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Journal of Pathology Informatics

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https://www.readbyqxmd.com/read/28400996/open-source-software-for-demand-forecasting-of-clinical-laboratory-test-volumes-using-time-series-analysis
#1
Emad A Mohammed, Christopher Naugler
BACKGROUND: Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400995/whatsapp-for-teaching-pathology-postgraduates-a-pilot-study
#2
Aditi Goyal, Nadeem Tanveer, Pooja Sharma
INTRODUCTION: Postgraduate students spend a sizeable proportion of their time on social media platforms such as WhatsApp and Facebook. This change in our social interaction needs to be accommodated in our teaching methods. To engage them and arouse their curiosity, WhatsApp is an ideal platform. Digital photography by cell phone cameras has made it possible to share cases and discuss them with students round the clock. OBJECTIVE: The primary aim of the study was to develop sharing and discussion of images using WhatsApp...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400994/pathological-diagnosis-of-gastric-cancers-with-a-novel-computerized-analysis-system
#3
Kosuke Oikawa, Akira Saito, Tomoharu Kiyuna, Hans Peter Graf, Eric Cosatto, Masahiko Kuroda
BACKGROUND: Recent studies of molecular biology have provided great advances for diagnostic molecular pathology. Automated diagnostic systems with computerized scanning for sampled cells in fluids or smears are now widely utilized. Automated analysis of tissue sections is, however, very difficult because they exhibit a complex mixture of overlapping malignant tumor cells, benign host-derived cells, and extracellular materials. Thus, traditional histological diagnosis is still the most powerful method for diagnosis of diseases...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400993/criteria-to-screen-molecular-tests-for-the-diagnosis-of-herpes-simplex-virus-in-the-central-nervous-system-have-no-propensity-to-harm
#4
Ronald George Hauser, Cynthia A Brandt, Richard A Martinello
OBJECTIVES: Investigators have ruled out herpes simplex virus (HSV) infection without the detection of herpes simplex deoxyribonucleic acid in cerebrospinal fluid (CSF) (i.e., HSV polymerase chain reaction [PCR]) by laboratory (normal CSF white blood cell count and protein) and clinical criteria (age ≥2 years, no history of human immunodeficiency virus or solid-organ transplant). Compared to HSV PCR of all samples, the algorithm saves money in test costs and may decrease exposure to acyclovir by illustrating the low probability that the patient has HSV...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400992/implementation-of-a-software-application-for-presurgical-case-history-review-of-frozen-section-pathology-cases
#5
Andrew P Norgan, Mathew L Okeson, Justin E Juskewitch, Kabeer K Shah, William R Sukov
BACKGROUND: The frozen section pathology practice at Mayo Clinic in Rochester performs ~20,000 intraoperative consultations a year (~70-80/weekday). To prepare for intraoperative consultations, surgical pathology fellows and residents review the case history, previous pathology, and relevant imaging the day before surgery. Before the work described herein, review of pending surgical pathology cases was a paper-based process requiring handwritten transcription from the electronic health record, a laborious and potentially error prone process...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400991/computer-science-biology-and-biomedical-informatics-academy-outcomes-from-5-years-of-immersing-high-school-students-into-informatics-research
#6
EDITORIAL
Andrew J King, Arielle M Fisher, Michael J Becich, David N Boone
The University of Pittsburgh's Department of Biomedical Informatics and Division of Pathology Informatics created a Science, Technology, Engineering, and Mathematics (STEM) pipeline in 2011 dedicated to providing cutting-edge informatics research and career preparatory experiences to a diverse group of highly motivated high-school students. In this third editorial installment describing the program, we provide a brief overview of the pipeline, report on achievements of the past scholars, and present results from self-reported assessments by the 2015 cohort of scholars...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28400990/classifications-of-multispectral-colorectal-cancer-tissues-using-convolution-neural-network
#7
Hawraa Haj-Hassan, Ahmad Chaddad, Youssef Harkouss, Christian Desrosiers, Matthew Toews, Camel Tanougast
BACKGROUND: Colorectal cancer (CRC) is the third most common cancer among men and women. Its diagnosis in early stages, typically done through the analysis of colon biopsy images, can greatly improve the chances of a successful treatment. This paper proposes to use convolution neural networks (CNNs) to predict three tissue types related to the progression of CRC: benign hyperplasia (BH), intraepithelial neoplasia (IN), and carcinoma (Ca). METHODS: Multispectral biopsy images of thirty CRC patients were retrospectively analyzed...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382227/performance-of-a-web-based-method-for-generating-synoptic-reports
#8
Megan A Renshaw, Scott A Renshaw, Mercy Mena-Allauca, Patricia P Carrion, Xiaorong Mei, Arniris Narciandi, Edwin W Gould, Andrew A Renshaw
CONTEXT: The College of American Pathologists (CAP) requires synoptic reporting of all tumor excisions. OBJECTIVE: To compare the performance of different methods of generating synoptic reports. METHODS: Completeness, amendment rates, rate of timely ordering of ancillary studies (KRAS in T4/N1 colon carcinoma), and structured data file extraction were compared for four different synoptic report generating methods. RESULTS: Use of the printed tumor protocols directly from the CAP website had the lowest completeness (84%) and highest amendment (1...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382226/a-randomized-study-comparing-digital-imaging-to-traditional-glass-slide-microscopy-for-breast-biopsy-and-cancer-diagnosis
#9
Joann G Elmore, Gary M Longton, Margaret S Pepe, Patricia A Carney, Heidi D Nelson, Kimberly H Allison, Berta M Geller, Tracy Onega, Anna N A Tosteson, Ezgi Mercan, Linda G Shapiro, Tad T Brunyé, Thomas R Morgan, Donald L Weaver
BACKGROUND: Digital whole slide imaging may be useful for obtaining second opinions and is used in many countries. However, the U.S. Food and Drug Administration requires verification studies. METHODS: Pathologists were randomized to interpret one of four sets of breast biopsy cases during two phases, separated by ≥9 months, using glass slides or digital format (sixty cases per set, one slide per case, n = 240 cases). Accuracy was assessed by comparing interpretations to a consensus reference standard...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382225/turning-microscopy-in-the-medical-curriculum-digital-experiences-from-the-faculty-of-health-and-medical-sciences-at-university-of-copenhagen
#10
Ben Vainer, Niels Werner Mortensen, Steen Seier Poulsen, Allan Have Sørensen, Jørgen Olsen, Hans Henrik Saxild, Flemming Fryd Johansen
Familiarity with the structure and composition of normal tissue and an understanding of the changes that occur during disease is pivotal to the study of the human body. For decades, microscope slides have been central to teaching pathology in medical courses and related subjects at the University of Copenhagen. Students had to learn how to use a microscope and envisage three-dimensional processes that occur in the body from two-dimensional glass slides. Here, we describe how a PathXL virtual microscopy system for teaching pathology and histology at the Faculty has recently been implemented, from an administrative, an economic, and a teaching perspective...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382224/recutclub-com-an-open-source-whole-slide-image-based-pathology-education-system
#11
Paul A Christensen, Nathan E Lee, Michael J Thrall, Suzanne Z Powell, Patricia Chevez-Barrios, S Wesley Long
BACKGROUND: Our institution's pathology unknown conferences provide educational cases for our residents. However, the cases have not been previously available digitally, have not been collated for postconference review, and were not accessible to a wider audience. Our objective was to create an inexpensive whole slide image (WSI) education suite to address these limitations and improve the education of pathology trainees. MATERIALS AND METHODS: We surveyed residents regarding their preference between four unique WSI systems...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382223/identification-of-histological-correlates-of-overall-survival-in-lower-grade-gliomas-using-a-bag-of-words-paradigm-a-preliminary-analysis-based-on-hematoxylin-eosin-stained-slides-from-the-lower-grade-glioma-cohort-of-the-cancer-genome-atlas
#12
Reid Trenton Powell, Adriana Olar, Shivali Narang, Ganesh Rao, Erik Sulman, Gregory N Fuller, Arvind Rao
BACKGROUND: Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO), which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs) (WHO Grade II-III) have fewer malignant characteristics than high-grade gliomas (WHO Grade IV), and a better clinical prognosis, however, accurate discrimination of overall survival (OS) remains a challenge...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28382222/summary-of-the-4-th-nordic-symposium-on-digital-pathology
#13
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/28197359/a-quantitative-approach-to-evaluate-image-quality-of-whole-slide-imaging-scanners
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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