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https://www.readbyqxmd.com/read/28432954/fully-automatic-left-ventricular-segmentation-from-long-axis-cardiac-cine-mr-scans
#1
Rahil Shahzad, Qian Tao, Oleh Dzyubachyk, Marius Staring, Boudewijn P F Lelieveldt, Rob J van der Geest
With an increasing number of large-scale population-based cardiac magnetic resonance (CMR) imaging studies being conducted nowadays, there comes the mammoth task of image annotation and image analysis. Such population-based studies would greatly benefit from automated pipelines, with an efficient CMR image analysis workflow. The purpose of this work is to investigate the feasibility of using a fully-automatic pipeline to segment the left ventricular endocardium and epicardium simultaneously on two orthogonal (vertical and horizontal) long-axis cardiac cine MRI scans...
April 13, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28431137/trapp-webserver-predicting-protein-binding-site-flexibility-and-detecting-transient-binding-pockets
#2
Antonia Stank, Daria B Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C Wade
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430956/achieving-high-reliability-in-histology-%C3%A2-an-improvement-series-to-reduce-errors
#3
Yael K Heher, Yigu Chen, Sergey Pyatibrat, Edward Yoon, Jeffrey D Goldsmith, Kenneth E Sands
Objectives: Despite sweeping medical advances in other fields, histology processes have by and large remained constant over the past 175 years. Patient label identification errors are a known liability in the laboratory and can be devastating, resulting in incorrect diagnoses and inappropriate treatment. The objective of this study was to identify vulnerable steps in the histology workflow and reduce the frequency of labeling errors (LEs). Methods: In this 36-month study period, a numerical step key (SK) was developed to capture LEs...
November 1, 2016: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28429389/evaluation-of-real-time-data-obtained-from-gravimetric-preparation-of-antineoplastic-agents-shows-medication-errors-with-possible-critical-therapeutic-impact-results-of-a-large-scale-multicentre-multinational-retrospective-study
#4
R Terkola, M Czejka, J Bérubé
WHAT IS KNOWN AND OBJECTIVE: Medication errors are a significant cause of morbidity and mortality especially with antineoplastic drugs, owing to their narrow therapeutic index. Gravimetric workflow software systems have the potential to reduce volumetric errors during intravenous antineoplastic drug preparation which may occur when verification is reliant on visual inspection. Our aim was to detect medication errors with possible critical therapeutic impact as determined by the rate of prevented medication errors in chemotherapy compounding after implementation of gravimetric measurement...
April 21, 2017: Journal of Clinical Pharmacy and Therapeutics
https://www.readbyqxmd.com/read/28429122/quantifying-golgi-structure-using-em-combining-volume-sem-and-stereology-for-higher-throughput
#5
REVIEW
Sophie Ferguson, Anna M Steyer, Terry M Mayhew, Yannick Schwab, John Milton Lucocq
Investigating organelles such as the Golgi complex depends increasingly on high-throughput quantitative morphological analyses from multiple experimental or genetic conditions. Light microscopy (LM) has been an effective tool for screening but fails to reveal fine details of Golgi structures such as vesicles, tubules and cisternae. Electron microscopy (EM) has sufficient resolution but traditional transmission EM (TEM) methods are slow and inefficient. Newer volume scanning EM (volume-SEM) methods now have the potential to speed up 3D analysis by automated sectioning and imaging...
April 20, 2017: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28428983/rapid-inducible-protein-displacement-in-plasmodiumin-vivo-and-in-vitro-using-knocksideways-technology
#6
Katie R Hughes, Andy P Waters
A deeper understanding of the biology of the Plasmodium parasite is essential in order to identify targets for interventions, with the ultimate aim of eliminating malaria. Determining the function(s) of essential proteins in Plasmodium has, until recently, been hampered by the lack of efficient conditional systems to abrogate proteins. We report the adaptation of a conditional technology, knocksideways (KS), for use in Plasmodium berghei, which can potentially rapidly inactivate proteins of interest through relocalisation...
March 14, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#7
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28426136/differentiating-signals-to-make-biological-sense-a-guide-through-databases-for-ms-based-non-targeted-metabolomics
#8
REVIEW
Alberto Gil de la Fuente, Emily Grace Armitage, Abraham Otero, Coral Barbas, Joanna Godzien
Metabolite identification is one of the most challenging steps in metabolomics studies and reflects one of the greatest bottlenecks in the entire workflow. The success of this step determines the success of the entire research, therefore the quality at which annotations are given requires special attention. A variety of tools and resources are available to aid metabolite identification or annotation, offering different and often complementary functionalities. In preparation for this article, almost 50 databases were reviewed, from which 17 were selected for discussion, chosen for their on-line ESI-MS functionality...
April 20, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28425748/a-field-analysis-trial-comparing-the-turnaround-times-of-routine-and-stat-red-blood-cell-immunohematology-testing
#9
Katie Sackett, Andrea Kjell, Abigail M Schneider, Claudia S Cohn
The turnaround time (TAT) for pre-transfusion testing is important for prompt clinical decision-making. TAT includes the time between the arrival of the sample and the initiation of testing, plus the processing time (PT) required to generate and report a result. The TAT in larger blood banks is mostly dependent upon the capability of the analyzer used. In smaller blood banks, where manual work is often performed, the TAT is dependent on availability and experience of staff, testing resources, and workload. Our site performed a comparative analysis of the ORTHO VISION® (Ortho Clinical Diagnostics, Raritan, NJ) and the Echo® (Immucor, Norcross, GA) blood bank analyzers, using the TAT and PT of standard blood bank tests as the outcome metrics...
January 2017: Immunohematology
https://www.readbyqxmd.com/read/28423853/square
#10
Carsten Oliver Schmidt, Christine Krabbe, Janka Schössow, Martin Albers, Dörte Radke, Jörg Henke
Valid scientific inferences from epidemiological and clinical studies require high data quality. Data generating departments therefore aim to detect data irregularities as early as possible in order to guide quality management processes. In addition, after the completion of data collections the obtained data quality must be evaluated. This can be challenging in complex studies due to a wide scope of examinations, numerous study variables, multiple examiners, devices, and examination centers. This paper describes a Java EE web application used to monitor and evaluate data quality in institutions with complex and multiple studies, named Square<sup>2</sup>...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423843/an-approach-for-the-support-of-semantic-workflows-in-electronic-health-records
#11
Marco Schweitzer, Alexander Hoerbst
With the unprecedented increase of healthcare data, technologies need to be both, highly efficient for the meaningful utilization of accessible data and flexible to adapt to future challenges and individual preferences. The OntoHealth system makes use of semantic technologies to enable flexible and individual interaction with Electronic Health Records (EHR) for physicians. This is achieved by the execution of formally modelled clinical workflows and the composition of Semantic Web Services (SWS). Several seamless components provide a service-oriented structure defined by individual designed EHR-workflows...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423821/using-healthcare-work-process-modelling-in-hospitals-to-increase-the-fit-between-the-healthcare-workflow-and-the-electronic-medical-record
#12
David Morquin, Roxana Ologeanu-Taddei, Ludivine Watbled
As with other organizations, hospitals tend to promote unrealistic expectations related to software implementaton. Quite often the real issue is a misfit between the software and organizational factors. Our paper shows how work process modelling within the hospital can reduce this misfit according to the vision developped by the ergonomics and the management of information systems. This idea is supported by two cases in two different University Hospitals in France, in which using work process modelling lead to identification of problems and their causes, and solutions...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423803/business-rules-to-improve-secondary-data-use-of-electronic-healthcare-systems
#13
Jonathan Blaisure, Werner Ceusters
The 'fit for purpose' paradigm used for data quality assessment in electronic healthcare record (EHR) systems is not so fit when assessed in the light of secondary data use. An analysis of the difficulties encountered in trying to use existing EHR data for cohort identification for prospective clinical trials and retrograde data analytics, revealed the root causes to fall in three categories: (1) issues in workflow and data registration, (2) preventable inadequacies in software configuration and personalization and (3) software development issues on the side of the vendor...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423760/uk-health-and-social-care-case-studies-iterative-technology-development
#14
Adie Blanchard, Laura Gilbert, Tom Dawson
As a result of increasing demand in the face of reducing resources, technology has been implemented in many social and health care services to improve service efficiency. This paper outlines the experiences of deploying a 'Software as a Service' application in the UK social and health care sectors. The case studies demonstrate that every implementation is different, and unique to each organisation. Technology design and integration can be facilitated by ongoing engagement and collaboration with all stakeholders, flexible design, and attention to interoperability to suit services and their workflows...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423751/web-validation-service-for-ensuring-adherence-to-the-dicom-standard
#15
Jorge Miguel Silva, Tiago Marques Godinho, David Silva, Carlos Costa
The DICOM Standard has been fundamental for ensuring the interoperability of Picture Archive and Communications Systems (PACS). By compiling rigorously to the standard, medical imaging equipment and applications from different vendors can share their data, and create integrated workflows which contributes to better quality healthcare services. However, DICOM is a complex, flexible and very extensive standard. Thus, it is difficult to attest the conformity of data structures produced by DICOM applications resulting in unexpected behaviors, errors and malfunctions...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423156/creation-of-an-internal-teledermatology-store-and-forward-system-in-an-existing-electronic-health-record-a-pilot-study-in-a-safety-net-public-health-and-hospital-system
#16
Zachary A Carter, Shauna Goldman, Kristen Anderson, Xiaxiao Li, Linda S Hynan, Benjamin F Chong, Arturo R Dominguez
Importance: External store-and-forward (SAF) teledermatology systems operate separately from the primary health record and have many limitations, including care fragmentation, inadequate communication among clinicians, and privacy and security concerns, among others. Development of internal SAF workflows within existing electronic health records (EHRs) should be the standard for large health care organizations for delivering high-quality dermatologic care, improving access, and capturing other telemedicine benchmark data...
April 19, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#17
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422179/heritability-maps-of-human-face-morphology-through-large-scale-automated-three-dimensional-phenotyping
#18
Dimosthenis Tsagkrasoulis, Pirro Hysi, Tim Spector, Giovanni Montana
The human face is a complex trait under strong genetic control, as evidenced by the striking visual similarity between twins. Nevertheless, heritability estimates of facial traits have often been surprisingly low or difficult to replicate. Furthermore, the construction of facial phenotypes that correspond to naturally perceived facial features remains largely a mystery. We present here a large-scale heritability study of face geometry that aims to address these issues. High-resolution, three-dimensional facial models have been acquired on a cohort of 952 twins recruited from the TwinsUK registry, and processed through a novel landmarking workflow, GESSA (Geodesic Ensemble Surface Sampling Algorithm)...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421332/the-statin-associated-muscle-symptom-clinical-index-sams-ci-revision-for-clinical-use-content-validation-and-inter-rater-reliability
#19
Robert S Rosenson, Kate Miller, Martha Bayliss, Robert J Sanchez, Marie T Baccara-Dinet, Daniela Chibedi-De-Roche, Beth Taylor, Irfan Khan, Garen Manvelian, Michelle White, Terry A Jacobson
PURPOSE: The Statin-Associated Muscle Symptom Clinical Index (SAMS-CI) is a method for assessing the likelihood that a patient's muscle symptoms (e.g., myalgia or myopathy) were caused or worsened by statin use. The objectives of this study were to prepare the SAMS-CI for clinical use, estimate its inter-rater reliability, and collect feedback from physicians on its practical application. METHODS: For content validity, we conducted structured in-depth interviews with its original authors as well as with a panel of independent physicians...
April 18, 2017: Cardiovascular Drugs and Therapy
https://www.readbyqxmd.com/read/28421225/using-telephony-data-to-facilitate-discovery-of-clinical-workflows
#20
Donald W Rucker
BACKGROUND:  Discovery of clinical workflows to target for redesign using methods such as Lean and Six Sigma is difficult. VoIP telephone call pattern analysis may complement direct observation and EMR-based tools in understanding clinical workflows at the enterprise level by allowing visualization of institutional telecommunications activity. OBJECTIVE:  To build an analytic framework mapping repetitive and high-volume telephone call patterns in a large medical center to their associated clinical units using an enterprise unified communications server log file and to support visualization of specific call patterns using graphical networks...
April 19, 2017: Applied Clinical Informatics
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