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https://www.readbyqxmd.com/read/28339516/improving-a-full-text-search-engine-the-importance-of-negation-detection-and-family-history-context-to-identify-cases-in-a-biomedical-data-warehouse
#1
Nicolas Garcelon, Antoine Neuraz, Vincent Benoit, Rémi Salomon, Anita Burgun
Objective: The repurposing of electronic health records (EHRs) can improve clinical and genetic research for rare diseases. However, significant information in rare disease EHRs is embedded in the narrative reports, which contain many negated clinical signs and family medical history. This paper presents a method to detect family history and negation in narrative reports and evaluates its impact on selecting populations from a clinical data warehouse (CDW). Materials and Methods: We developed a pipeline to process 1...
October 20, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28335399/an-eddy-current-testing-platform-system-for-pipe-defect-inspection-based-on-an-optimized-eddy-current-technique-probe-design
#2
Damhuji Rifai, Ahmed N Abdalla, Ramdan Razali, Kharudin Ali, Moneer A Faraj
The use of the eddy current technique (ECT) for the non-destructive testing of conducting materials has become increasingly important in the past few years. The use of the non-destructive ECT plays a key role in the ensuring the safety and integrity of the large industrial structures such as oil and gas pipelines. This paper introduce a novel ECT probe design integrated with the distributed ECT inspection system (DSECT) use for crack inspection on inner ferromagnetic pipes. The system consists of an array of giant magneto-resistive (GMR) sensors, a pneumatic system, a rotating magnetic field excitation source and a host PC acting as the data analysis center...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#3
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334975/apricot-an-integrated-computational-pipeline-for-the-sequence-based-identification-and-characterization-of-rna-binding-proteins
#4
Malvika Sharan, Konrad U Förstner, Ana Eulalio, Jörg Vogel
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334822/posigene-automated-and-easy-to-use-pipeline-for-genome-wide-detection-of-positively-selected-genes
#5
Arne Sahm, Martin Bens, Matthias Platzer, Karol Szafranski
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334360/hla-ma-simple-yet-powerful-matching-of-samples-using-hla-typing-results
#6
Clemens Messerschmidt, Manuel Holtgrewe, Dieter Beule
Summary: We propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method OptiType. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple, fast, and robust matching of samples from whole genome, exome, and RNA-seq data. Our approach uses information from small but genetically highly variable regions and thus complements approaches that rely on genome or exon-wide variant profiles...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334241/rmats-dvr-rmats-discovery-of-differential-variants-in-rna
#7
Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing
Motivation: RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334167/identification-of-genetic-outliers-due-to-sub-structure-and-cryptic-relationships
#8
Daniel Schlauch, Heide Fier, Christoph Lange
Motivation: In order to minimize the effects of genetic confounding on the analysis of high-throughput genetic association studies, e.g. (whole-genome) sequencing (WGS) studies, genome-wide association studies (GWAS), etc., we propose a general framework to assess and to test formally for genetic heterogeneity among study subjects. As the approach fully utilizes the recent ancestor information captured by rare variants, it is especially powerful in WGS studies. Even for relatively moderate sample sizes, the proposed testing framework is able to identify study subjects that are genetically too similar, e...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334086/pseudoalignment-for-metagenomic-read-assignment
#9
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Motivation: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains...
February 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333980/evaluating-alignment-and-variant-calling-software-for-mutation-identification-in-c-elegans-by-whole-genome-sequencing
#10
Harold E Smith, Sijung Yun
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria...
2017: PloS One
https://www.readbyqxmd.com/read/28333907/the-effect-of-placing-flow-diverting-stents-in-intracranial-collateral-arteries-of-miniature-pig
#11
Jiwei Wang, Yanan Ding, Qiuxia Wang, Yanan Wang, Shiqing Mu, Lixin Bi, Youxiang Li
BACKGROUND Flow-diverting stent (FDS) has been suggested as an effective intracranial aneurysm treatment. However, the effects of FDS on collateral branches of an aneurysm parent artery still remain unknown. Thus, the present study aimed to comprehensively evaluate the effects of placing a FDS in the intracranial collateral artery, using a miniature pig animal model. MATERIAL AND METHODS Ten healthy miniature pigs were included in the study: one pig was reserved as a control and the remaining nine pigs were placed in three experimental groups: FDS (i...
March 23, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28332378/quantitative-computed-tomographic-volumetry-after-treatment-of-a-giant-intracranial-aneurysm-with-a-pipeline-embolization-device
#12
Woong Jae Lee, Jun Soo Byun, Jae Kyun Kim, Taek Kyun Nam
Recently developed flow diverters, such as the pipeline embolization device (PED), allow for safe and efficacious treatment of giant intracranial aneurysms, with high occlusion rates and a low incidence of complications. However, incomplete obliteration after PED treatment may lead to aneurysm regrowth and delayed rupture. Herein, we report a case of a partially thrombosed giant aneurysm of the cavernous internal carotid artery that showed progressive recanalization at 1-3 months after application of a PED...
May 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28331889/unsupervised-labeling-of-glomerular-boundaries-using-gabor-filters-and-statistical-testing-in-renal-histology
#13
Brandon Ginley, John E Tomaszewski, Rabi Yacoub, Feng Chen, Pinaki Sarder
The glomerulus is the blood filtering unit of the kidney. Each human kidney contains [Formula: see text] glomeruli. Several renal conditions originate from structural damage to glomerular microcompartments, such as proteinuria, the excessive loss of blood proteins into urine. The gold standard for evaluating structural damage in renal pathology is histopathological and immunofluorescence examination of needle biopsies under a light microscope. This method is limited by qualitative or semiquantitative manual scoring approaches to the evaluation of glomerular structural features...
April 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28331841/resistance-testing-for-the-treatment-of-chronic-hepatitis-c-with-direct-acting-antivirals-when-and-for-how-long
#14
Ana Belén Pérez, Natalia Chueca, Federico García
The need to test for resistance associated substitutions (RAS) has been intensively debated in the past two years. In the absence of pangenotypic combinations, it seems reasonable that, if available, RAS testing in the NS5A gene at baseline for genotypes 1a and 3 may help to avoid overtreatment in terms of ribavirin usage and/or prolonged treatment duration. When patients fail treatment, RAS testing may also be useful to guide the selection of the new regimen, especially for those that need urgent retreatment and that have failed a combination including an NS5A inhibitor...
March 2017: Germs
https://www.readbyqxmd.com/read/28331587/a-simple-fast-and-repeatable-survey-method-for-underwater-visual-3d-benthic-mapping-and-monitoring
#15
Oscar Pizarro, Ariell Friedman, Mitch Bryson, Stefan B Williams, Joshua Madin
Visual 3D reconstruction techniques provide rich ecological and habitat structural information from underwater imagery. However, an unaided swimmer or diver struggles to navigate precisely over larger extents with consistent image overlap needed for visual reconstruction. While underwater robots have demonstrated systematic coverage of areas much larger than the footprint of a single image, access to suitable robotic systems is limited and requires specialized operators. Furthermore, robots are poor at navigating hydrodynamic habitats such as shallow coral reefs...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28330825/streamlining-workflow-and-automation-to-accelerate-laboratory-scale-protein-production
#16
REVIEW
Jennifer Konczal, Christopher H Gray
Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli...
March 18, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28330331/identification-and-quantification-of-novel-rna-isoforms-in-horn-cancer-of-bos-indicus-by-comprehensive-rna-seq
#17
Subhash J Jakhesara, Prakash G Koringa, Neelam M Nathani, Chaitanya G Joshi
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330144/upcot-an-integrated-pipeline-tool-for-clustering-upstream-dna-sequences-of-orthologous-genes-in-prokaryotic-genomes
#18
P V Parvati Sai Arun, Jogadhenu S S Prakash
UpCoT is a pipeline tool developed by automating the series of steps involved in prediction of cis-regulatory elements. UpCoT generates orthologs for each gene in target genome using bi-directional best blast hit against the reference genomes, then identifies potential orthologous transcriptional units using intergenic distance. Finally it generates the FASTA files containing upstream sequences of orthologous transcriptional units of each gene in target genome. The inputs of UpCoT are protein sequence files (*...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#19
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#20
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
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