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https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#1
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/28653599/microrna-539-inhibits-the-epithelial-mesenchymal-transition-of-esophageal-cancer-cells-by-twist-related-protein-1-mediated-modulation-of-melanoma-associated-antigen-a4-magea4
#2
Zhili Cao, Xiang Zheng, Lei Cao, Naixin Liang
MicroRNAs (miR) play key roles in cancers, yet the potential molecular mechanisms of miR-539 on esophageal squamous cell carcinoma (ESCC) are not well understood. Screened by informatics method, Twist-related protein 1 (TWIST1) was hypothesized to be a possible target gene of miR-539. Since the melanoma associated antigen (MAGE) A4 is reported to be up-regulated by TWIST1, this study aimed to examine the biological functions and mechanism involving TWIST1 and MAGE4 of miR-539 in ESCC. MiR-539 mimics or scrambled miRs were transfected into human ESCC TE3 cells to interfere the expression of miR-539...
June 12, 2017: Oncology Research
https://www.readbyqxmd.com/read/28653026/mono-di-and-tri-ssrs-data-extraction-storage-from-1403-virus-genomes-with-next-generation-retrieval-mechanism
#3
K V S S R Murthy, K V V Satyanarayana
Now a day׳s SSRs occupy the dominant role in different areas of bio-informatics like new virus identification, DNA finger printing, paternity & maternity identification, disease identification, future disease expectations and possibilities etc., Due to their wide applications in various fields and their significance, SSRs have been the area of interest for many researchers. In the SSRs extraction, retrieval algorithms are used; if retrieval algorithms quality is improved then automatically SSRs extraction system will achieve the most relevant results...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28648871/creation-of-an-open-framework-for-point-of-care-computer-assisted-reporting-and-decision-support-tools-for-radiologists
#4
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/28647790/should-degree-programs-in-biomedical-and-health-informatics-be-dedicated-or-integrated-reflections-and-recommendations-after-more-than-40%C3%A2-years-of-medical-informatics-education-at-tu-braunschweig-including-10%C3%A2-years-of-b-sc-and-15%C3%A2-years-of-m-sc-integrated
#5
Reinhold Haux, Michael Marschollek, Klaus-Hendrik Wolf, Ute Zeisberg
Education in biomedical and health informatics (BMHI) has been established in many countries throughout the world. For degree programs in BMHI we can distinguish between those that are completely stand-alone or dedicated to the discipline vs. those that are integrated within another program. After running integrated degree medical informatics programs at TU Braunschweig for 10 years at the B.Sc. and for 15 years at the M.Sc level, we (1) report about this educational approach, (2) analyze recommendations on, implementations of, and experiences with degree educational programs in BMHI worldwide, (3) summarize our lessons learned with the integrated approach at TU Braunschweig, and (4) suggest an answer to the question, whether degree programs in biomedical and health informatics should be dedicated or integrated...
July 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28640683/the-public-health-practitioner-of-the-future
#6
Paul Campbell Erwin, Ross C Brownson
The requisite capacities and capabilities of the public health practitioner of the future are being driven by multiple forces of change, including public health agency accreditation, climate change, health in all policies, social media and informatics, demographic transitions, globalized travel, and the repercussions of the Affordable Care Act. We describe five critical capacities and capabilities that public health practitioners can build on to successfully prepare for and respond to these forces of change: systems thinking and systems methods, communication capacities, an entrepreneurial orientation, transformational ethics, and policy analysis and response...
June 22, 2017: American Journal of Public Health
https://www.readbyqxmd.com/read/28637687/inhibition-of-cdk4-6-by-palbociclib-significantly-extends-survival-in-medulloblastoma-patient-derived-xenograft-mouse-models
#7
Michelle L Cook Sangar, Laura A Genovesi, Madison W Nakamoto, Melissa J Davis, Sue E Knoblaugh, Pengxiang Ji, Amanda Millar, Brandon Wainwright, James M Olson
  <p>Bioinformatics analysis followed by in vivo studies in patient-derived xenograft models were used to identify and validate CDK 4/6 inhibition as an effective therapeutic strategy for medulloblastoma, particularly Group 3 MYC-amplified tumors which have the worst clinical prognosis.</p> <br />Experimental Design: <p>A protein interaction network derived from a Sleeping Beauty mutagenesis model of medulloblastoma was used to identify potential novel therapeutic targets.  The top hit from this analysis was validated in vivo using patient-derived xenograft models of medulloblastoma implanted subcutaneously in the flank and orthotopically in the cerebellum of mice...
June 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28637638/the-gap-in-medical-informatics-and-continuing-education-between-the-united-states-and-china-a-comparison-of-conferences-in-2016
#8
Jun Liang, Kunyan Wei, Qun Meng, Zhenying Chen, Jiajie Zhang, Jianbo Lei
BACKGROUND: China launched its second health reform in 2010 with considerable investments in medical informatics (MI). However, to the best of our knowledge, research on the outcomes of this ambitious undertaking has been limited. OBJECTIVE: Our aim was to understand the development of MI and the state of continuing education in China and the United States from the perspective of conferences. METHODS: We conducted a quantitative and qualitative analysis of four MI conferences in China and two in the United States: China Medical Information Association Annual Symposium (CMIAAS), China Hospital Information Network Annual Conference (CHINC), China Health Information Technology Exchange Annual Conference (CHITEC), China Annual Proceeding of Medical Informatics (CPMI) versus the American Medical Informatics Association (AMIA) and Healthcare Information and Management Systems Society (HIMSS)...
June 21, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28637208/unit-conversions-between-loinc-codes
#9
Ronald G Hauser, Douglas B Quine, Alex Ryder, Sheldon Campbell
Logical Observation Identifiers Names and Codes (LOINC) is the most widely used controlled vocabulary to identify laboratory tests. A given laboratory test can often be reported in more than 1 unit of measure (eg, grams or moles), and LOINC defines unique codes for each unit. Consequently, an identical laboratory test performed by 2 different clinical laboratories may have different LOINC codes. The absence of unit conversions between compatible LOINC codes impedes data aggregation and analysis of laboratory results...
June 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28636770/a-technology-training-protocol-for-meeting-qsen-goals-focusing-on-meaningful-learning
#10
Shuhong Luo, Melanie Kalman
The purpose of this paper is to describe and discuss how we designed and developed a 12-step technology training protocol. The protocol is meant to improve meaningful learning in technology education so that nursing students are able to meet the informatics requirements of Quality and Safety Education in Nursing competencies. When designing and developing the training protocol, we used a simplified experiential learning model that addressed the core features of meaningful learning: to connect new knowledge with students' prior knowledge and real-world workflow...
June 21, 2017: Nursing Forum
https://www.readbyqxmd.com/read/28636063/solving-interoperability-in-translational-health-perspectives-of-students-from-the-international-partnership-in-health-informatics-education-iphie-2016-master-class
#11
Anne M Turner, Julio C Facelli, Monique Jaspers, Thomas Wetter, Daniel Pfeifer, Laël Cranmer Gatewood, Terry Adam, Yu-Chuan Li, Ming-Chin Lin, R Scott Evans, Anna Beukenhorst, Hugo Johan Theodoore van Mens, Esmee Tensen, Christian Bock, Laura Fendrich, Peter Seitz, Julian Suleder, Ranyah Aldelkhyyel, Kent Bridgeman, Zhen Hu, Aaron Sattler, Shin-Yi Guo, Islam Md Mohaimenul Mohaimenul, Dina Nur Anggraini Ningrum, Hsin-Ru Tung, Jiantano Bian, Joseph M Plasek, Casey Rommel, Juandalyn Burke, Harkirat Sohih
BACKGROUND: In the summer of 2016 an international group of biomedical and health informatics faculty and graduate students gathered for the 16th meeting of the International Partnership in Health Informatics Education (IPHIE) masterclass at the University of Utah campus in Salt Lake City, Utah. This international biomedical and health informatics workshop was created to share knowledge and explore issues in biomedical health informatics (BHI). OBJECTIVE: The goal of this paper is to summarize the discussions of biomedical and health informatics graduate students who were asked to define interoperability, and make critical observations to gather insight on how to improve biomedical education...
June 20, 2017: Applied Clinical Informatics
https://www.readbyqxmd.com/read/28633483/an-informatics-research-agenda-to-support-patient-and-family-empowerment-and-engagement-in-care-and-recovery-during-and-after-hospitalization
#12
Sarah Collins, Patricia Dykes, David W Bates, Brittany Couture, Ronen Rozenblum, Jennifer Prey, Kristin O'Reilly, Patricia Q Bourie, Cindy Dwyer, S Ryan Greysen, Jeffery Smith, Michael Gropper, Anuj K Dalal
As part of an interdisciplinary acute care patient portal task force with members from 10 academic medical centers and professional organizations, we held a national workshop with 71 attendees representing over 30 health systems, professional organizations, and technology companies. Our consensus approach identified 7 key sociotechnical and evaluation research focus areas related to the consumption and capture of information from patients, care partners (eg, family, friends), and clinicians through portals in the acute and post-acute care settings...
June 17, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28628741/amplicon-competition-enables-end-point-quantitation-of-nucleic-acids-following-isothermal-amplification
#13
Yu Sherry Jiang, Apollo Stacy, Marvin Whiteley, Andrew D Ellington, Sanchita Bhadra
It is inherently difficult to quantitate nucleic acid analytes with most isothermal amplification assays. We have now developed loop-mediated isothermal amplification (LAMP) reactions in which competition between defined numbers of 'false' and 'true' amplicons leads to order of magnitude quantitation via a single end-point determination. These thresholded LAMP reactions were successfully used to directly and quantitatively estimate the numbers of nucleic acids in complex biospecimens, including directly from cells and in sewage, with the values obtained closely correlating with qPCR quantitations...
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28625502/a-computable-phenotype-improves-cohort-ascertainment-in-a-pediatric-pulmonary-hypertension-registry
#14
Alon Geva, Jessica L Gronsbell, Tianxi Cai, Tianrun Cai, Shawn N Murphy, Jessica C Lyons, Michelle M Heinz, Marc D Natter, Nandan Patibandla, Jonathan Bickel, Mary P Mullen, Kenneth D Mandl
OBJECTIVES: To compare registry and electronic health record (EHR) data mining approaches for cohort ascertainment in patients with pediatric pulmonary hypertension (PH) in an effort to overcome some of the limitations of registry enrollment alone in identifying patients with particular disease phenotypes. STUDY DESIGN: This study was a single-center retrospective analysis of EHR and registry data at Boston Children's Hospital. The local Informatics for Integrating Biology and the Bedside (i2b2) data warehouse was queried for billing codes, prescriptions, and narrative data related to pediatric PH...
June 15, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28623185/a-web-based-data-collection-platform-for-multisite-randomized-behavioral-intervention-trials-development-key-software-features-and-results-of-a-user-survey
#15
Riddhi A Modi, Michael J Mugavero, Rivet K Amico, Jeanne Keruly, Evelyn Byrd Quinlivan, Heidi M Crane, Alfredo Guzman, Anne Zinski, Solange Montue, Katya Roytburd, Anna Church, James H Willig
BACKGROUND: Meticulous tracking of study data must begin early in the study recruitment phase and must account for regulatory compliance, minimize missing data, and provide high information integrity and/or reduction of errors. In behavioral intervention trials, participants typically complete several study procedures at different time points. Among HIV-infected patients, behavioral interventions can favorably affect health outcomes. In order to empower newly diagnosed HIV positive individuals to learn skills to enhance retention in HIV care, we developed the behavioral health intervention Integrating ENGagement and Adherence Goals upon Entry (iENGAGE) funded by the National Institute of Allergy and Infectious Diseases (NIAID), where we deployed an in-clinic behavioral health intervention in 4 urban HIV outpatient clinics in the United States...
June 16, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28616866/vocal-palsy-increases-the-risk-of-lower-respiratory-tract-infection-in-low-risk-low-morbidity-patients-undergoing-thyroidectomy-for-benign-disease-a-big-data-analysis
#16
S A R Nouraei, J Allen, H Kaddour, S E Middleton, P Aylin, A Darzi, N S Tolley
OBJECTIVES: Thyroidectomy is the commonest and most rapidly-growing operation which places normally-functioning laryngeal nerves at risk of injury. Laryngeal palsy is a major risk-factor for dysphonia, dysphagia, and less commonly, airway obstruction. We investigated the association between post-thyroidectomy vocal palsy and long-term risks of pneumonia and laryngeal failure. DESIGN: An N=near-all analysis of the English administrative dataset using a previously-validated informatics algorithm to identify young and otherwise low-risk patients undergoing thyroidectomy for benign disease...
June 14, 2017: Clinical Otolaryngology
https://www.readbyqxmd.com/read/28614444/expected-hazards-and-hospital-beds-in-host-cities-of-the-2014-fifa-world-cup-in-brazil
#17
Elaine Silva Miranda, Kimberley Shoaf, Raulino Sabino da Silva, Carolina Figueiredo Freitas, Claudia Garcia Serpa Osorio-de-Castro
Planning for mass gatherings involves health system preparedness based on an understanding of natural and technological hazards identified through prior risk assessment. We present the expected hazards reported by health administrators of the host cities for the 2014 FIFA World Cup in Brazil and discuss the hazards considering minimal available public hospital beds in the 12 cities at the time of the event. Four different groups of respondents were interviewed: pharmaceutical service administrators and overall health administrators at both the municipal and hospital levels...
June 12, 2017: Cadernos de Saúde Pública
https://www.readbyqxmd.com/read/28609004/post-fine-needle-aspiration-biopsy-communication-and-the-integrated-and-standardized-cytopathology-report
#18
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
#19
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
#20
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
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