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Ioannis Konstantinos Karabagias
The objectives of the present study were: (a) to evaluate the aroma evolution of raw lamb packaged in multi-layer coating film and stored at 4 ± 1 °C, with respect to storage time and (b) to investigate whether specific aldehyde ratios could serve as markers of lamb meat freshness and degree of oxidation. Volatile compounds were determined using headspace solid phase microextraction coupled to gas chromatography/mass spectrometry. Results showed that the most dominant volatiles were 2,2,4,6,6-pentamethyl-heptane, hexanal, 1-octen-3-ol, 1-hexanol, carbon disulfide and p -cymene...
March 16, 2018: Foods (Basel, Switzerland)
Laura E Erban, Stephen B Balogh, Daniel E Campbell, Henry A Walker
Urban water systems consist of natural and engineered flows of water interacting in complex ways. System complexity can be understood via mass conservative models that account for the interrelationships among all major flows and storages. We have developed a generic urban water system model in the R package CityWaterBalance . CityWaterBalance provides a reproducible workflow for studying urban water systems by facilitating automated retrievals of open data and post-processing with open source R functions. It allows the user to 1) rapidly assemble a quantitative, comprehensive assessment of flows thorough an urban area, and 2) easily change the spatial and temporal boundaries of analysis...
February 1, 2018: Open Water
Thomas Tängdén, Pier Giorgio Cojutti, Jason A Roberts, Federico Pea
BACKGROUND AND OBJECTIVES: Valganciclovir is used as oral prophylaxis for cytomegalovirus (CMV) infection in kidney transplant recipients. However, limited pharmacokinetic data exist to guide dosing in this patient group. This study aimed to describe the population pharmacokinetics of valganciclovir in a large sample of kidney transplant recipients and predict optimal dosing based on Monte Carlo simulations. METHODS: Therapeutic drug monitoring (TDM) data from adult kidney transplant recipients who received valganciclovir prophylaxis during a 10-year study period were collected retrospectively...
March 15, 2018: Clinical Pharmacokinetics
Todd R Kramer
This case report examines a vesiculopustular reaction which occurred in a young Marine 9 d after receiving the smallpox vaccination. Review of the CDC guidelines, ACAM2000 package insert, and literature surrounding the smallpox vaccine reveals several well-established adverse cutaneous reactions associated with vaccination. These dermatologic reactions are typically mild and self-limited, but do have the potential to be life threatening - especially in those with immunocompromise. Unfortunately, the correct diagnosis can often be difficult to make, as many of these rashes share similar characteristics...
March 13, 2018: Military Medicine
Li Yin, Xueqiang Guo, Chunyan Zhang, Zhihui Cai, Cunshuan Xu
The priming stage is the first step of liver regeneration (LR). This stage is characterized by the transition from G0 to cell cycle for 4 hours in rat. In this study, individual gene level and gene set level (GSEA) was performed to identify the candidate genes and significantly changed biological processes at 2 h after partial hepatectomy (PH). The leading edge analysis is performed to identify the key genes and iRegulon was employed for transcription factor (TF) analysis. A total of 53 differentially expressed genes were identified using RMA package based on R language at 2 h after PH, including the transcription factor, enzyme and cytokine...
February 20, 2018: Oncotarget
Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik
BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. RESULTS: We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs...
March 15, 2018: Genome Biology
J H C de Roo, T M Bosch, A van Rhijn, R Del Canho
BACKGROUND: Medication is not always delivered in a safe dosing format. Up to 33% of medication errors can be attributed to confusing packaging or labelling. CASE DESCRIPTION: A 6-year-old boy with ADHD, for which he was being treated with methylphenidate and pipamperone drops, was brought to the A&E department with signs of severe encephalopathy. He had apparently been given pipamperone in streams rather than in drops in the previous months. The pipamperone level in his blood was raised to toxic levels...
2018: Nederlands Tijdschrift Voor Geneeskunde
Lu Zeng, R Daniel Kortschak, Joy M Raison, Terry Bertozzi, David L Adelson
Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements...
2018: PloS One
Hongfang Li, Yuzhi Zhen, Yunshuang Geng, Junyan Feng, Jun Wang, Hongsong Zhang
BACKGROUND The aim of this study was to identify some key genes related to the pathogenesis of thoracic aortic aneurysm (TAA) and gain more insights to the molecular mechanism of TAA. MATERIAL AND METHODS The expression profile of GSE9106 was downloaded from the Gene Expression Omnibus (GEO) database. The data contained 58 TAA peripheral blood samples and 36 normal peripheral blood samples. The differently expressed genes (DEGs) between the TAA samples and the normal samples were identified via limma package of R...
March 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Arvid Sjölander
Measures of causal effects play a central role in epidemiology. A wide range of measures exist, which are designed to give relevant answers to substantive epidemiological research questions. However, due to mathematical convenience and software limitations most studies only report odds ratios for binary outcomes and hazard ratios for time-to-event outcomes. In this paper we show how logistic regression models and Cox proportional hazards regression models can be used to estimate a wide range of causal effect measures, with the R-package stdReg...
March 14, 2018: European Journal of Epidemiology
Øystein A Haaland, Rolv T Lie, Julia Romanowska, Miriam Gjerdevik, Håkon K Gjessing, Astanand Jugessur
Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry...
2018: Frontiers in Genetics
Benedikt G Brink, Justin Meskas, Ryan R Brinkman
Motivation: Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high- throughput...
March 9, 2018: Bioinformatics
Azam Peyvandipour, Nafiseh Saberian, Adib Shafi, Michele Donato, Sorin Draghici
Motivation: Identification of novel therapeutic effects for existing U.S. Food and Drug Administration (FDA)-approved drugs, drug repurposing, is an approach aimed to dramatically shorten the drug discovery process, which is costly, slow and risky. Several computational approaches use transcriptional data to find potential repurposing candidates. The main hypothesis of such approaches is that if gene expression signature of a particular drug is opposite to the gene expression signature of a disease, that drug may have a potential therapeutic effect on the disease...
March 9, 2018: Bioinformatics
Huan Liu, Tianjiao Xia, Fangxia Xu, Zhengliang Ma, Xiaoping Gu
Neuropathic pain is a chronic pain state associated with multiple etiologies that results in considerable social and economic burden. The identification of key genes associated with neuropathic pain is important for the development of novel therapies. Therefore, the present study downloaded the gene expression profile GSE15041 from the Gene Expression Omnibus database. The unverified gene chip was removed and the microarray data was normalized following quality control. The limma package in R was used to screen the differentially expressed genes (DEGs), followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis...
March 9, 2018: Molecular Medicine Reports
Junchi Yang, Lumin Bo, Ting Han, Dan Ding, Mingming Nie, Kai Yin
Gastric cancer (GC) has a high incidence and mortality rate. If discovered late, GC tends to have a poor prognosis. Improvements in the prognostic accuracy of GC through combined analysis of multiple relevant genes and clinical factors may solve this problem. In the present study, GSE62254 (including 300 GC tissues), obtained from the Gene Expression Omnibus database, was used as a training set, and the mRNA‑sequencing data of GC (including 384 GC tissues) downloaded from the Cancer Genome Atlas database served as a validation set...
March 9, 2018: Molecular Medicine Reports
Ping Xu, Yu-di He, Ze-Ming Yu, Kai Luo, Huai-Ya Xie, Pei-Mei Zou, Xiao Gu, Shi-Rui Wang, Jian-Fang Cai, Qun Xu, Hang Li, Xue-Wang Li
Objective To compare the efficacy and safety of tacrolimus with those of cyclosporine in treating idiopathic membranous nephropathy (IMN) via network meta-analysis. Methods Databases including PubMed,Embase,CENTRAL (Cochrane),Wanfang Database,CNKI,and VIP citation database were searched for relevant studies according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Package Meta 4.5.0 and Gemtc 0.8.1 in R 3.3.1 were used to analyze the included studies. Results In this network meta-analysis,the complete remission rate (RR=0...
February 28, 2018: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
Remco R Bouckaert, Claire Bowern, Quentin D Atkinson
It remains a mystery how Pama-Nyungan, the world's largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social or technological advantages allowed rapid language replacement from the Gulf Plains region during the mid-Holocene. Others have proposed expansions from refugia linked to climatic changes after the last ice age or, more controversially, during the initial colonization of Australia. Here, we combine basic vocabulary data from 306 Pama-Nyungan languages with Bayesian phylogeographic methods to explicitly model the expansion of the family across Australia and test between these origin scenarios...
March 12, 2018: Nature Ecology & Evolution
Y Wang, X Mi, G J M Rosa, Z Chen, P Lin, S Wang, Z Bao
Neural networks (NN) have emerged as a new tool for genomic selection (GS) in animal breeding. However, the properties of NN used in GS for the prediction of phenotypical outcomes are not well characterized due to the problem of over-parameterization of NN and difficulties in using whole-genome marker sets as high-dimensional NN input. In this note, we have developed an R package called snnR that could find an optimal sparse structure of a NN by minimizing the square error subject to a penalty on the L1-norm of the parameters (weights and biases), therefore solve the problem of over-parameterization in NN...
February 24, 2018: Journal of Animal Science
Suzanne Jolley, Elizabeth Kuipers, Catherine Stewart, Sophie Browning, Karen Bracegirdle, Nedah Basit, Kimberley Gin, Colette Hirsch, Richard Corrigall, Partha Banerjea, Grainne Turley, Daniel Stahl, Kristin R Laurens
OBJECTIVES: Health care guidelines recommend psychological interventions for childhood unusual experiences that are associated with distress or adverse functional impact (UEDs), based on adult, rather than child-specific, evidence. We report the first randomized controlled evaluation of the acceptability and potential clinical utility of cognitive behavioural therapy for childhood UEDs (CBT-UED). DESIGN: Pilot randomized controlled trial. METHODS: Participants aged 8-14 years were recruited from referrals to community services for children with emotional/behavioural problems and screened for self-reported UEDs...
March 12, 2018: British Journal of Clinical Psychology
Zheng Wei, Wei Zhang, Huan Fang, Yanda Li, Xiaowo Wang
Summary: ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines...
March 7, 2018: Bioinformatics
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