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Journal of Pathology Informatics

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https://www.readbyqxmd.com/read/28197359/a-quantitative-approach-to-evaluate-image-quality-of-whole-slide-imaging-scanners
#1
Prarthana Shrestha, R Kneepkens, J Vrijnsen, D Vossen, E Abels, B Hulsken
CONTEXT: The quality of images produced by whole slide imaging (WSI) scanners has a direct influence on the readers' performance and reliability of the clinical diagnosis. Therefore, WSI scanners should produce not only high quality but also consistent quality images. AIM: We aim to evaluate reproducibility of WSI scanners based on the quality of images produced over time and among multiple scanners. The evaluation is independent of content or context of test specimen...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28163977/generating-unique-ids-from-patient-identification-data-using-security-models
#2
Emad A Mohammed, Jonathan C Slack, Christopher T Naugler
BACKGROUND: The use of electronic health records (EHRs) has continued to increase within healthcare systems in the developed and developing nations. EHRs allow for increased patient safety, grant patients easier access to their medical records, and offer a wealth of data to researchers. However, various bioethical, financial, logistical, and information security considerations must be addressed while transitioning to an EHR system. The need to encrypt private patient information for data sharing is one of the foremost challenges faced by health information technology...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28163976/reporting-gleason-grade-score-in-synoptic-reports-of-radical-prostatectomies
#3
Andrew A Renshaw, Mercy Mena-Allauca, Edwin W Gould
CONTEXT: The format of a synoptic report can significantly affect the accuracy, speed, and preference with which a reader can retrieve information. OBJECTIVE: The objective of this study is to compare different formats of Gleason grading/score in synoptic reports of radical prostatectomies. METHODS: The performance of 16 nonpathologists (cancer registrars, MDs, medical non-MDs, and nonmedical) at identifying specific information in various formatted synoptic reports using a computerized quiz that measured both accuracy and speed...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28163975/use-of-application-containers-and-workflows-for-genomic-data-analysis
#4
Wade L Schulz, Thomas J S Durant, Alexa J Siddon, Richard Torres
BACKGROUND: The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. METHODS: Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28163974/enhancements-in-localized-classification-for-uterine-cervical-cancer-digital-histology-image-assessment
#5
Peng Guo, Haidar Almubarak, Koyel Banerjee, R Joe Stanley, Rodney Long, Sameer Antani, George Thoma, Rosemary Zuna, Shelliane R Frazier, Randy H Moss, William V Stoecker
BACKGROUND: In previous research, we introduced an automated, localized, fusion-based approach for classifying uterine cervix squamous epithelium into Normal, CIN1, CIN2, and CIN3 grades of cervical intraepithelial neoplasia (CIN) based on digitized histology image analysis. As part of the CIN assessment process, acellular and atypical cell concentration features were computed from vertical segment partitions of the epithelium region to quantize the relative distribution of nuclei. METHODS: Feature data was extracted from 610 individual segments from 61 images for epithelium classification into categories of Normal, CIN1, CIN2, and CIN3...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28163973/how-to-interpret-the-results-of-medical-time-series-data-analysis-classical-statistical-approaches-versus-dynamic-bayesian-network-modeling
#6
Agnieszka Onisko, Marek J Druzdzel, R Marshall Austin
BACKGROUND: Classical statistics is a well-established approach in the analysis of medical data. While the medical community seems to be familiar with the concept of a statistical analysis and its interpretation, the Bayesian approach, argued by many of its proponents to be superior to the classical frequentist approach, is still not well-recognized in the analysis of medical data. AIM: The goal of this study is to encourage data analysts to use the Bayesian approach, such as modeling with graphical probabilistic networks, as an insightful alternative to classical statistical analysis of medical data...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28066684/pathology-report-data-extraction-from-relational-database-using-r-with-extraction-from-reports-on-melanoma-of-skin-as-an-example
#7
Jay J Ye
BACKGROUND: Different methods have been described for data extraction from pathology reports with varying degrees of success. Here a technique for directly extracting data from relational database is described. METHODS: Our department uses synoptic reports modified from College of American Pathologists (CAP) Cancer Protocol Templates to report most of our cancer diagnoses. Choosing the melanoma of skin synoptic report as an example, R scripting language extended with RODBC package was used to query the pathology information system database...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28066683/computer-based-image-analysis-in-breast-pathology
#8
REVIEW
Ziba Gandomkar, Patrick C Brennan, Claudia Mello-Thoms
Whole slide imaging (WSI) has the potential to be utilized in telepathology, teleconsultation, quality assurance, clinical education, and digital image analysis to aid pathologists. In this paper, the potential added benefits of computer-assisted image analysis in breast pathology are reviewed and discussed. One of the major advantages of WSI systems is the possibility of doing computer-based image analysis on the digital slides. The purpose of computer-assisted analysis of breast virtual slides can be (i) segmentation of desired regions or objects such as diagnostically relevant areas, epithelial nuclei, lymphocyte cells, tubules, and mitotic figures, (ii) classification of breast slides based on breast cancer (BCa) grades, the invasive potential of tumors, or cancer subtypes, (iii) prognosis of BCa, or (iv) immunohistochemical quantification...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28066682/detecting-and-segmenting-cell-nuclei-in-two-dimensional-microscopy-images
#9
Chi Liu, Fei Shang, John A Ozolek, Gustavo K Rohde
INTRODUCTION: Cell nuclei are important indicators of cellular processes and diseases. Segmentation is an essential stage in systems for quantitative analysis of nuclei extracted from microscopy images. Given the wide variety of nuclei appearance in different organs and staining procedures, a plethora of methods have been described in the literature to improve the segmentation accuracy and robustness. MATERIALS AND METHODS: In this paper, we propose an unsupervised method for cell nuclei detection and segmentation in two-dimensional microscopy images...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994941/a-multisite-validation-of-whole-slide-imaging-for-primary-diagnosis-using-standardized-data-collection-and-analysis
#10
Katy Wack, Laura Drogowski, Murray Treloar, Andrew Evans, Jonhan Ho, Anil Parwani, Michael C Montalto
CONTEXT: Text-based reporting and manual arbitration for whole slide imaging (WSI) validation studies are labor intensive and do not allow for consistent, scalable, and repeatable data collection or analysis. OBJECTIVE: The objective of this study was to establish a method of data capture and analysis using standardized codified checklists and predetermined synoptic discordance tables and to use these methods in a pilot multisite validation study. METHODS AND STUDY DESIGN: Fifteen case report form checklists were generated from the College of American Pathology cancer protocols...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994940/reflex-test-reminders-in-required-cancer-synoptic-templates-decrease-order-entry-error-an-analysis-of-mismatch-repair-immunohistochemical-orders-to-screen-for-lynch-syndrome
#11
Mark R Kilgore, Carrie A McIlwain, Rodney A Schmidt, Barbara M Norquist, Elizabeth M Swisher, Rochelle L Garcia, Mara H Rendi
BACKGROUND: Endometrial carcinoma (EC) is the most common extracolonic malignant neoplasm associated with Lynch syndrome (LS). LS is caused by autosomal dominant germline mutations in DNA mismatch repair (MMR) genes. Screening for LS in EC is often evaluated by loss of immunohistochemical (IHC) expression of DNA MMR enzymes MLH1, MSH2, MSH6, and PMS2 (MMR IHC). In July 2013, our clinicians asked that we screen all EC in patients ≤60 for loss of MMR IHC expression. Despite this policy, several cases were not screened or screening was delayed...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994939/pointwise-mutual-information-quantifies-intratumor-heterogeneity-in-tissue-sections-labeled-with-multiple-fluorescent-biomarkers
#12
Daniel M Spagnolo, Rekha Gyanchandani, Yousef Al-Kofahi, Andrew M Stern, Timothy R Lezon, Albert Gough, Dan E Meyer, Fiona Ginty, Brion Sarachan, Jeffrey Fine, Adrian V Lee, D Lansing Taylor, S Chakra Chennubhotla
BACKGROUND: Measures of spatial intratumor heterogeneity are potentially important diagnostic biomarkers for cancer progression, proliferation, and response to therapy. Spatial relationships among cells including cancer and stromal cells in the tumor microenvironment (TME) are key contributors to heterogeneity. METHODS: We demonstrate how to quantify spatial heterogeneity from immunofluorescence pathology samples, using a set of 3 basic breast cancer biomarkers as a test case...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994938/the-utility-of-including-pathology-reports-in-improving-the-computational-identification-of-patients
#13
Wei Chen, Yungui Huang, Brendan Boyle, Simon Lin
BACKGROUND: Celiac disease (CD) is a common autoimmune disorder. Efficient identification of patients may improve chronic management of the disease. Prior studies have shown searching International Classification of Diseases-9 (ICD-9) codes alone is inaccurate for identifying patients with CD. In this study, we developed automated classification algorithms leveraging pathology reports and other clinical data in Electronic Health Records (EHRs) to refine the subset population preselected using ICD-9 code (579...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27994937/the-growing-need-for-microservices-in-bioinformatics
#14
Christopher L Williams, Jeffrey C Sica, Robert T Killen, Ulysses G J Balis
OBJECTIVE: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27761297/erratum-antibody-supervised-deep-learning-for-quantification-of-tumor-infiltrating-immune-cells-in-hematoxylin-and-eosin-stained-breast-cancer-samples
#15
(no author information available yet)
[This corrects the article on p. 38 in vol. 7, PMID: 27688929.].
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688931/rates-of-provision-of-clinical-information-in-the-skin-biopsy-requisition-form-and-corresponding-encounter-visit-note
#16
Meredith A Olson, Christine M Lohse, Nneka I Comfere
BACKGROUND: The skin biopsy requisition form (RF) serves as a key communication tool for transfer of relevant information related to skin biopsy between clinicians and pathologists. Clinical information in the skin biopsy RF is frequently missing or incomplete. OBJECTIVE: To determine the rates of provision of critical clinical information necessary for histopathologic interpretation in the skin biopsy RF and encounter visit note (EVN). METHODS: A retrospective review of 300 RFs and corresponding EVNs from May 1 to 7, 2012, in a tertiary care dermatology practice...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688930/a-novel-leadership-fellowship-in-digital-pathology
#17
Bethany Jill Williams, Darren Treanor
No abstract text is available yet for this article.
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688929/antibody-supervised-deep-learning-for-quantification-of-tumor-infiltrating-immune-cells-in-hematoxylin-and-eosin-stained-breast-cancer-samples
#18
Riku Turkki, Nina Linder, Panu E Kovanen, Teijo Pellinen, Johan Lundin
BACKGROUND: Immune cell infiltration in tumor is an emerging prognostic biomarker in breast cancer. The gold standard for quantification of immune cells in tissue sections is visual assessment through a microscope, which is subjective and semi-quantitative. In this study, we propose and evaluate an approach based on antibody-guided annotation and deep learning to quantify immune cell-rich areas in hematoxylin and eosin (H&E) stained samples. METHODS: Consecutive sections of formalin-fixed parafin-embedded samples obtained from the primary tumor of twenty breast cancer patients were cut and stained with H&E and the pan-leukocyte CD45 antibody...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688928/experience-of-maintaining-laboratory-educational-website-s-sustainability
#19
Izak B Dimenstein
Laboratory methodology websites are specialized niche websites. The visibility of a niche website transforms it into an authority site on a particular "niche of knowledge." This article presents some ways in which a laboratory methodology website can maintain its sustainability. The optimal composition of the website includes a basic content, a blog, and an ancillary part. This article discusses experimenting with the search engine optimization query results page. Strategic placement of keywords and even phrases, as well as fragmentation of the post's material, can improve the website's visibility to search engines...
2016: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/27688927/a-novel-method-for-morphological-pleomorphism-and-heterogeneity-quantitative-measurement-named-cell-feature-level-co-occurrence-matrix
#20
Akira Saito, Yasushi Numata, Takuya Hamada, Tomoyoshi Horisawa, Eric Cosatto, Hans-Peter Graf, Masahiko Kuroda, Yoichiro Yamamoto
BACKGROUND: Recent developments in molecular pathology and genetic/epigenetic analysis of cancer tissue have resulted in a marked increase in objective and measurable data. In comparison, the traditional morphological analysis approach to pathology diagnosis, which can connect these molecular data and clinical diagnosis, is still mostly subjective. Even though the advent and popularization of digital pathology has provided a boost to computer-aided diagnosis, some important pathological concepts still remain largely non-quantitative and their associated data measurements depend on the pathologist's sense and experience...
2016: Journal of Pathology Informatics
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