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https://www.readbyqxmd.com/read/29036693/icg-a-wiki-driven-knowledgebase-of-internal-control-genes-for-rt-qpcr-normalization
#1
Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang, Wanzhu Zuo, Yang Zhang, Wenming Zhao, Yiming Bao, Jingfa Xiao, Songnian Hu, Lili Hao, Zhang Zhang
Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036627/using-uncertainty-to-link-and-rank-evidence-from-biomedical-literature-for-model-curation
#2
Chrysoula Zerva, Riza Batista-Navarro, Philip Day, Sophia Ananiadou
Motivation: In recent years, there has been great progress in the field of automated curation of biomedical networks and models, aided by text mining methods that provide evidence from literature. Such methods must not only extract snippets of text that relate to model interactions, but also be able to contextualize the evidence and provide additional confidence scores for the interaction in question. Although various approaches calculating confidence scores have focused primarily on the quality of the extracted information, there has been little work on exploring the textual uncertainty conveyed by the author...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036607/endoscopic-and-histopathologic-reflux-associated-mucosal-damage-in-the-remnant-esophagus-following-transthoracic-esophagectomy-for-cancer-5-year-long-term-follow-up
#3
H F Fuchs, H M Schmidt, M Meissner, S Brinkmann, M Maus, M Bludau, W Schröder, A H Hölscher, J M Leers
Gastroesophageal reflux is a common problem following esophagectomy and reconstruction with gastric interposition. Despite a routine prescription of proton pump inhibitors, reflux-associated mucosal damage in the remnant esophagus is frequently observed. Purpose of this study is to evaluate mucosal damage in the esophageal remnant during long-term follow-up and to compare the prevalence of this damage between the subgroups of esophageal squamous cell and adenocarcinoma. All patients undergoing transthoracic Ivor-Lewis esophagectomy were prospectively entered in our IRB approved database...
September 21, 2017: Diseases of the Esophagus: Official Journal of the International Society for Diseases of the Esophagus
https://www.readbyqxmd.com/read/29036597/faucet-streaming-de-novo-assembly-graph-construction
#4
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/29036573/complexviewer-visualization-of-curated-macromolecular-complexes
#5
Colin W Combe, Marine Dumousseau Sivade, Henning Hermjakob, Joshua Heimbach, Birgit H M Meldal, Gos Micklem, Sandra Orchard, Juri Rappsilber
Summary: Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex. Availability and implementation: freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036562/nandb-number-and-brightness-in-r-with-a-novel-automatic-detrending-algorithm
#6
Rory Nolan, Luis A J Alvarez, Jonathan Elegheert, Maro Iliopoulou, G Maria Jakobsdottir, Marina Rodriguez-Muñoz, A Radu Aricescu, Sergi Padilla-Parra
Summary: An R package for performing number and brightness image analysis, with the implementation of a novel automatic detrending algorithm. Availability and implementation: Available at https://github.com/rorynolan/nandb for all platforms. Contact: rnolan@well.ox.ac.uk or spadilla@well.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
July 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#7
(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/29036507/ggseqlogo-a-versatile-r-package-for-drawing-sequence-logos
#8
Omar Wagih
Summary: Sequence logos have become a crucial visualization method for studying underlying sequence patterns in the genome. Despite this, there remains a scarcity of software packages that provide the versatility often required for such visualizations. ggseqlogo is an R package built on the ggplot2 package that aims to address this issue. ggseqlogo offers native illustration of publication-ready DNA, RNA and protein sequence logos in a highly customizable fashion with features including multi-logo plots, qualitative and quantitative colour schemes, annotation of logos and integration with other plots...
July 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036452/a-nonparametric-significance-test-for-sampled-networks
#9
Andrew Elliott, Elizabeth Leicht, Alan Whitmore, Gesine Reinert, Felix Reed-Tsochas
Motivation: Our work is motivated by an interest in constructing a protein-protein interaction network that captures key features associated with Parkinson's disease. While there is an abundance of subnetwork construction methods available, it is often far from obvious which subnetwork is the most suitable starting point for further investigation. Results: We provide a method to assess whether a subnetwork constructed from a seed list (a list of nodes known to be important in the area of interest) differs significantly from a randomly generated subnetwork...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036307/irys-extract
#10
Rani Arielly, Yuval Ebenstein
Summary: Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser. Availability and implementation: Irys Extract has been developed in Matlab R2015a, it was tested to work with IrysView 2...
July 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036273/scoop-an-accurate-and-fast-predictor-of-protein-stability-curves-as-a-function-of-temperature
#11
Fabrizio Pucci, Jean Marc Kwasigroch, Marianne Rooman
Motivation: The molecular bases of protein stability remain far from elucidated even though substantial progress has been made through both computational and experimental investigations. One of the most challenging goals is the development of accurate prediction tools of the temperature dependence of the standard folding free energy Δ G ( T ). Such predictors have an enormous series of potential applications, which range from drug design in the biopharmaceutical sector to the optimization of enzyme activity for biofuel production...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036271/cancer-hallmarks-analytics-tool-chat-a-text-mining-approach-to-organize-and-evaluate-scientific-literature-on-cancer
#12
Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo, Johan Högberg, Ulla Stenius, Anna Korhonen
Motivation: To understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29035817/electroformation-of-double-vesicles-using-an-amplitude-modulated-electric-field
#13
Salah Eddine Ghellab, Qingchuan Li, Thomas Fuhs, Hongmei Bi, Xiaojun Han
Double vesicles are a promising model to mimic eukaryotic cells, yet effective preparation methods with high yields and stable double vesicles are scarce. Previously reported electroformation methods were mainly based on sinusoidal AC fields. Using a combination of sinusoidal and amplitude modulated (AM) electric fields lipid double vesicles could be produced for the first time by a simple electroformation process. First lipid domes formed in a sinusoidal AC field. The domes grew into tubes during the subsequent application of an AM field...
October 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29035809/synthesis-of-hollow-nico2o4-nanospheres-with-large-specific-surface-area-for-asymmetric-supercapacitors
#14
Kaibing Xu, Jianmao Yang, Junqing Hu
Hollow micro-/nanostructured electrode materials with high active surface area are highly desirable for achieving outstanding electrochemical properties. Herein, we report the successful synthesis of hierarchical hollow NiCo2O4 nanospheres with high surface area as electrode materials for supercapacitors. Electrochemical measurements prove that such electrode materials exhibit excellent electrochemical behavior with a specific capacitance reaching 1229 F/g at 1 A/g, remarkable rate performance (∼83.6% retention from 1 to 25 A/g) and good cycling performance (86...
September 30, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/29035518/manipulation-and-assessment-of-charge-and-spin-delocalization-in-mixed-valent-triarylamine-vinylruthenium-conjugates
#15
Christopher Hassenrück, Rainer F Winter
Triarylamine-vinylruthenium conjugates (4-RC6H4)2N{C6H4-4-CH═CHRu(CO)Cl(P(i)Pr3)2}, with R = CHO (1-CHO), C(═O)Me (1-Ac), COOMe (1-E), and Me (1-Me), have been prepared and investigated in their neutral, mono- and dioxidized states by cyclic voltammetry, IR, and UV/vis/near-infrared spectroelectrochemistry, electron paramagnetic resonance spectroscopy, and quantum-chemical calculations. Electron-withdrawing substituents at the triarylamine moiety shift the charge and spin density toward the more electron-rich vinylruthenium site in comparison to the 4-OMe-substituted triarylamine-vinylruthenium conjugate 1-OMe...
October 16, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29035040/orally-administrated-baker-s-yeast-beta-glucan-promotes-glucose-and-lipid-homeostasis-in-the-livers-of-ob-ob-mice
#16
Yan Cao, Ying Sun, Siwei Zou, Mengxia Li, Xiaojuan Xu
Baker's yeast glucan (BYG) has been reported to be anti-diabetic. Herein, further study on the effect of orally administrated BYG on glucose and lipid homeostasis in the livers of ob/ob mice was performed. It was found that BYG decreased the blood glucose and the hepatic glucose and lipid disorders. Western blotting analysis revealed that BYG up-regulated p-AKT and p-AMPK, and down-regulated p-Acc in the liver. Furthermore, RNA-Seq analysis indicated that BYG down-regulated genes responsible for gluconeogenesis (G6pase and Got1), fatty acid biosynthesis (Acly, Acc, Fas, etc...
October 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29034731/effects-of-omega-3-fatty-acids-on-bone-turnover-markers-in-postmenopausal-women-systematic-review-and-meta-analysis
#17
D Shen, X Zhang, Z Li, H Bai, L Chen
AIM: There is conflicting evidence regarding the effects of omega-3 fatty acids on bone turnover markers in postmenopausal women. Thus, we systematically reviewed the efficacy of omega-3 fatty acids by conducting a meta-analysis of available randomized controlled trials. METHODS: PubMed, Embase, Cochrane Library and Scopus were searched in December 2016. The standardized mean difference (SMD) or weighted mean difference (WMD) and the corresponding 95% confidence intervals (CIs) were calculated using a fixed-effects model...
October 16, 2017: Climacteric: the Journal of the International Menopause Society
https://www.readbyqxmd.com/read/29034704/the-role-of-nutrition-and-hydration-in-disease-prevention-and-patient-safety
#18
Omorogieva Ojo
Omorogieva Ojo, Senior Lecturer in Primary Care at the University of Greenwich, O.Ojo@greenwich.ac.uk , looks at the importance of nutrition and hydration across healthcare settings.
October 12, 2017: British Journal of Nursing: BJN
https://www.readbyqxmd.com/read/29034437/management-of-early-anal-cancer-need-for-guidelines-and-standardisation
#19
Michael P Jones, Susan Carroll, Jarad Martin, Richard Hillman, Andrew Grulich, Dianne O'Connell, Christopher Young, Isobel Mary Poynten
PURPOSE: The optimal management of early squamous cell carcinoma of the anal canal (AC) is yet to be determined. This study investigated current practice in the management of early AC. METHODS: A patterns of care survey was completed by Australian surgeons and radiation oncologists. Specific topics addressed were as follows: geographical location of practice, staging of disease, treatment approaches to T1N0 tumours and grade 3 anal intra-epithelial neoplasia (AIN3) lesions, radiotherapy planning, toxicities, follow-up and clinical trial involvement...
October 15, 2017: International Journal of Colorectal Disease
https://www.readbyqxmd.com/read/29033856/possible-facilitative-effects-of-repeated-anodal-transcranial-direct-current-stimulation-on-functional-outcome-1-month-later-in-schizophrenia-an-open-trial
#20
Zui Narita, Takuma Inagawa, Kazuki Sueyoshi, Crystal Lin, Tomiki Sumiyoshi
Recent research on neuromodulation techniques, such as transcranial direct current stimulation (tDCS), for the treatment of schizophrenia has mainly focused on psychotic symptoms. We aimed to determine whether repetitive tDCS is efficacious in improving determinants of outcome, such as cognitive function, daily living skills, and depressive mood in patients with schizophrenia. Twenty-eight patients underwent tDCS (2 mA × 20 min) two times per day for 5 consecutive days. The anodal electrode was placed over the left dorsolateral prefrontal cortex while the cathodal electrode was placed over the right supraorbital region...
2017: Frontiers in Psychiatry
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