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https://www.readbyqxmd.com/read/29040923/six-factors-of-adult-dyslexia-assessed-by-cognitive-tests-and-self-report-questions-very-high-predictive-validity
#1
Peter Tamboer, Harrie C M Vorst, Peter F de Jong
The Multiple Diagnostic Digital Dyslexia Test for Adults (MDDDT-A) consists of 12 newly developed tests and self-report questions in the Dutch language. Predictive validity and construct validity were investigated and compared with validity of a standard test battery of dyslexia (STB) in a sample of 154 students. There are three main results. First, various analyses of principal components showed that six or more factors of dyslexia can be distinguished (rapid naming, spelling, reading, short-term memory, confusion, phonology, attention, complexity)...
October 14, 2017: Research in Developmental Disabilities
https://www.readbyqxmd.com/read/29040755/the-omics-dashboard-for-interactive-exploration-of-gene-expression-data
#2
Suzanne Paley, Karen Parker, Aaron Spaulding, Jean-Francois Tomb, Paul O'Maille, Peter D Karp
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, energy metabolism, regulation and central dogma. Each of those panels contains a series of X-Y plots depicting expression levels of subsystems of that panel, e.g. subsystems within the central dogma panel include transcription, translation and protein maturation and folding...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040741/identification-of-new-protein-protein-and-protein-dna-interactions-linked-with-wood-formation-in-populus-trichocarpa
#3
H Earl Petzold, Stephen B Rigoulot, Chengsong Zhao, Bidisha Chanda, Xiaoyan Sheng, Mingzhe Zhao, Xiaoyan Jia, Allan W Dickerman, Eric P Beers, Amy M Brunner
Cellular processes, such as signal transduction and cell wall deposition, are organized by macromolecule interactions. Experimentally determined protein-protein interactions (PPIs) and protein-DNA interactions (PDIs) relevant to woody plant development are sparse. To begin to develop a Populus trichocarpa Torr. & A. Gray wood interactome, we applied the yeast-two-hybrid (Y2H) assay in different ways to enable the discovery of novel PPIs and connected networks. We first cloned open reading frames (ORFs) for 361 genes markedly upregulated in secondary xylem compared with secondary phloem and performed a binary Y2H screen with these proteins...
October 10, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29040702/literacy-outcomes-in-deaf-students-with-cochlear-implants-current-state-of-the-knowledge
#4
Connie Mayer, Beverly J Trezek
The purpose of this paper is to examine the available peer-reviewed research regarding literacy achievement in deaf children with cochlear implants. A related goal is to identify gaps in the empirical literature and suggest directions for future research. Included in this review are studies that exclusively report reading and writing outcomes for groups of students. A total of 21 studies were identified, representing those published over approximately a 20-year time period (1997-2016) and collectively reporting the literacy outcomes for over 1,000 cochlear implant users...
October 5, 2017: Journal of Deaf Studies and Deaf Education
https://www.readbyqxmd.com/read/29040683/quantitating-translational-control-mrna-abundance-dependent-and-independent-contributions-and-the-mrna-sequences-that-specify-them
#5
Jingyi Jessica Li, Guo-Liang Chew, Mark D Biggin
Translation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an 'amplification exponent'. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040406/matam-reconstruction-of-phylogenetic-marker-genes-from-short-sequencing-reads-in-metagenomes
#6
Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet
Motivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#7
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040282/colorectal-carcinoma-tumour-budding-and-podia-formation-in-the-xenograft-microenvironment
#8
Friedrich Prall, Claudia Maletzki, Maja Hühns, Mathias Krohn, Michael Linnebacher
Tumour budding and podia formation are well-appreciated in surgical pathology as an aggressive invasion phenotype of colorectal carcinoma cells that is attained in the microenvironment of the invasive margin. In this study, we addressed how tumour budding and podia formation feature in xenografts. Primary colorectal carcinomas (N = 44) of various molecular types (sporadic standard type, high-degree microsatellite-unstable, CpG island methylator phenotype) were transplanted subcutaneously into T and B cell-deficient NSG mice, making possible immunohistochemistry with routine surgical pathology antibodies...
2017: PloS One
https://www.readbyqxmd.com/read/29040021/flexible-sigmoidoscopy-and-ct-colonography-screening-patients-experience-with-and-factors-for-undergoing-screening-insight-from-the-proteus-colon-trial
#9
Carlo Senore, Loredana Correale, Daniele Regge, Cesare Hassan, Gabriella Iussich, Marco Silvani, Arrigo Arrigoni, Lia Morra, Nereo Segnan
Purpose To compare the acceptability of computed tomographic (CT) colonography and flexible sigmoidoscopy (FS) screening and the factors predicting CT colonographic screening participation, targeting participants in a randomized screening trial. Materials and Methods Eligible individuals aged 58 years (n = 1984) living in Turin, Italy, were randomly assigned to be invited to screening for colorectal cancer with FS or CT colonography. After individuals who had died or moved away (n = 28) were excluded, 264 of 976 (27...
October 17, 2017: Radiology
https://www.readbyqxmd.com/read/29036997/-mean-blood-pressure-among-the-adults-in-china-2010-2012-based-on-the-results-of-mercury-sphygmomanometer-and-converted-electronic-sphygmomanometer
#10
D M Yu, P Fu, W T Yu, H J Guo, X G Yang, W H Zhao, L Y Zhao
Objective: To analyze the average systolic blood pressure (SBP) and diastolic blood pressure (DBP) among adults aged 18 years old and above in China between 2010 and 2012; and to compare the difference in the results measured by mercury sphygmomanometer and converted electronic sphygmomanometer. Methods: The data was collected from Chinese Nutrition and Health Surveillance in 2010-2012. 120 428 adults aged 18 years old and above were selected from 150 survey counties (districts) of 31 provinces in China Mainland, by multi-stage stratified and probability proportion to size (PPS) cluster randomization sampling method...
October 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/29036717/evaluation-of-occupational-radiation-dose-in-transcatheter-aortic-valve-implantation
#11
Anette Aarsnes, Gry Dahle, Erik Fosse, Kjell Arne Rein, Lars Aaberge, Anne Catrine T Martinsen
Occupational doses during fluoroscopy in interventional procedures vary largely (Kim et al. (Occupational radiation doses to operators performing cardiac catheterization procedures. Health Phys. 2008;94:211-227)). In transcatheter aortic valve implantation, the operators' positions and use of radiation shielding are particularly related to the entry choice on the patient's heart. This study evaluates how occupational doses depend on operator positioning during transfemoral and transaortal access. Occupational dosimetric readings were collected with electronic dosemeters on two cardiothoracic surgeons and one cardiologist during 31 procedures...
September 23, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29036644/roles-of-female-and-male-genotype-in-post-mating-responses-in-drosophila-melanogaster-roles-of-female-and-male-genotype-in-female-drosophila-melanogaster-transcriptional-physiological-and-behavioral-responses-to-mating
#12
Sofie Y N Delbare, Clement Y Chow, Mariana F Wolfner, Andrew G Clark
Mating induces a multitude of changes in female behavior, physiology and gene expression. Interactions between female and male genotype lead to variation in post-mating phenotypes and reproductive success. So far, few female molecules responsible for these interactions have been identified. Here, we used Drosophila melanogaster from five geographically dispersed populations to investigate such female x male genotypic interactions at the female transcriptomic and phenotypic levels. Females from each line were singly-mated to males from the same five lines, for a total of 25 combinations...
October 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036597/faucet-streaming-de-novo-assembly-graph-construction
#13
Roye Rozov, Gil Goldshlager, Eran Halperin, Ron Shamir
Motivation: We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased. Results: Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#14
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036581/secondary-use-of-electronic-health-record-data-for-clinical-workflow-analysis
#15
Michelle R Hribar, Sarah Read-Brown, Isaac H Goldstein, Leah G Reznick, Lorinna Lombardi, Mansi Parikh, Winston Chamberlain, Michael F Chiang
Objective: Outpatient clinics lack guidance for tackling modern efficiency and productivity demands. Workflow studies require large amounts of timing data that are prohibitively expensive to collect through observation or tracking devices. Electronic health records (EHRs) contain a vast amount of timing data - timestamps collected during regular use - that can be mapped to workflow steps. This study validates using EHR timestamp data to predict outpatient ophthalmology clinic workflow timings at Oregon Health and Science University and demonstrates their usefulness in 3 different studies...
September 26, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#16
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036486/comparison-of-padc-neutron-detectors-from-different-suppliers
#17
M Caresana, A Parravicini, S Coria, A Stabilini, F Assenmacher, E G Yukihara
The objective of this study was to compare poly-allyl diglycol carbonate (PADC) track detectors from different suppliers for linear energy transfer (LET) spectrometry and neutron dosimetry. PADCs are commonly used for passive personal neutron dosimetry, where a common approach is to couple the PADC with a plastic radiator to generate secondary charged particles. The neutron dose can be estimated using the track density or the average LET of the secondary particles. The characterisation of PADC in terms of LET spectrometric capability and neutron sensitivity was previously performed using PADC from Intercast S...
September 29, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29036421/lrcstats-a-tool-for-evaluating-long-reads-correction-methods
#18
Sean La, Ehsan Haghshenas, Cedric Chauve
Motivation: Third-generation sequencing (TGS) platforms that generate long reads, such as PacBio and Oxford Nanopore technologies, have had a dramatic impact on genomics research. However, despite recent improvements, TGS reads suffer from high-error rates and the development of read correction methods is an active field of research. This motivates the need to develop tools that can evaluate the accuracy of noisy long reads correction tools. Results: We introduce LRCstats, a tool that measures the accuracy of long reads correction tools...
August 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036419/an-accurate-algorithm-for-the-detection-of-dna-fragments-from-dilution-pool-sequencing-experiments
#19
Vikas Bansal
Motivation: The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention...
July 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036413/smooth-quantile-normalization
#20
Stephanie C Hicks, Kwame Okrah, Joseph N Paulson, John Quackenbush, Rafael A Irizarry, Héctor Corrada Bravo
Between-sample normalization is a critical step in genomic data analysis to remove systematic bias and unwanted technical variation in high-throughput data. Global normalization methods are based on the assumption that observed variability in global properties is due to technical reasons and are unrelated to the biology of interest. For example, some methods correct for differences in sequencing read counts by scaling features to have similar median values across samples, but these fail to reduce other forms of unwanted technical variation...
July 10, 2017: Biostatistics
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