - 2000 - Accuracy, Utility, and Cost of Frozen Section Marg.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T4XG8BUQ/abstract\;jsessionid=38996782539257F27A0FF75D0B452897.html:text/html}
}

@article{cooper_nucleus_2000,
	title = {The {Nucleus} during {Mitosis}},
	url = {http://www.ncbi.nlm.nih.gov/books/NBK9890/},
	abstract = {A unique feature of the nucleus is that it disassembles and re-forms each time most cells divide. At the beginning of mitosis, the chromosomes condense, the nucleolus disappears, and the nuclear envelope breaks down, resulting in the release of most of the contents of the nucleus into the cytoplasm. At the end of mitosis, the process is reversed: The chromosomes decondense, and nuclear envelopes re-form around the separated sets of daughter chromosomes. Chapter 14 presents a comprehensive discussion of mitosis; in this section we will consider the mechanisms involved in the disassembly and re-formation of the nucleus. The process is controlled largely by reversible phosphorylation and dephosphorylation of nuclear proteins resulting from the action of the Cdc2 protein kinase, which is a critical regulator of mitosis in all eukaryotic cells.},
	language = {en},
	urldate = {2016-07-02},
	author = {Cooper, Geoffrey M.},
	year = {2000},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IKQE6D87/NBK9890.html:text/html}
}

@inproceedings{naik_automated_2008,
	title = {Automated gland and nuclei segmentation for grading of prostate and breast cancer histopathology},
	doi = {10.1109/ISBI.2008.4540988},
	abstract = {Automated detection and segmentation of nuclear and glandular structures is critical for classification and grading of prostate and breast cancer histopathology. In this paper, we present a methodology for automated detection and segmentation of structures of interest in digitized histopathology images. The scheme integrates image information from across three different scales: (1) low- level information based on pixel values, (2) high-level information based on relationships between pixels for object detection, and (3) domain-specific information based on relationships between histological structures. Low-level information is utilized by a Bayesian classifier to generate a likelihood that each pixel belongs to an object of interest. High-level information is extracted in two ways: (i) by a level-set algorithm, where a contour is evolved in the likelihood scenes generated by the Bayesian classifier to identify object boundaries, and (ii) by a template matching algorithm, where shape models are used to identify glands and nuclei from the low-level likelihood scenes. Structural constraints are imposed via domain- specific knowledge in order to verify whether the detected objects do indeed belong to structures of interest. In this paper we demonstrate the utility of our glandular and nuclear segmentation algorithm in accurate extraction of various morphological and nuclear features for automated grading of (a) prostate cancer, (b) breast cancer, and (c) distinguishing between cancerous and benign breast histology specimens. The efficacy of our segmentation algorithm is evaluated by comparing breast and prostate cancer grading and benign vs. cancer discrimination accuracies with corresponding accuracies obtained via manual detection and segmentation of glands and nuclei.},
	booktitle = {5th {IEEE} {International} {Symposium} on {Biomedical} {Imaging}: {From} {Nano} to {Macro}, 2008. {ISBI} 2008},
	author = {Naik, S. and Doyle, S. and Agner, S. and Madabhushi, A. and Feldman, M. and Tomaszewski, J.},
	month = may,
	year = {2008},
	keywords = {automated gland segmentation, Bayesian classifier, Bayesian methods, Breast cancer, breast cancer histopathology, cancer, Cancer detection, Data mining, Detection, Glands, Grading, Image segmentation, image segmentation, Layout, level-set algorithm, mammography, medical computing, medical image processing, nuclei segmentation, Object detection, Pixel, Prostate cancer, prostate cancer, Segmentation},
	pages = {284--287},
	file = {04540988.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/A6R7USNI/04540988.pdf:application/pdf;IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/2X8WUB9N/Naik et al. - 2008 - Automated gland and nuclei segmentation for gradin.html:text/html}
}

@article{popovici_joint_2016,
	title = {Joint analysis of histopathology image features and gene expression in breast cancer},
	volume = {17},
	issn = {1471-2105},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864935/},
	doi = {10.1186/s12859-016-1072-z},
	abstract = {Background
Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-host interactions that is not accessible through these techniques. Thus, integrating the histopathology images in the biomarker discovery workflow could potentially lead to the identification of new image-based biomarkers and the refinement or even replacement of the existing genomic and proteomic signatures. However, extracting meaningful and robust image features to be mined jointly with genomic (and clinical, etc.) data represents a real challenge due to the complexity of the images.

Results
We developed a framework for integrating the histopathology images in the biomarker discovery workflow based on the bag-of-features approach – a method that has the advantage of being assumption-free and data-driven. The images were reduced to a set of salient patterns and additional measurements of their spatial distribution, with the resulting features being directly used in a standard biomarker discovery application. We demonstrated this framework in a search for prognostic biomarkers in breast cancer which resulted in the identification of several prognostic image features and a promising multimodal (imaging and genomic) prognostic signature. The source code for the image analysis procedures is freely available.

Conclusions
The framework proposed allows for a joint analysis of images and gene expression data. Its application to a set of breast cancer cases resulted in image-based and combined (image and genomic) prognostic scores for relapse-free survival.

Electronic supplementary material
The online version of this article (doi:10.1186/s12859-016-1072-z) contains supplementary material, which is available to authorized users.},
	urldate = {2016-06-27},
	journal = {BMC Bioinformatics},
	author = {Popovici, Vlad and Budinská, Eva and Čápková, Lenka and Schwarz, Daniel and Dušek, Ladislav and Feit, Josef and Jaggi, Rolf},
	month = may,
	year = {2016},
	pmid = {27170365},
	pmcid = {PMC4864935},
	file = {12859_2016_Article_1072.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/SG6SCWN9/12859_2016_Article_1072.pdf:application/pdf}
}

@misc{health_exporting_????,
	type = {{WebContent}},
	title = {Exporting {Medical} {Devices}},
	url = {http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/ImportingandExportingDevices/ExportingMedicalDevices/default.htm},
	language = {en},
	urldate = {2015-11-22},
	author = {Health, Center for Devices {and} Radiological},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/3EKWMSUS/default.html:text/html}
}

@misc{health_medical_????-1,
	type = {{WebContent}},
	title = {Medical {Device} {User} {Fee} {Amendments} ({MDUFA})},
	url = {http://www.fda.gov/ForIndustry/UserFees/MedicalDeviceUserFee/ucm20081521.htm},
	language = {en},
	urldate = {2015-11-22},
	author = {Health, Center for Devices {and} Radiological},
	file = {Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/RXZW674G/ucm20081521.html:text/html}
}

@article{campbell_learning_2011-1,
	title = {Learning with {Support} {Vector} {Machines}},
	volume = {5},
	issn = {1939-4608},
	url = {http://www.morganclaypool.com.libproxy.tulane.edu:2048/doi/abs/10.2200/S00324ED1V01Y201102AIM010},
	doi = {10.2200/S00324ED1V01Y201102AIM010},
	number = {1},
	urldate = {2016-07-05},
	journal = {Synthesis Lectures on Artificial Intelligence and Machine Learning},
	author = {Campbell, Colin and Ying, Yiming},
	month = feb,
	year = {2011},
	pages = {1--95},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JQ98UN3X/Campbell and Ying - 2011 - Learning with Support Vector Machines.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/7K2SX5FP/S00324ED1V01Y201102AIM010.html:text/html}
}

@article{emmadi_evaluation_2012,
	title = {Evaluation of {Resection} {Margins} in {Breast} {Conservation} {Therapy}: {The} {Pathology} {Perspective}\&\#x2014;{Past}, {Present}, and {Future}, {Evaluation} of {Resection} {Margins} in {Breast} {Conservation} {Therapy}: {The} {Pathology} {Perspective}\&\#x2014;{Past}, {Present}, and {Future}},
	volume = {2012, 2012},
	issn = {2090-1402, 2090-1402},
	shorttitle = {Evaluation of {Resection} {Margins} in {Breast} {Conservation} {Therapy}},
	url = {http://www.hindawi.com/journals/ijso/2012/180259/abs/, http://www.hindawi.com/journals/ijso/2012/180259/abs/},
	doi = {10.1155/2012/180259, 10.1155/2012/180259},
	abstract = {Tumor surgical resection margin status is important for any malignant lesion. When this occurs in conjunction with efforts to preserve or conserve the afflicted organ, these margins become extremely important. With the demonstration of no difference in overall survival between mastectomy versus lumpectomy and radiation for breast carcinoma, there is a definite trend toward smaller resections combined with radiation, constituting \&\#x201c;breast-conserving therapy.\&\#x201d; Tumor-free margins are therefore key to the success of this treatment protocol. We discuss the various aspects of margin status in this setting, from a pathology perspective, incorporating the past and current practices with a brief glimpse of emerging future techniques., Tumor surgical resection margin status is important for any malignant lesion. When this occurs in conjunction with efforts to preserve or conserve the afflicted organ, these margins become extremely important. With the demonstration of no difference in overall survival between mastectomy versus lumpectomy and radiation for breast carcinoma, there is a definite trend toward smaller resections combined with radiation, constituting \&\#x201c;breast-conserving therapy.\&\#x201d; Tumor-free margins are therefore key to the success of this treatment protocol. We discuss the various aspects of margin status in this setting, from a pathology perspective, incorporating the past and current practices with a brief glimpse of emerging future techniques.},
	language = {en},
	urldate = {2016-06-24},
	journal = {International Journal of Surgical Oncology, International Journal of Surgical Oncology},
	author = {Emmadi, Rajyasree and Wiley, Elizabeth L. and Emmadi, Rajyasree and Wiley, Elizabeth L.},
	month = nov,
	year = {2012},
	pages = {e180259},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/E4NWNBCX/Emmadi et al. - 2012 - Evaluation of Resection Margins in Breast Conserva.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/6X2688NF/180259.html:application/xhtml+xml}
}

@article{cannizzaro_endomicroscopy_2012,
	title = {Endomicroscopy and {Cancer}: {A} {New} {Approach} to the {Visualization} of {Neoangiogenesis}},
	volume = {2012},
	issn = {1687-6121},
	shorttitle = {Endomicroscopy and {Cancer}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263616/},
	doi = {10.1155/2012/537170},
	abstract = {Probe-based Confocal Laser Endomicroscopy (pCLE) is a novel imaging technique for gastrointestinal endoscopy providing in vivo microscopy at subcellular resolution. It offers the possibility to analyze neoangiogenesis and vessel density in vivo. Angiogenetic switch is essential in cancer progression. Aim of the paper was to review the use of this imaging tool to analyze colorectal and gastric cancers vascularization in vivo. The aim is to provide the possibility of combining diagnostic evidences with vascularization and molecular profile to evaluate the efficacy of an antiangiogenic treatment in association with conventional therapy. pCLE can be considered a revolutionary method for real-time assessment of changes in vascularization pattern in this tumors and it may open the possibility to address the use of anti-angiogenic therapy in order to improve the outcome of the treatment.},
	urldate = {2016-06-21},
	journal = {Gastroenterology Research and Practice},
	author = {Cannizzaro, Renato and Mongiat, Maurizio and Canzonieri, Vincenzo and Fornasarig, Mara and Maiero, Stefania and De Re, Valli and Todaro, Federico and De Paoli, Paolo and Spessotto, Paola},
	year = {2012},
	pmid = {22287958},
	pmcid = {PMC3263616},
	file = {PubMed Central Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/JVW6U4EE/Cannizzaro et al. - 2012 - Endomicroscopy and Cancer A New Approach to the V.pdf:application/pdf}
}

@article{barton_ahmed_2011,
	title = {The {Ahmed} {Baerveldt} {Comparison} {Study}: {Methodology}, {Baseline} {Patient} {Characteristics}, and {Intraoperative} {Complications}},
	volume = {118},
	issn = {0161-6420},
	shorttitle = {The {Ahmed} {Baerveldt} {Comparison} {Study}},
	url = {http://www.sciencedirect.com/science/article/pii/S0161642010007529},
	doi = {10.1016/j.ophtha.2010.07.015},
	abstract = {Purpose
The Ahmed Baerveldt Comparison (ABC) Study compares the long-term outcomes and complications of the Ahmed glaucoma valve (AGV; model FP7; New World Medical, Los Ranchos, CA) and the Baerveldt glaucoma implant (BGI; model 101-350; Abbott Medical Optics, Abbott Park, IL).
Design
Multicenter, randomized, controlled clinical trial.
Participants
Two hundred seventy-six glaucoma patients at 16 clinical centers worldwide who were 18 to 85 years of age with inadequately controlled intraocular pressure (IOP; ≥18 mmHg) in whom placement of an aqueous shunt was planned.
Methods
Study patients were randomized to undergo implantation of an AGV or a BGI.
Main Outcome Measures
Failure, defined as IOP \&gt;21 mmHg or not reduced by 20\% less than baseline or IOP ≤5 mmHg (2 consecutive visits after 3 months), additional glaucoma surgery, removal of the implant, or loss of light perception vision.
Results
A total of 276 patients were enrolled between October 2006 and April 2008, including 143 in the AGV group and 133 in the BGI group. The mean age±standard deviation (SD) of patients enrolled was 63±14 years, and 52\% were male. The mean baseline IOP±SD was 31.5±11.8 mmHg. Except for a 13\% higher prevalence of hypertension in the AGV group, no significant differences in baseline demographic or ocular characteristics were observed between the study groups. Intraoperative complications occurred in 11 (8\%) patients in the AGV group and in 16 (12\%) patients in the BGI group (P = 0.31).
Conclusions
The ABC Study should yield valuable prospective data comparing 2 commonly used aqueous shunts in clinical practice.
Financial Disclosure(s)
Proprietary or commercial disclosure may be found after the references.},
	number = {3},
	urldate = {2015-11-22},
	journal = {Ophthalmology},
	author = {Barton, Keith and Gedde, Steven J. and Budenz, Donald L. and Feuer, William J. and Schiffman, Joyce},
	month = mar,
	year = {2011},
	pages = {435--442},
	file = {ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T8I87RH8/S0161642010007529.html:text/html}
}

@article{wan_automated_????,
	title = {Automated grading of breast cancer histopathology using cascaded ensemble with combination of multi-level image features},
	issn = {0925-2312},
	url = {http://www.sciencedirect.com/science/article/pii/S0925231216305471},
	doi = {10.1016/j.neucom.2016.05.084},
	abstract = {We present a novel image-analysis based method for automatically distinguishing low, intermediate, and high grades of breast cancer in digitized histopathology. A multiple level feature set, including pixel-, object-, and semantic-level features derived from convolutional neural networks (CNN), is extracted from 106 hematoxylin and eosin stained breast biopsy tissue studies from 106 women patients. These multi-level features allow not only characterization of cancer morphology, but also extraction of structural and interpretable information within the histopathological images. In this study, an improved hybrid active contour model based segmentation method was used to segment nuclei from the images. The semantic-level features were extracted by a CNN approach, which described the proportions of nuclei belonging to the different grades, in conjunction with pixel-level (texture) and object-level (architecture) features, to create an integrated set of image attributes that can potentially outperform either subtype of features individually. We utilized a cascaded approach to train multiple support vector machine (SVM) classifiers using combinations of feature subtypes to enable the possibility of maximizing the performance by leveraging different feature sets extracted from multiple levels. Final class (cancer grade) was determined by combining the scores produced by the individual SVM classifiers. By employing a light (three-layer) CNN model and parallel computing, the presented approach is computationally efficient and applicable to large-scale datasets. The method achieved an accuracy of 0.92 for low versus high, 0.77 for low versus intermediate, and 0.76 for intermediate versus high, and an overall accuracy of 0.69 when discriminating low, intermediate, and high grades of histopathological breast cancer images. This suggested that our grading method could be useful in developing a computational diagnostic tool for differentiating breast cancer grades, which might enable objective and reproducible alternative for diagnosis.},
	urldate = {2016-06-25},
	journal = {Neurocomputing},
	author = {Wan, Tao and Cao, Jiajia and Chen, Jianhui and Qin, Zengchang},
	keywords = {Breast cancer grading, Cascaded ensemble, Convolutional neural networks, histopathology, Multi-level features},
	file = {1-s2.0-S0925231216305471-main.pdf:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/F3HTW9EN/1-s2.0-S0925231216305471-main.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/NS9C5RHT/S0925231216305471.html:text/html}
}

@article{beck_systematic_2011,
	title = {Systematic {Analysis} of {Breast} {Cancer} {Morphology} {Uncovers} {Stromal} {Features} {Associated} with {Survival}},
	volume = {3},
	copyright = {Copyright © 2011, American Association for the Advancement of Science},
	issn = {1946-6234, 1946-6242},
	url = {http://stm.sciencemag.org/content/3/108/108ra113},
	doi = {10.1126/scitranslmed.3002564},
	abstract = {An Automated Pathologist Reads Cancer Biopsies
How is a camera different from the human eye? Only the eye’s images undergo extensive secondary processing as they are interpreted by the human brain. But what if we could program a computer to do the secondary processing? A pathologist reading a cancer biopsy slide matches his or her brain’s memory of certain cancer-related features (tubules, atypical nuclei, and mitosis) against the tissue. This decades-old scoring system is still standard in most places for prognosis and treatment of cancer, despite its variability and often unreliability. Now, Beck et al. have created an automated pathologist by replacing the human brain with sophisticated image processing software and instructing it to find quantitative aspects of breast cancer tissue that predict prognosis. The software located a set of features that strongly predicted breast cancer outcome in both training and validation samples.
With an image analysis protocol they termed C-Path, the authors set their program loose on a set of samples from patients in the Netherlands. From more than 6000 features, the software found a set that were associated with samples from patients who had died sooner. The key aspect of this analysis was that these features were not predefined by a pathologist as being relevant to cancer; instead, the software itself found the cancer-related features among the very large set of measurements of the image. Classifying the tissue as epithelial or stromal, an important part of cancer diagnosis, took a bit of extra work: The authors needed to provide the software with some hand-marked samples so it could learn the difference. The C-Path score yielded information above and beyond that from many other measures of cancer severity including pathology grade, estrogen receptor status, tumor size, and lymph node status. In another, completely independent group of women from Vancouver, the C-Path score was also associated with overall survival.
An unexpected finding was that the features that were the best predictors of patient survival were not from the cancer itself but were from the adjacent stromal tissue. Women with worse outcomes tended to have thin cords of epithelial cells infiltrating the stroma, which resulted in high-risk stromal matrix variability scores. These patients also tended to have more inflammatory cells in the stroma (picked up as dark areas by the software). Replacing the human brain with an unbiased image processing system can extract more information from microcopy images and discover new biological aspects of cancer tissue.
Automated quantification of thousands of morphologic features in microscopic images of breast cancer allows the construction of a robust prognostic model.
Automated quantification of thousands of morphologic features in microscopic images of breast cancer allows the construction of a robust prognostic model.},
	language = {en},
	number = {108},
	urldate = {2015-09-02},
	journal = {Science Translational Medicine},
	author = {Beck, Andrew H. and Sangoi, Ankur R. and Leung, Samuel and Marinelli, Robert J. and Nielsen, Torsten O. and Vijver, Marc J. van de and West, Robert B. and Rijn, Matt van de and Koller, Daphne},
	month = nov,
	year = {2011},
	pmid = {22072638},
	pages = {108ra113--108ra113},
	file = {Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/9RGKJGSE/Beck et al. - 2011 - Systematic Analysis of Breast Cancer Morphology Un.pdf:application/pdf;Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/T43D93CF/Beck et al. - 2011 - Systematic Analysis of Breast Cancer Morphology Un.html:text/html}
}

@article{veta_breast_2014,
	title = {Breast {Cancer} {Histopathology} {Image} {Analysis}: {A} {Review}},
	volume = {61},
	issn = {0018-9294},
	shorttitle = {Breast {Cancer} {Histopathology} {Image} {Analysis}},
	doi = {10.1109/TBME.2014.2303852},
	abstract = {This paper presents an overview of methods that have been proposed for the analysis of breast cancer histopathology images. This research area has become particularly relevant with the advent of whole slide imaging (WSI) scanners, which can perform cost-effective and high-throughput histopathology slide digitization, and which aim at replacing the optical microscope as the primary tool used by pathologist. Breast cancer is the most prevalent form of cancers among women, and image analysis methods that target this disease have a huge potential to reduce the workload in a typical pathology lab and to improve the quality of the interpretation. This paper is meant as an introduction for nonexperts. It starts with an overview of the tissue preparation, staining and slide digitization processes followed by a discussion of the different image processing techniques and applications, ranging from analysis of tissue staining to computer-aided diagnosis, and prognosis of breast cancer patients.},
	number = {5},
	journal = {IEEE Transactions on Biomedical Engineering},
	author = {Veta, M. and Pluim, J.P.W. and van Diest, P.J. and Viergever, M.A.},
	month = may,
	year = {2014},
	keywords = {biological specimen preparation, biological tissues, biomedical optical imaging, Breast cancer, breast cancer histopathology image analysis, breast cancer patient prognosis, cancer, computer-aided diagnosis, cost-effective histopathology slide digitization, digital pathology, high-throughput histopathology slide digitization, histopathology, Image analysis, image analysis, image processing applications, image processing techniques, Image segmentation, mammography, medical image processing, Microscopy, object detection, object segmentation, optical microscope, Pathology, pathology lab workload reduction, quality improvement, tissue preparation, tissue staining, Tumors, whole slide imaging, WSI scanners},
	pages = {1400--1411},
	file = {IEEE Xplore Abstract Record:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IJMT5CGH/Veta et al. - 2014 - Breast Cancer Histopathology Image Analysis A Rev.html:text/html;IEEE Xplore Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/R8C2H3RK/R8C2H3RK.pdf:application/pdf}
}

@article{giunchi_revised_2014,
	title = {Revised {Gleason} {Grading} {System} {Is} a {Better} {Predictor} of {Indolent} {Prostate} {Cancer} at the {Time} of {Diagnosis}: {Retrospective} {Clinical}-{Pathological} {Study} on {Matched} {Biopsy} and {Radical} {Prostatectomy} {Specimens}},
	volume = {12},
	issn = {1558-7673},
	shorttitle = {Revised {Gleason} {Grading} {System} {Is} a {Better} {Predictor} of {Indolent} {Prostate} {Cancer} at the {Time} of {Diagnosis}},
	url = {http://www.sciencedirect.com/science/article/pii/S1558767314000172},
	doi = {10.1016/j.clgc.2014.01.009},
	abstract = {Introduction/Background
The increase of prostate cancer diagnosis after the introduction of prostate-specific antigen (PSA) screening resulted in overtreatment of patients with low risk tumors. The histological Gleason score (GS) revised in 2005 by the International Society of Urological Pathology (ISUP) is currently the most reliable tool to separate aggressive from indolent prostate cancer.
Materials and Methods
Using the new 2005 GS criteria we retrospectively evaluated biopsy and surgical samples of 1344 patients who underwent radical prostatectomy in our institution. According to the new GS criteria we then selected 134 patients who would have been suitable for active surveillance at the time of biopsy (at least 2 positive cores, PSA \&lt; 10 ng/mL, GS ≤ 6). We finally assessed the accuracy of the revised GS in biopsy to predict indolent cancer in the prostatectomy specimens.
Results
The mean GS increased from 6 to 7 after histological revision in biopsy and prostatectomy specimens. Histological revision determined a significant decrease of patients with GS ≤ 6 and an increase of those with GS ≥ 7 (all P \&lt; .001). The average of pathologically indolent disease (organ-confined, GS ≤ 6 at surgery, tumor of any volume) significantly decreased after histological revision (P \&lt; .001).
Conclusion
The revised ISUP 2005 criteria for Gleason grading provided better stratification of GS ≤ 6 prostate cancer and improved the accuracy for the histological diagnosis of indolent prostate cancer in biopsy and radical prostatectomy specimens.},
	number = {5},
	urldate = {2016-12-12},
	journal = {Clinical Genitourinary Cancer},
	author = {Giunchi, Francesca and Brunocilla, Eugenio and Borghesi, Marco and Rizzi, Simona and Ricci, Martina Sofia and Romagnoli, Daniele and Martorana, Giuseppe and Schiavina, Riccardo and Fiorentino, Michelangelo},
	month = oct,
	year = {2014},
	keywords = {Active surveillance, Gleason grading, histopathology, Indolent tumor, PROSTATE cancer},
	pages = {325--329},
	file = {ScienceDirect Full Text PDF:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/IIX379M8/Giunchi et al. - 2014 - Revised Gleason Grading System Is a Better Predict.pdf:application/pdf;ScienceDirect Snapshot:/Users/geekypete/Library/Application Support/Zotero/Profiles/cioj7j1h.default/zotero/storage/8XB3D37X/S1558767314000172.html:text/html}
}

@article{rodriguez_stress-dependent_1994-1,
	title = {Stress-dependent finite growth in soft elastic tissues},
	volume = {27},
	issn = {0021-9290},
	abstract = {Growth and remodeling in tissues may be modulated by mechanical factors such as stress. For example, in cardiac hypertrophy, alterations in wall stress arising from changes in mechanical loading lead to cardiac growth and remodeling. A general continuum formulation for finite volumetric growth in soft elastic tissues is therefore proposed. The shape change of an unloaded tissue during growth is described by a mapping analogous to the deformation gradient tensor. This mapping is decomposed into a transformation of the local zero-stress reference state and an accompanying elastic deformation that ensures the compatibility of the total growth deformation. Residual stress arises from this elastic deformation. Hence, a complete kinematic formulation for growth in general requires a knowledge of the constitutive law for stress in the tissue. Since growth may in turn be affected by stress in the tissue, a general form for the stress-dependent growth law is proposed as a relation between the symmetric growth-rate tensor and the stress tensor. With a thick-walled hollow cylinder of incompressible, isotropic hyperelastic material as an example, the mechanics of left ventricular hypertrophy are investigated. The results show that transmurally uniform pure circumferential growth, which may be similar to eccentric ventricular hypertrophy, changes the state of residual stress in the heart wall. A model of axially loaded bone is used to test a simple stress-dependent growth law in which growth rate depends on the difference between the stress due to loading and a predetermined growth equilibrium stress.},
	language = {eng},
	number = {4},
	journal = {Journal of Biomechanics},
	author = {Rodriguez, E. K. and Hoger, A. and McCulloch, A. D.},
	month = apr,
	year = {1994},
	pmid = {8188726},
	keywords = {Bone and Bones, Bone Development, Elasticity, Elastic Tissue, Heart, Humans, Hypertrophy, Hypertrophy, Left Ventricular, Mathematics, Models, Biological, Stress, Mechanical},
	pages = {455--467}
}