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Imaging informatics

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https://www.readbyqxmd.com/read/28730549/creation-and-curation-of-the-society-of-imaging-informatics-in-medicine-hackathon-dataset
#1
Marc Kohli, James J Morrison, Judy Wawira, Matthew B Morgan, Jason Hostetter, Brad Genereaux, Mohannad Hussain, Steve G Langer
In order to support innovation, the Society of Imaging Informatics in Medicine (SIIM) elected to create a collaborative computing experience called a "hackathon." The SIIM Hackathon has always consisted of two components, the event itself and the infrastructure and resources provided to the participants. In 2014, SIIM provided a collection of servers to participants during the annual meeting. After initial server setup, it was clear that clinical and imaging "test" data were also needed in order to create useful applications...
July 20, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#2
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28648871/creation-of-an-open-framework-for-point-of-care-computer-assisted-reporting-and-decision-support-tools-for-radiologists
#3
Tarik K Alkasab, Bernardo C Bizzo, Lincoln L Berland, Sujith Nair, Pari V Pandharipande, H Benjamin Harvey
Decreasing unnecessary variation in radiology reporting and producing guideline-concordant reports is fundamental to radiology's success in value-based payment models and good for patient care. In this article, we present an open authoring system for point-of-care clinical decision support tools integrated into the radiologist reporting environment referred to as the computer-assisted reporting and decision support (CAR/DS) framework. The CAR/DS authoring system, described herein, includes: (1) a definition format for representing radiology clinical guidelines as structured, machine-readable Extensible Markup Language documents and (2) a user-friendly reference implementation to test the fidelity of the created definition files with the clinical guideline...
June 22, 2017: Journal of the American College of Radiology: JACR
https://www.readbyqxmd.com/read/28609000/the-role-of-informatics-in-patient-centered-care-and-personalized-medicine
#4
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/28608010/transcriptome-architecture-of-adult-mouse-brain-revealed-by-sparse-coding-of-genome-wide-in-situ-hybridization-images
#5
Yujie Li, Hanbo Chen, Xi Jiang, Xiang Li, Jinglei Lv, Meng Li, Hanchuan Peng, Joe Z Tsien, Tianming Liu
Highly differentiated brain structures with distinctly different phenotypes are closely correlated with the unique combination of gene expression patterns. Using a genome-wide in situ hybridization image dataset released by Allen Mouse Brain Atlas, we present a data-driven method of dictionary learning and sparse coding. Our results show that sparse coding can elucidate patterns of transcriptome organization of mouse brain. A collection of components obtained from sparse coding display robust region-specific molecular signatures corresponding to the canonical neuroanatomical subdivisions including fiber tracts and ventricular systems...
June 12, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28551930/-laboratory-tests-and-radiological-imaging-diagnostic-tools-that-share-information-and-can-be-functionally-integrated
#6
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/28538724/applying-systems-level-spectral-imaging-and-analysis-to-reveal-the-organelle-interactome
#7
Alex M Valm, Sarah Cohen, Wesley R Legant, Justin Melunis, Uri Hershberg, Eric Wait, Andrew R Cohen, Michael W Davidson, Eric Betzig, Jennifer Lippincott-Schwartz
The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28514892/single-case-cognitive-neuropsychology-in-the-age-of-big-data
#8
Jared Medina, Simon Fischer-Baum
Historically, single-case studies of brain-damaged individuals have contributed substantially to our understanding of cognitive processes. However, the role of single-case cognitive neuropsychology has diminished with the proliferation of techniques that measure neural activity in humans. Instead, large-scale informatics approaches in which data are gathered from hundreds of neuroimaging studies have become popular. It has been claimed that utilizing these informatics approaches can address problems found in single imaging studies...
May 17, 2017: Cognitive Neuropsychology
https://www.readbyqxmd.com/read/28365740/effective-biomedical-document-classification-for-identifying-publications-relevant-to-the-mouse-gene-expression-database-gxd
#9
Xiangying Jiang, Martin Ringwald, Judith Blake, Hagit Shatkay
The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28358291/feasibility-and-utility-of-an-integrated-medical-imaging-and-informatics-smartphone-system-for-management-of-acute-stroke
#10
Kristina Shkirkova, Eftitan Y Akam, Josephine Huang, Sunil A Sheth, May Nour, Conrad W Liang, Michael McManus, Van Trinh, Gary Duckwiler, Jason Tarpley, Fernando Vinuela, Jeffrey L Saver
Background Rapid dissemination and coordination of clinical and imaging data among multidisciplinary team members are essential for optimal acute stroke care. Aim To characterize the feasibility and utility of the Synapse Emergency Room mobile (Synapse ERm) informatics system. Methods We implemented the Synapse ERm system for integration of clinical data, computerized tomography, magnetic resonance, and catheter angiographic imaging, and real-time stroke team communications, in consecutive acute neurovascular patients at a Comprehensive Stroke Center...
January 1, 2017: International Journal of Stroke: Official Journal of the International Stroke Society
https://www.readbyqxmd.com/read/28348249/deciphering-tissue-morphodynamics-using-bioimage-informatics
#11
REVIEW
Alexandre C Dufour, Anneliene H Jonker, Jean-Christophe Olivo-Marin
In recent years developmental biology has greatly benefited from the latest advances in fluorescence microscopy techniques. Consequently, quantitative and automated analysis of this data is becoming a vital first step in the quest for novel insights into the various aspects of development. Here we present an introductory overview of the various image analysis methods proposed for developmental biology images, with particular attention to openly available software packages. These tools, as well as others to come, are rapidly paving the way towards standardized and reproducible bioimaging studies at the whole-tissue level...
May 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28280932/bits-and-bytes-the-future-of-radiology-lies-in-informatics-and-information-technology
#12
James A Brink, Ronald L Arenson, Thomas M Grist, Jonathan S Lewin, Dieter Enzmann
Advances in informatics and information technology are sure to alter the practice of medical imaging and image-guided therapies substantially over the next decade. Each element of the imaging continuum will be affected by substantial increases in computing capacity coincident with the seamless integration of digital technology into our society at large. This article focuses primarily on areas where this IT transformation is likely to have a profound effect on the practice of radiology. KEY POINTS: • Clinical decision support ensures consistent and appropriate resource utilization...
March 9, 2017: European Radiology
https://www.readbyqxmd.com/read/28220414/quantitative-analysis-of-ligand-induced-endocytosis-of-flagellin-sensing-2-using-automated-image-segmentation
#13
Michelle E Leslie, Antje Heese
Plants are equipped with a suite of plant pattern recognition receptors (PRRs) that must be properly trafficked to and from the plasma membrane (PM), which serves as the host-pathogen interface, for robust detection of invading pathogenic microbes. Recognition of bacterial flagellin, or the derived peptide flg22, is facilitated by the PM-localized PRR, FLAGELLIN SENSING 2 (FLS2). Upon flg22 binding, FLS2 is rapidly internalized from the PM into endosomal compartments and subsequently degraded. To understand better the integration of FLS2 endocytosis and signaling outputs, we developed methods for the quantitative analysis of FLS2 trafficking using freely available bioimage informatic tools...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28161513/the-burden-of-proof-the-current-state-of-atrial-fibrillation-prevention-and-treatment-trials
#14
Rosita Zakeri, David R Van Wagoner, Hugh Calkins, Tom Wong, Heather M Ross, E Kevin Heist, Timothy E Meyer, Peter R Kowey, Robert J Mentz, John G Cleland, Bertram Pitt, Faiez Zannad, Cecilia Linde
Atrial fibrillation (AF) is an age-related arrhythmia of enormous socioeconomic significance. In recent years, our understanding of the basic mechanisms that initiate and perpetuate AF has evolved rapidly, catheter ablation of AF has progressed from concept to reality, and recent studies suggest lifestyle modification may help prevent AF recurrence. Emerging developments in genetics, imaging, and informatics also present new opportunities for personalized care. However, considerable challenges remain. These include a paucity of studies examining AF prevention, modest efficacy of existing antiarrhythmic therapies, diverse ablation technologies and practice, and limited evidence to guide management of high-risk patients with multiple comorbidities...
May 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28144731/-erratum-to-annual-report-of-the-working-group-on-informatics-innovative-imaging-and-biobanking-of-the-german-society-for-pathology
#15
G Kayser, G Haroske
No abstract text is available yet for this article.
January 31, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28100277/stress-echo-2020-the-international-stress-echo-study-in-ischemic-and-non-ischemic-heart-disease
#16
MULTICENTER STUDY
Eugenio Picano, Quirino Ciampi, Rodolfo Citro, Antonello D'Andrea, Maria Chiara Scali, Lauro Cortigiani, Iacopo Olivotto, Fabio Mori, Maurizio Galderisi, Marco Fabio Costantino, Lorenza Pratali, Giovanni Di Salvo, Eduardo Bossone, Francesco Ferrara, Luna Gargani, Fausto Rigo, Nicola Gaibazzi, Giuseppe Limongelli, Giuseppe Pacileo, Maria Grazia Andreassi, Bruno Pinamonti, Laura Massa, Marco A R Torres, Marcelo H Miglioranza, Clarissa Borguezan Daros, José Luis de Castro E Silva Pretto, Branko Beleslin, Ana Djordjevic-Dikic, Albert Varga, Attila Palinkas, Gergely Agoston, Dario Gregori, Paolo Trambaiolo, Sergio Severino, Ayana Arystan, Marco Paterni, Clara Carpeggiani, Paolo Colonna
BACKGROUND: Stress echocardiography (SE) has an established role in evidence-based guidelines, but recently its breadth and variety of applications have extended well beyond coronary artery disease (CAD). We lack a prospective research study of SE applications, in and beyond CAD, also considering a variety of signs in addition to regional wall motion abnormalities. METHODS: In a prospective, multicenter, international, observational study design, > 100 certified high-volume SE labs (initially from Italy, Brazil, Hungary, and Serbia) will be networked with an organized system of clinical, laboratory and imaging data collection at the time of physical or pharmacological SE, with structured follow-up information...
January 18, 2017: Cardiovascular Ultrasound
https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#17
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28087400/plus-disease-in-retinopathy-of-prematurity-diagnostic-trends-in-2016-versus-2007
#18
MULTICENTER STUDY
Chace Moleta, J Peter Campbell, Jayashree Kalpathy-Cramer, R V Paul Chan, Susan Ostmo, Karyn Jonas, Michael F Chiang
PURPOSE: To identify any temporal trends in the diagnosis of plus disease in retinopathy of prematurity (ROP) by experts. DESIGN: Reliability analysis. METHODS: ROP experts were recruited in 2007 and 2016 to classify 34 wide-field fundus images of ROP as plus, pre-plus, or normal, coded as "3," "2," and "1," respectively, in the database. The main outcome was the average calculated score for each image in each cohort. Secondary outcomes included correlation on the relative ordering of the images in 2016 vs 2007, interexpert agreement, and intraexpert agreement...
April 2017: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/28077885/designing-and-implementation-of-retina-image-drawing-system-and-automatic-report-generation-from-retina-examinations
#19
Reza Safdari, Mehrshad Mokhtaran, Shahram Tahmasebian
INTRODUCTION: Electronic medical records as one of major parts of electronic health records is an important application of Medical Informatics. EMR includes different types of data, Graphical items being one of these data types. To this end, a standard structure for storing and recovering and finally exchanging this data type is required. In order to standardize information items in this research, UMLS standard is used. In this research, graphical information from fondues designing in retina surgery forms is used for the task of implementation...
October 2016: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/28057585/an-overview-of-data-science-uses-in-bioimage-informatics
#20
REVIEW
Anatole Chessel
This review aims at providing a practical overview of the use of statistical features and associated data science methods in bioimage informatics. To achieve a quantitative link between images and biological concepts, one typically replaces an object coming from an image (a segmented cell or intracellular object, a pattern of expression or localisation, even a whole image) by a vector of numbers. They range from carefully crafted biologically relevant measurements to features learnt through deep neural networks...
January 3, 2017: Methods: a Companion to Methods in Enzymology
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