keyword
MENU ▼
Read by QxMD icon Read
search

r package

keyword
https://www.readbyqxmd.com/read/27923011/feasibility-and-acceptability-of-health-communication-interventions-within-a-combination-intervention-strategy-for-improving-linkage-and-retention-in-hiv-care-in-mozambique
#1
Roberta Sutton, Maria Lahuerta, Fatima Abacassamo, Laurence Ahoua, Maria Tomo, Matthew R Lamb, Batya Elul
BACKGROUND: Challenges to ensuring timely linkage to and retention in HIV care are well documented. Combination intervention strategies can be effective in improving the HIV care continuum. Data on feasibility and acceptability of intervention types within intervention packages are limited. METHODS: The Engage4Health study assessed the effectiveness of a combination intervention strategy to increase linkage and retention among adults newly diagnosed with HIV in Mozambique...
January 1, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/27922550/a-novel-abcc6-haplotype-is-associated-with-azathioprine-drug-response-in-myasthenia-gravis
#2
Lara Colleoni, Barbara Galbardi, Claudia Barzago, Silvia Bonanno, Sara Franzi, Rita Frangiamore, Giorgia Camera, Maria Foti, Donatella Biancolini, Eleonora Canioni, Lorenzo Maggi, Carlo Antozzi, Renato Mantegazza, Pia Bernasconi, Dimos Kapetis
OBJECTIVE: We investigated the association of single nucleotide polymorphisms (SNPs) in drug-metabolizing enzymes and transporters (DMETs) with the response to azathioprine (AZA) in patients affected by myasthenia gravis (MG) to determine possible genotype-phenotype correlations. PATIENTS AND METHODS: Genomic DNA from 180 AZA-treated MG patients was screened through the Affymetrix DMET platform, which characterizes 1931 SNPs in 225 genes. The significant SNPs, identified to be involved in AZA response, were subsequently validated by allelic discrimination and direct sequencing...
December 2, 2016: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/27920952/a-methodology-for-the-design-of-experiments-in-computational-intelligence-with-multiple-regression-models
#3
Carlos Fernandez-Lozano, Marcos Gestal, Cristian R Munteanu, Julian Dorado, Alejandro Pazos
The design of experiments and the validation of the results achieved with them are vital in any research study. This paper focuses on the use of different Machine Learning approaches for regression tasks in the field of Computational Intelligence and especially on a correct comparison between the different results provided for different methods, as those techniques are complex systems that require further study to be fully understood. A methodology commonly accepted in Computational intelligence is implemented in an R package called RRegrs...
2016: PeerJ
https://www.readbyqxmd.com/read/27920488/evalmsa-a-program-to-evaluate-multiple-sequence-alignments-and-detect-outliers
#4
Alvaro Chiner-Oms, Fernando González-Candelas
We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#5
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27918183/finding-structure-in-data-using-multivariate-tree-boosting
#6
Patrick J Miller, Gitta H Lubke, Daniel B McArtor, C S Bergeman
Technology and collaboration enable dramatic increases in the size of psychological and psychiatric data collections, but finding structure in these large data sets with many collected variables is challenging. Decision tree ensembles such as random forests (Strobl, Malley, & Tutz, 2009) are a useful tool for finding structure, but are difficult to interpret with multiple outcome variables which are often of interest in psychology. To find and interpret structure in data sets with multiple outcomes and many predictors (possibly exceeding the sample size), we introduce a multivariate extension to a decision tree ensemble method called gradient boosted regression trees (Friedman, 2001)...
December 2016: Psychological Methods
https://www.readbyqxmd.com/read/27917150/nurse-led-intervention-to-improve-knowledge-of-medications-in-survivors-of-stroke-or-transient-ischemic-attack-a-cluster-randomized-controlled-trial
#7
Muideen T Olaiya, Dominique A Cadilhac, Joosup Kim, David Ung, Mark R Nelson, Velandai K Srikanth, Christopher F Bladin, Richard P Gerraty, Sharyn M Fitzgerald, Thanh G Phan, Judith Frayne, Amanda G Thrift
INTRODUCTION: Limited evidence exists on effective interventions to improve knowledge of preventive medications in patients with chronic diseases, such as stroke. We investigated the effectiveness of a nurse-led intervention, where a component was to improve knowledge of prevention medications, in patients with stroke or transient ischemic attack (TIA). METHODS: Prospective sub-study of the Shared Team Approach between Nurses and Doctors for Improved Risk Factor Management, a randomized controlled trial of risk factor management...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27916580/annual-revision-rates-of-partial-versus-total-knee-arthroplasty-a-comparative-meta-analysis
#8
REVIEW
Harshvardhan Chawla, Jelle P van der List, Alexander B Christ, Maximiliano R Sobrero, Hendrik A Zuiderbaan, Andrew D Pearle
BACKGROUND: Utilization of unicompartmental knee arthroplasty (UKA) and patellofemoral arthroplasty (PFA) as alternatives to total knee arthroplasty (TKA) for unicompartmental knee osteoarthritis (OA) has increased. However, no single resource consolidates survivorship data between TKA and partial resurfacing options for each variant of unicompartmental OA. This meta-analysis compared survivorship between TKA and medial UKA (MUKA), lateral UKA (LUKA) and PFA using annual revision rate as a standardized metric...
December 1, 2016: Knee
https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#9
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913041/impact-of-lymph-node-evaluation-in-adjuvant-and-neoadjuvant-chemotherapy-settings-on-survival-outcomes-in-wilms-tumour-a-review-of-185-cases-from-a-single-institution
#10
Ronica H Nanda, Bahig M Shehata, Nasim Khoshnam, Megan Durham, Sungjin Kim, Wasim Selwanes, Zhengjia Chen, Chao Zhang, Natia Esiashvili
It is unclear if lymph node sampling in Wilms tumour, though critical for staging purposes, affects survival outcomes. The value of lymph node sampling in patients treated with neoadjuvant chemotherapy (NAC) is even more uncertain. We reviewed our institutional data to determine the impact of lymph node sampling on survival, as well as its role in the context of NAC. A total of 185 patients with Wilms tumour treated at our institution were included in this analysis. The number of nodes sampled (≤7, or >7), lymph node status (unknown, negative, or positive), pathological stage, and use of neoadjuvant chemotherapy were analysed for survival outcomes...
November 29, 2016: Pathology
https://www.readbyqxmd.com/read/27910574/the-development-of-an-improved-streak-tube-for-fusion-diagnostics
#11
J R Howorth, J S Milnes, Y Fisher, A Jadwin, R Boni, P A Jaanimagi
The fusion diagnostic community, including the National Ignition Facility, the Laboratory for Laser Energetics, Megajoule in France, and others require optical recording instruments with precise time resolution covering a dynamic range of many orders of magnitude. In 2012, LLE, Photek, and Sydor Instruments embarked on the re-design of an improved streak tube for fusion diagnostics. As a baseline we started with the Photek ST-Y streak tube which is a member of the RCA design dating back to 1957, because the tube body can accommodate a 35 mm long photocathode, and consequently more fibre coupled diagnostic channels than smaller designs...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910345/heat-flux-estimates-of-power-balance-on-proto-mpex-with-ir-imaging
#12
M Showers, T M Biewer, J B O Caughman, D C Donovan, R H Goulding, J Rapp
The Prototype Material Plasma Exposure eXperiment (Proto-MPEX) at Oak Ridge National Laboratory (ORNL) is a precursor linear plasma device to the Material Plasma Exposure eXperiment (MPEX), which will study plasma material interactions (PMIs) for future fusion reactors. This paper will discuss the initial steps performed towards completing a power balance on Proto-MPEX to quantify where energy is lost from the plasma, including the relevant diagnostic package implemented. Machine operating parameters that will improve Proto-MPEX's performance may be identified, increasing its PMI research capabilities...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910308/an-instrument-for-measuring-scintillators-efficiently-based-on-silicon-photomultipliers
#13
M J Yang, Z M Zhang, Y J Wang, D W Li, W Zhou, H H Tang, Y T Liu, P Chai, L Shuai, X C Huang, S Q Liu, M L Zhu, X P Jiang, Y W Zhang, T Li, B Ma, S F Sun, L Y Sun, Q Wang, Z R Lu, T Zhang, L Wei
An instrument used for measuring multiple scintillators' light output and energy resolution was developed. The instrument consisted of a light sensor array which was composed of 64 discrete SiPMs (Silicon Photomultipliers), a corresponding individual channel readout electronics system, and a data processing algorithm. A Teflon grid and a large interval between adjacent SiPMs were employed to eliminate the optical cross talk among scintillators. The scintillators' light output was obtained by comparing with a reference sample with known light output...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909058/secreted-glioblastoma-nanovesicles-contain-intracellular-signaling-proteins-and-active-ras-incorporated-in-a-farnesylation-dependent-manner
#14
Natalie Luhtala, Aaron Aslanian, John R Yates, Tony Hunter
Glioblastomas (GBMs) are malignant brain tumors with a median survival of less than 18 months. Redundancy of signaling pathways represented within GBMs contributes to their therapeutic resistance. Exosomes are extracellular nanovesicles released from cells and present in human biofluids that represent a possible biomarker of tumor signaling state that could aid in personalized treatment. Herein, we demonstrate that mouse GBM cell-derived extracellular nanovesicles resembling exosomes from an H-RasV12 myr-Akt mouse model for GBM are enriched for intracellular signaling cascade proteins (GO: 0007242) and Ras protein signal transduction (GO: 0007265), and contain active Ras...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27906902/comparison-of-transcriptome-between-type-2-diabetes-mellitus-and-impaired-fasting-glucose
#15
Ying Cui, Wen Chen, Jinfeng Chi, Lei Wang
BACKGROUND The aim of this study was to compare the transcriptome between impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM), and further research their molecular mechanisms. MATERIAL AND METHODS The original microarray GSE21321, including miRNA and mRNA expression profiles, was downloaded from the GEO database. Data preprocessing was processed by limma package, and differentially expressed genes (DGs) and miRNA (DMs) were screened. Then, the regulatory relationships among miRNA, TF, and genes were screened and the regulatory network was constructed...
December 1, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/27905985/tlr7-8-agonist-induces-a-post-entry-samhd1-independent-block-to-hiv-1-infection-of-monocytes
#16
Henning Hofmann, Bénédicte Vanwalscappel, Nicolin Bloch, Nathaniel R Landau
BACKGROUND: Monocytes, the primary myeloid cell-type in peripheral blood, are resistant to HIV-1 infection as a result of the lentiviral restriction factor SAMHD1. Toll-like receptors recognize microbial pathogen components, inducing the expression of antiviral host proteins and proinflammatory cytokines. TLR agonists that mimic microbial ligands have been found to have activity against HIV-1 in macrophages. The induction of restriction factors in monocytes by TLR agonist activation has not been well studied...
December 1, 2016: Retrovirology
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#17
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27902843/ridge-estimation-of-the-var-1-model-and-its-time-series-chain-graph-from-multivariate-time-course-omics-data
#18
Viktorian Miok, Saskia M Wilting, Wessel N van Wieringen
Omics experiments endowed with a time-course design may enable us to uncover the dynamic interplay among genes of cellular processes. Multivariate techniques (like VAR(1) models describing the temporal and contemporaneous relations among variates) that may facilitate this goal are hampered by the high-dimensionality of the resulting data. This is resolved by the presented ridge regularized maximum likelihood estimation procedure for the VAR(1) model. Information on the absence of temporal and contemporaneous relations may be incorporated in this procedure...
November 7, 2016: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/27902803/alphasim-software-for-breeding-program-simulation
#19
Anne-Michelle Faux, Gregor Gorjanc, R Chris Gaynor, Mara Battagin, Stefan M Edwards, David L Wilson, Sarah J Hearne, Serap Gonen, John M Hickey
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902800/aghmatrix-r-package-to-construct-relationship-matrices-for-autotetraploid-and-diploid-species-a-blueberry-example
#20
Rodrigo R Amadeu, Catherine Cellon, James W Olmstead, Antonio A F Garcia, Marcio F R Resende, Patricio R Muñoz
Progress in the rate of improvement in autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction and selection methodologies in autopolyploids are lacking. The objectives of this research were to (i) develop an R package for autopolyploids to construct the relationship matrix derived from pedigree information that accounts for autopolyploidy and double reduction and (ii) use the package to estimate the level and effect of double reduction in an autotetraploid blueberry breeding population with extensive pedigree information...
November 2016: Plant Genome
keyword
keyword
66475
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"