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https://www.readbyqxmd.com/read/29341027/developing-deep-learning-applications-for-life-science-and-pharma-industry
#1
Daniel Siegismund, Vasily Tolkachev, Stephan Heyse, Beate Sick, Oliver Duerr, Stephan Steigele
Deep Learning has boosted artificial intelligence over the past 5 years and is seen now as one of the major technological innovation areas, predicted to replace lots of repetitive, but complex tasks of human labor within the next decade. It is also expected to be 'game changing' for research activities in pharma and life sciences, where large sets of similar yet complex data samples are systematically analyzed. Deep learning is currently conquering formerly expert domains especially in areas requiring perception, previously not amenable to standard machine learning...
January 16, 2018: Drug Research
https://www.readbyqxmd.com/read/29334632/capillary-electrophoresis-mass-spectrometry-for-targeted-and-untargeted-analysis-of-the-sub-5%C3%A2-kda-urine-metabolome-of-patients-with-prostate-or-bladder-cancer-a-feasibility-study
#2
Matthew S MacLennan, Miranda G M Kok, Laiel Soliman, Alan So, Antonio Hurtado-Coll, David D Y Chen
Targeted and untargeted analyses of the sub-5 kDa urine metabolome of genitourinary cancer patients (prostate and/or bladder) were performed without chemical derivatization using capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS). For targeted analysis, endogenous levels of sarcosine and 5 other amino acid metabolites implicated in the progression of prostate cancer were quantified in four patients and in a pooled urine sample from healthy volunteers. An untargeted analysis (m/z 50 to 850) of patient urine was performed using the same CE-ESI-MS system identifying over 400 distinct molecular features per patient...
January 7, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29317516/digital-pathology-access-and-usage-in-the-uk-results-from-a-national-survey-on-behalf-of-the-national-cancer-research-institute-s-cm-path-initiative
#3
Bethany Jill Williams, Jessica Lee, Karin A Oien, Darren Treanor
AIM: To canvass the UK pathology community to ascertain current levels of digital pathology usage in clinical and academic histopathology departments, and prevalent attitudes to digital pathology. METHODS: A 15-item survey was circulated to National Health Service and academic pathology departments across the UK using the SurveyMonkey online survey tool. Responses were sought at a departmental or institutional level. Where possible, departmental heads were approached and asked to complete the survey, or forward it to the most relevant individual in their department...
January 9, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29288495/pan-cancer-insights-from-the-cancer-genome-atlas-the-pathologist-s-perspective
#4
REVIEW
Lee A D Cooper, Elizabeth G Demicco, Joel H Saltz, Reid T Powell, Arvind Rao, Alexander J Lazar
The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of selected tumor types to advance understanding of disease and provide an open-access resource for worldwide cancer research. Thirty-three tumor types (selected by histology or tissue of origin, to include both common and rare diseases), comprising over 11,000 specimens were subjected to DNA sequencing, copy number and methylation analysis, and transcriptomic, proteomic, and histologic evaluation...
December 30, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29279774/a-novel-white-blood-cells-segmentation-algorithm-based-on-adaptive-neutrosophic-similarity-score
#5
A I Shahin, Yanhui Guo, K M Amin, Amr A Sharawi
Background: White blood cells (WBCs) play a crucial role in the diagnosis of many diseases according to their numbers or morphology. The recent digital pathology equipments investigate and analyze the blood smear images automatically. The previous automated segmentation algorithms worked on healthy and non-healthy WBCs separately. Also, such algorithms had employed certain color components which leak adaptively with different datasets. Methods: In this paper, a novel segmentation algorithm for WBCs in the blood smear images is proposed using multi-scale similarity measure based on the neutrosophic domain...
December 2018: Health Information Science and Systems
https://www.readbyqxmd.com/read/29246889/nerve-terminals-at-the-human-corneoscleral-limbus
#6
Mouhamed A Al-Aqaba, Fady S Anis, Imran Mohammed, Harminder S Dua
AIMS: To demonstrate and characterise distinct subepithelial compact nerve endings (CNE) at the human corneoscleral limbus. METHODS: Ten fresh human donor corneoscleral discs (mean age, 67 years) and 26 organ-cultured corneoscleral rims (mean age, 59 years) were studied. All samples were subjected to enzyme histochemical staining related to endogenous acetylcholinesterase present in nerve tissue and H&E staining. Whole-mount en face imaging with NanoZoomer digital pathology microscope and serial cross-section imaging with light microscope were undertaken...
December 15, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/29241972/towards-machine-learned-quality-control-a-benchmark-for-sharpness-quantification-in-digital-pathology
#7
Gabriele Campanella, Arjun R Rajanna, Lorraine Corsale, Peter J Schüffler, Yukako Yagi, Thomas J Fuchs
Pathology is on the verge of a profound change from an analog and qualitative to a digital and quantitative discipline. This change is mostly driven by the high-throughput scanning of microscope slides in modern pathology departments, reaching tens of thousands of digital slides per month. The resulting vast digital archives form the basis of clinical use in digital pathology and allow large scale machine learning in computational pathology. One of the most crucial bottlenecks of high-throughput scanning is quality control (QC)...
September 25, 2017: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
https://www.readbyqxmd.com/read/29233930/critical-research-gaps-and-recommendations-to-inform-research-prioritisation-for-more-effective-prevention-and-improved-outcomes-in-colorectal-cancer
#8
REVIEW
Mark Lawler, Deborah Alsina, Richard A Adams, Annie S Anderson, Gina Brown, Nicola S Fearnhead, Stephen W Fenwick, Stephen P Halloran, Daniel Hochhauser, Mark A Hull, Viktor H Koelzer, Angus G K McNair, Kevin J Monahan, Inke Näthke, Christine Norton, Marco R Novelli, Robert J C Steele, Anne L Thomas, Lisa M Wilde, Richard H Wilson, Ian Tomlinson
OBJECTIVE: Colorectal cancer (CRC) leads to significant morbidity/mortality worldwide. Defining critical research gaps (RG), their prioritisation and resolution, could improve patient outcomes. DESIGN: RG analysis was conducted by a multidisciplinary panel of patients, clinicians and researchers (n=71). Eight working groups (WG) were constituted: discovery science; risk; prevention; early diagnosis and screening; pathology; curative treatment; stage IV disease; and living with and beyond CRC...
January 2018: Gut
https://www.readbyqxmd.com/read/29219668/multispectral-imaging-reveals-hyper-active-tgf-%C3%AE-signaling-in-colorectal-cancer
#9
Lei Yang, Zheng Liu, Jinjing Tan, Hongwei Dong, Xiaojing Zhang
Advances in multiplex immunohistochemistry (IHC) techniques and digital pathology platforms allow quantification of multiple proteins at same tissue section and produce continuous data. TGF-β signaling plays crucial and complex roles in colorectal cancer (CRC). We here aimed to investigate clinical pathological relevant of proteins involved in TGF-β signaling at CRC tissues. Multiplex fluorescent IHC was used to quantitative analysis. The levels of eight proteins (TGF-β1, TGFBRI, TGFBRII, SMAD4, SMAD2/3, p-SMAD2/3, SMAD1/5/9, and p-SMAD1/5/9) were determined in TMA sections...
December 8, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/29203879/qupath-open-source-software-for-digital-pathology-image-analysis
#10
Peter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman, Jacqueline A James, Manuel Salto-Tellez, Peter W Hamilton
QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath's flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29193851/survival-of-corneal-nerve-sheath-structures-in-organ-cultured-donor-corneas
#11
Virinder K Dhillon, Mohamed S Elalfy, Marco Messina, Mouhamed Al-Aqaba, Harminder S Dua
PURPOSE: To study the morphology of human corneal nerves in eye bank organ-cultured corneas and in corneal grafts post-transplantation. METHODS: Thirty-seven organ-cultured corneas were divided into: Group-A, anterior 300-400 μm of 20 corneas used for Descemets stripping endothelial keratoplasty, and Group-B, 17 full-thickness corneas unsuitable for transplantation. Corneas whole mounts were stained for nerves using acetylcholinesterase technique and examined by NanoZoomer digital pathology microscope...
November 29, 2017: Acta Ophthalmologica
https://www.readbyqxmd.com/read/29162012/meeting-report-tissue-based-image-analysis
#12
Chandra Saravanan, Vanessa Schumacher, Danielle Brown, Robert Dunstan, Jean-Rene Galarneau, Marielle Odin, Sasmita Mishra
Quantitative image analysis (IA) is a rapidly evolving area of digital pathology. Although not a new concept, the quantification of histological features on photomicrographs used to be cumbersome, resource-intensive, and limited to specialists and specialized laboratories. Recent technological advances like highly efficient automated whole slide digitizer (scanner) systems, innovative IA platforms, and the emergence of pathologist-friendly image annotation and analysis systems mean that quantification of features on histological digital images will become increasingly prominent in pathologists' daily professional lives...
October 2017: Toxicologic Pathology
https://www.readbyqxmd.com/read/29138761/a-metastasis-biomarker-metasite-breast%C3%A2-score-is-associated-with-distant-recurrence-in-hormone-receptor-positive-her2-negative-early-stage-breast-cancer
#13
Joseph A Sparano, Robert Gray, Maja H Oktay, David Entenberg, Thomas Rohan, Xiaonan Xue, Michael Donovan, Michael Peterson, Anthony Shuber, Douglas A Hamilton, Timothy D'Alfonso, Lori J Goldstein, Frank Gertler, Nancy E Davidson, John Condeelis, Joan Jones
Metastasis is the primary cause of death in early-stage breast cancer. We evaluated the association between a metastasis biomarker, which we call "Tumor Microenviroment of Metastasis" (TMEM), and risk of recurrence. TMEM are microanatomic structures where invasive tumor cells are in direct contact with endothelial cells and macrophages, and which serve as intravasation sites for tumor cells into the circulation. We evaluated primary tumors from 600 patients with Stage I-III breast cancer treated with adjuvant chemotherapy in trial E2197 (NCT00003519), plus endocrine therapy for hormone receptor (HR)+ disease...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#14
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29128479/adipocyte-size-variability-in-benign-and-malignant-lipomatous-tumors-and-morphologic-mimics-a-quantitative-definition-using-digital-pathology
#15
Gregory R Bean, Kwun Wah Wen, Andrew E Horvai
Among well-differentiated lipomatous lesions, variability in adipocyte size has been proposed as a morphologic feature of malignancy. Specifically, normal adipose tissue and benign lipomas tend to contain adipocytes of uniform size, whereas atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDL) are described as containing adipocytes with a conspicuous variation in cell size. However, this proposed variance has never been objectively, quantitatively correlated with diagnosis. Using whole slide scanning combined with semiautomated digital image analysis, we aimed to quantitatively test the hypothesis that variance in adipocyte size is a feature of malignancy in well-differentiated lipomatous tumors...
November 8, 2017: Human Pathology
https://www.readbyqxmd.com/read/29109450/interactive-phenotyping-of-large-scale-histology-imaging-data-with-histomicsml
#16
Michael Nalisnik, Mohamed Amgad, Sanghoon Lee, Sameer H Halani, Jose Enrique Velazquez Vega, Daniel J Brat, David A Gutman, Lee A D Cooper
Whole-slide imaging of histologic sections captures tissue microenvironments and cytologic details in expansive high-resolution images. These images can be mined to extract quantitative features that describe tissues, yielding measurements for hundreds of millions of histologic objects. A central challenge in utilizing this data is enabling investigators to train and evaluate classification rules for identifying objects related to processes like angiogenesis or immune response. In this paper we describe HistomicsML, an interactive machine-learning system for digital pathology imaging datasets...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29100980/the-limbic-and-neocortical-contribution-of-%C3%AE-synuclein-tau-and-amyloid-%C3%AE-to-disease-duration-in-dementia-with-lewy-bodies
#17
Tanis J Ferman, Naoya Aoki, Julia E Crook, Melissa E Murray, Neill R Graff-Radford, Jay A van Gerpen, Ryan J Uitti, Zbigniew K Wszolek, Jonathan Graff-Radford, Otto Pedraza, Kejal Kantarci, Bradley F Boeve, Dennis W Dickson
INTRODUCTION: We sought to assess the individual and combined contribution of limbic and neocortical α-synuclein, tau, and amyloid β (Aβ) to duration of illness in dementia with Lewy bodies (DLB). METHODS: Quantitative digital pathology of limbic and neocortical α-synuclein, tau, and Aβ was assessed in 49 patients with clinically probable DLB. Regression modeling examined the unique and shared contribution of each pathology to the variance of illness duration...
October 31, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/29092947/an-image-analysis-resource-for-cancer-research-piip-pathology-image-informatics-platform-for-visualization-analysis-and-management
#18
Anne L Martel, Dan Hosseinzadeh, Caglar Senaras, Yu Zhou, Azadeh Yazdanpanah, Rushin Shojaii, Emily S Patterson, Anant Madabhushi, Metin N Gurcan
Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Thus far, new plugins have been developed and incorporated into the platform for out of focus detection, region of interest transformation, and IHC slide analysis...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29092945/the-digital-slide-archive-a-software-platform-for-management-integration-and-analysis-of-histology-for-cancer-research
#19
David A Gutman, Mohammed Khalilia, Sanghoon Lee, Michael Nalisnik, Zach Mullen, Jonathan Beezley, Deepak R Chittajallu, David Manthey, Lee A D Cooper
Tissue-based cancer studies can generate large amounts of histology data in the form of glass slides. These slides contain important diagnostic, prognostic, and biological information and can be digitized into expansive and high-resolution whole-slide images using slide-scanning devices. Effectively utilizing digital pathology data in cancer research requires the ability to manage, visualize, share, and perform quantitative analysis on these large amounts of image data, tasks that are often complex and difficult for investigators with the current state of commercial digital pathology software...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29049424/diagnostic-accuracy-of-virtual-pathology-vs-traditional-microscopy-in-a-large-dermatopathology-study
#20
Michael N Kent, Thomas G Olsen, Theresa A Feeser, Katherine C Tesno, John C Moad, Michael P Conroy, Mary Jo Kendrick, Sean R Stephenson, Michael R Murchland, Ayesha U Khan, Elizabeth A Peacock, Alexa Brumfiel, Michael A Bottomley
Importance: Digital pathology represents a transformative technology that impacts dermatologists and dermatopathologists from residency to academic and private practice. Two concerns are accuracy of interpretation from whole-slide images (WSI) and effect on workflow. Studies of considerably large series involving single-organ systems are lacking. Objective: To evaluate whether diagnosis from WSI on a digital microscope is inferior to diagnosis of glass slides from traditional microscopy (TM) in a large cohort of dermatopathology cases with attention on image resolution, specifically eosinophils in inflammatory cases and mitotic figures in melanomas, and to measure the workflow efficiency of WSI compared with TM...
October 11, 2017: JAMA Dermatology
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