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https://www.readbyqxmd.com/read/28636001/wataa-atlas-of-protein-hydration-exploring-synergies-between-data-mining-and-ab-initio-calculations
#1
Jiří Černý, Bohdan Schneider, Lada Biedermannová
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28634172/identifying-an-oxygenation-index-threshold-for-increased-mortality-in-acute-respiratory-failure
#2
Brandon G Hammond, Pamela Garcia-Filion, Paul Kang, Mounica Y Rao, Brigham C Willis, Heidi J Dalton
BACKGROUND: The objective of this work was to examine current oxygenation index (OI) data and outcomes using electronic medical record data to identify a specific OI value associated with mortality. METHODS: This study was a retrospective electronic medical record data review from the pediatric ICU of Phoenix Children's Hospital, with data mining for variables to calculate OIs on subjects age 1 month to 20 y mechanically ventilated >24 h, excluding those with known intracardiac shunts or cyanotic heart disease...
June 20, 2017: Respiratory Care
https://www.readbyqxmd.com/read/28633385/timiner-ngs-data-mining-pipeline-for-cancer-immunology-and-immunotherapy
#3
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Summary: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing (NGS) data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from NGS data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates, and quantification of tumor immunogenicity...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632895/genome-mining-reveals-high-incidence-of-putative-lipopeptide-biosynthesis-nrps-pks-clusters-containing-fatty-acyl-amp-ligase-genes-in-biofilm-forming-cyanobacteria
#4
Tomáš Galica, Pavel Hrouzek, Jan Mareš
Cyanobacterial lipopeptides exhibit antimicrobial and antifungal bioactivities with potential for use in pharmaceutical research. However, due to their haemolytic activity and cytotoxic effects against human cells, they may pose a health issue if produced in substantial amounts in the environment. In bacteria, lipopeptides can be synthesized via several well-evidenced mechanisms. In one of them, fatty acyl-AMP ligase (FAAL) initiates the biosynthesis by activation of a fatty acyl residue. We have performed a bioinformatic survey of the cyanobacterial genomic information available in the public databases for the presence of FAAL-containing non-ribosomal peptide synthetase/polyketide synthetase (NRPS/PKS) biosynthetic clusters, as a genetic basis for lipopeptide biosynthesis...
June 20, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28632437/conscientious-classification-a-data-scientist-s-guide-to-discrimination-aware-classification
#5
Brian d'Alessandro, Cathy O'Neil, Tom LaGatta
Recent research has helped to cultivate growing awareness that machine-learning systems fueled by big data can create or exacerbate troubling disparities in society. Much of this research comes from outside of the practicing data science community, leaving its members with little concrete guidance to proactively address these concerns. This article introduces issues of discrimination to the data science community on its own terms. In it, we tour the familiar data-mining process while providing a taxonomy of common practices that have the potential to produce unintended discrimination...
June 2017: Big Data
https://www.readbyqxmd.com/read/28631050/analgesia-nociception-index-ani-monitoring-in-patients-with-thoracic-paravertebral-block-a-randomized-controlled-study
#6
Nurseda Dundar, Alparslan Kus, Yavuz Gurkan, Kamil Toker, Mine Solak
The goal of the study was to evaluate the effectiveness of analgesia nociception index (ANI) monitoring during intraoperative period for patients with thoracic paravertebral block (TPVB) undergoing breast surgery under general anesthesia. This prospective randomized trial was performed after receiving ethics committee approval in 44 patients who were scheduled to undergo breast surgery under general anesthesia. TPVB was performed in the preoperative period using 20 mL of bupivacaine 0.25% at T4 level. Anesthesia maintenance was provided with sevoflurane in O2: air mixture and remifentanil infusion...
June 19, 2017: Journal of Clinical Monitoring and Computing
https://www.readbyqxmd.com/read/28629168/assessing-statistically-significant-heavy-metal-concentrations-in-abandoned-mine-areas-via-hot-spot-analysis-of-portable-xrf-data
#7
Sung-Min Kim, Yosoon Choi
To develop appropriate measures to prevent soil contamination in abandoned mining areas, an understanding of the spatial variation of the potentially toxic trace elements (PTEs) in the soil is necessary. For the purpose of effective soil sampling, this study uses hot spot analysis, which calculates a z-score based on the Getis-Ord Gi* statistic to identify a statistically significant hot spot sample. To constitute a statistically significant hot spot, a feature with a high value should also be surrounded by other features with high values...
June 18, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28627690/data-mining-and-pathway-analysis-of-glucose-6-phosphate-dehydrogenase-with-natural-language-processing
#8
Long Chen, Chunhua Zhang, Yanling Wang, Yuqian Li, Qiaoqiao Han, Huixin Yang, Yuechun Zhu
Human glucose-6-phosphate dehydrogenase (G6PD) is a crucial enzyme in the pentose phosphate pathway, and serves an important role in biosynthesis and the redox balance. G6PD deficiency is a major cause of neonatal jaundice and acute hemolyticanemia, and recently, G6PD has been associated with diseases including inflammation and cancer. The aim of the present study was to conduct a search of the National Center for Biotechnology Information PubMed library for articles discussing G6PD. Genes that were identified to be associated with G6PD were recorded, and the frequency at which each gene appeared was calculated...
June 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28627269/profiling-and-identification-of-chlorogenic-acid-metabolites-in-rats-by-ultra-high-performance-liquid-chromatography-coupled-with-linear-ion-trap-orbitrap-mass-spectrometer
#9
Fei Wang, Zhanpeng Shang, Lulu Xu, Zhibin Wang, Wenjing Zhao, XiaoDan Mei, Jianqiu Lu, Jiangyu Zhang
1. Chlorogenic acids (CGAs), one kind of major bioactive constituents isolated from Flos Lonicerae Japonicae, possess many biological activities, such as antibacterial, antioxidant, and antiviral activities. In this study, we established an efficient strategy using ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MS) to profile the in vivo metabolic fate of CGAs in rat urine and plasma. 2. The extract from Flos Lonicerae Japonicae was orally administrated to Sprague-Dawley (SD) rats at a dose of 1000 mg/kg body weight...
June 19, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/28626796/determining-underground-mining-work-postures-using-motion-capture-and-digital-human-modeling
#10
Timothy J Lutz, Joseph P DuCarme, Adam K Smith, Dean Ambrose
According to Mine Safety and Health Administration (MSHA) data, during 2008-2012 in the U.S., there were, on average, 65 lost-time accidents per year during routine mining and maintenance activities involving remote-controlled continuous mining machines (CMMs). To address this problem, the National Institute for Occupational Safety and Health (NIOSH) is currently investigating the implementation and integration of existing and emerging technologies in underground mines to provide automated, intelligent proximity detection (iPD) devices on CMMs...
December 27, 2016: Journal of Environment and Health Sciences
https://www.readbyqxmd.com/read/28626598/design-concerns-of-room-and-pillar-retreat-panels
#11
Ted M Klemetti, Morgan M Sears, Ihsan B Tulu
Why do some room and pillar retreat panels encounter abnormal conditions? What factors deserve the most consideration during the planning and execution phases of mining and what can be done to mitigate those abnormal conditions when they are encountered? To help answer these questions, and to determine some of the relevant factors influencing the conditions of room and pillar (R & P) retreat mining entries, four consecutive R & P retreat panels were evaluated. This evaluation was intended to reinforce the influence of topographic changes, depth of cover, multiple-seam interactions, geological conditions, and mining geometry...
January 2017: International Journal of Mining Science and Technology
https://www.readbyqxmd.com/read/28626527/systematic-data-mining-reveals-synergistic-h3r-mchr1-ligands
#12
David Schaller, Stefanie Hagenow, Gina Alpert, Alexandra Naß, Robert Schulz, Marcel Bermudez, Holger Stark, Gerhard Wolber
In this study, we report a ligand-centric data mining approach that guided the identification of suitable target profiles for treating obesity. The newly developed method is based on identifying target pairs for synergistic positive effects and also encompasses the exclusion of compounds showing a detrimental effect on obesity treatment (off-targets). Ligands with known activity against obesity-relevant targets were compared using fingerprint representations. Similar compounds with activities to different targets were evaluated for the mechanism of action since activation or deactivation of drug targets determines the pharmacological effect...
June 8, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28626492/cross-formational-flow-of-water-into-coalbed-methane-reservoirs-controls-on-relative-permeability-curve-shape-and-production-profile
#13
Alireza Salmachi, C Özgen Karacan
Coalbed methane (CBM) wells tend to produce large volumes of water, especially when there is hydraulic connectivity between coalbed and nearby formations. Cross-formational flow between producing coal and adjacent formations can have significant production and environmental implications, affecting economic viability of production from these shallow reservoirs. Such flows can also affect how much gas can be removed from a coalbed prior to mining and thus can have implications for methane control in mining as well...
March 2017: Environmental Earth Sciences
https://www.readbyqxmd.com/read/28625880/predicting-biomedical-metadata-in-cedar-a-study-of-gene-expression-omnibus-geo
#14
Maryam Panahiazar, Michel Dumontier, Olivier Gevaert
A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metadata values. We evaluate our framework in the context of experimental metadata from the Gene Expression Omnibus (GEO). We applied four rule mining algorithms to the most common structured metadata elements (sample type, molecular type, platform, label type and organism) from over 1,3 million GEO records...
June 15, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28625679/phenotype-databases-for-genetic-screens-in-human-cells
#15
Benedikt Rauscher, Erica Valentini, Ulrike Hardeland, Michael Boutros
Genetic screens are powerful tools to identify components that make up biological systems. Perturbations introduced by methods such as RNA interference (RNAi) or CRISPR/Cas9-mediated genome editing lead to biological phenotypes that can be examined to understand the molecular function of genes in the cell. Over the years, many of such experiments have been conducted providing a wealth of knowledge about genotype-to-phenotype relationships. These data are a rich source of information and it is in a common interest to make them available in a simplified and integrated format...
June 15, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28625502/a-computable-phenotype-improves-cohort-ascertainment-in-a-pediatric-pulmonary-hypertension-registry
#16
Alon Geva, Jessica L Gronsbell, Tianxi Cai, Tianrun Cai, Shawn N Murphy, Jessica C Lyons, Michelle M Heinz, Marc D Natter, Nandan Patibandla, Jonathan Bickel, Mary P Mullen, Kenneth D Mandl
OBJECTIVES: To compare registry and electronic health record (EHR) data mining approaches for cohort ascertainment in patients with pediatric pulmonary hypertension (PH) in an effort to overcome some of the limitations of registry enrollment alone in identifying patients with particular disease phenotypes. STUDY DESIGN: This study was a single-center retrospective analysis of EHR and registry data at Boston Children's Hospital. The local Informatics for Integrating Biology and the Bedside (i2b2) data warehouse was queried for billing codes, prescriptions, and narrative data related to pediatric PH...
June 15, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28623888/ub-isap-a-streamlined-unix-pipeline-for-mining-unique-viral-vector-integration-sites-from-next-generation-sequencing-data
#17
Atul Kamboj, Claus V Hallwirth, Ian E Alexander, Geoffrey B McCowage, Belinda Kramer
BACKGROUND: The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. RESULTS: We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28621740/a-multi-disciplinary-approach-to-remote-sensing-through-low-cost-uavs
#18
Gabriela Calvario, Basilio Sierra, Teresa E Alarcón, Carmen Hernandez, Oscar Dalmau
The use of Unmanned Aerial Vehicles (UAVs) based on remote sensing has generated low cost monitoring, since the data can be acquired quickly and easily. This paper reports the experience related to agave crop analysis with a low cost UAV. The data were processed by traditional photogrammetric flow and data extraction techniques were applied to extract new layers and separate the agave plants from weeds and other elements of the environment. Our proposal combines elements of photogrammetry, computer vision, data mining, geomatics and computer science...
June 16, 2017: Sensors
https://www.readbyqxmd.com/read/28621718/using-small-rna-seq-data-to-detect-sirna-duplexes-induced-by-plant-viruses
#19
Xiaoran Niu, Yu Sun, Ze Chen, Rugang Li, Chellappan Padmanabhan, Jishou Ruan, Jan F Kreuze, KaiShu Ling, ZhangJun Fei, Shan Gao
Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28620857/distribution-of-potentially-toxic-elements-ptes-in-tailings-soils-and-plants-around-gol-e-gohar-iron-mine-a-case-study-in-iran
#20
Naghmeh Soltani, Behnam Keshavarzi, Farid Moore, Armin Sorooshian, Mohamad Reza Ahmadi
This study investigated the concentration of potentially toxic elements (PTEs) including Al, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sb, V, and Zn in 102 soils (in the Near and Far areas of the mine), 7 tailings, and 60 plant samples (shoots and roots of Artemisia sieberi and Zygophylum species) collected at the Gol-E-Gohar iron ore mine in Iran. The elemental concentrations in tailings and soil samples (in Near and Far areas) varied between 7.4 and 35.8 mg kg(-1) for As (with a mean of 25.39 mg kg(-1) for tailings), 7...
June 15, 2017: Environmental Science and Pollution Research International
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