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https://www.readbyqxmd.com/read/29452334/seed-2-a-user-friendly-platform-for-amplicon-high-throughput-sequencing-data-analyses
#1
Tomáš Vetrovský, Petr Baldrian, Daniel Morais, Bonnie Berger
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29448925/insecticide-resistance-evolution-with-mixtures-and-sequences-a-model-based-explanation
#2
Andy South, Ian M Hastings
BACKGROUND: Insecticide resistance threatens effective vector control, especially for mosquitoes and malaria. To manage resistance, recommended insecticide use strategies include mixtures, sequences and rotations. New insecticides are being developed and there is an opportunity to develop use strategies that limit the evolution of further resistance in the short term. A 2013 review of modelling and empirical studies of resistance points to the advantages of mixtures. However, there is limited recent, accessible modelling work addressing the evolution of resistance under different operational strategies...
February 15, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29444234/threadna-predicting-dna-mechanics-contribution-to-sequence-selectivity-of-proteins-along-whole-genomes
#3
Jasmin Cevost, Cédric Vaillant, Sam Meyer, Burkhard Rost
Motivation: Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA's response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein-DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29437890/brain-transcriptome-databases-a-user-s-guide
#4
Jason M Keil, Adel Qalieh, Kenneth Y Kwan
Transcriptional programs instruct the generation and maintenance of diverse subtypes of neural cells, establishment of distinct brain regions, formation and function of neural circuits, and ultimately behavior. Spatiotemporal and cell type-specific analyses of the transcriptome, the sum total of all RNA transcripts in a cell or an organ, can provide insights into the role of genes in brain development and function, and their potential contribution to disorders of the brain. In the previous decade, advances in sequencing technology and funding from the National Institutes of Health and private foundations for large-scale genomics projects have led to a growing collection of brain transcriptome databases...
February 7, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29433429/the-management-of-children-with-bronchiolitis-in-the-australasian-hospital-setting-development-of-a-clinical-practice-guideline
#5
Sharon O'Brien, Sally Wilson, Fenella J Gill, Elizabeth Cotterell, Meredith L Borland, Edward Oakley, Stuart R Dalziel
BACKGROUND: Bronchiolitis is the commonest respiratory infection in children less than 12 months and cause of hospitalisation in infants under 6 months of age in Australasia. Unfortunately there is substantial variation in management, despite high levels of supporting evidence. This paper reports on the process, strengths and challenges of the hybrid approach used to develop the first Australasian management guideline relevant to the local population. METHOD: An adaption of the nine steps recommended by the National Health and Medical Research Council (NHMRC) and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology were utilised...
February 12, 2018: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/29433427/methcna-a-database-for-integrating-genomic-and-epigenomic-data-in-human-cancer
#6
Gaofeng Deng, Jian Yang, Qing Zhang, Zhi-Xiong Xiao, Haoyang Cai
BACKGROUND: The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29432475/high-throughput-tabular-data-processor-platform-independent-graphical-tool-for-processing-large-data-sets
#7
Piotr Madanecki, Magdalena Bałut, Patrick G Buckley, J Renata Ochocka, Rafał Bartoszewski, David K Crossman, Ludwine M Messiaen, Arkadiusz Piotrowski
High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks...
2018: PloS One
https://www.readbyqxmd.com/read/29432199/effect-of-a-combination-of-flip-and-zooming-stimuli-on-the-performance-of-a-visual-brain-computer-interface-for-spelling
#8
Jiao Cheng, Jing Jin, Ian Daly, Yu Zhang, Bei Wang, Xingyu Wang, Andrzej Cichocki
Brain-computer interface (BCI) systems can allow their users to communicate with the external world by recognizing intention directly from their brain activity without the assistance of the peripheral motor nervous system. The P300-speller is one of the most widely used visual BCI applications. In previous studies, a flip stimulus (rotating the background area of the character) that was based on apparent motion, suffered from less refractory effects. However, its performance was not improved significantly. In addition, a presentation paradigm that used a "zooming" action (changing the size of the symbol) has been shown to evoke relatively higher P300 amplitudes and obtain a better BCI performance...
February 13, 2018: Biomedizinische Technik. Biomedical Engineering
https://www.readbyqxmd.com/read/29431017/touchless-computer-interfaces-in-hospitals-a-review
#9
Seán Cronin, Gavin Doherty
The widespread use of technology in hospitals and the difficulty of sterilising computer controls has increased opportunities for the spread of pathogens. This leads to an interest in touchless user interfaces for computer systems. We present a review of touchless interaction with computer equipment in the hospital environment, based on a systematic search of the literature. Sterility provides an implied theme and motivation for the field as a whole, but other advantages, such as hands-busy settings, are also proposed...
February 1, 2018: Health Informatics Journal
https://www.readbyqxmd.com/read/29429018/mobcdb-a-comprehensive-database-integrating-multi-omics-data-on-breast-cancer-for-precision-medicine
#10
Bingbing Xie, Zifeng Yuan, Yadong Yang, Zhidan Sun, Shuigeng Zhou, Xiangdong Fang
BACKGROUND: Breast cancer is one of the most frequently diagnosed cancers among women worldwide, characterized by diverse biological heterogeneity. It is well known that complex and combined gene regulation of multi-omics is involved in the occurrence and development of breast cancer. RESULTS: In this paper, we present the Multi-Omics Breast Cancer Database (MOBCdb), a simple and easily accessible repository that integrates genomic, transcriptomic, epigenomic, clinical, and drug response data of different subtypes of breast cancer...
February 10, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29428417/juicebox-js-provides-a-cloud-based-visualization-system-for-hi-c-data
#11
James T Robinson, Douglass Turner, Neva C Durand, Helga Thorvaldsdóttir, Jill P Mesirov, Erez Lieberman Aiden
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute...
February 5, 2018: Cell Systems
https://www.readbyqxmd.com/read/29427936/eurecon-equidistant-uniform-rigid-body-ensemble-constructor
#12
P Popov, S Grudinin
Conformational ensembles comprise one of the fundamental concepts in statistical bioinformatics and appear in a variety of applications, e.g. molecular docking, virtual screening, searching for pharmacophores, etc. High-throughput applications require billions of conformations to be considered, thus, one often uses the rigid-body representation of molecules or its fragments to cope with the computational cost. Of particular interest is generation of the near-native conformational ensembles, which consist of conformations structurally close to the biologically relevant ones...
February 2, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29426813/the-use-of-communication-apps-by-medical-staff-in-the-australian-health-care-system-survey-study-on-prevalence-and-use
#13
Amanda Nikolic, Nilmini Wickramasinghe, Damian Claydon-Platt, Vikram Balakrishnan, Philip Smart
BACKGROUND: The use of communication apps on mobile phones offers an efficient, unobtrusive, and portable mode of communication for medical staff. The potential enhancements in patient care and education appear significant, with clinical details able to be shared quickly within multidisciplinary teams, supporting rapid integration of disparate information, and more efficient patient care. However, sharing patient data in this way also raises legal and ethical issues. No data is currently available demonstrating how widespread the use of these apps are, doctor's attitudes towards them, or what guides clinician choice of app...
February 9, 2018: JMIR Medical Informatics
https://www.readbyqxmd.com/read/29425634/quantifying-medical-student-clinical-experiences-via-an-icd-code-logging-app
#14
Fred Rawlins, Cameron Sumpter, Dean Sutphin, Harold R Garner
OBJECTIVES: The logging of ICD Diagnostic, Procedure and Drug codes is one means of tracking the experience of medical students' clinical rotations. The goal is to create a web-based computer and mobile application to track the progress of trainees, monitor the effectiveness of their training locations and be a means of sampling public health status. MATERIALS AND METHODS: We have developed a web-based app in which medical trainees make entries via a simple and quick interface optimized for both mobile devices and personal computers...
March 2018: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29425632/electronic-health-record-on-the-go-device-form-factor-and-fitts-law
#15
Frank A Drews, Jonathan R Zadra, Jeremy Gleed
PURPOSE: With electronic health records (EHRs) becoming ubiquitous, computer use in exam rooms during patient-provider interactions is commonplace. Although computer use brings many benefits to providers, and patients generally rate computer-use as having a positive impact, the use of mobile devices could eliminate existing issues, for example allowing providers to enter or review records while face-to-face with patients. Using mobile devices increases flexibility of providers, but also creates challenges associated with the mobile device itself...
March 2018: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29425308/inform-inference-of-network-response-modules
#16
Veer Singh Marwah, Pia Anneli Sofia Kinaret, Angela Serra, Giovanni Scala, Antti Lauerma, Vittorio Fortino, Dario Greco, Oliver Stegle
Summary: Detecting and interpreting responsive modules from gene expression data by using network-based approaches is a common but laborious task. It often requires the application of several computational methods implemented in different software packages, forcing biologists to compile complex analytical pipelines. Here we introduce INfORM (Inference of NetwOrk Response Modules), an R shiny application that enables non-expert users to detect, evaluate, and select gene modules with high statistical and biological significance...
February 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29425248/electrooculography-based-continuous-eye-writing-recognition-system-for-efficient-assistive-communication-systems
#17
Fuming Fang, Takahiro Shinozaki
Human-computer interface systems whose input is based on eye movements can serve as a means of communication for patients with locked-in syndrome. Eye-writing is one such system; users can input characters by moving their eyes to follow the lines of the strokes corresponding to characters. Although this input method makes it easy for patients to get started because of their familiarity with handwriting, existing eye-writing systems suffer from slow input rates because they require a pause between input characters to simplify the automatic recognition process...
2018: PloS One
https://www.readbyqxmd.com/read/29423863/a-framework-for-2-stage-global-sensitivity-analysis-of-gastroplus%C3%A2-compartmental-models
#18
Megerle L Scherholz, James Forder, Ioannis P Androulakis
Parameter sensitivity and uncertainty analysis for physiologically based pharmacokinetic (PBPK) models are becoming an important consideration for regulatory submissions, requiring further evaluation to establish the need for global sensitivity analysis. To demonstrate the benefits of an extensive analysis, global sensitivity was implemented for the GastroPlus™ model, a well-known commercially available platform, using four example drugs: acetaminophen, risperidone, atenolol, and furosemide. The capabilities of GastroPlus were expanded by developing an integrated framework to automate the GastroPlus graphical user interface with AutoIt and for execution of the sensitivity analysis in MATLAB®...
February 8, 2018: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/29423736/itemplate-a-template-based-eye-movement-data-analysis-approach
#19
Naiqi G Xiao, Kang Lee
Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method...
February 8, 2018: Behavior Research Methods
https://www.readbyqxmd.com/read/29417688/pagani-toolkit-parallel-graph-theoretical-analysis-package-for-brain-network-big-data
#20
Haixiao Du, Mingrui Xia, Kang Zhao, Xuhong Liao, Huazhong Yang, Yu Wang, Yong He
The recent collection of unprecedented quantities of neuroimaging data with high spatial resolution has led to brain network big data. However, a toolkit for fast and scalable computational solutions is still lacking. Here, we developed the PArallel Graph-theoretical ANalysIs (PAGANI) Toolkit based on a hybrid central processing unit-graphics processing unit (CPU-GPU) framework with a graphical user interface to facilitate the mapping and characterization of high-resolution brain networks. Specifically, the toolkit provides flexible parameters for users to customize computations of graph metrics in brain network analyses...
February 7, 2018: Human Brain Mapping
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