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https://www.readbyqxmd.com/read/30514161/meta-analysis-of-non-statistically-significant-unreported-effects
#1
Anton Albajes-Eizagirre, Aleix Solanes, Joaquim Radua
Published studies in Medicine (and virtually any other discipline) sometimes report that a difference or correlation did not reach statistical significance but do not report its effect size or any statistic from which the latter may be derived. Unfortunately, meta-analysts should not exclude these studies because their exclusion would bias the meta-analytic outcome, but also they cannot be included as null effect sizes because this strategy is also associated to bias. To overcome this problem, we have developed MetaNSUE, a novel method based on multiple imputations of the censored information...
December 4, 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/30513083/augmenting-geovisual-analytics-of-social-media-data-with-heterogeneous-information-network-mining-cognitive-plausibility-assessment
#2
Alexander Savelyev, Alan M MacEachren
This paper investigates the feasibility, from a user perspective, of integrating a heterogeneous information network mining (HINM) technique into SensePlace3 (SP3), a web-based geovisual analytics environment. The core contribution of this paper is a user study that determines whether an analyst with minimal background can comprehend the network data modeling metaphors employed by the resulting system, whether they can employ said metaphors to explore spatial data, and whether they can interpret the results of such spatial analysis correctly...
2018: PloS One
https://www.readbyqxmd.com/read/30511150/bioinformatics-protocols-for-quickly-obtaining-large-scale-data-sets-for-phylogenetic-inferences
#3
Hugo López-Fernández, Pedro Duque, Sílvia Henriques, Noé Vázquez, Florentino Fdez-Riverola, Cristina P Vieira, Miguel Reboiro-Jato, Jorge Vieira
Useful insight into the evolution of genes and gene families can be provided by the analysis of all available genome datasets rather than just a few, which are usually those of model species. Handling and transforming such datasets into the desired format for downstream analyses is, however, often a difficult and time-consuming task for researchers without a background in informatics. Therefore, we present two simple and fast protocols for data preparation, using an easy-to-install, open-source, cross-platform software application with user-friendly, rich graphical user interface (SEDA; http://www...
December 3, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/30509317/hiv-related-data-among-key-populations-to-inform-evidence-based-responses-protocol-of-a-systematic-review
#4
Amrita Rao, Sheree Schwartz, Keith Sabin, Tisha Wheeler, Jinkou Zhao, James Hargreaves, Stefan Baral
BACKGROUND: Key populations who bear a disproportionate burden of HIV, including female sex workers, men who have sex with men, people who use drugs, transgender people, and incarcerated populations, have been understudied, especially in the context of broadly generalized HIV epidemics. Program and investment planning documents often do not take into account the data that do exist. Prior systematic reviews have been comprehensive, but lack sustainability and relevance over time. This review aims to synthesize all available data for key populations and present the data through an accessible, updatable user-friendly graphic interface...
December 3, 2018: Systematic Reviews
https://www.readbyqxmd.com/read/30507938/tammicol-tool-for-analysis-of-the-morphology-of-microbial-colonies
#5
Hayden Tronnolone, Jennifer M Gardner, Joanna F Sundstrom, Vladimir Jiranek, Stephen G Oliver, Benjamin J Binder
Many microbes are studied by examining colony morphology via two-dimensional top-down images. The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background, producing a binary image. While this may be achieved manually for a single colony, this process is infeasible for large datasets containing thousands of images. The software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol) has been developed to efficiently and automatically convert colony images to binary...
December 3, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/30501333/a-scalable-hardware-and-software-control-apparatus-for-experiments-with-hybrid-quantum-systems
#6
Elia Perego, Marco Pomponio, Amelia Detti, Lucia Duca, Carlo Sias, Claudio E Calosso
Modern experiments with fundamental quantum systems - like ultracold atoms, trapped ions, and single photons - are managed by a control system formed by a number of input/output electronic channels governed by a computer. In hybrid quantum systems, where two or more quantum systems are combined and made to interact, establishing an efficient control system is particularly challenging due to the higher complexity, especially when each single quantum system is characterized by a different time scale. Here we present a new control apparatus specifically designed to efficiently manage hybrid quantum systems...
November 2018: Review of Scientific Instruments
https://www.readbyqxmd.com/read/30500879/crispr-local-a-local-single-guide-rna-sgrna-design-tool-for-non-reference-plant-genomes
#7
Jiamin Sun, Hao Liu, Jianxiao Liu, Shikun Cheng, Yong Peng, Qinghua Zhang, Jianbing Yan, Hai-Jun Liu, Ling-Ling Chen
Summary: CRISPR-Local is a high-throughput local tool for designing sgRNAs in plants and other organisms that factors in genetic variation and is optimized to generate genome-wide sgRNAs. CRISPR-Local outperforms other sgRNA design tools in the following respects: (1) designing sgRNAs suitable for non-reference varieties; (2) screening for sgRNAs that are capable of simultaneously targeting multiple genes; (3) saving computational resources by avoiding repeated calculations from multiple submissions; and (4) running offline, with both command-line and graphical user interface modes, and the ability to export multiple formats for further batch analysis or visualization...
November 30, 2018: Bioinformatics
https://www.readbyqxmd.com/read/30500432/applications-of-flika-a-python-based-image-processing-and-analysis-platform-for-studying-local-events-of-cellular-calcium-signaling
#8
Kyle L Ellefsen, Jeffrey T Lock, Brett Settle, Carley A Karsten, Ian Parker
The patterning of cytosolic Ca2+ signals underlies their ubiquitous ability to specifically regulate numerous cellular processes. Advances in fluorescence microscopy have made it possible to image these signals with unprecedented temporal and spatial resolution. However, this is a double-edged sword, as the resulting enormous data sets necessitate development of software to automate image processing and analysis. Here, we describe Flika, an open source, graphical user interface program written in the Python environment that contains a suite of built-in image processing tools to enable intuitive visualization of image data and analysis...
November 27, 2018: Biochimica et biophysica acta. Molecular cell research
https://www.readbyqxmd.com/read/30489639/hierarchical-multi-population-viability-analysis
#9
Douglas R Leasure, Seth J Wenger, Nathan D Chelgren, Helen M Neville, Daniel C Dauwalter, Robin Bjork, Kurt A Fesenmyer, Jason B Dunham, Mary M Peacock, Charlie H Luce, Abby C Lute, Daniel J Isaak
Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models...
November 29, 2018: Ecology
https://www.readbyqxmd.com/read/30487099/influences-of-augmented-reality-head-worn-display-type-and-user-interface-design-on-performance-and-usability-in-simulated-warehouse-order-picking
#10
Sunwook Kim, Maury A Nussbaum, Joseph L Gabbard
Limited information is available regarding the effective use of workplace head-worn displays (HWD), especially the choices of HWD types and user interface (UI) designs. We explored how different HWD types and UI designs affect perceived workload, usability, visual discomfort, and job performance during a simulated warehouse job involving order picking and part assembly. Sixteen gender-balanced participants completed the simulated job in all combinations of two HWD types (binocular vs. monocular) and four UIs, the latter of which manipulated information mode (text-vs...
January 2019: Applied Ergonomics
https://www.readbyqxmd.com/read/30483089/web-based-interfaces-for-virtual-c-elegans-neuron-model-definition-network-configuration-behavioral-experiment-definition-and-experiment-results-visualization
#11
Gorka Epelde, Fearghal Morgan, Andoni Mujika, Frank Callaly, Peter Leškovský, Brian McGinley, Roberto Álvarez, Axel Blau, Finn Krewer
The Si elegans platform targets the complete virtualization of the nematode Caenorhabditis elegans , and its environment. This paper presents a suite of unified web-based Graphical User Interfaces (GUIs) as the main user interaction point, and discusses their underlying technologies and methods. The user-friendly features of this tool suite enable users to graphically create neuron and network models, and behavioral experiments, without requiring knowledge of domain-specific computer-science tools. The framework furthermore allows the graphical visualization of all simulation results using a worm locomotion and neural activity viewer...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/30475995/gencof-a-graphical-user-interface-to-rapidly-remove-human-genome-contaminants-from-metagenomic-datasets
#12
Matthew D Czajkowski, Daniel P Vance, Steven A Frese, Giorgio Casaburi
Summary: The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programming knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use...
November 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/30475729/eyelid-drive-system-an-assistive-technology-employing-inductive-sensing-of-eyelid-movement
#13
Philip Graybill, Mehdi Kiani
This paper presents the design, development, and validation of the Eyelid Drive System (EDS), an assistive technology comprising a specialized pair of glasses and millimeter-sized passive resonators, attached to the wearer's eyelids, that transduce eyelid movement (blinking and winking) through inductive sensing. The theory of operation and design optimization with simulations are presented. A proof-of-concept prototype EDS was constructed using a pair of non-prescription glasses and commercial-off-the-shelf components...
November 20, 2018: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/30450913/msstatsqc-2-0-r-bioconductor-package-for-statistical-quality-control-of-mass-spectrometry-based-proteomic-experiments
#14
Eralp Dogu, Sara Mohammad Taheri, Roger Olivella, Florian Marty, Ian Lienert, Lukas Reiter, Eduardo Sabidó, Olga Vitek
MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted Selected Reaction Monitoring experiments. This manuscript presents an extension, MSstatsQC 2.0, that supports experiments with global Data-Dependent and Data-Independent acquisition. The extension implements data processing and analyses that are specific to these acquisition types. It relies on the state-of-the-art methods of statistical process control to detect deviations from optimal performance of various metrics (such as intensity and retention time of chromatographic peaks), and to summarize the results across multiple metrics and analytes...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30443441/an-open-source-feature-extraction-tool-for-the-analysis-of-peripheral-physiological-data
#15
Mohsen Nabian, Yu Yin, Jolie Wormwood, Karen S Quigley, Lisa F Barrett, Sarah Ostadabbas
Electrocardiogram, electrodermal activity, electromyogram, continuous blood pressure, and impedance cardiography are among the most commonly used peripheral physiological signals (biosignals) in psychological studies and healthcare applications, including health tracking, sleep quality assessment, disease early-detection/diagnosis, and understanding human emotional and affective phenomena. This paper presents the development of a biosignal-specific processing toolbox (Bio-SP tool) for preprocessing and feature extraction of these physiological signals according to the state-of-the-art studies reported in the scientific literature and feedback received from the field experts...
2018: IEEE Journal of Translational Engineering in Health and Medicine
https://www.readbyqxmd.com/read/30441276/a-32-channel-wireless-configurable-system-for-electrical-stimulation-of-the-stomach
#16
Zaid Abukhalaf, Amir Javan-Khoshkholgh, Wahib Alrofati, Aydin Farajidavar
We have designed and developed a configurable system that can generate and deliver a variety of electrical pulses suitable for gastrointestinal studies. The system is composed of a front-end unit, and a back-end unit that is connected to a computer. The front-end unit contains a stimulating module with 32 channels configured to generate two different current pulses, simultaneously. Commercial off-the-shelf components were used to develop front- and back-end units. A graphical user interface was designed in LabVIEW that allows configuration of the stimulation pulses through the back-end unit in real-time...
July 2018: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/30441218/identification-of-the-relationships-between-noncontact-capacitive-sensing-signals-and-continuous-grasp-forces-preliminary-study
#17
Enhao Zheng, Qining Wang, Hong Qiao
This study explores the relationships between noncontact capacitive sensing signals and continuous grasp forces. It is a crucial step towards the volitional control of robotic systems based on the noncontact sensing approach. We firstly designed a measurement system including the capacitive sensing front-ends, the grasp force sensor, the signal sampling circuits and the graphic user interface. The capacitive sensing front-end was specifically designed for human forearm signal sampling, which was worn outside of the clothes...
July 2018: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/30440990/a-configurable-portable-system-for-ambulatory-monitoring-of-gastric-bioelectrical-activity-and-delivering-electrical-stimulation
#18
Wahib Alrofati, Amir Javan-Khoshkholgh, Rui Bao, Qi Kang, Nadi Abu Mahfouz, Aydin Farajidavar
The purpose of this paper is to develop and validate a configurable system that can wirelessly acquire gastric electrical activity called slow waves, and deliver high energy electrical pulses to modulate its activity. The system is composed of a front-end unit, and an external stationary backend unit that is connected to a computer. The front-end unit contains a recording module with four channels, and a stimulating module with two channels. Commercial off-theshelf components were used to develop front- and back-end units...
July 2018: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/30440829/eye-hand-coordination-assessment-metrics-using-a-multi-platform-haptic-system-with-eye-tracking-and-motion-capture-feedback
#19
N Pernalete, A Raheja, M Segura, D Menychtas, T Wieczorek, S Carey
In this paper, we discuss the possibility to determine assessment metrics for eye-hand coordination, using a mapping between a robotic haptic device to a virtual environment, and correlating it with the eye-gaze and upper arm movements. Our goal is to develop, implement and refine a system that will assess and improve eye-hand coordination in individuals with disabilities. A detailed analysis of patterns was conducted by therapists in order to select various levels of difficulty that could be included in the system, and which would yield the greatest benefit in terms of assessment of coordination as well as in training...
July 2018: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/30428831/funcexplorer-a-tool-for-fast-data-driven-functional-characterisation-of-high-throughput-expression-data
#20
Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
BACKGROUND: A widely applied approach to extract knowledge from high-throughput genomic data is clustering of gene expression profiles followed by functional enrichment analysis. This type of analysis, when done manually, is highly subjective and has limited reproducibility. Moreover, this pipeline can be very time-consuming and resource-demanding as enrichment analysis is done for tens to hundreds of clusters at a time. Thus, the task often needs programming skills to form a pipeline of different software tools or R packages to enable an automated approach...
November 14, 2018: BMC Genomics
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