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"Digital pathology"

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https://www.readbyqxmd.com/read/28507795/digital-analysis-and-epigenetic-regulation-of-the-signature-of-rejection-in-colorectal-cancer
#1
Viktor H Koelzer, Lena Sokol, Stefan Zahnd, Lucine Christe, Heather Dawson, Martin D Berger, Daniel Inderbitzin, Inti Zlobec, Alessandro Lugli
The immune system plays a pivotal role in the development and progression of colorectal cancer (CRC). Tumor immune rejection has been previously linked to the activation of the interferon-stimulated genes (ISG) STAT1, IRF-5 and IRF-1. Specific immunoregulatory microRNAs (miRNAs) may impact the expression of these ISG in the tumor microenvironment. In this translational study, we develop a digital image analysis protocol to identify the ISG-gene expression signature and investigate miRNA expression in the immediate environment of invading cancer cells...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28480122/the-need-for-careful-data-collection-for-pattern-recognition-in-digital-pathology
#2
Raphaël Marée
Effective pattern recognition requires carefully designed ground-truth datasets. In this technical note, we first summarize potential data collection issues in digital pathology and then propose guidelines to build more realistic ground-truth datasets and to control their quality. We hope our comments will foster the effective application of pattern recognition approaches in digital pathology.
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28475271/why-is-digital-pathology-in-cytopathology-lagging-behind-surgical-pathology
#3
Matthew G Hanna, Liron Pantanowitz
No abstract text is available yet for this article.
May 5, 2017: Cancer
https://www.readbyqxmd.com/read/28472544/an-optimized-image-analysis-algorithm-for-detecting-nuclear-signals-in-digital-whole-slides-for-histopathology
#4
Róbert Paulik, Tamás Micsik, Gábor Kiszler, Péter Kaszál, János Székely, Norbert Paulik, Eszter Várhalmi, Viktória Prémusz, Tibor Krenács, Béla Molnár
Nuclear estrogen receptor (ER), progesterone receptor (PR) and Ki-67 protein positive tumor cell fractions are semiquantitatively assessed in breast cancer for prognostic and predictive purposes. These biomarkers are usually revealed using immunoperoxidase methods resulting in diverse signal intensity and frequent inhomogeneity in tumor cell nuclei, which are routinely scored and interpreted by a pathologist during conventional light-microscopic examination. In the last decade digital pathology-based whole slide scanning and image analysis algorithms have shown tremendous development to support pathologists in this diagnostic process, which can directly influence patient selection for targeted- and chemotherapy...
May 4, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28467215/a-systematic-analysis-of-discordant-diagnoses-in-digital-pathology-compared-with-light-microscopy
#5
Bethany J Williams, Philip DaCosta, Edward Goacher, Darren Treanor
CONTEXT: - Relatively little is known about the significance and potential impact of glass-digital discordances, and this is likely to be of importance when considering digital pathology adoption. OBJECTIVE: - To apply evidence-based medicine to collect and analyze reported instances of glass-digital discordance from the whole slide imaging validation literature. DESIGN: - We used our prior systematic review protocol to identify studies assessing the concordance of light microscopy and whole slide imaging between 1999 and 2015...
May 3, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28446788/resolution-enhanced-fourier-ptychographic-microscopy-based-on-high-numerical-aperture-illuminations
#6
Jiasong Sun, Chao Zuo, Liang Zhang, Qian Chen
High-resolution and wide field-of-view (FOV) microscopic imaging plays a central role in diverse applications such as high-throughput screening and digital pathology. However, conventional microscopes face inherent trade-offs between the spatial resolution and FOV, which are fundamental limited by the space-bandwidth product (SBP) of the optical system. The resolution-FOV tradeoff can be effectively decoupled in Fourier ptychography microscopy (FPM), however, to date, the effective imaging NA achievable with a typical FPM system is still limited to the range of 0...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446544/cellular-expression-of-pd-l1-in-the-peripheral-blood-of-lung-cancer-patients-is-associated-with-worse-survival
#7
Daniel J Boffa, Ryon P Graf, Michelle C Salazar, Jessica Hoag, David Lu, Rachel Krupa, Jessica Louw, Lyndsey Dugan, Yipeng Wang, Mark Landers, Mahipal Suraneni, Stephanie B Greene, Samir Makani, Marisa Magaña, Lyudmila Bazhenova, Ryan V Dittamore, Jorge Nieva
BACKGROUND: Lung cancer treatment has become increasingly dependent upon invasive biopsies to profile tumors for personalized therapy. Recently, tumor expression of PD-L1 has gained interest as a potential predictor of response to immunotherapy. Circulating biomarkers present an opportunity for tumor profiling without the risks of invasive procedures. We characterized PD-L1 expression within populations of nucleated cells in the peripheral blood of lung cancer patients in hopes of expanding the role of liquid biopsy in this setting...
April 26, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28440660/implementation-of-whole-slide-imaging-for-clinical-purposes-issues-to-consider-from-the-perspective-of-early-adopters
#8
Andrew J Evans, Mohamed E Salama, Walter H Henricks, Liron Pantanowitz
CONTEXT: - There is growing interest in the use of digital pathology, especially whole slide imaging, for diagnostic purposes. Many issues need to be considered when incorporating this technology into a clinical laboratory. The College of American Pathologists established a Digital Pathology Committee to support the development of College programs related to digital pathology. One of its many initiatives was a panel discussion entitled "Implementing Whole-Slide Imaging for Clinical Use: What to Do and What to Avoid," given for 3 years at the College's annual meetings starting in 2014...
April 25, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28430222/impact-of-partial-coherence-on-the-apparent-optical-transfer-function-derived-from-the-response-to-amplitude-edges
#9
S Mojtaba Shakeri, Lucas J van Vliet, Sjoerd Stallinga
We present an investigation of the impact of partial coherence on optical imaging systems with the focus on whole slide imaging (WSI) systems for digital pathology. The investigation is based on the analysis of the edge response of the optical system, which gives rise to an apparent optical transfer function (OTF) that can be linked to two elementary complex functions Q and U. The function Q is directly related to the transmission cross coefficient (TCC) and can be identified with the performance function first introduced by Kintner and Sillitto...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28426134/metastasis-detection-from-whole-slide-images-using-local-features-and-random-forests
#10
Mira Valkonen, Kimmo Kartasalo, Kaisa Liimatainen, Matti Nykter, Leena Latonen, Pekka Ruusuvuori
Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. With accurate methods using image analysis and machine learning, significant speed-up, and savings in costs through increased throughput in histological assessment could be achieved. This article describes a machine learning approach for detection of cancerous tissue from scanned whole slide images. Our method is based on feature engineering and supervised learning with a random forest model...
April 20, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28423830/bridging-the-semantic-gap-between-diagnostic-histopathology-and-image-analysis
#11
Lamine Traore, Yannick Kergosien, Daniel Racoceanu
With the wider acceptance of Whole Slide Images (WSI) in histopathology domain, automatic image analysis algorithms represent a very promising solution to support pathologist's laborious tasks during the diagnosis process, to create a quantification-based second opinion and to enhance inter-observer agreement. In this context, reference vocabularies and formalization of the associated knowledge are especially needed to annotate histopathology images with labels complying with semantic standards. In this work, we elaborate a sustainable triptych able to bridge the gap between pathologists and image analysis scientists...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28421181/mct1-in-invasive-ductal-carcinoma-monocarboxylate-metabolism-and-aggressive-breast-cancer
#12
Jennifer M Johnson, Paolo Cotzia, Roberto Fratamico, Lekha Mikkilineni, Jason Chen, Daniele Colombo, Mehri Mollaee, Diana Whitaker-Menezes, Marina Domingo-Vidal, Zhao Lin, Tingting Zhan, Madalina Tuluc, Juan Palazzo, Ruth C Birbe, Ubaldo E Martinez-Outschoorn
Introduction: Monocarboxylate transporter 1 (MCT1) is an importer of monocarboxylates such as lactate and pyruvate and a marker of mitochondrial metabolism. MCT1 is highly expressed in a subgroup of cancer cells to allow for catabolite uptake from the tumor microenvironment to support mitochondrial metabolism. We studied the protein expression of MCT1 in a broad group of breast invasive ductal carcinoma specimens to determine its association with breast cancer subtypes and outcomes. Methods: MCT1 expression was evaluated by immunohistochemistry on tissue micro-arrays (TMA) obtained through our tumor bank...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28418027/accurate-and-reproducible-invasive-breast-cancer-detection-in-whole-slide-images-a-deep-learning-approach-for-quantifying-tumor-extent
#13
Angel Cruz-Roa, Hannah Gilmore, Ajay Basavanhally, Michael Feldman, Shridar Ganesan, Natalie N C Shih, John Tomaszewski, Fabio A González, Anant Madabhushi
With the increasing ability to routinely and rapidly digitize whole slide images with slide scanners, there has been interest in developing computerized image analysis algorithms for automated detection of disease extent from digital pathology images. The manual identification of presence and extent of breast cancer by a pathologist is critical for patient management for tumor staging and assessing treatment response. However, this process is tedious and subject to inter- and intra-reader variability. For computerized methods to be useful as decision support tools, they need to be resilient to data acquired from different sources, different staining and cutting protocols and different scanners...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382222/summary-of-the-4-th-nordic-symposium-on-digital-pathology
#14
Claes Lundström, Marie Waltersson, Anders Persson, Darren Treanor
The Nordic symposium on digital pathology (NDP) was created to promote knowledge exchange across stakeholders in health care, industry, and academia. In 2016, the 4(th) NDP installment took place in Linköping, Sweden, promoting development and collaboration in digital pathology for the benefit of routine care advances. This article summarizes the symposium, gathering 170 attendees from 13 countries. This summary also contains results from a survey on integrated diagnostics aspects, in particular radiology-pathology collaboration...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28381191/expression-and-associations-of-traf1-bmi-1-aldh1-and-lin28b-in-oral-squamous-cell-carcinoma
#15
Tian-Fu Wu, Yi-Cun Li, Si-Rui Ma, Bing-Liu, Wen-Feng Zhang, Zhi-Jun Sun
Tumor necrosis factor receptor-associated factor 1, an adaptor protein of tumor necrosis factor 2, is involved in classical nuclear factor (NF)-κB activation and lymphocyte recruitment. However, less is known about the expression and association of tumor necrosis factor receptor-associated factor 1 with cancer stem cell markers in oral squamous cell carcinoma. This study aimed to investigate the expression of tumor necrosis factor receptor-associated factor 1 and stem cell characteristic markers (lin28 homolog B, B cell-specific Moloney murine leukemia virus integration site 1, and aldehyde dehydrogenase 1) in oral squamous cell carcinoma and analyze their relations...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28352074/optimized-mass-spectrometry-analysis-workflow-with-polarimetric-guidance-for-ex-vivo-and-in-situ-sampling-of-biological-tissues
#16
Michael Woolman, Adam Gribble, Emma Bluemke, Jing Zou, Manuela Ventura, Nicholas Bernards, Megan Wu, Howard J Ginsberg, Sunit Das, Alex Vitkin, Arash Zarrine-Afsar
Spatially Targeted Mass Spectrometry (MS) analysis using survey scans with an imaging modality often requires consecutive tissue slices, because of the tissue damage during survey scan or due to incompatible sample preparation requirements between the survey modality and MS. We report two spatially targeted MS analysis workflows based on polarized light imaging guidance that use the same tissue sample for survey and targeted analysis. The first workflow is applicable for thin-slice analysis, and uses transmission-polarimetry-guided Desorption ElectroSpray Ionization Mass Spectrometry (DESI-MS), and confirmatory H&E histopathology analysis on the same slice; this is validated using quantitative digital pathology methods...
March 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28347240/computer-aided-prognosis-on-breast-cancer-with-hematoxylin-and-eosin-histopathology-images-a-review
#17
REVIEW
Jia-Mei Chen, Yan Li, Jun Xu, Lei Gong, Lin-Wei Wang, Wen-Lou Liu, Juan Liu
With the advance of digital pathology, image analysis has begun to show its advantages in information analysis of hematoxylin and eosin histopathology images. Generally, histological features in hematoxylin and eosin images are measured to evaluate tumor grade and prognosis for breast cancer. This review summarized recent works in image analysis of hematoxylin and eosin histopathology images for breast cancer prognosis. First, prognostic factors for breast cancer based on hematoxylin and eosin histopathology images were summarized...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28325451/multiview-boosting-digital-pathology-analysis-of-prostate-cancer
#18
Jin Tae Kwak, Stephen M Hewitt
BACKGROUND AND OBJECTIVE: Various digital pathology tools have been developed to aid in analyzing tissues and improving cancer pathology. The multi-resolution nature of cancer pathology, however, has not been fully analyzed and utilized. Here, we develop an automated, cooperative, and multi-resolution method for improving prostate cancer diagnosis. METHODS: Digitized tissue specimen images are obtained from 5 tissue microarrays (TMAs). The TMAs include 70 benign and 135 cancer samples (TMA1), 74 benign and 89 cancer samples (TMA2), 70 benign and 115 cancer samples (TMA3), 79 benign and 82 cancer samples (TMA4), and 72 benign and 86 cancer samples (TMA5)...
April 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28320627/maximal-ambient-noise-levels-and-type-of-voice-material-required-for-valid-use-of-smartphones-in-clinical-voice-research
#19
Jean Lebacq, Jean Schoentgen, Giovanna Cantarella, Franz Thomas Bruss, Claudia Manfredi, Philippe DeJonckere
PURPOSE: Smartphone technology provides new opportunities for recording standardized voice samples of patients and transmitting the audio files to the voice laboratory. This drastically improves the achievement of baseline designs, used in research on efficiency of voice treatments. However, the basic requirement is the suitability of smartphones for recording and digitizing pathologic voices (mainly characterized by period perturbations and noise) without significant distortion. In a previous article, this was tested using realistic synthesized deviant voice samples (/a:/) with three precisely known levels of jitter and of noise in all combinations...
March 17, 2017: Journal of Voice: Official Journal of the Voice Foundation
https://www.readbyqxmd.com/read/28275608/design-and-implementation-of-the-retinoblastoma-collaborative-laboratory
#20
Seemi Qaiser, Alice Limo, Josiah Gichana, Kahaki Kimani, Jessie Githanga, Wairimu Waweru, Elizabeth A O Dimba, Helen Dimaras
PURPOSE: The purpose of this work was to describe the design and implementation of a digital pathology laboratory, the Retinoblastoma Collaborative Laboratory (RbCoLab) in Kenya. METHOD: The RbCoLab is a central lab in Nairobi that receives retinoblastoma specimens from all over Kenya. Specimens were processed using evidence-based standard operating procedures. Images were produced by a digital scanner, and pathology reports were disseminated online. RESULTS: The lab implemented standard operating procedures aimed at improving the accuracy, completeness, and timeliness of pathology reports, enhancing the care of Kenyan retinoblastoma patients...
January 2017: Ocular Oncology and Pathology
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