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Aaron M Drucker, Patrick Fleming, An-Wen Chan
Systematic reviews are increasingly utilized in the medical literature to summarize available evidence on a research question. Like other studies, systematic reviews are at risk for bias from a number of sources. A systematic review should be based on a formal protocol developed and made publicly available before the conduct of the review; deviations from a protocol with selective presentation of data can result in reporting bias. Evidence selection bias occurs when a systematic review does not identify all available data on a topic...
November 2016: Journal of Investigative Dermatology
Daniel T Goon, Constance A Nsibambi, Milton Chebet
BACKGROUND: Scant information exist on screen time behavior of South Africa children and whether they do not meet the recommendation of American Association of Pediatrics (AAP) concerning screen time activity for children is only speculative. Therefore, the purpose of this study was to examine the time spent in sedentary activities, especially screen time of South African children with regard to gender. METHODS: This cross-sectional study involved a random sample of 1136 school children (548 boys; 588 girls) aged 9-13 years attending public schools in Central Pretoria, South Africa...
December 2016: Minerva Pediatrica
Jun Li, Wei Zhen, Dengkai Long, Ling Ding, Anhui Gong, Chenghong Xiao, Weike Jiang, Xiaoqing Liu, Tao Zhou, Luqi Huang
Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P...
2016: PloS One
(no author information available yet)
Reports an error in "Does Reading a Single Passage of Literary Fiction Really Improve Theory of Mind? An Attempt at Replication" by Maria Eugenia Panero, Deena Skolnick Weisberg, Jessica Black, Thalia R. Goldstein, Jennifer L. Barnes, Hiram Brownell and Ellen Winner (Journal of Personality and Social Psychology, Advanced Online Publication, Sep 19, 2016, np). In the article, due to an error in stimulus construction, four items (three authors, one foil) were omitted from the ART presented to all participants tested by Research Group 1...
November 2016: Journal of Personality and Social Psychology
David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
S P Pfeifer
Sequencing has revolutionized biology by permitting the analysis of genomic variation at an unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it accessible for a wide range of research topics. However, the produced data contain subtle but complex types of errors, biases and uncertainties that impose several statistical and computational challenges to the reliable detection of variants. To tap the full potential of high-throughput sequencing, a thorough understanding of the data produced as well as the available methodologies is required...
October 19, 2016: Heredity
Elena Grassi, Elisa Mariella, Antonio Lembo, Ivan Molineris, Paolo Provero
BACKGROUND: Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3'UTRs have been found to play an important role in this context, since alternative 3' UTRs could lead to differences for example in regulation by microRNAs and cellular localization of the transcripts thus altering their fate. RESULTS: We propose a strategy to identify the genes undergoing regulation of 3' UTR length using RNA sequencing data obtained from standard libraries, thus widely applicable to data originally obtained to perform classical differential expression analyses...
October 18, 2016: BMC Bioinformatics
Eduard Poltavskiy, J David Spence, Jeehyoung Kim, Heejung Bang
In the modern era, with high-throughput technology and large data size, associational studies are actively being generated. Some have statistical and clinical validity and utility, or at least have biologically plausible relationships, while others may not. Recently, the potential effect of birth month on lifetime disease risks has been studied in a phenome-wide model. We evaluated the associations between birth month and 5 cardiovascular disease-related outcomes in an independent registry of 8,346 patients from Ontario, Canada in 1977-2014...
2016: Online Journal of Public Health Informatics
Regan W Bergmark, Emily Gliklich, Rong Guo, Richard E Gliklich
BACKGROUND: Texting while driving and other cell-phone reading and writing activities are high-risk activities associated with motor vehicle collisions and mortality. This paper describes the development and preliminary evaluation of the Distracted Driving Survey (DDS) and score. METHODS: Survey questions were developed by a research team using semi-structured interviews, pilot-tested, and evaluated in young drivers for validity and reliability. Questions focused on texting while driving and use of email, social media, and maps on cellular phones with specific questions about the driving speeds at which these activities are performed...
December 2016: Injury Epidemiology
Michael P Heaton, Timothy P L Smith, Jacky K Carnahan, Veronica Basnayake, Jiansheng Qiu, Barry Simpson, Theodore S Kalbfleisch
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle...
2016: F1000Research
Daniel P Russo, Marlene T Kim, Wenyi Wang, Daniel Pinolini, Sunil Shende, Judy Strickland, Thomas Hartung, Hao Zhu
: We have developed a public Chemical In vitro - In vivo Profiling (CIIPro) portal, which can automatically extract in vitro biological data from public resources (i.e. PubChem) for user-supplied compounds. For compounds with in vivo target activity data (e.g. animal toxicity testing results), the integrated cheminformatics algorithm will optimize the extracted biological data using in vitro - in vivo correlations. The resulting in vitro biological data for target compounds can be used for read-across risk assessment of target compounds...
October 14, 2016: Bioinformatics
Yi Zhou, Wenjuan Yu, Huan Zhong, Jianlin Li, Hongxia Li, Feng He, Jie Zhou, Yongkai Tang, Juhua Yu, Fan Yu
Common carp (Cyprinus carpio) is a widespread freshwater fish and economically important species in China and other East Asian countries. Recent studies suggest that insulin can alter the expression of immune genes and, thus, can be regarded as an immunomodulatory hormone. To understand the mechanism of the immune response to insulin, we performed a comparative RNA-seq transcriptome analysis using livers from common carp injected with insulin (5 μg/g bodyweight) or saline as a control. After filtering the low-quality reads and removing the adaptors, the clean raw reads were assembled into 60,421 unigenes with mean length of 746...
October 11, 2016: Fish & Shellfish Immunology
Bruno Louro, João Pedro Marques, Deborah M Power, Adelino V M Canário
The gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax) are the most important aquaculture species in the Mediterranean Sea and since the last decade it has been seen an exponential increase in their available molecular resources. In order to improve accessibility to transcriptome resources, Expressed Sequence Tags (ESTs), mRNA sequences and raw read sequences were assembled and deposited in BLAST queryable databases. The publicly available sea bream and sea bass sequences (6...
October 11, 2016: Marine Genomics
M O Burford Reiskind, K Coyle, H V Daniels, P Labadie, M H Reiskind, N B Roberts, R B Roberts, J Schaff, E L Vargo
The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish...
November 2016: Molecular Ecology Resources
Michael W Metzler
One of the grand challenges of our time is to educate children and youth to live physically active and healthy lives today and into adulthood. To do so, we must first agree that the highest mission priority for physical education programs in schools is that of public health promotion through physical activity. Under that mission, school physical education programs from preschool to Grade 12 (P-12) would be designed, implemented, resourced, and evaluated to help children meet the recommended 60 min of daily physical activity...
October 13, 2016: Research Quarterly for Exercise and Sport
Dieter Böning
In modern societies there is strong belief in scientific progress. But unfortunately a parallel partial regress occurs because of often evitable mistakes. Mistakes are mainly forgetting, erroneous theories, errors in experiments and manuscripts, prejudice, selected publication of "positive" results and fraud. An example for forgetting is that methods introduced decades ago are used without knowing the underlying theories: basic articles are no longer read nor cited. This omission may cause incorrect interpretation of results...
October 13, 2016: International Journal of Sports Physiology and Performance
Bin Wang, Yuxi Zhou, Song Leng, Liyuan Zheng, Hong Lv, Fei Wang, Li-Hai Tan, Yimin Sun
Developmental dyslexia (DD) is a neurodevelopment disorder characterized by reading disabilities without apparent etiologies. Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a structural craniofacial malformation featured by isolated orofacial abnormalities. Despite substantial phenotypic differences, potential linkage between these two disorders has been suggested as prevalence of DD among NSCL/P patients was much higher than that in general populations. Previous neuroimaging studies observed impaired short-term memory in patients with DD and NSCL/P, respectively...
October 13, 2016: Journal of Human Genetics
Ank E Nijhawan, Princess A Iroh, Larry S Brown, Daniel Winetsky, Esmaeil Porsa
BACKGROUND: Tuberculosis (TB) disproportionately affects immigrants, HIV-infected individuals, and those living in crowded settings such as homeless shelters and correctional facilities. Although the majority of jails and prisons use a tuberculin skin test (TST) for latent tuberculosis infection (LTBI) screening, limited data exist on the clinical performance and costs of the TST compared to interferon gamma release assays (IGRAs) in this setting. METHODS: A prospective pilot study comparing cost between TST and an IGRA (QuantiFERON Gold In-tube, QFT-GIT) for the detection of LTBI in a convenience sample of inmates entering the Dallas County Jail (DCJ) was conducted June-October 2014...
October 12, 2016: BMC Infectious Diseases
Irene Saugar, Brian Molloy, Eloisa Sanz, María Blanca Sánchez, María Fernández-Lobato, Antonio Jiménez
Antibiotic A201A produced by Saccharothrix mutabilis subsp. capreolus NRRL3817 contains an aminonucleoside (N(6), N(6)-dimethyl-3'-amino-3'-deoxyadenosyl), a polyketide (α-methyl-p-coumaric acid) and a disaccharide moiety. The heterologous expression in Streptomyces lividans and Streptomyces coelicolor of a S. mutabilis genomic region of ~34 kb results in the production of A201A, which was identified by microbiological, biochemical and physicochemical approaches, and indicating that this region may contain the entire A201A biosynthetic gene cluster (ata)...
October 12, 2016: Journal of Antibiotics
Ning Yu, Yaping Liang, Xinxiang Peng, Xuewen Hou
BACKGROUND: ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. FINDINGS: In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases...
December 2016: Rice
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