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https://www.readbyqxmd.com/read/28453675/circosvcf-circos-visualization-of-whole-genome-sequence-variations-stored-in-vcf-files
#1
E Drori, D Levy, P Smirin-Yosef, O Rahimi, M Salmon-Divon
Summary: Visualization of whole-genomic variations in a meaningful manner assists researchers in gaining new insights into the underlying data, especially when it comes in the context of whole genome comparisons. CircosVCF is a web based visualization tool for genome-wide variant data described in VCF files, using circos plots. The user friendly interface of CircosVCF supports an interactive design of the circles in the plot, and the integration of additional information such as experimental data or annotations...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453673/vexor-an-integrative-environment-for-prioritization-of-functional-variants-in-fine-mapping-analysis
#2
Audrey Lemaçon, Charles Joly Beauparlant, Penny Soucy, Jamie Allen, Douglas Easton, Peter Kraft, Jacques Simard, Arnaud Droit
Motivation: The identification of the functional variants responsible for observed genome-wide association studies (GWAS) signals is one of the most challenging tasks of the post-GWAS research era. Several tools have been developed to annotate genetic variants by their genomic location and potential functional implications. Each of these tools has its own requirements and internal logic, which forces the user to become acquainted with each interface. Results: From an awareness of the amount of work needed to analyze a single locus, we have built a flexible, versatile and easy-to-use web interface designed to help in prioritizing variants and predicting their potential functional implications...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453653/the-bologna-annotation-resource-bar-3-0-improving-protein-functional-annotation
#3
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453553/a-tool-for-discovering-drug-sensitivity-and-gene-expression-associations-in-cancer-cells
#4
Yong Qin, Anthony P Conley, Elizabeth A Grimm, Jason Roszik
The sensitivity of cancer cells to anticancer drugs is a crucial factor for developing effective treatments. However, it is still challenging to precisely predict the effectiveness of therapeutics in humans within a complex genomic and molecular context. We developed an interface which allows the user to rapidly explore drug sensitivity and gene expression associations. Predictions for how expression of various genes affect anticancer drug activity are available for all genes for a set of therapeutics based on data from various cell lines of different origin in the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer projects...
2017: PloS One
https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#5
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28449074/fireprot-web-server-for-automated-design-of-thermostable-proteins
#6
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomas Martinek, David Bednar, Jiri Damborsky
There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28447862/high-reliability-microcontroller-nerve-stimulator-for-assistance-in-regional-anaesthesia-procedures
#7
Carlos A Ferri, Antonio A F Quevedo
In the last decades, the use of nerve stimulators to aid in regional anaesthesia has been shown to benefit the patient since it allows a better location of the nerve plexus, leading to correct positioning of the needle through which the anaesthetic is applied. However, most of the nerve stimulators available in the market for this purpose do not have the minimum recommended features for a good stimulator, and this can lead to risks to the patient. Thus, this study aims to develop an equipment, using embedded electronics, which meets all the characteristics, for a successful blockade...
April 27, 2017: Journal of Medical Engineering & Technology
https://www.readbyqxmd.com/read/28447860/remote-sensing-of-physiological-signs-using-a-machine-vision-system
#8
Ali Al-Naji, Kim Gibson, Javaan Chahl
The aim of this work is to remotely measure heart rate (HR) and respiratory rate (RR) using a video camera from long range (> 50 m). The proposed system is based on imperceptible signals produced from blood circulation, including skin colour variations and head motion. As these signals are not visible to the naked eye and to preserve the signal strength in the video, we used an improved video magnification technique to enhance these invisible signals and detect the physiological activity within the subject...
April 27, 2017: Journal of Medical Engineering & Technology
https://www.readbyqxmd.com/read/28446258/touchscreen-interventions-and-the-well-being-of-people-with-dementia-and-caregivers-a-systematic-review
#9
Charlie Tyack, Paul M Camic
BACKGROUND: Dementia can have significant detrimental impacts on the well-being of those with the disease and their carers. A range of computer-based interventions, including touchscreen-based interventions have been researched for use with this population in the hope that they might improve psychological well-being. This article reviews touchscreen-based interventions designed to be used by people with dementia (PWD), with a specific focus in assessing their impact on well-being. METHOD: The data bases, PsycInfo, ASSIA, Medline, CINAHL, and Cochrane Reviews were searched for touchscreen-based interventions designed to be used by PWD with reported psychological well-being outcomes...
April 27, 2017: International Psychogeriatrics
https://www.readbyqxmd.com/read/28443681/preventing-the-forgotten-ureteral-stent-by-using-a-mobile-point-of-care-application
#10
Justin Bradley Ziemba, Wesley Ludwig, Leticia Ruiz, Eduardo Carvalhal, Brian Matlaga
INTRODUCTION: The forgotten ureteral stent (FUS) can lead to patient morbidity. To date, tracking ureteral stents is a cumbersome task, given their high frequency of insertion and variable indwelling times. To simplify this process, an application was developed to track patients with indwelling ureteral stents. We report our initial user-experience and clinical outcomes with this application. METHODS: Ureteral Stent Tracker™ (UST) is a secure, HIPPA compliant, cloud based point-of-care (POC) application...
April 26, 2017: Journal of Endourology
https://www.readbyqxmd.com/read/28442630/discovering-relationships-between-nuclear-receptor-signaling-pathways-genes-and-tissues-in-transcriptomine
#11
Lauren B Becnel, Scott A Ochsner, Yolanda F Darlington, Apollo McOwiti, Wasula H Kankanamge, Michael Dehart, Alexey Naumov, Neil J McKenna
We previously developed a web tool, Transcriptomine, to explore expression profiling data sets involving small-molecule or genetic manipulations of nuclear receptor signaling pathways. We describe advances in biocuration, query interface design, and data visualization that enhance the discovery of uncharacterized biology in these pathways using this tool. Transcriptomine currently contains about 45 million data points encompassing more than 2000 experiments in a reference library of nearly 550 data sets retrieved from public archives and systematically curated...
April 25, 2017: Science Signaling
https://www.readbyqxmd.com/read/28441977/detecting-clusters-in-atom-probe-data-with-gaussian-mixture-models
#12
Jennifer Zelenty, Andrew Dahl, Jonathan Hyde, George D W Smith, Michael P Moody
Accurately identifying and extracting clusters from atom probe tomography (APT) reconstructions is extremely challenging, yet critical to many applications. Currently, the most prevalent approach to detect clusters is the maximum separation method, a heuristic that relies heavily upon parameters manually chosen by the user. In this work, a new clustering algorithm, Gaussian mixture model Expectation Maximization Algorithm (GEMA), was developed. GEMA utilizes a Gaussian mixture model to probabilistically distinguish clusters from random fluctuations in the matrix...
April 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28441476/sboldesigner-2-an-intuitive-tool-for-structural-genetic-design
#13
Michael Zhang, James Alastair McLaughlin, Anil Wipat, Chris J Myers
As the Synthetic Biology Open Language (SBOL) data and visual standards gain acceptance for describing genetic designs in a detailed and reproducible way, there is an increasing need for an intuitive sequence editor tool that biologists can use that supports these standards. This paper describes SBOLDesigner 2, a genetic design automation (GDA) tool that natively supports both the SBOL data model (Version 2.1) and SBOL Visual (Version 1.0). This software is enabled to fetch and store parts and designs from SBOL repositories, such as SynBioHub...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28439836/prediction-of-mirna-mrna-interactions-using-mirgate
#14
Eduardo Andrés-León, Gonzalo Gómez-López, David G Pisano
miRGate ( http://mirgate.bioinfo.cnio.es /) is a freely available database that contains predicted and experimentally validated microRNA-messenger RNA (miRNA-mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3'-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28438724/toward-a-more-usable-home-based-video-telemedicine-system-a-heuristic-evaluation-of-the-clinician-user-interfaces-of-home-based-video-telemedicine-systems
#15
Sruthy Agnisarman, Shraddhaa Narasimha, Kapil Chalil Madathil, Brandon Welch, Fnu Brinda, Aparna Ashok, James McElligott
BACKGROUND: Telemedicine is the use of technology to provide and support health care when distance separates the clinical service and the patient. Home-based telemedicine systems involve the use of such technology for medical support and care connecting the patient from the comfort of their homes with the clinician. In order for such a system to be used extensively, it is necessary to understand not only the issues faced by the patients in using them but also the clinician. OBJECTIVES: The aim of this study was to conduct a heuristic evaluation of 4 telemedicine software platforms-Doxy...
April 24, 2017: JMIR Human Factors
https://www.readbyqxmd.com/read/28437440/synthesizer-expediting-synthesis-studies-from-context-free-data-with-information-retrieval-techniques
#16
Lisa M Gandy, Jordan Gumm, Benjamin Fertig, Anne Thessen, Michael J Kennish, Sameer Chavan, Luigi Marchionni, Xiaoxin Xia, Shambhavi Shankrit, Elana J Fertig
Scientists have unprecedented access to a wide variety of high-quality datasets. These datasets, which are often independently curated, commonly use unstructured spreadsheets to store their data. Standardized annotations are essential to perform synthesis studies across investigators, but are often not used in practice. Therefore, accurately combining records in spreadsheets from differing studies requires tedious and error-prone human curation. These efforts result in a significant time and cost barrier to synthesis research...
2017: PloS One
https://www.readbyqxmd.com/read/28437115/development-and-implementation-of-advanced-fitting-methods-for-the-calculation-of-accurate-molecular-structures
#17
Marco Mendolicchio, Emanuele Penocchio, Daniele Licari, Nicola Tasinato, Vincenzo Barone
The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of dynamical and environmental effects in tuning their overall behavior. For this purpose the so-called semi-experimental approach, based on a non-linear least-squares fit of the moments of inertia associated to a set of available isotopologues, allows one to obtain very accurate results, without the unfavorable computational cost characterizing high-level quantum chemical methods...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28436857/real-time-triple-modal-photoacoustic-ultrasound-and-magnetic-resonance-fusion-imaging-of-humans
#18
Sara Park, Jongseong Jang, Jeesu Kim, Young Soo Kim, Chulhong Kim
Imaging that fuses multiple modes has become a useful tool for diagnosis and therapeutic monitoring. As a next step, real-time fusion imaging has attracted interest as for a tool to guide surgery. One widespread fusion imaging technique in surgery combines real-time ultrasound (US) imaging and preacquired magnetic resonance (MR) imaging. However, US imaging visualizes only structural information with relatively low contrast. Here, we present a photoacoustic (PA), US, and MR fusion imaging system which integrates a clinical PA and US imaging system with an optical tracking-based navigation subsystem...
April 24, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28436837/passive-bci-in-operational-environments-insights-recent-advances-and-future-trends
#19
Pietro Arico, Gianluca Borghini, Gianluca Di Flumeri, Nicolina Sciaraffa, Alfredo Colosimo, Fabio Babiloni
OBJECTIVE: this mini-review aims to highlight recent important aspects to consider and evaluate when passive Brain-Computer Interface (pBCI) systems would be developed and used in operational environments, and remarks future directions of their applications. METHODS: Electroencephalography (EEG)-based pBCI has become an important tool for real-time analysis of brain activity, since it could potentially provide, covertly - without distracting the user from the main task - and objectively - not affected by the subjective judgement of an observer or the user itself - information about the operator cognitive state...
April 17, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28431949/classification-of-eeg-signals-to-identify-variations-in-attention-during-motor-task-execution
#20
Susan Aliakbaryhosseinabadi, Ernest Nlandu Kamavuako, Ning Jiang, Dario Farina, Natalie Mrachacz-Kersting
BACKGROUND: Brain-computer interface (BCI) systems in neuro-rehabilitation use brain signals to control external devices. User status such as attention affects BCI performance; thus detecting the user's attention drift due to internal or external factors is essential for high detection accuracy. NEW METHOD: An auditory oddball task was applied to divert the users' attention during a simple ankle dorsiflexion movement. Electroencephalogram signals were recorded from eighteen channels...
April 18, 2017: Journal of Neuroscience Methods
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