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https://www.readbyqxmd.com/read/29145615/iptmnet-an-integrated-resource-for-protein-post-translational-modification-network-discovery
#1
Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136637/transcriptional-profiling-of-toll-like-receptor-2-deficient-primary-murine-brain-cells-during-toxoplasma-gondii-infection
#2
Kousuke Umeda, Sachi Tanaka, Fumiaki Ihara, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
BACKGROUND: Toxoplasma gondii is capable of persisting in the brain, although it is efficiently eliminated by cellular immune responses in most other sites. While Toll-like receptor 2 (TLR2) reportedly plays important roles in protective immunity against the parasite, the relationship between neurological disorders induced by T. gondii infection and TLR2 function in the brain remains controversial with many unknowns. In this study, primary cultured astrocytes, microglia, neurons, and peritoneal macrophages obtained from wild-type and TLR2-deficient mice were exposed to T...
2017: PloS One
https://www.readbyqxmd.com/read/29133314/decisional-needs-assessment-of-patients-with-complex-care-needs-in-primary-care-a-participatory-systematic-mixed-studies-review-protocol
#3
Mathieu Bujold, Pierre Pluye, France Légaré, Jeannie Haggerty, Genevieve C Gore, Reem El Sherif, Marie-Eve Poitras, Marie-Claude Beaulieu, Marie-Dominique Beaulieu, Paula L Bush, Yves Couturier, Beatrice Débarges, Justin Gagnon, Anik Giguère, Roland Grad, Vera Granikov, Serge Goulet, Catherine Hudon, Bernardo Kremer, Edeltraut Kröger, Irina Kudrina, Bertrand Lebouché, Christine Loignon, Marie-Therese Lussier, Cristiano Martello, Quynh Nguyen, Rebekah Pratt, Benoit Rihoux, Ellen Rosenberg, Isabelle Samson, Nicolas Senn, David Li Tang, Masashi Tsujimoto, Isabelle Vedel, Bruno Ventelou, Michel Wensing
INTRODUCTION: Patients with complex care needs (PCCNs) often suffer from combinations of multiple chronic conditions, mental health problems, drug interactions and social vulnerability, which can lead to healthcare services overuse, underuse or misuse. Typically, PCCNs face interactional issues and unmet decisional needs regarding possible options in a cascade of interrelated decisions involving different stakeholders (themselves, their families, their caregivers, their healthcare practitioners)...
November 12, 2017: BMJ Open
https://www.readbyqxmd.com/read/29132408/using-semantics-for-representing-experimental-protocols
#4
Olga Giraldo, Alexander García, Federico López, Oscar Corcho
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory...
November 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29126123/pedam-a-database-for-pediatric-disease-annotation-and-medicine
#5
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Xin Li, Yunxiang Liang, Dongming Guo, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29123525/identification-of-new-features-from-known-bacterial-protective-vaccine-antigens-enhances-rational-vaccine-design
#6
Edison Ong, Mei U Wong, Yongqun He
With many protective vaccine antigens reported in the literature and verified experimentally, how to use the knowledge mined from these antigens to support rational vaccine design and study underlying design mechanism remains unclear. In order to address the problem, a systematic bioinformatics analysis was performed on 291 Gram-positive and Gram-negative bacterial protective antigens with experimental evidence manually curated in the Protegen database. The bioinformatics analyses evaluated included subcellular localization, adhesin probability, peptide signaling, transmembrane α-helix and β-barrel, conserved domain, Clusters of Orthologous Groups, and Gene Ontology functional annotations...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#7
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29122011/entity-recognition-in-the-biomedical-domain-using-a-hybrid-approach
#8
Marco Basaldella, Lenz Furrer, Carlo Tasso, Fabio Rinaldi
BACKGROUND: This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles. METHOD: The approach uses a two-stage pipeline, combining a dictionary-based entity recognizer with a machine-learning classifier. First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29115469/microrna%C3%A2-512%C3%A2-3p-is-upregulated-and-promotes-proliferation-and-cell-cycle-progression-in-prostate-cancer-cells
#9
Zhigang Rao, Ziqi He, Yi He, Zonghua Guo, Dongbo Kong, Jufang Liu
Prostate cancer (PCa) is the most commonly diagnosed cancer in males worldwide. MicroRNAs (miRNAs/miRs) are small non‑coding RNAs that participate in the regulation of various biological processes by regulating post‑transcriptional gene expression. However, whether dysregulation of miRNA expression may be associated with the carcinogenesis of PCa remains to be elucidated. The present study identified differentially expressed miRNAs in PCa by analyzing two publicly available gene expression datasets, GSE14857 and GSE21036...
October 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#10
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29113811/incorporating-gene-ontology-into-fuzzy-relational-clustering-of-microarray-gene-expression-data
#11
Animesh Kumar Paul, Pintu Chandra Shill
The product of gene expression works together in the cell for each living organism in order to achieve different biological processes. Many proteins are involved in different roles depending on the environment of the organism for the functioning of the cell. In this paper, we propose gene ontology (GO) annotations based semi-supervised clustering algorithm called GO fuzzy relational clustering (GO-FRC) where one gene is allowed to be assigned to multiple clusters which are the most biologically relevant behavior of genes...
November 4, 2017: Bio Systems
https://www.readbyqxmd.com/read/29113073/an-ontology-based-reasoning-framework-for-querying-satellite-images-for-disaster-monitoring
#12
Marjan Alirezaie, Andrey Kiselev, Martin Längkvist, Franziska Klügl, Amy Loutfi
This paper presents a framework in which satellite images are classified and augmented with additional semantic information to enable queries about what can be found on the map at a particular location, but also about paths that can be taken. This is achieved by a reasoning framework based on qualitative spatial reasoning that is able to find answers to high level queries that may vary on the current situation. This framework called SemCityMap, provides the full pipeline from enriching the raw image data with rudimentary labels to the integration of a knowledge representation and reasoning methods to user interfaces for high level querying...
November 5, 2017: Sensors
https://www.readbyqxmd.com/read/29109515/chemical-similarity-enrichment-analysis-chemrich-as-alternative-to-biochemical-pathway-mapping-for-metabolomic-datasets
#13
Dinesh Kumar Barupal, Oliver Fiehn
Metabolomics answers a fundamental question in biology: How does metabolism respond to genetic, environmental or phenotypic perturbations? Combining several metabolomics assays can yield datasets for more than 800 structurally identified metabolites. However, biological interpretations of metabolic regulation in these datasets are hindered by inherent limits of pathway enrichment statistics. We have developed ChemRICH, a statistical enrichment approach that is based on chemical similarity rather than sparse biochemical knowledge annotations...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29106618/eram-encyclopedia-of-rare-disease-annotations-for-precision-medicine
#14
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Yunxiang Liang, Dongming Guo, Xin Li, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM)...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106451/ploc-mhum-predict-subcellular-localization-of-multi-location-human-proteins-via-general-pseaac-to-winnow-out-the-crucial-go-information
#15
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Motivation: For in-depth understanding the functions of proteins in a cell, the knowledge of their subcellular localization is indispensable. The current study is focused on human protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for both basic research and drug design...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29101418/-the-big-data-game-on-the-ludic-constitution-of-the-collaborative-production-of-knowledge-in-high-energy-physics-at-cern
#16
Anne Dippel
This article looks at how games and play contribute to the big data-driven production of knowledge in High-Energy Physics, with a particular focus on the Large Hadron Collider (LHC) at the European Organization for Nuclear Research (CERN), where the author has been conducting anthropological fieldwork since 2014. The ludic (playful) aspect of knowledge production is analyzed here in three different dimensions: the Symbolic, the Ontological, and the Epistemic. The first one points towards CERN as place where a cosmological game of probability is played with the help of Monte-Carlo simulations...
December 2017: NTM
https://www.readbyqxmd.com/read/29081784/eqtls-regulating-transcript-variations-associated-with-rapid-internode-elongation-in-deepwater-rice
#17
Takeshi Kuroha, Keisuke Nagai, Yusuke Kurokawa, Yoshiaki Nagamura, Miyako Kusano, Hideshi Yasui, Motoyuki Ashikari, Atsushi Fukushima
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29079755/a-proteome-view-of-structural-functional-and-taxonomic-characteristics-of-major-protein-domain-clusters
#18
Chia-Tsen Sun, Austin W T Chiang, Ming-Jing Hwang
Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29076113/a-knowledge-modeling-approach-to-integrate-multiple-clinical-practice-guidelines-to-provide-evidence-based-clinical-decision-support-for-managing-comorbid-conditions
#19
Samina Abidi
Clinical management of comorbidities is a challenge, especially in a clinical decision support setting, as it requires the safe and efficient reconciliation of multiple disease-specific clinical procedures to formulate a comorbid therapeutic plan that is both effective and safe for the patient. In this paper we pursue the integration of multiple disease-specific Clinical Practice Guidelines (CPG) in order to manage co-morbidities within a computerized Clinical Decision Support System (CDSS). We present a CPG integration framework-termed as COMET (Comorbidity Ontological Modeling & ExecuTion) that manifests a knowledge management approach to model, computerize and integrate multiple CPG to yield a comorbid CPG knowledge model that upon execution can provide evidence-based recommendations for handling comorbid patients...
October 26, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/29069413/wormbase-2017-molting-into-a-new-stage
#20
Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller, Cecilia Nakamura, Paulo Nuin, Michael Paulini, Daniela Raciti, Faye Rodgers, Matt Russell, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul Kersey, Tim Schedl, Lincoln Stein, Paul W Sternberg
WormBase ( http://www.wormbase.org ) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans , and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations...
October 24, 2017: Nucleic Acids Research
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