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https://www.readbyqxmd.com/read/28434056/beyond-the-primary-endpoint-paradigm-a-test-of-intervention-effect-in-hiv-behavioral-intervention-trials-with-numerous-correlated-outcomes
#1
Jessica M Harwood, Robert E Weiss, W Scott Comulada
Behavioral interventions are increasingly based on holistic approaches to health with an understanding that health-related behaviors are linked. A motivating example is provided by the Philani study, an intervention trial conducted to improve the health of South African mothers and their children. Inter-related health problems around maternal alcohol use, malnutrition, and HIV were addressed; multiple endpoints were targeted. The traditional hypothesis testing paradigm that tests significance on one primary outcome did not suffice...
April 22, 2017: Prevention Science: the Official Journal of the Society for Prevention Research
https://www.readbyqxmd.com/read/28433372/intrinsic-fertility-of-human-oocytes
#2
Sherman J Silber, Keiichi Kato, Naoki Aoyama, Akiko Yabuuchi, Helen Skaletsky, Yuting Fan, Kazunori Shinohara, Noriyuki Yatabe, Tamotsu Kobayashi
OBJECTIVE: To study the intrinsic fertility of the human oocyte. DESIGN: A large retrospective study of natural cycle single embryo transfer (ET) IVF cycles. SETTING: Private IVF clinic, university, and private hospital. PATIENT(S): Patients were enrolled consecutively over an 8-year period in a single ET natural cycle protocol. INTERVENTION(S): A total of 13,949 oocyte retrievals with natural IVF single ET...
April 19, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28432442/smokeless-tobacco-products-harbor-diverse-bacterial-microbiota-that-differ-across-products-and-brands
#3
Eoghan M Smyth, Prachi Kulkarni, Emma Claye, Stephen Stanfill, Robert Tyx, Cynthia Maddox, Emmanuel F Mongodin, Amy R Sapkota
Smokeless tobacco products contain numerous chemical compounds, including known human carcinogens. Other smokeless tobacco constituents, including bacteria, may also contribute to adverse health effects among smokeless tobacco users. However, there is a lack of data regarding the microbial constituents of smokeless tobacco. Our goal was to characterize the bacterial microbiota of different smokeless tobacco products and evaluate differences across product types and brands. DNA was extracted from 15 brands of smokeless tobacco products (including dry snuff, moist snuff, snus, and Swedish snus) and 6 handmade products (e...
April 22, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28431121/starbeast2-brings-faster-species-tree-inference-and-accurate-estimates-of-substitution-rates
#4
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28428869/rapid-maximum-likelihood-ancestral-state-reconstruction-of-continuous-characters-a-rerooting-free-algorithm
#5
Eric W Goolsby
Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428828/bioinformatics-analysis-of-key-genes-and-latent-pathway-interactions-based-on-the-anaplastic-thyroid-carcinoma-gene-expression-profile
#6
Yun Huang, Yiming Tao, Xinying Li, Shi Chang, Bo Jiang, Feng Li, Zhi-Ming Wang
Anaplastic thyroid carcinoma (ATC) is an aggressive malignant disease in older adults with a high mortality rate. The present study aimed to examine several key genes and pathways, which are associated with ATC. The GSE33630 gene expression profile was downloaded from the Gene Expression Omnibus database, which included 11 ATC and 45 normal thyroid samples. The differentially expressed genes (DEGs) in ATC were identified using the Limma package in R. The Gene Ontology functions and Kyoto Encyclopedia of Genes and Genomes pathways of the selected DEGs were enriched using the Database for Annotation, Visualization and Integrated Discovery...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28420363/context-matters-sources-of-variability-in-weekend-physical-activity-among-families-a-repeated-measures-study
#7
Robert J Noonan, Stuart J Fairclough, Zoe R Knowles, Lynne M Boddy
BACKGROUND: Family involvement is an essential component of effective physical activity (PA) interventions in children. However, little is known about the PA levels and characteristics of PA among families. This study used a repeated measures design and multiple data sources to explore the variability and characteristics of weekend PA among families. METHODS: Families (including a 'target' child aged 9-11 years, their primary caregiver(s) and siblings aged 6-8 years) were recruited through primary schools in Liverpool, UK...
April 18, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28419287/prediction-algorithm-for-surgical-intervention-in-neonatal-brachial-plexus-palsy
#8
Thomas J Wilson, Kate W C Chang, Lynda J S Yang
BACKGROUND: Neonatal brachial plexus palsy (NBPP) results in reduced function of the affected arm with profound ramifications on quality of life. Advances in surgical technique have shown improvements in outcomes for appropriately selected patients. Patient selection, however, remains difficult. OBJECTIVE: To develop a decision algorithm that could be applied at the individual patient level, early in life, to reliably predict persistent NBPP that would benefit from surgery...
April 17, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28419235/a-bayesian-group-sparse-multi-task-regression-model-for-imaging-genetics
#9
Keelin Greenlaw, Elena Szefer, Jinko Graham, Mary Lesperance, Farouk S Nathoo
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28418939/exploring-the-molecular-pathogenesis-and-biomarkers-of-high-risk-oral-premalignant-lesions-on-the-basis-of-long-noncoding-rna-expression-profiling-by-serial-analysis-of-gene-expression
#10
Hongcheng Jia, Xuan Wang, Zheng Sun
Oral premalignant lesions (OPLs) have malignant transformation potential, with no reliable markers available. This study aimed to assess molecular events to identify biomarkers that can reflect high-risk lesions as predictive factors to tailor clinical decision for patients on the basis of long noncoding RNAs (lncRNA) expression profiling by serial analysis of gene expression. The GSE31021 and GSE8127 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs were identified using the LIMMA package in R language...
April 17, 2017: European Journal of Cancer Prevention
https://www.readbyqxmd.com/read/28416950/trapr-r-package-for-statistical-analysis-and-visualization-of-rna-seq-data
#11
Jae Hyun Lim, Soo Youn Lee, Ju Han Kim
High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#12
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28416883/application-of-electrolysed-oxidising-water-as-a-sanitiser-to-extend-the-shelf-life-of-seafood-products-a-review
#13
REVIEW
Fera R Dewi, Roger Stanley, Shane M Powell, Christopher M Burke
Electrolysed oxidising water (E.O. water) is produced by electrolysis of sodium chloride to yield primarily chlorine based oxidising products. At neutral pH this results in hypochlorous acid in the un-protonated form which has the greatest oxidising potential and ability to penetrate microbial cell walls to disrupt the cell membranes. E.O. water has been shown to be an effective method to reduce microbial contamination on food processing surfaces. The efficacy of E.O. water against pathogenic bacteria such as Listeria monocytogenes, Escherichia coli and Vibrio parahaemolyticus has also been extensively confirmed in growth studies of bacteria in culture where the sanitising agent can have direct contact with the bacteria...
April 2017: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28416645/performance-stability-of-silicon-oxide-coated-plastic-parenteral-vials
#14
Christopher M Weikart, Carlo G Pantano, Jeff R Schallenberger
A new packaging system was developed for parenteral pharmaceuticals that combines the best attributes of plastic and glass without their respective drawbacks. This technological advancement is based on the synergy between high precision injection-molded plastics and plasma coating technology. The result is a shatter resistant, optically clear, low particulate and chemically durable packaging system. The demand for this product is driven by the expanding market, regulatory constraints and product recalls for injectable drugs and biologics packaged in traditional glass materials...
April 17, 2017: PDA Journal of Pharmaceutical Science and Technology
https://www.readbyqxmd.com/read/28415721/robust-in-silico-identification-of-cancer-cell-lines-based-on-next-generation-sequencing
#15
Raik Otto, Christine Sers, Ulf Leser
Cancer cell lines (CCL) are important tools for cancer researchers world-wide. However, handling of cancer cell lines is error-prone, and critical errors such as misidentification and cross-contamination occur more often than acceptable. Based on the fact that CCL today very often are sequenced (partly or entirely) anyway as part of the studies performed, we developed Uniquorn, a computational method that reliably identifies CCL samples based on variant profiles derived from whole exome or whole genome sequencing...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415613/promoter-dna-methylation-analysis-reveals-a-combined-diagnosis-of-cpg-based-biomarker-for-prostate-cancer
#16
Yuanyuan Tang, Shusuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
BACKGROUND: Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. MATERIALS AND METHODS: The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414553/gd-rda-a-new-regularized-discriminant-analysis-for-high-dimensional-data
#17
Yan Zhou, Baoxue Zhang, Gaorong Li, Tiejun Tong, Xiang Wan
High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identification of which type of diseases a new patient belongs to has been recognized as an important problem. For high-dimensional small sample size data, the classical discriminant methods suffer from the singularity problem and are, therefore, no longer applicable in practice. In this article, we propose a geometric diagonalization method for the regularized discriminant analysis. We then consider a bias correction to further improve the proposed method...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28413470/identification-of-genes-associated-with-the-effect-of-inflammation-on-the-neurotransmission-of-vascular-smooth-muscle-cell
#18
Shujie Gan, Shenlong Qiu, Yiwen Feng, Yanping Zhang, Qin Qian, Zhong Wan, Jingdong Tang
Vascular smooth muscle cell (VSMC) accumulation and hypertrophy are common in vascular disorders, and inflammation has a crucial role in the development of these diseases. To investigate the effect of inflammation on the neurotransmission of VSMC, bioinformatic analysis was performed, following next generation sequencing. Genes of lipopolysaccharide (LPS)-treated A7r5 cells and phosphate-buffered saline (PBS)-treated A7r5 cells were sequenced via next generation sequencing, and each assay was repeated three times...
April 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28413437/gostag-gene-ontology-subtrees-to-tag-and-annotate-genes-within-a-set
#19
Brian D Bennett, Pierre R Bushel
BACKGROUND: Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times there are hundreds of statistically significant GO terms per gene set. Comparing enriched categories between a large number of analyses and identifying the term within the GO hierarchy with the most connections is challenging. Furthermore, ascertaining biological themes representative of the samples can be highly subjective from the interpretation of the enriched categories...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28410574/comparison-of-different-cell-type-correction-methods-for-genome-scale-epigenetics-studies
#20
COMPARATIVE STUDY
Akhilesh Kaushal, Hongmei Zhang, Wilfried J J Karmaus, Meredith Ray, Mylin A Torres, Alicia K Smith, Shu-Li Wang
BACKGROUND: Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular heterogeneity. Algorithms have been developed to measure or adjust for this heterogeneity, and some have been compared in the literature. However, with new methods available, it is unknown whether the findings will be consistent, if not which method(s) perform better. RESULTS: Methods: We compared eight cell-type correction methods including the method in the minfi R package, the method by Houseman et al...
April 14, 2017: BMC Bioinformatics
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