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https://www.readbyqxmd.com/read/29450704/gulf-arabic-nouns-and-verbs-a-standardized-set-of-319-object-pictures-and-141-action-pictures-with-predictors-of-naming-latencies
#1
Tariq Khwaileh, Eiman Mustafawi, Ruth Herbert, David Howard
Standardized pictorial stimuli and predictors of successful picture naming are not readily available for Gulf Arabic. On the basis of data obtained from Qatari Arabic, a variety of Gulf Arabic, the present study provides norms for a set of 319 object pictures and a set of 141 action pictures. Norms were collected from healthy speakers, using a picture-naming paradigm and rating tasks. Norms for naming latencies, name agreement, visual complexity, image agreement, imageability, age of acquisition, and familiarity were established...
February 15, 2018: Behavior Research Methods
https://www.readbyqxmd.com/read/29450543/mutation-in-the-zebrafish-cct2-gene-leads-to-abnormalities-of-cell-cycle-and-cell-death-in-the-retina-a-model-of-cct2-related-leber-congenital-amaurosis
#2
Yuriko Minegishi, Naoki Nakaya, Stanislav I Tomarev
Purpose: The compound heterozygous mutations in the β subunit of chaperonin containing TCP-1 (CCT), encoded by CCT2, lead to the Leber congenital amaurosis (LCA). In this study, a cct2 mutant line of zebrafish was established to investigate the role of CCT2 mutations in LCA in vertebrates. Methods: A cct2 mutant zebrafish line was produced using the CRISPR-Cas9 system. Changes in the eyes of developing wild-type and mutant larvae were monitored using microscopy, immunostaining, TUNEL, and EdU assays...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29448075/improving-mass-univariate-analysis-of-neuroimaging-data-by-modelling-important-unknown-covariates-application-to-epigenome-wide-association-studies
#3
Bryan Guillaume, Changqing Wang, Joann Poh, Mo Jun Shen, Mei Lyn Ong, Pei Fang Tan, Neerja Karnani, Michael Meaney, Anqi Qiu
Statistical inference on neuroimaging data is often conducted using a mass-univariate model, equivalent to fitting a linear model at every voxel with a known set of covariates. Due to the large number of linear models, it is challenging to check if the selection of covariates is appropriate and to modify this selection adequately. The use of standard diagnostics, such as residual plotting, is clearly not practical for neuroimaging data. However, the selection of covariates is crucial for linear regression to ensure valid statistical inference...
February 12, 2018: NeuroImage
https://www.readbyqxmd.com/read/29447948/roles-of-ihh-signaling-in-chondroprogenitor-function-in-postnatal-condylar-cartilage
#4
Naito Kurio, Cheri Saunders, Till E Bechtold, Imad Salhab, Hyun-Duck Nah, Sayantani Sinha, Paul C Billings, Maurizio Pacifici, Eiki Koyama
Condylar articular cartilage in mouse temporomandibular joint develops from progenitor cells near the articulating surface that proliferate, undergo chondrogenesis and mature into hypertrophic chondrocytes. However, it remains unclear how these processes are regulated, particularly postnatally. Here we focused on the apical polymorphic layer rich in progenitors and asked whether the phenotype and fate of the cells require signaling by Indian hedgehog (Ihh) previously studied in developing long bones. In condyles in newborn mice, the apical polymorphic/progenitor cell layer was ~10 cell layer-thick and expressed the articular matrix marker Tenascin-C (Tn-C), and the underlying thick cell layer expressed Tn-C as well as the chondrogenic master regulator Sox9...
February 12, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29447401/ramwas-fast-methylome-wide-association-study-pipeline-for-enrichment-platforms
#5
Andrey A Shabalin, Mohammad W Hattab, Shaunna L Clark, Robin F Chan, Gaurav Kumar, Karolina A Aberg, Edwin J C G van den Oord, Inanc Birol
Motivation: Enrichment-based technologies can provide measurements of DNA methylation at tens of millions of CpGs for thousands of samples. Existing tools for methylome-wide association studies cannot analyze data sets of this size and lack important features like principal component analysis, combined analysis with SNP data, and outcome predictions that are based on all informative methylation sites. Results: We present a Bioconductor R package called RaMWAS with a full set of tools for large-scale methylome-wide association studies...
February 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29445897/brdu-edu-dual-labeling-to-determine-the-cell-cycle-dynamics-of-defined-cellular-subpopulations
#6
Lachlan Harris, Oressia Zalucki, Michael Piper
Measuring the mean duration of synthesis-phase (T s ) and of the total cell-cycle (T c ) within progenitor cell populations can provide important insights into the biology governing these cells. Rather than a passive process that shows little variability across cellular contexts, the cell-cycle is instead highly regulated. For example, in the rodent forebrain, T s is selectively lengthened in radial glial progenitor cells undergoing symmetric versus asymmetric division. This lengthening is thought to minimize the potential for copying errors that can occur during DNA replication...
February 14, 2018: Journal of Molecular Histology
https://www.readbyqxmd.com/read/29444662/a-systematic-approach-to-rna-associated-motif-discovery
#7
Tian Gao, Jiang Shu, Juan Cui
BACKGROUND: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective...
February 14, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29444237/compression-of-genomic-sequencing-reads-via-hash-based-reordering-algorithm-and-analysis
#8
Shubham Chandak, Kedar Tatwawadi, Tsachy Weissman, Inanc Birol
Motivation: New Generation Sequencing (NGS) technologies for genome sequencing produce large amounts of short genomic reads per experiment, which are highly redundant and compressible. However, general-purpose compressors are unable to exploit this redundancy due to the special structure present in the data. Results: We present a new algorithm for compressing reads both with and without preserving the read order. In both cases, it achieves 1.4×-2× compression gain over state-of-the-art read compression tools for datasets containing as many as 3 billion Illumina reads...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444235/squeakr-an-exact-and-approximate-k-mer-counting-system
#9
Prashant Pandey, Michael A Bender, Rob Johnson, Rob Patro, Bonnie Berger
Motivation: k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444205/ssbio-a-python-framework-for-structural-systems-biology
#10
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol Kavvas, Jonathan M Monk, Zhen Zhang, Bernhard O Palsson, Alfonso Valencia
Summary: Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The ssbio package provides an automated pipeline to construct high quality genomescale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows...
February 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29443925/pclass-protein-quaternary-structure-classification-by-using-bootstrapping-strategy-as-model-selection
#11
Chi-Chou Huang, Chi-Chang Chang, Chi-Wei Chen, Shao-Yu Ho, Hsung-Pin Chang, Yen-Wei Chu
Protein quaternary structure complex is also known as a multimer, which plays an important role in a cell. The dimer structure of transcription factors is involved in gene regulation, but the trimer structure of virus-infection-associated glycoproteins is related to the human immunodeficiency virus. The classification of the protein quaternary structure complex for the post-genome era of proteomics research will be of great help. Classification systems among protein quaternary structures have not been widely developed...
February 14, 2018: Genes
https://www.readbyqxmd.com/read/29438560/hiite-hiv-1-incidence-and-infection-time-estimator
#12
Sung Yong Park, Tanzy M T Love, Shivankur Kapoor, Ha Youn Lee, John Hancock
Motivation: Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting...
February 9, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29438558/kmgene-a-unified-r-package-for-gene-based-association-analysis-for-complex-traits
#13
Qi Yan, Zhou Fang, Wei Chen, Oliver Stegle
Summary: In this report, we introduce an R package KMgene for performing gene-based association tests for familial, multivariate or longitudinal traits using kernel machine (KM) regression under a generalized linear mixed model (GLMM) framework. Extensive simulations were performed to evaluate the validity of the approaches implemented in KMgene. Availability: http://cran.r-project.org/web/packages/KMgene. Contact: qi.yan@chp.edu or wei.chen@chp...
February 9, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29435935/neonatal-rat-cardiomyocytes-isolation-culture-and-determination-of-micrornas-effects-in-proliferation
#14
Lichan Tao, Yihua Bei, Yongqin Li, Junjie Xiao
Cardiomyocytes loss is a major contributor for many cardiovascular diseases including heart failure and myocardial infarction. Although extremely limited, adult cardiomyocytes are able to proliferate. Understanding the molecular mechanisms controlling cardiomyocytes proliferation is extremely important for enhancing cardiomyocyte proliferation to promote cardiac regeneration and repair. MicroRNAs (miRNAs, miRs) are powerful controllers of many essential biological processes including cell proliferation. Here, we described in detail a protocol for isolation and culture of neonatal rat cardiomyocytes and the determination of miRNAs' effects in proliferation based on two well-established methods including EdU and Ki67 immunofluorescent stainings...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29434381/ismp-adverse-drug-reactions-influenza-vaccine-induced-stevens-johnson-syndrome-vilazodone-induced-nightmares-dabigatran-induced-pustular-eruptions-neurotoxic-and-cardiotoxic-symptoms-after-cannabis-concentrate-exposure-rosuvastatin-induced-skin-eruption
#15
Michael A Mancano
The purpose of this feature is to heighten awareness of specific adverse drug reactions (ADRs), discuss methods of prevention, and promote reporting of ADRs to the US Food and Drug Administration's (FDA) MedWatch program (800-FDA-1088). If you have reported an interesting, preventable ADR to MedWatch, please consider sharing the account with our readers. Write to Dr. Mancano at ISMP, 200 Lakeside Drive, Suite 200, Horsham, PA 19044 (phone: 215-707-4936; e-mail: mmancano@temple.edu). Your report will be published anonymously unless otherwise requested...
February 2018: Hospital Pharmacy
https://www.readbyqxmd.com/read/29433427/methcna-a-database-for-integrating-genomic-and-epigenomic-data-in-human-cancer
#16
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/29432533/crossplan-systematic-planning-of-genetic-crosses-to-validate-mathematical-models
#17
Aditya Pratapa, Neil Adames, Pavel Kraikivski, Nicholas Franzese, John J Tyson, Jean Peccoud, T M Murali, Bonnie Berger
Motivation: Mathematical models of cellular processes can systematically predict the phenotypes of novel combinations of multi-gene mutations. Searching for informative predictions and prioritizing them for experimental validation is challenging since the number of possible combinations grows exponentially in the number of mutations. Moreover, keeping track of the crosses needed to make new mutants and planning sequences of experiments is unmanageable when the experimenter is deluged by hundreds of potentially informative predictions to test...
February 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29432522/wdl-rf-predicting-bioactivities-of-ligand-molecules-acting-with-g-protein-coupled-receptors-by-combining-weighted-deep-learning-and-random-forest
#18
Jiansheng Wu, Qiuming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K B Chan, Xiaoyan Ke, Yang Zhang, Jonathan Wren
Motivation: Precise assessment of ligand bioactivities (including IC50, EC50, Ki, Kd, etc.) is essential for virtual screening and lead compound identification. However, not all ligands have experimentally-determined activities. In particular, many G protein-coupled receptors (GPCRs), which are the largest integral membrane protein family and represent targets of nearly 40% drugs on the market, lack published experimental data about ligand interactions. Computational methods with the ability to accurately predict the bioactivity of ligands can help efficiently address this problem...
February 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29432517/spectral-clustering-based-on-learning-similarity-matrix
#19
Seyoung Park, Hongyu Zhao, Inanc Birol
Motivation: Single-cell RNA-sequencing (scRNA-seq) technology can generate genome-wide expression data at the single-cell levels. One important objective in scRNA-seq analysis is to cluster cells where each cluster consists of cells belonging to the same cell type based on gene expression patterns. Results: We introduce a novel spectral clustering framework that imposes sparse structures on a target matrix. Specifically, we utilize multiple doubly stochastic similarity matrices to learn a similarity matrix, motivated by the observation that each similarity matrix can be a different informative representation of the data...
February 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29432514/improving-snp-prioritization-and-pleiotropic-architecture-estimation-by-incorporating-prior-knowledge-using-graph-gpa
#20
Hang J Kim, Zhenning Yu, Andrew Lawson, Hongyu Zhao, Dongjun Chung, Oliver Stegle
Availability: graph-GPA is implemented as an R package 'GGPA', which is publicly available at http://dongjunchung.github.io/GGPA/. DDNet, a web interface to query diseases of interest and download a prior disease graph obtained from a text mining of biomedical literature, is publicly available at http://www.chunglab.io/ddnet/. Contact: chungd@musc.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
February 8, 2018: Bioinformatics
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