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Pathology informatics

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https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#1
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#2
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/29092947/an-image-analysis-resource-for-cancer-research-piip-pathology-image-informatics-platform-for-visualization-analysis-and-management
#3
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/29054270/the-peptidome-comes-of-age-mass-spectrometry-based-characterization-of-the-circulating-cancer-peptidome
#4
David W Greening, Eugene A Kapp, Richard J Simpson
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases...
2017: Enzymes
https://www.readbyqxmd.com/read/28939981/-annual-report-2017-of-the-working-group-on-informatics-digital-pathology-and-biobanks
#5
G Kayser, G Haroske
No abstract text is available yet for this article.
September 22, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28913416/using-focused-laboratory-management-and-quality-improvement-projects-to-enhance-resident-training-and-foster-scholarship
#6
Matthew D Krasowski, Bradley A Ford, J Stacey Klutts, Chris S Jensen, Angela S Briggs, Robert A Robinson, Leslie A Bruch, Nitin J Karandikar
Training in patient safety, quality, and management is widely recognized as an important element of graduate medical education. These concepts have been intertwined in pathology graduate medical education for many years, although training programs face challenges in creating explicit learning opportunities in these fields. Tangibly involving pathology residents in management and quality improvement projects has the potential to teach and reinforce key concepts and further fulfill Accreditation Council for Graduate Medical Education goals for pursuing projects related to patient safety and quality improvement...
January 2017: Acad Pathol
https://www.readbyqxmd.com/read/28828200/pathedex-uncovering-high-explanatory-visual-diagnostics-heuristics-using-digital-pathology-and-multiscale-gaze-data
#7
Dmitriy Shin, Mikhail Kovalenko, Ilker Ersoy, Yu Li, Donald Doll, Chi-Ren Shyu, Richard Hammer
BACKGROUND: Visual heuristics of pathology diagnosis is a largely unexplored area where reported studies only provided a qualitative insight into the subject. Uncovering and quantifying pathology visual and nonvisual diagnostic patterns have great potential to improve clinical outcomes and avoid diagnostic pitfalls. METHODS: Here, we present PathEdEx, an informatics computational framework that incorporates whole-slide digital pathology imaging with multiscale gaze-tracking technology to create web-based interactive pathology educational atlases and to datamine visual and nonvisual diagnostic heuristics...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28828198/teaching-digital-pathology-the-international-school-of-digital-pathology-and-proposed-syllabus
#8
Vincenzo Della Mea, Antonino Carbone, Carla Di Loreto, Gloria Bueno, Paolo De Paoli, Marcial García-Rojo, David de Mena, Annunziata Gloghini, Mohammad Ilyas, Arvydas Laurinavicius, Allan Rasmusson, Massimo Milione, Riccardo Dolcetti, Marco Pagani, Andrea Stoppini, Sandro Sulfaro, Michelangelo Bartolo, Emanuela Mazzon, H Peter Soyer, Liron Pantanowitz
Digital pathology is an interdisciplinary field where competency in pathology, laboratory techniques, informatics, computer science, information systems, engineering, and even biology converge. This implies that teaching students about digital pathology requires coverage, expertise, and hands-on experience in all these disciplines. With this in mind, a syllabus was developed for a digital pathology summer school aimed at professionals in the aforementioned fields, as well as trainees and doctoral students. The aim of this communication is to share the context, rationale, and syllabus for this school of digital pathology...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28688028/novel-assessment-of-interstitial-lung-disease-using-the-computer-aided-lung-informatics-for-pathology-evaluation-and-rating-caliper-software-system-in-idiopathic-inflammatory-myopathies
#9
Patompong Ungprasert, Katelynn M Wilton, Floranne C Ernste, Sanjay Kalra, Cynthia S Crowson, Srinivasan Rajagopalan, Brian J Bartholmai
PURPOSE: To evaluate the correlation between measurements from quantitative thoracic high-resolution CT (HRCT) analysis with "Computer-Aided Lung Informatics for Pathology Evaluation and Rating" (CALIPER) software and measurements from pulmonary function tests (PFTs) in patients with idiopathic inflammatory myopathies (IIM)-associated interstitial lung disease (ILD). METHODS: A cohort of patients with IIM-associated ILD seen at Mayo Clinic was identified from medical record review...
October 2017: Lung
https://www.readbyqxmd.com/read/28684129/chemokine-isoforms-and-processing-in-inflammation-and-immunity
#10
REVIEW
Paul Proost, Sofie Struyf, Jo Van Damme, Pierre Fiten, Estefania Ugarte-Berzal, Ghislain Opdenakker
The first dimension of chemokine heterogeneity is reflected by their discovery and purification as natural proteins. Each of those chemokines attracted a specific inflammatory leukocyte type. With the introduction of genomic technologies, a second wave of chemokine heterogeneity was established by the discovery of putative chemokine-like sequences and by demonstrating chemotactic activity of the gene products in physiological leukocyte homing. In the postgenomic era, the third dimension of chemokine heterogeneity is the description of posttranslational modifications on most chemokines...
July 3, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28609004/post-fine-needle-aspiration-biopsy-communication-and-the-integrated-and-standardized-cytopathology-report
#11
Martha B Pitman, W Stephen Black-Schaffer
Communication between cytopathologists and patients and their care team is a critical component of accurate and timely patient management. The most important single means of communication for the cytopathologist is through the cytopathology report. Implementation of standardized terminology schemes and structured, templated reporting facilitates the ability of the cytopathologist to provide a comprehensive and integrated report. Cytopathology has been among the pathology subspecialties that have led the way in developing standardized reporting, beginning with the 1954 Papanicolaou classification scheme for cervical-vaginal cytology and continuing through the Bethesda systems for gynecological cytology and several nongynecological cytology systems...
June 2017: Cancer
https://www.readbyqxmd.com/read/28609000/the-role-of-informatics-in-patient-centered-care-and-personalized-medicine
#12
Matthew G Hanna, Liron Pantanowitz
The practice of cytopathology has dramatically changed due to advances in genomics and information technology. Cytology laboratories have accordingly become increasingly dependent on pathology informatics support to meet the emerging demands of precision medicine. Pathology informatics deals with information technology in the laboratory, and the impact of this technology on workflow processes and staff who interact with these tools. This article covers the critical role that laboratory information systems, electronic medical records, and digital imaging plays in patient-centered personalized medicine...
June 2017: Cancer
https://www.readbyqxmd.com/read/28586416/bridging-the-gap-between-reproducibility-and-translation-data-resources-and-approaches
#13
Caroline J Zeiss, Linda K Johnson
Animal research has constituted a fundamental means to achieve groundbreaking therapies for human disease. However, for complex diseases, promising preclinical results have failed to translate to the clinic. Reasons for this disparity are multifactorial. These include the challenges inherent in modeling complex disease in animals, as well issues of study design, reproducibility and operational norms within the biomedical research enterprise. In this issue, we explore the range of information resources available for the comparative study of disease, as well as challenges to the ultimate translation of preclinical findings...
July 1, 2017: ILAR Journal
https://www.readbyqxmd.com/read/28551930/-laboratory-tests-and-radiological-imaging-diagnostic-tools-that-share-information-and-can-be-functionally-integrated
#14
Michael Mayer
In spite of apparent disparity between the specialties of radiological imaging, pathology and laboratory analysis, the medical diagnostic information that these sources provide have a lot in common and can be effectively utilized by sharing quantitative and qualitative results through modern information technology processes. Informaticsbased integration of radiological imaging, digital images of anatomical and molecular pathology and clinical laboratory results enables earlier, more sensitive and precise diagnosis, resulting in the more efficient treatment of patients...
March 2017: Harefuah
https://www.readbyqxmd.com/read/28542177/mycophenolate-mofetil-for-scleroderma-related-interstitial-lung-disease-a-real-world-experience
#15
Misbah Baqir, Ashima Makol, Thomas G Osborn, Brian J Bartholmai, Jay H Ryu
BACKGROUND AND OBJECTIVE: Interstitial lung disease (ILD) remains the number one cause of mortality in scleroderma (SSc). Our goal was to determine the effectiveness of mycophenolate mofetil (MMF) in treating SSc-ILD in a retrospective study. METHODS: A retrospective, computer-assisted search was performed to identify patients with SSc-ILD treated with MMF from 1997 through 2014. We used a novel software tool, Computer-Aided Lung Informatics for Pathology Evaluation and Rating (CALIPER), to quantify parenchymal lung abnormalities on high-resolution computed tomography...
2017: PloS One
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
#16
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/28398175/interactive-design-of-patient-oriented-video-games-for-rehabilitation-concept-and-application
#17
Giorgia Lupinacci, Gianluca Gatti, Corrado Melegari, Saverio Fontana
PURPOSE: Serious video-games are innovative tools used to train the motor skills of subjects affected by neurological disorders. They are often developed to train a specific type of patients and the rules of the game are standardly defined. A system that allows the therapist to design highly patient-oriented video-games, without specific informatics skills, is proposed. METHOD: The system consists of one personal computer, two screens, a Kinect™ sensor and a specific software developed here for the design of the video-games...
April 11, 2017: Disability and Rehabilitation. Assistive Technology
https://www.readbyqxmd.com/read/28393503/-bilateral-submandibulectomy-for-the-treatment-of-drooling-in-pediatric-age-10-years-of-experience
#18
A S Marinho, C Sousa, A Coelho, J Barbosa-Sequeira, M Recamán, F Carvalho
INTRODUCTION: Sialorrhea is a medical problem and can become a social issue, common in children with neurological disabilities. The bilateral submandibulectomy is one of the available treatment options for managing this pathology. AIM OF THE STUDY: The aim of this study is to evaluate the effectiveness of bilateral submandibulectomy in the management of sialorrhea in children with neurological disabilities through the parents' satisfaction grade. PATIENTS AND METHODS: We retrospectively analyzed 91 bilateral submandibulectomies for a period of time of 10 years (2004-2015)...
July 10, 2016: Cirugía Pediátrica: Organo Oficial de la Sociedad Española de Cirugía Pediátrica
https://www.readbyqxmd.com/read/28392728/external-quality-assessment-beyond-the-analytical-phase-an-australian-perspective
#19
REVIEW
Tony Badrick, Stephanie Gay, Euan J McCaughey, Andrew Georgiou
External Quality Assessment (EQA) is the verification, on a recurring basis, that laboratory results conform to expectations for the quality required for patient care. It is now widely recognised that both the pre- and post-laboratory phase of testing, termed the diagnostic phases, are a significant source of laboratory errors. These errors have a direct impact on both the effectiveness of the laboratory and patient safety. Despite this, Australian laboratories tend to be focussed on very narrow concepts of EQA, primarily surrounding test accuracy, with little in the way of EQA programs for the diagnostic phases...
February 15, 2017: Biochemia Medica: časopis Hrvatskoga Društva Medicinskih Biokemičara
https://www.readbyqxmd.com/read/28365743/automated-pdf-highlighting-to-support-faster-curation-of-literature-for-parkinson-s-and-alzheimer-s-disease
#20
Honghan Wu, Anika Oellrich, Christine Girges, Bernard de Bono, Tim J P Hubbard, Richard J B Dobson
Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator...
January 1, 2017: Database: the Journal of Biological Databases and Curation
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