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https://www.readbyqxmd.com/read/29042212/morfpred-plus-computational-identification-of-morfs-in-protein-sequences-using-physicochemical-properties-and-hmm-profiles
#1
Ronesh Sharma, Maitsetseg Bayarjargal, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma
Motivation Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. Method In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences...
October 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29036693/icg-a-wiki-driven-knowledgebase-of-internal-control-genes-for-rt-qpcr-normalization
#2
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/29036542/database-resources-of-the-big-data-center-in-2018
#3
(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/29029599/liverwiki-a-wiki-based-database-for-human-liver
#4
Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu
BACKGROUND: Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort...
October 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29028899/phandango-an-interactive-viewer-for-bacterial-population-genomics
#5
James Hadfield, Nicholas J Croucher, Richard J Goater, Khalil Abudahab, David M Aanensen, Simon R Harris
Summary: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29025823/standing-collaboration-a-study-protocol-for-developing-clinical-standards
#6
Louise K Wiles, Peter D Hibbert, Jacqueline H Stephens, Enrico Coiera, Johanna Westbrook, Jeffrey Braithwaite, Ric O Day, Ken M Hillman, William B Runciman
INTRODUCTION: Despite widespread availability of clinical practice guidelines (CPGs), considerable gaps continue between the care that is recommended ('appropriate care') and the care provided. Problems with current CPGs are commonly cited as barriers to providing 'appropriate care'.Our study aims to develop and test an alternative method to keep CPGs accessible and up to date. This method aims to mitigate existing problems by using a single process to develop clinical standards (embodied in clinical indicators) collaboratively with researchers, healthcare professionals, patients and consumers...
October 11, 2017: BMJ Open
https://www.readbyqxmd.com/read/28982479/nurse-led-immunotreatment-decision-coaching-in-people-with-multiple-sclerosis-decims-feasibility-testing-pilot-randomised-controlled-trial-and-mixed-methods-process-evaluation
#7
A C Rahn, S Köpke, I Backhus, J Kasper, K Anger, B Untiedt, A Alegiani, I Kleiter, I Mühlhauser, C Heesen
BACKGROUND: Treatment decision-making is complex for people with multiple sclerosis. Profound information on available options is virtually not possible in regular neurologist encounters. The "nurse decision coach model" was developed to redistribute health professionals' tasks in supporting immunotreatment decision-making following the principles of informed shared decision-making. OBJECTIVES: To test the feasibility of a decision coaching programme and recruitment strategies to inform the main trial...
August 26, 2017: International Journal of Nursing Studies
https://www.readbyqxmd.com/read/28949323/a-global-reference-database-of-crowdsourced-cropland-data-collected-using-the-geo-wiki-platform
#8
Juan Carlos Laso Bayas, Myroslava Lesiv, François Waldner, Anne Schucknecht, Martina Duerauer, Linda See, Steffen Fritz, Dilek Fraisl, Inian Moorthy, Ian McCallum, Christoph Perger, Olha Danylo, Pierre Defourny, Javier Gallego, Sven Gilliams, Ibrar Ul Hassan Akhtar, Swarup Jyoti Baishya, Mrinal Baruah, Khangsembou Bungnamei, Alfredo Campos, Trishna Changkakati, Anna Cipriani, Krishna Das, Keemee Das, Inamani Das, Kyle Frankel Davis, Purabi Hazarika, Brian Alan Johnson, Ziga Malek, Monia Elisa Molinari, Kripal Panging, Chandra Kant Pawe, Ana Pérez-Hoyos, Parag Kumar Sahariah, Dhrubajyoti Sahariah, Anup Saikia, Meghna Saikia, Peter Schlesinger, Elena Seidacaru, Kuleswar Singha, John W Wilson
A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed...
September 26, 2017: Scientific Data
https://www.readbyqxmd.com/read/28949071/radiation-therapy-students-perceptions-of-a-wiki
#9
Gay Dungey, Peter Gallagher
BACKGROUND: This pilot study aimed to gain the perceptions of first-year students using a wiki as a learning tool for the Bachelor of Radiation Therapy degree in New Zealand. Literature suggests that wikis have great potential as an educational tool for both lecturers and students, because they encourage collaborative learning and resource sharing. In 2015, the 'Otago Wiki' platform was introduced as a part of the degree. METHODS: The first-year students were allocated into groups of four...
September 26, 2017: Clinical Teacher
https://www.readbyqxmd.com/read/28894890/new-prognostic-factor-telomerase-reverse-transcriptase-promotor-mutation-presents-without-mr-imaging-biomarkers-in-primary-glioblastoma
#10
Tunc F Ersoy, Vera C Keil, Dariusch R Hadizadeh, Gerrit H Gielen, Rolf Fimmers, Andreas Waha, Barbara Heidenreich, Rajiv Kumar, Hans H Schild, Matthias Simon
PURPOSE: Magnetic resonance (MR) imaging biomarkers can assist in the non-invasive assessment of the genetic status in glioblastomas (GBMs). Telomerase reverse transcriptase (TERT) promoter mutations are associated with a negative prognosis. This study was performed to identify MR imaging biomarkers to forecast the TERT mutation status. METHODS: Pre-operative MRIs of 64/67 genetically confirmed primary GBM patients (51/67 TERT-mutated with rs2853669 polymorphism) were analyzed according to Visually AcceSAble Rembrandt Images (VASARI) ( https://wiki...
September 11, 2017: Neuroradiology
https://www.readbyqxmd.com/read/28883196/from-a-content-delivery-portal-to-a-knowledge-management-system-for-standardized-cancer-documentation
#11
Danijela Schlue, Sebastian Mate, Jörg Haier, Dennis Kadioglu, Hans-Ulrich Prokosch, Bernhard Breil
Heterogeneous tumor documentation and its challenges of interpretation of medical terms lead to problems in analyses of data from clinical and epidemiological cancer registries. The objective of this project was to design, implement and improve a national content delivery portal for oncological terms. Data elements of existing handbooks and documentation sources were analyzed, combined and summarized by medical experts of different comprehensive cancer centers. Informatics experts created a generic data model based on an existing metadata repository...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28879061/a-practical-guide-to-build-de-novo-assemblies-for-single-tissues-of-non-model-organisms-the-example-of-a-neotropical-frog
#12
Santiago Montero-Mendieta, Manfred Grabherr, Henrik Lantz, Ignacio De la Riva, Jennifer A Leonard, Matthew T Webster, Carles Vilà
Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog...
2017: PeerJ
https://www.readbyqxmd.com/read/28870259/rdfio-extending-semantic-mediawiki-for-interoperable-biomedical-data-management
#13
Samuel Lampa, Egon Willighagen, Pekka Kohonen, Ali King, Denny Vrandečić, Roland Grafström, Ola Spjuth
BACKGROUND: Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data. This stresses the need for efficient ways of integrating these data in a coherent description of biological systems. In many cases, biological data needs organization before integration. This is not seldom a collaborative effort, and it is thus important that tools for data integration support a collaborative way of working. Wiki systems with support for structured semantic data authoring, such as Semantic MediaWiki, provide a powerful solution for collaborative editing of data combined with machine-readability, so that data can be handled in an automated fashion in any downstream analyses...
September 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28836922/a-neutral-control-condition-for-hypnosis-experiments-wiki-text
#14
Katalin Varga, Zoltán Kekecs, P S Myhre, Emese Józsa
A new control condition called Wiki is introduced. Key themes of each test suggestion of the Stanford Hypnotic Susceptibility Scale, Form C, were matched by a corresponding extract from Wikipedia.org. The authors compared phenomenological reports of participants across 4 conditions: hypnosis split into high and low hypnotizable subgroups, music, and Wiki condition, using the Phenomenology of Consciousness Inventory. High hypnotizables undergoing hypnosis reported higher altered experience and altered states of awareness than individuals in the Wiki condition, supporting the authors' hypothesis that the Wiki condition does not evoke an altered state of consciousness (internal dialogue, volitional control, and self-awareness did not differ)...
October 2017: International Journal of Clinical and Experimental Hypnosis
https://www.readbyqxmd.com/read/28672236/developing-and-applying-metamodels-of-high-resolution-process-based-simulations-for-high-throughput-exposure-assessment-of-organic-chemicals-in-riverine-ecosystems
#15
M Craig Barber, Kristin K Isaacs, Caroline Tebes-Stevens
As defined by Wikipedia (https://en.wikipedia.org/wiki/Metamodeling), "(a) metamodel or surrogate model is a model of a model, and metamodeling is the process of generating such metamodels." The goals of metamodeling include, but are not limited to (1) developing functional or statistical relationships between a model's input and output variables for model analysis, interpretation, or information consumption by users' clients; (2) quantifying a model's sensitivity to alternative or uncertain forcing functions, initial conditions, or parameters; and (3) characterizing the model's response or state space...
December 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28663021/comparative-analysis-of-diabetes-self-management-education-programs-in-the-european-union-member-states
#16
Sarama Saha, Henna Riemenschneider, Gabriele Müller, Diane Levin-Zamir, Stephan Van den Broucke, Peter E H Schwarz
Diabetes self-management education (DSME) is generally considered as an integral part of diabetes care. The availability of different types of self-management in the European Union Member States (EUMS) remains uncertain. The aim of this study is to perform a comparative analysis of existing DSME programs (DSMEP) implemented in EUMS. Unpublished data regarding DSME in the EUMS was assessed with Diabetes Literacy Survey using wiki tool (WT) targeting patients and different stakeholders. An additional literature review (LR) was performed in PubMed to identify published studies regarding DSMEP in the EUMS from 2004 to 2014...
June 26, 2017: Primary Care Diabetes
https://www.readbyqxmd.com/read/28608851/a-global-dataset-of-crowdsourced-land-cover-and-land-use-reference-data
#17
Steffen Fritz, Linda See, Christoph Perger, Ian McCallum, Christian Schill, Dmitry Schepaschenko, Martina Duerauer, Mathias Karner, Christopher Dresel, Juan-Carlos Laso-Bayas, Myroslava Lesiv, Inian Moorthy, Carl F Salk, Olha Danylo, Tobias Sturn, Franziska Albrecht, Liangzhi You, Florian Kraxner, Michael Obersteiner
Global land cover is an essential climate variable and a key biophysical driver for earth system models. While remote sensing technology, particularly satellites, have played a key role in providing land cover datasets, large discrepancies have been noted among the available products. Global land use is typically more difficult to map and in many cases cannot be remotely sensed. In-situ or ground-based data and high resolution imagery are thus an important requirement for producing accurate land cover and land use datasets and this is precisely what is lacking...
June 13, 2017: Scientific Data
https://www.readbyqxmd.com/read/28583426/studying-behaviors-among-neurosurgery-residents-using-web-2-0-analytic-tools
#18
Benjamin Davidson, Naif M Alotaibi, Daipayan Guha, Sandi Amaral, Abhaya V Kulkarni, Andres M Lozano
BACKGROUND: Web 2.0 technologies (e.g., blogs, social networks, and wikis) are increasingly being used by medical schools and postgraduate training programs as tools for information dissemination. These technologies offer the unique opportunity to track metrics of user engagement and interaction. Here, we employ Web 2.0 tools to assess academic behaviors among neurosurgery residents. METHODS: We performed a retrospective review of all educational lectures, part of the core Neurosurgery Residency curriculum at the University of Toronto, posted on our teaching website (www...
June 2, 2017: Journal of Surgical Education
https://www.readbyqxmd.com/read/28562810/teaching-learning-evaluation-on-the-icnp%C3%A2-using-virtual-learning-environment
#19
Carolina Costa Valcanti Avelino, Lívia Cristina Scalon da Costa, Soraia Matilde Marques Buchhorn, Denismar Alves Nogueira, Sueli Leiko Takamatsu Goyatá
Objective: Evaluating the teaching-learning process of undergraduates and nursing professionals on the International Classification for Nursing Practice (ICNP®) through a course on Moodle Platform. Method: Mixed research conducted with 51 nursing students and nurses. Many technological and educational resources were used. To collect data, two semi-structured questionnaires were applied and focus groups were carried out. Statistical and thematic analysis of the data was performed...
May 2017: Revista Brasileira de Enfermagem
https://www.readbyqxmd.com/read/28518075/leveraging-cyverse-resources-for-de-novo-comparative-transcriptomics-of-underserved-non-model-organisms
#20
Blake L Joyce, Asher K Haug-Baltzell, Jonathan P Hulvey, Fiona McCarthy, Upendra Kumar Devisetty, Eric Lyons
This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g. executing bash commands, visualization and management of large data sets. All command line code and further explanations of each command or step can be found on the wiki (https://wiki.cyverse.org/wiki/x/dgGtAQ). The Discovery Environment and Atmosphere platforms are connected together through the CyVerse Data Store...
May 9, 2017: Journal of Visualized Experiments: JoVE
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