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https://www.readbyqxmd.com/read/29223040/the-ascidian-embryo-teratogenicity-assay-in-ciona-intestinalis-as-a-new-teratological-screening-to-test-the-mixture-effect-of-the-co-exposure-to-ethanol-and-fluconazole
#1
Maria Battistoni, Silvia Mercurio, Gentile Francesco Ficetola, Francesca Cristiana Metruccio, Elena Menegola, Roberta Pennati
The aim of this work was to evaluate the Ascidian Embryo Teratogenicity assay (AET) as new alternative invertebrate model to test the developmental effects of the co-exposure to ethanol and fluconazole. Ciona intestinalis embryos were exposed to the azolic fungicide fluconazole, (FLUCO, 7.8-250μM), to ethanol (Eth, 0.01-0.5%) and to their mixture (0.01% Eth+FLUCO 7.8-250μM) from neurula to larval stage. At the end of the exposure period, larvae were morphologically evaluated and benchmark analysis performed by using the PROAST modelling software...
December 2, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/29221386/finite-temperature-dynamics-of-a-holstein-polaron-the-thermo-field-dynamics-approach
#2
Lipeng Chen, Yang Zhao
Combining the multiple Davydov D2 Ansatz with the method of thermo-field dynamics, we study finite temperature dynamics of a Holstein polaron on a lattice. It has been demonstrated, using the hierarchy equations of motion method as a benchmark, that our approach provides an efficient, robust description of finite temperature dynamics of the Holstein polaron in the simultaneous presence of diagonal and off-diagonal exciton-phonon coupling. The method of thermo-field dynamics handles temperature effects in the Hilbert space with key numerical advantages over other treatments of finite-temperature dynamics based on quantum master equations in the Liouville space or wave function propagation with Monte Carlo importance sampling...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29221381/study-of-li-atom-diffusion-in-amorphous-li3po4-with-neural-network-potential
#3
Wenwen Li, Yasunobu Ando, Emi Minamitani, Satoshi Watanabe
To clarify atomic diffusion in amorphous materials, which is important in novel information and energy devices, theoretical methods having both reliability and computational speed are eagerly anticipated. In the present study, we applied neural network (NN) potentials, a recently developed machine learning technique, to the study of atom diffusion in amorphous materials, using Li3PO4 as a benchmark material. The NN potential was used together with the nudged elastic band, kinetic Monte Carlo, and molecular dynamics methods to characterize Li vacancy diffusion behavior in the amorphous Li3PO4 model...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29220515/busco-applications-from-quality-assessments-to-gene-prediction-and-phylogenomics
#4
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220512/a-survey-and-evaluations-of-histogram-based-statistics-in-alignment-free-sequence-comparison
#5
Brian B Luczak, Benjamin T James, Hani Z Girgis
Motivation: Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. Results: We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares...
December 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#6
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#7
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220475/improving-average-ranking-precision-in-user-searches-for-biomedical-research-datasets
#8
Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
https://biocaddie.org/benchmark-data.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220467/query-expansion-using-mesh-terms-for-dataset-retrieval-ohsu-at-the-biocaddie-2016-dataset-retrieval-challenge
#9
Theodore B Wright, David Ball, William Hersh
https://biocaddie.org/benchmark-data.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220453/a-publicly-available-benchmark-for-biomedical-dataset-retrieval-the-reference-standard-for-the-2016-biocaddie-dataset-retrieval-challenge
#10
Trevor Cohen, Kirk Roberts, Anupama E Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu
https://biocaddie.org/benchmark-data.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220442/benchmarking-distributed-data-warehouse-solutions-for-storing-genomic-variant-information
#11
Marek S Wiewiórka, Dawid P Wysakowicz, Michal J Okoniewski, Tomasz Gambin
https://github.com/ZSI-Bio/variantsdwh.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220321/end-to-end-blind-image-quality-assessment-using-deep-neural-networks
#12
Kede Ma, Wentao Liu, Kai Zhang, Zhengfang Duanmu, Zhou Wang, Wangmeng Zuo
We propose a multi-task end-to-end optimized deep neural network (MEON) for blind image quality assessment (BIQA). MEON consists of two sub-networks-a distortion identification network and a quality prediction network-sharing the early layers. Unlike traditional methods used for training multi-task networks, our training process is performed in two steps. In the first step, we train a distortion type identification sub-network, for which large-scale training samples are readily available. In the second step, starting from the pre-trained early layers and the outputs of the first sub-network, we train a quality prediction sub-network using a variant of the stochastic gradient descent method...
March 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29220315/background-modeling-by-stability-of-adaptive-features-in-complex-scenes
#13
Dan Yang, Chenqiu Zhao, Xiaohong Zhang, Sheng Huang
The single-feature-based background model often fails in complex scenes, since a pixel is better described by several features, which highlight different characteristics of it. Therefore, the multi-feature-based background model has drawn much attention recently. In this paper, we propose a novel multi-feature-based background model, named stability of adaptive feature (SoAF) model, which utilizes the stabilities of different features in a pixel to adaptively weigh the contributions of these features for foreground detection...
March 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29220078/using-the-seven-bridges-cancer-genomics-cloud-to-access-and-analyze-petabytes-of-cancer-data
#14
Raunaq Malhotra, Isheeta Seth, Erik Lehnert, Jing Zhao, Gaurav Kaushik, Elizabeth H Williams, Anurag Sethi, Brandi N Davis-Dusenbery
Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high-performance cluster, which could take several weeks even with a highly optimized network connection. The National Cancer Institute (NCI) initiated the Cancer Genomics Cloud Pilots program to provide researchers with the resources to process data with cloud computational resources...
December 8, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/29219070/predicting-human-splicing-branchpoints-by-combining-sequence-derived-features-and-multi-label-learning-methods
#15
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order to guide wet experiments, we develop computational methods to predict human splicing branchpoints. RESULTS: Considering the fact that an intron may have multiple branchpoints, we transform the branchpoint prediction as the multi-label learning problem, and attempt to predict branchpoint sites from intron sequences...
December 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29218879/an-ultra-fast-and-scalable-quantification-pipeline-for-transposable-elements-from-next-generation-sequencing-data
#16
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M Shulman, Zhandong Liu
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218467/antibiotic-prescription-and-clinical-management-of-common-infections-among-general-practitioners-in-latvia-lithuania-and-sweden-a-pilot-survey-with-a-simple-protocol
#17
Uga Dumpis, Annika Hahlin, Sonata Varvuolyte, Stephan Stenmark, Sarmīte Veide, Rolanda Valinteliene, Asta Jurkeviciene, Johan Struwe
Comparative information on diagnosis-related antibiotic prescribing patterns are scarce from primary care within and between countries. To describe and compare antibiotic prescription and routine management of infections in primary care in Latvia (LV), Lithuania (LT) and two study sites in Sweden (SE), a cross-sectional observational study on patients who consulted due to sypmtoms compatible with infection was undetraken. Infection and treatment was detected and recorded by physicians only. Data was collected from altogether 8786 consecutive patients with infections in the three countries...
December 7, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29218430/cpdock-the-complementarity-plot-for-docking-of-proteins-implementing-multi-dielectric-continuum-electrostatics
#18
Sankar Basu
The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6...
December 7, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29218420/an-improved-pathological-brain-detection-system-based-on-two-dimensional-pca-and-evolutionary-extreme-learning-machine
#19
Deepak Ranjan Nayak, Ratnakar Dash, Banshidhar Majhi
Pathological brain detection has made notable stride in the past years, as a consequence many pathological brain detection systems (PBDSs) have been proposed. But, the accuracy of these systems still needs significant improvement in order to meet the necessity of real world diagnostic situations. In this paper, an efficient PBDS based on MR images is proposed that markedly improves the recent results. The proposed system makes use of contrast limited adaptive histogram equalization (CLAHE) to enhance the quality of the input MR images...
December 7, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29218117/basis-and-statistical-design-of-the-passive-hiv-1-antibody-mediated-prevention-amp-test-of-concept-efficacy-trials
#20
Peter B Gilbert, Michal Juraska, Allan C deCamp, Shelly Karuna, Srilatha Edupuganti, Nyaradzo Mgodi, Deborah J Donnell, Carter Bentley, Nirupama Sista, Philip Andrew, Abby Isaacs, Yunda Huang, Lily Zhang, Edmund Capparelli, Nidhi Kochar, Jing Wang, Susan H Eshleman, Kenneth H Mayer, Craig A Magaret, John Hural, James G Kublin, Glenda Gray, David C Montefiori, Margarita M Gomez, David N Burns, Julie McElrath, Julie Ledgerwood, Barney S Graham, John R Mascola, Myron Cohen, Lawrence Corey
Background: Anti-HIV-1 broadly neutralizing antibodies (bnAbs) have been developed as potential agents for prevention of HIV-1 infection. The HIV Vaccine Trials Network and the HIV Prevention Trials Network are conducting the Antibody Mediated Prevention (AMP) trials to assess whether, and how, intravenous infusion of the anti-CD4 binding site bnAb, VRC01, prevents HIV-1 infection. These are the first test-of-concept studies to assess HIV-1 bnAb prevention efficacy in humans. Methods: The AMP trials are two parallel phase 2b HIV-1 prevention efficacy trials conducted in two cohorts: 2700 HIV-uninfected men and transgender persons who have sex with men in the United States, Peru, Brazil, and Switzerland; and 1500 HIV-uninfected sexually active women in seven countries in sub-Saharan Africa...
January 2017: Statistical Communications in Infectious Diseases
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