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https://www.readbyqxmd.com/read/28340498/academic-difficulties-in-children-with-prenatal-alcohol-exposure-presence-profile-and-neural-correlates
#1
Leila Glass, Eileen M Moore, Natacha Akshoomoff, Kenneth Lyons Jones, Edward P Riley, Sarah N Mattson
BACKGROUND: Academic achievement was evaluated in children with heavy prenatal alcohol exposure to determine potential strengths and weaknesses, evaluate the utility of different definitions for identifying low academic performance, and explore the neural correlates that may underlie academic performance. METHODS: Children (8 to 16 years) were assessed using the WIAT-II. Patterns of performance were examined in 2 subject groups: children with heavy prenatal alcohol exposure (n = 67) and controls (n = 61)...
March 24, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#2
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340218/user-centered-design-of-discharge-warnings-tool-for-colorectal-surgery-patients
#3
Aanand D Naik, Molly J Horstman, Linda T Li, Michael K Paasche-Orlow, Bryan Campbell, Whitney L Mills, Levi I Herman, Daniel A Anaya, Barbara W Trautner, David H Berger
Objectives: Readmission following colorectal surgery, typically due to surgery-related complications, is common. Patient-centered discharge warnings may guide recognition of early complication signs after colorectal surgery. Materials and Methods: User-centered design of a discharge warnings tool consisted of iterative health literacy review and a heuristic evaluation with human factors and clinical experts as well as patient end users to establish content validity and usability...
March 16, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339981/transcriptome-analysis-of-comb-and-testis-from-rose-comb-silky-chicken-r1-r1-and-beijing-fatty-wild-type-chicken-r-r
#4
Y Wang, J Li, C Feng, Y Zhao, X Hu, N Li
Rose-comb was one of the chicken comb-variants first used by Bateson and Punnet in 1902 to demonstrate Mendelian inheritance in animals. Rose-comb is a monogenic trait that has been widely described in chickens. It is caused by a large structural rearrangement that leads to mis-expression of transcription factor MNR2 on chromosome 7. Rose-comb has pleiotropic effects in homozygous roosters, which is associated with poor sperm mobility. It was postulated that this is caused by the disruption of the CCDC108 gene located at the distal inversion breakpoint...
March 2, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339816/post-mortem-toxicology-in-young-sudden-cardiac-death-victims-a-nationwide-cohort-study
#5
Thea Bjune, Bjarke Risgaard, Line Kruckow, Charlotte Glinge, Ole Ingemann-Hansen, Peter Mygind Leth, Kristian Linnet, Jytte Banner, Bo Gregers Winkel, Jacob Tfelt-Hansen
Aims: Several drugs increase the risk of ventricular fibrillation and sudden cardiac death (SCD). We aimed to investigate in detail the toxicological findings of all young SCD throughout Denmark. Methods and results: Deaths in persons aged 1-49 years were included over a 10-year period. Death certificates and autopsy reports were retrieved and read to identify cases of sudden death and establish cause of death. All medico-legal autopsied SCD were included and toxicological reports collected...
February 27, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28339752/testing-shoulder-pain-mapping
#6
Levent Bayam, Rajendra Arumilli, Ian Horsley, Fatma Bayam, Lee Herrington, Lennard Funk
Objective. : A previous study on shoulder pain mapping showed specific pain patterns for common shoulder disorders. This study aimed to test those patterns for accuracy, modify shoulder pain mapping as needed, and observe their reliability and validity. Methods. : This prospective study used a two-step process and was undertaken to determine its potential utility in daily practice. New shoulder pain patients marked their pain, its character and severity, on a custom-made mapping form...
February 22, 2017: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/28339460/evaluating-implementation-of-a-fire-prevention-injury-prevention-briefing-in-children-s-centres-cluster-randomised-controlled-trial
#7
Toity Deave, Adrian Hawkins, Arun Kumar, Mike Hayes, Nicola Cooper, Michael Watson, Joanne Ablewhite, Carol Coupland, Alex Sutton, Gosia Majsak-Newman, Lisa McDaid, Trudy Goodenough, Kate Beckett, Elaine McColl, Richard Reading, Denise Kendrick
BACKGROUND: Many developed countries have high mortality rates for fire-related deaths in children aged 0-14 years with steep social gradients. Evidence-based interventions to promote fire safety practices exist, but the impact of implementing a range of these interventions in children's services has not been assessed. We developed an Injury Prevention Briefing (IPB), which brought together evidence about effective fire safety interventions and good practice in delivering interventions; plus training and facilitation to support its use and evaluated its implementation...
2017: PloS One
https://www.readbyqxmd.com/read/28335417/dna-sequencing-sensors-an-overview
#8
REVIEW
Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro
The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger...
March 14, 2017: Sensors
https://www.readbyqxmd.com/read/28334836/trypanosoma-brucei-rap1-maintains-telomere-and-subtelomere-integrity-by-suppressing-terra-and-telomeric-rna-dna-hybrids
#9
Vishal Nanavaty, Ranjodh Sandhu, Sanaa E Jehi, Unnati M Pandya, Bibo Li
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, thereby evading the host's immune response. VSGs are monoallelically expressed from subtelomeric expression sites (ESs), and VSG switching exploits subtelomere plasticity. However, subtelomere integrity is essential for T. brucei viability. The telomeric transcript, TERRA, was detected in T. brucei previously. We now show that the active ES-adjacent telomere is transcribed. We find that TbRAP1, a telomere protein essential for VSG silencing, suppresses VSG gene conversion-mediated switching...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334828/flexible-crispr-library-construction-using-parallel-oligonucleotide-retrieval
#10
Abigail Read, Shaojian Gao, Eric Batchelor, Ji Luo
CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334395/pore-guis-for-parallel-and-real-time-processing-of-minion-sequence-data
#11
Robert Stewart, Mick Watson
Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs. Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334390/seqarray-a-storage-efficient-high-performance-data-format-for-wgs-variant-calls
#12
Xiuwen Zheng, Stephanie M Gogarten, Michael Lawrence, Adrienne Stilp, Matthew P Conomos, Bruce S Weir, Cathy Laurie, David Levine
Motivation: Whole-genome sequencing (WGS) data is being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package "SeqArray" for storing variant calls in an arrayoriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#13
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334366/vcnet-vector-based-gene-co-expression-network-construction-and-its-application-to-rna-seq-data
#14
Zengmiao Wang, Huaying Fang, Nelson Leung-Sang Tang, Minghua Deng
Motivation: Building gene co-expression network (GCN) from gene expression data is an important field of bioinformatic research. Nowadays, RNA-seq data provides high dimensional information to quantify gene expressions in term of read counts for individual exons of genes. Such an increase in the dimension of expression data during the transition from microarray to RNA-seq era made many previous co-expression analysis algorithms based on simple univariate correlation no longer applicable...
March 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334252/individualized-prediction-of-reading-comprehension-ability-using-gray-matter-volume
#15
Zaixu Cui, Mengmeng Su, Liangjie Li, Hua Shu, Gaolang Gong
Reading comprehension is a crucial reading skill for learning and putatively contains 2 key components: reading decoding and linguistic comprehension. Current understanding of the neural mechanism underlying these reading comprehension components is lacking, and whether and how neuroanatomical features can be used to predict these 2 skills remain largely unexplored. In the present study, we analyzed a large sample from the Human Connectome Project (HCP) dataset and successfully built multivariate predictive models for these 2 skills using whole-brain gray matter volume features...
March 10, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28334241/rmats-dvr-rmats-discovery-of-differential-variants-in-rna
#16
Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing
Motivation: RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334218/reconciliation-between-operational-taxonomic-units-and-species-boundaries
#17
Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek-Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for a bacterial species. Our results show that the robustness of such a generalized cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene...
March 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334202/selecting-between-sample-rna-seq-normalization-methods-from-the-perspective-of-their-assumptions
#18
Ciaran Evans, Johanna Hardin, Daniel M Stoebel
RNA-Seq is a widely used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An underemphasized feature of normalization is the assumptions on which the methods rely and how the validity of these assumptions can have a substantial impact on the performance of the methods...
February 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334183/comparative-transcriptional-analysis-of-the-host-specialized-aphids-aphis-gossypii-hemiptera-aphididae
#19
Yuan-Chen Zhang, Hai-Xia Lei, Ning-Hui Miao, Xiang-Dong Liu
Host specialization is an ubiquitous character in aphid populations. Many polyphagous aphid populations usually consist of several subpopulations that have strong fidelity to a specific host or a subset of host range. Host specialization is an evolutional result of food habit of insects. However, genetic basis and molecular mechanism of host specialization are still unclear. In this study, we presented a comparative analysis on global gene expression profiles of three lineages of Aphis gossypii Glover: cotton-specialized (CO), cucurbit-specialized (CU), and CU reared on cowpea (CU-cowpea), using RNA-Seq method...
February 17, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334140/circular-rna-identification-based-on-multiple-seed-matching
#20
Yuan Gao, Jinyang Zhang, Fangqing Zhao
Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage...
February 28, 2017: Briefings in Bioinformatics
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