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https://read.qxmd.com/read/30783007/an-integrative-database-of-%C3%AE-lactamase-enzymes-sequences-structures-functions-and-phylogenetic-trees
#1
Vivek Keshri, Seydina M Diene, Adrien Estienne, Justine Dardaillon, Olivier Chabrol, Laurent Tichit, Jean-Marc Rolain, Didier Raoult, Pierre Pontarotti
Beta-lactamase enzymes have attracted substential medical attention from researchers and clinicians because of their clinical, ecological, and evolutionary interest. Here, we present an online comprehensive database of β-lactamase enzymes. The current database is manually curated and incorporates the primary amino acid sequences, closest structural information in the external structure database (Protein Data Bank) and the functional profiles and phylogenetic trees of the four molecular classes (A, B, C, and D) of β-lactamases...
February 19, 2019: Antimicrobial Agents and Chemotherapy
https://read.qxmd.com/read/30782956/microsimulation-model-for-the-health-economic-evaluation-of-osteoporosis-interventions-study-protocol
#2
Lei Si, John A Eisman, Tania Winzenberg, Kerrie M Sanders, Jacqueline R Center, Tuan V Nguyen, Andrew J Palmer
INTRODUCTION: Osteoporosis is a systemic skeletal disease that is characterised by reduced bone strength and increased fracture risk. Osteoporosis-related fractures impose enormous disease and economic burden to the society. Although many treatments and health interventions are proven effective to prevent fractures, health economic evaluation adds evidence to their economic merits. Computer simulation modelling is a useful approach to extrapolate clinical and economic outcomes from clinical trials and it is increasingly used in health economic evaluation...
February 18, 2019: BMJ Open
https://read.qxmd.com/read/30782112/slim-a-flexible-web-application-for-the-reproducible-processing-of-environmental-dna-metabarcoding-data
#3
Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski, Tristan Cordier
BACKGROUND: High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR amplification, it is possible to multiplex hundreds of samples in a single sequencing run. The analysis of millions of sequences spread into hundreds to thousands of samples prompts for efficient, automated yet flexible analysis pipelines. Various algorithms and software have been developed to perform one or multiple processing steps, such as paired-end reads assembly, chimera filtering, Operational Taxonomic Unit (OTU) clustering and taxonomic assignment...
February 19, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30776757/modeling-mesobionano-systems-with-mbn-studio-made-easy
#4
Gennady B Sushko, Ilia A Solov'yov, Andrey V Solov'yov
This paper introduces MesoBioNano (MBN) Studio - a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization, molecular dynamics, and kinetic Monte Carlo simulations. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner...
February 7, 2019: Journal of Molecular Graphics & Modelling
https://read.qxmd.com/read/30772429/vgsc2-second-generation-vector-graph-toolkit-of-genome-synteny-and-collinearity
#5
Yiqing Xu, Qi'ang Wang, Luis Tanon-Reyes, Feng Cheng, Changwei Bi, Ning Ye, Guoxin Wu
Synteny and collinearity analysis is a standard investigative strategy done in many comparative genomic studies to understand genomic conservation and evolution. Currently, most visualization toolkits of synteny and collinearity do not emphasize the graphical representation of the results, especially the lack of extensible format on vector graphics outputs. This limitation becomes more apparent as 3rd generation sequencing brings high-throughput data, requiring relatively higher resolution for the resulting images...
February 14, 2019: Genomics
https://read.qxmd.com/read/30767762/funmappone-a-tool-to-hierarchically-organize-and-visually-navigate-functional-gene-annotations-in-multiple-experiments
#6
Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki, Dario Greco
BACKGROUND: Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations, such as ontologies and molecular pathways. Annotating results from omics experiments into functional categories is essential not only to understand the underlying regulatory dynamics but also to compare multiple experimental conditions at a higher level of abstraction...
February 15, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30755466/maxquant-live-enables-global-targeting-of-more-than-25-000-peptides
#7
Christoph Wichmann, Florian Meier, Sebastian Virreira Winter, Andreas-David Brunner, Jürgen Cox, Matthias Mann
Mass spectrometry (MS)-based proteomics is often performed in a shotgun format, in which as many peptide precursors as possible are selected from full or MS1 scans so that their fragment spectra can be recorded in MS2 scans. While achieving great proteome depths, shotgun proteomics cannot guarantee that each precursor will be fragmented in each run. In contrast, targeted proteomics aims to reproducibly and sensitively record a restricted number of precursor/fragment combinations in each run, based on pre-scheduled mass-to-charge and retention time windows...
February 12, 2019: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/30738105/vibrotactile-piezoelectric-stimulation-system-with-precise-and-versatile-timing-control-for-somatosensory-research
#8
Limin Sun, Yoshio Okada
BACKGROUND: Tactile stimulations systems are useful for studying the somatosensory system in children because they are innocuous and safe. Stimulators based on piezoelectric actuator are useful, but there is still a need for such systems capable of providing accurate and versatile control of timing and pattern of activation. NEW METHOD: We have implemented a vibrotactile stimulating system useful for behavioral and electroencephalography (EEG) and magnetoencephalography (MEG) research...
February 6, 2019: Journal of Neuroscience Methods
https://read.qxmd.com/read/30735162/excyt-a-graphical-user-interface-for-streamlining-analysis-of-high-dimensional-cytometry-data
#9
John-William Sidhom, Debebe Theodros, Benjamin Murter, Jelani C Zarif, Sudipto Ganguly, Drew M Pardoll, Alexander Baras
With the advent of flow cytometers capable of measuring an increasing number of parameters, scientists continue to develop larger panels to phenotypically explore characteristics of their cellular samples. However, these technological advancements yield high-dimensional data sets that have become increasingly difficult to analyze objectively within traditional manual-based gating programs. In order to better analyze and present data, scientists partner with bioinformaticians with expertise in analyzing high-dimensional data to parse their flow cytometry data...
January 16, 2019: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/30734206/psychopy2-experiments-in-behavior-made-easy
#10
Jonathan Peirce, Jeremy R Gray, Sol Simpson, Michael MacAskill, Richard Höchenberger, Hiroyuki Sogo, Erik Kastman, Jonas Kristoffer Lindeløv
PsychoPy is an application for the creation of experiments in behavioral science (psychology, neuroscience, linguistics, etc.) with precise spatial control and timing of stimuli. It now provides a choice of interface; users can write scripts in Python if they choose, while those who prefer to construct experiments graphically can use the new Builder interface. Here we describe the features that have been added over the last 10 years of its development. The most notable addition has been that Builder interface, allowing users to create studies with minimal or no programming, while also allowing the insertion of Python code for maximal flexibility...
February 7, 2019: Behavior Research Methods
https://read.qxmd.com/read/30722041/the-radish-genome-database-radishgd-an-integrated-information-resource-for-radish-genomics
#11
Hee-Ju Yu, Seunghoon Baek, Young-Joon Lee, Ara Cho, Jeong-Hwan Mun
Radish (Raphanus sativus L.) is an important root vegetable crop in the family Brassicaceae, which provides diverse nutrients for human health and is closely related to the Brassica crop species. Recently, we sequenced and assembled the radish genome into nine chromosome pseudomolecules. In addition, we developed diverse genomic resources, including genetic maps, molecular markers, transcriptome, genome-wide methylation and variome data. In this study, we describe the radish genome database (RadishGD), including details of data sets that we generated and the web interface that allows access to these data...
January 1, 2019: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/30714642/us-pro-an-application-enabling-efficient-high-throughput-ultrasound-video-processing
#12
Adrian D Haimovich, Zachary Lehmann, R Andrew Taylor
We describe a new graphical user interface-based application, US-Pro, designed to enable customized, high-throughput ultrasound video anonymization and dynamic cropping before output to video or high-efficiency disk storage. This application is distributed in a Docker container environment, which supports facile software installation on the most commonly used operating systems, as well as local processing of data sets, precluding the external transfer of electronic protected health information. The US-Pro application will facilitate the reproducible production of large-scale ultrasound video data sets for varied applications, including machine-learning analysis, educational distribution, and quality assurance review...
February 4, 2019: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://read.qxmd.com/read/30710333/chap-open-source-software-for-processing-and-analyzing-pupillometry-data
#13
Ronen Hershman, Avishai Henik, Noga Cohen
Pupil dilation is an effective indicator of cognitive and affective processes. Although several eyetracker systems on the market can provide effective solutions for pupil dilation measurement, there is a lack of tools for processing and analyzing the data provided by these systems. For this reason, we developed CHAP: open-source software written in MATLAB. This software provides a user-friendly graphical user interface for processing and analyzing pupillometry data. Our software creates uniform conventions for the preprocessing and analysis of pupillometry data and provides a quick and easy-to-use tool for researchers interested in pupillometry...
February 1, 2019: Behavior Research Methods
https://read.qxmd.com/read/30704396/genesysv-a-fast-intuitive-and-scalable-genome-exploration-open-source-tool-for-variants-generated-from-high-throughput-sequencing-projects
#14
Mohammad Zia, Paul Spurgeon, Adrian Levesque, Thomas Furlani, Jianxin Wang
BACKGROUND: High throughput sequencing technologies have been increasingly used in basic genetic research as well as in clinical applications. More and more variants underlying Mendelian and complex diseases are being discovered and documented using these technologies. However, identifying and obtaining a short list of candidate disease-causing variants remains challenging for most of the users after variant calling, especially for people without computational skills. RESULTS: We developed GenESysV (Genome Exploration System for Variants) as a scalable, intuitive and user-friendly open source tool...
January 31, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30698997/design-of-microplate-compatible-illumination-panels-for-a-semiautomated-benchtop-pipetting-system
#15
Pierre Baillargeon, Kervin Coss-Flores, Fakhar Singhera, Justin Shumate, Hannah Williams, Lina DeLuca, Timothy P Spicer, Louis Scampavia
Microplates are an essential tool used in laboratories for storing research materials and performing assays. Many types of laboratory automation exist that greatly reduce the effort needed to utilize microplates; however, there are cases where the use of such automation is not feasible or practical. In these instances, researchers must work in an environment where liquid handling operations are performed manually with handheld pipetting devices. This type of work is tedious and error-prone as it relies on researchers to manually track a significant amount of metadata, including transfer volumes, plate barcodes, well contents, and well locations...
January 30, 2019: SLAS Technology
https://read.qxmd.com/read/30695766/fluka-particle-therapy-tool-for-monte-carlo-independent-calculation-of-scanned-proton-and-carbon-ion-beam-therapy
#16
Wioletta Sandra Kozłowska, Till Tobias Böhlen, Caterina Cuccagna, Alfredo Ferrari, Francesco Fracchiolla, Dietmar Georg, Giuseppe Magro, Andrea Mairani, Marco Schwarz, Vasilis Vlachoudis
While Monte Carlo (MC) codes are considered as the gold standard for dosimetric calculations, the availability of user friendly MC codes suited for particle therapy is limited. Based on the FLUKA MC code and its graphical user interface (GUI) Flair, we developed an easy-to-use tool which enables simple and reliable simulations for particle therapy. In this paper we provide an overview of functionalities of the tool and with the presented clinical, proton and carbon ion therapy examples we demonstrate its reliability and the usability in the clinical environment and show its flexibility for research purposes...
January 29, 2019: Physics in Medicine and Biology
https://read.qxmd.com/read/30694229/qresp-a-tool-for-curating-discovering-and-exploring-reproducible-scientific-papers
#17
Marco Govoni, Milson Munakami, Aditya Tanikanti, Jonathan H Skone, Hakizumwami B Runesha, Federico Giberti, Juan de Pablo, Giulia Galli
We propose a strategy and present a simple tool to facilitate scientific data reproducibility by making available, in a distributed manner, all data and procedures presented in scientific papers, together with metadata to render them searchable and discoverable. In particular, we describe a graphical user interface (GUI), Qresp, to curate papers (i.e. generate metadata) and to explore curated papers and automatically access the data presented in scientific publications.
January 29, 2019: Scientific Data
https://read.qxmd.com/read/30693385/an-effective-detection-mechanism-for-localizing-macular-region-and-grading-maculopathy
#18
C R Dhivyaa, M Vijayakumar
The eye disease is prominent in many nations including India and is said to affect up to 80% patients having diabetes. Diabetic Retinopathy is the medical term for denoting the damages to retina caused due to diabetes mellitus. Implying K means Clustering algorithm for coarse segmentation, hard distils are identified with better accuracy than the classical approaches. The variance based methods for segmenting hard distils are reviewed in the surveys and had to be improved. To remove the background features from the picture and conserve computational costs, a mathematical morphological method is used to reconstruct the image features for better segmentation...
January 28, 2019: Journal of Medical Systems
https://read.qxmd.com/read/30688551/stiffness-and-energy-storage-characteristics-of-energy-storage-and-return-prosthetic-feet
#19
Nicholas D Womac, Richard R Neptune, Glenn K Klute
BACKGROUND: Mechanical properties of prosthetic feet can significantly influence amputee gait, but how they vary with respect to limb loading and orientation is infrequently reported. OBJECTIVE: The objective of this study is to measure stiffness and energy storage characteristics of prosthetic feet across limb loading and a range of orientations experienced in typical gait. STUDY DESIGN: This study included mechanical testing. METHODS: Force-displacement data were collected at combinations of 15 sagittal and 5 coronal orientations and used to calculate stiffness and energy storage across prosthetic feet, stiffness categories, and heel wedge conditions...
January 28, 2019: Prosthetics and Orthotics International
https://read.qxmd.com/read/30687579/a-miniature-configurable-wireless-system-for-recording-gastric-electrophysiological-activity-and-delivering-high-energy-electrical-stimulation
#20
Rui Wang, Zaid Abukhalaf, Amir Javan-Khoshkholgh, Tim H-H Wang, Shameer Sathar, Peng Du, Timothy R Angeli, Leo K Cheng, Greg O'Grady, Niranchan Paskaranandavadivel, Aydin Farajidavar
The purpose of this paper is to develop and validate a miniature 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 back-end unit that is connected to a computer. The front-end unit contains a recording module with three channels, and a single-channel stimulation module. Commercial off-the-shelf components were used to develop front- and back-end units...
June 2018: IEEE journal on emerging and selected topics in circuits and systems
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