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https://www.readbyqxmd.com/read/28090814/personalized-dynamic-prediction-of-death-according-to-tumour-progression-and-high-dimensional-genetic-factors-meta-analysis-with-a-joint-model
#1
Takeshi Emura, Masahiro Nakatochi, Shigeyuki Matsui, Hirofumi Michimae, Virginie Rondeau
Developing a personalized risk prediction model of death is fundamental for improving patient care and touches on the realm of personalized medicine. The increasing availability of genomic information and large-scale meta-analytic data sets for clinicians has motivated the extension of traditional survival prediction based on the Cox proportional hazards model. The aim of our paper is to develop a personalized risk prediction formula for death according to genetic factors and dynamic tumour progression status based on meta-analytic data...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28090517/semi-parametric-regression-model-for-survival-data-graphical-visualization-with-r
#2
EDITORIAL
Zhongheng Zhang
Cox proportional hazards model is a semi-parametric model that leaves its baseline hazard function unspecified. The rationale to use Cox proportional hazards model is that (I) the underlying form of hazard function is stringent and unrealistic, and (II) researchers are only interested in estimation of how the hazard changes with covariate (relative hazard). Cox regression model can be easily fit with coxph() function in survival package. Stratified Cox model may be used for covariate that violates the proportional hazards assumption...
December 2016: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28090458/efficient-isolation-of-sperm-with-high-dna-integrity-and-stable-chromatin-packaging-by-a-combination-of-density-gradient-centrifugation-and-magnetic-activated-cell-sorting
#3
Hee-Jun Chi, Su-Jin Kwak, Seok-Gi Kim, Youn-Young Kim, Ji-Young Park, Chang-Seok Yoo, Il-Hae Park, Hong-Gil Sun, Jae-Won Kim, Kyeong-Ho Lee
OBJECTIVE: This study was carried out to investigate the correlations of the sperm DNA fragmentation index (DFI) with semen parameters and apoptosis, and to investigate the effects of density-gradient centrifugation (DGC) and magnetic-activated cell sorting (MACS) on reducing the proportion of sperm with DNA fragmentation and protamine deficiency. METHODS: Semen analysis and a sperm DNA fragmentation assay were performed to assess the correlations between semen parameters and the DFI in 458 semen samples...
December 2016: Clinical and Experimental Reproductive Medicine
https://www.readbyqxmd.com/read/28089956/robust-causal-inference-using-directed-acyclic-graphs-the-r-package-dagitty
#4
Johannes Textor, Benito van der Zander, Mark S Gilthorpe, Maciej Liśkiewicz, George T H Ellison
Directed acyclic graphs (DAGs), which offer systematic representations of causal relationships, have become an established framework for the analysis of causal inference in epidemiology, often being used to determine covariate adjustment sets for minimizing confounding bias. DAGitty is a popular web application for drawing and analysing DAGs. Here we introduce the R package 'dagitty', which provides access to all of the capabilities of the DAGitty web application within the R platform for statistical computing, and also offers several new functions...
January 15, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28088763/scater-pre-processing-quality-control-normalization-and-visualization-of-single-cell-rna-seq-data-in-r
#5
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. RESULTS: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088185/igc-an-integrated-analysis-package-of-gene-expression-and-copy-number-alteration
#6
Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang
BACKGROUND: With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28088176/ttca-an-r-package-for-the-identification-of-differentially-expressed-genes-in-time-course-microarray-data
#7
Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
BACKGROUND: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28086803/compendium-of-tcdd-mediated-transcriptomic-response-datasets-in-mammalian-model-systems
#8
Stephenie D Prokopec, Kathleen E Houlahan, Ren X Sun, John D Watson, Cindy Q Yao, Jamie Lee, Christine P'ng, Renee Pang, Alexander H Wu, Lauren C Chong, Ashley B Smith, Nicholas J Harding, Ivy D Moffat, Jere Lindén, Sanna Lensu, Allan B Okey, Raimo Pohjanvirta, Paul C Boutros
BACKGROUND: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute lethality. The severity of toxicity is highly dependent on the aryl hydrocarbon receptor (AHR). Binding of TCDD to the AHR leads to changes in transcription of numerous genes. Studies evaluating the transcriptional changes brought on by TCDD may provide valuable insight into the role of the AHR in human health and disease...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081565/leucine-rich-%C3%AE-2-glycoprotein-a-novel-neutrophil-granule-protein-and-modulator-of-myelopoiesis
#9
Lawrence J Druhan, Amanda Lance, Shimena Li, Andrea E Price, Jacob T Emerson, Sarah A Baxter, Jonathan M Gerber, Belinda R Avalos
Leucine-rich α2 glycoprotein (LRG1), a serum protein produced by hepatocytes, has been implicated in angiogenesis and tumor promotion. Our laboratory previously reported the expression of LRG1 in murine myeloid cell lines undergoing neutrophilic granulocyte differentiation. However, the presence of LRG1 in primary human neutrophils and a role for LRG1 in regulation of hematopoiesis have not been previously described. Here we show that LRG1 is packaged into the granule compartment of human neutrophils and secreted upon neutrophil activation to modulate the microenvironment...
2017: PloS One
https://www.readbyqxmd.com/read/28081045/changes-in-the-distribution-of-sex-partners-in-the-united-states-2002-to-2011-2013
#10
Christopher R Harper, Patricia J Dittus, Jami S Leichliter, Sevgi O Aral
OBJECTIVE: The purpose of the current analysis is to examine subgroup differences in the distribution of opposite-sex sex partners in the United States across an approximate 10-year period to identify patterns that may inform sexually transmitted infection research and prevention. METHODS: Data were drawn from the 2002 and 2011-2013 National Survey of Family Growth, a US probability-based household survey focusing on sexual and reproductive health. The measures included in this analysis were lifetime opposite-sex sex partners and opposite-sex sex partners in the past year...
February 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#11
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077933/bayespop-probabilistic-population-projections
#12
Hana Ševčíková, Adrian E Raftery
We describe bayesPop, an R package for producing probabilistic population projections for all countries. This uses probabilistic projections of total fertility and life expectancy generated by Bayesian hierarchical models. It produces a sample from the joint posterior predictive distribution of future age- and sex-specific population counts, fertility rates and mortality rates, as well as future numbers of births and deaths. It provides graphical ways of summarizing this information, including trajectory plots and various kinds of probabilistic population pyramids...
December 2016: Journal of Statistical Software
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#13
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28075205/a-genomic-and-protein-protein-interaction-analyses-of-nonsyndromic-hearing-impairment-in-cameroon-using-targeted-genomic-enrichment-and-massively-parallel-sequencing
#14
Kamogelo Lebeko, Noluthando Manyisa, Emile R Chimusa, Nicola Mulder, Collet Dandara, Ambroise Wonkam
Hearing impairment (HI) is one of the leading causes of disability in the world, impacting the social, economic, and psychological well-being of the affected individual. This is particularly true in sub-Saharan Africa, which carries one of the highest burdens of this condition. Despite this, there are limited data on the most prevalent genes or mutations that cause HI among sub-Saharan Africans. Next-generation technologies, such as targeted genomic enrichment and massively parallel sequencing, offer new promise in this context...
January 11, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28073760/better-diagnostic-signatures-from-rnaseq-data-through-use-of-auxiliary-co-data
#15
Putri W Novianti, Barbara C Snoek, Saskia M Wilting, Mark A van de Wiel
: Our aim is to improve omics based prediction and feature selection using multiple sources of auxiliary information: co-data. Adaptive group regularized ridge regression (GRridge) was proposed to achieve this by estimating additional group-based penalty parameters through an empirical Bayes method at a low computational cost. We illustrate the GRridge method and software on RNA sequencing data sets. The method boosts the performance of an ordinary ridge regression and outperforms other classifiers...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073756/feature-selection-using-a-one-dimensional-na%C3%A3-ve-bayes-classifier-increases-the-accuracy-of-support-vector-machine-classification-of-cdr3-repertoires
#16
Mattia Cinelli, Yuxin Sun, Katharine Best, James M Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain
MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073755/advanced-boolean-modeling-of-biological-networks-applied-to-systems-pharmacology
#17
Itziar Irurzun-Arana, José Martín Pastor, Iñaki F Trocóniz, José David Gómez-Mantilla
MOTIVATION: Literature on complex diseases is abundant but not always quantitative. Many molecular pathways are qualitatively well described but this information cannot be used in traditional quantitative mathematical models employed in drug development. Tools for analysis of discrete networks are useful to capture the available information in the literature but have not been efficiently integrated by the pharmaceutical industry. We propose an expansion of the usual analysis of discrete networks that facilitates the identification/validation of therapeutic targets...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28072703/screening-the-key-micrornas-and-transcription-factors-in-prostate-cancer-based-on-microrna-functional-synergistic-relationships
#18
Fan Feng, Jitao Wu, Zhenli Gao, Shengqiang Yu, Yuanshan Cui
Prostate cancer (PC) is a common neoplasm, and metastatic PC remains incurable. The study aims to screen key microRNAs (miRNAs) and transcription factors (TFs) involved in PC.The miRNA expression profile dataset (GSE45604) was downloaded from Gene Expression Omnibus database, including 50 PC and 10 normal specimens. Differentially expressed miRNAs (DEmiRNAs) were identified through limma package in R, and DEmiRNA-DEmiRNA co-regulation network was constructed based on the number of co-regulated target genes...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28071686/identification-of-temporal-genes-involved-in-the-mechanisms-of-spinal-cord-injury
#19
S Ma, J Wang, L Liu, L Xia, R Tao
OBJECTIVES: As a high-cost neurological disability, spinal cord injury (SCI) can result in permanent paralysis and loss of sensation. To identify the temporal genes involved in the pathogenesis of SCI, we analysed the expression profile of GSE45006. METHODS: GSE45006 was downloaded from Gene Expression Omnibus, including 20 SCI samples (samples at 1 day, 3 days, 1 week, 2 weeks and 8 weeks after injury, four repetitions for each time point) and 4 normal samples...
January 10, 2017: Spinal Cord
https://www.readbyqxmd.com/read/28071028/influence-of-impurities-in-raw-material-on-sensory-and-physicochemical-properties-of-cold-pressed-rapeseedoil-produced-from-conventionally-and-ecologically-grown-seeds
#20
Małgorzata Wroniak, Agnieszka Rękas, Katarzyna Ratusz
BACKGROUND: The main problem of cold-pressed technology is its low yield and the varying quality of the end product, which is dependent on the quality of the raw material, technological process applied and also on conditions of packaging and storage. The effects of different contents of impurities in rapeseed on the sensory, physicochemical properties and oxidative stability of rapeseed oil produced by cold-pressing were investigated. METHODS: Cold-pressed oil produced from conventionally grown rapeseeds (individual cultivars and industrial seeds) and certified ecological rapeseeds...
July 2016: Acta Scientiarum Polonorum. Technologia Alimentaria
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