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https://www.readbyqxmd.com/read/28545254/bacterial-virus-ontology-coordinating-across-databases
#1
Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted...
May 23, 2017: Viruses
https://www.readbyqxmd.com/read/28541580/genes-and-gene-clusters-related-to-genotype-and-drought-induced-variation-in-saccharification-potential-lignin-content-and-wood-anatomical-traits-in-populus-nigra%C3%A2
#2
Henning Wildhagen, Shanty Paul, Mike Allwright, Hazel K Smith, Marta Malinowska, Sabine K Schnabel, M João Paulo, Federica Cattonaro, Vera Vendramin, Simone Scalabrin, Dennis Janz, Cyril Douthe, Oliver Brendel, Cyril Buré, David Cohen, Irène Hummel, Didier Le Thiec, Fred van Eeuwijk, Joost J B Keurentjes, Jaume Flexas, Michele Morgante, Paul Robson, Marie-Béatrice Bogeat-Triboulot, Gail Taylor, Andrea Polle
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential...
May 24, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28540678/semantic-technologies-and-bio-ontologies
#3
Fernando Gutierrez
As information available through data repositories constantly grows, the need for automated mechanisms for linking, querying, and sharing data has become a relevant factor both in research and industry. This situation is more evident in research fields such as the life sciences, where new experiments by different research groups are constantly generating new information regarding a wide variety of related study objects. However, current methods for representing information and knowledge are not suited for machine processing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28533479/the-landscape-of-dna-methylation-mediated-regulation-of-long-non-coding-rnas-in-breast-cancer
#4
Chunlong Zhang, Xinyu Wang, Xuecang Li, Ning Zhao, Yihan Wang, Xiaole Han, Ce Ci, Jian Zhang, Meng Li, Yan Zhang
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28532419/a-survey-of-the-complex-transcriptome-from-the-highly-polyploid-sugarcane-genome-using-full-length-isoform-sequencing-and-de-novo-assembly-from-short-read-sequencing
#5
Nam V Hoang, Agnelo Furtado, Patrick J Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P Thirugnanasambandam, Frederik C Botha, Robert J Henry
BACKGROUND: Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS: The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28524641/nursing-philosophy-2016-response-to-peter-allmark-s-article-aristotle-for-nursing
#6
Beverly J B Whelton
Preparing to lecture on Aristotle's contribution to Nursing at the International Philosophy of Nursing Conference August 22, 2016, in Quebec City, Quebec, Canada, I came upon the recently published article by my IPONS colleague, Allmark (2016), "Aristotle for Nursing." Allmark (2016) provides a comprehensive and understandable overview of Aristotle's philosophical system including the substantial nature of being and the four causes of change. Nurses using Aristotle to support practice and theoretical research will benefit from a careful reading of Allmark to enrich their use of the realist understanding of knowledge of nature (epistemology) and the matter-form causal relationships within natural being (ontology and teleology)...
May 19, 2017: Nursing Philosophy: An International Journal for Healthcare Professionals
https://www.readbyqxmd.com/read/28521733/nfpscanner-a-webtool-for-knowledge-based-deciphering-of-biomedical-networks
#7
Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo, Fei Li
BACKGROUND: Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis...
May 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28515914/analysis-of-the-function-of-microrna-375-in-humans-using-bioinformatics
#8
Xiaohua Chen, Baoxia Li, Rongcheng Luo, Sina Cai, Cao Zhang, Xiaolong Cao
MicroRNA-375 (miR-375) is expressed at low levels in many types of solid tumor, particularly in gastrointestinal tumors. It is considered to be important in the development of cancer and certain diseases. Thus, more detailed knowledge is required on the particular functions of miR-375. miRs function by regulating target genes. Therefore, in the current study, miRWalk (which includes the data from 10 prediction software programs) was used to predict the target genes of miR-375. The genes, which were co-predicted using five different software programs were further analyzed using Database for Annotation, Visualization and Integrated Discovery online software [including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis]...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28515735/time-course-transcriptome-analysis-of-compatible-and-incompatible-pollen-stigma-interactions-in-brassica-napus-l
#9
Tong Zhang, Changbin Gao, Yao Yue, Zhiquan Liu, Chaozhi Ma, Guilong Zhou, Yong Yang, Zhiqiang Duan, Bing Li, Jing Wen, Bin Yi, Jinxiong Shen, Jinxing Tu, Tingdong Fu
Brassica species exhibit both compatible and incompatible pollen-stigma interactions, however, the underlying molecular mechanisms remain largely unknown. Here, RNA-seq technology was applied in a comprehensive time-course experiment (2, 5, 10, 20, and 30 min) to explore gene expression during compatible/incompatible pollen-stigma interactions in stigma. Moderate changes of gene expression were observed both in compatible pollination (PC) and incompatible pollination (PI) within 10 min, whereas drastic changes showed up by 30 min, especially in PI...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28508772/concept-based-retrieval-from-critical-incident-reports
#10
Kerstin Denecke
BACKGROUND: Critical incident reporting systems (CIRS) are used as a means to collect anonymously entered information of incidents that occurred for example in a hospital. Analyzing this information helps to identify among others problems in the workflow, in the infrastructure or in processes. OBJECTIVES: The entire potential of these sources of experiential knowledge remains often unconsidered since retrieval of relevant reports and their analysis is difficult and time-consuming, and the reporting systems often do not provide support for these tasks...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28503356/towards-an-obesity-cancer-knowledge-base-biomedical-entity-identification-and-relation-detection
#11
Juan Antonio Lossio-Ventura, William Hogan, François Modave, Amanda Hicks, Josh Hanna, Yi Guo, Zhe He, Jiang Bian
Obesity is associated with increased risks of various types of cancer, as well as a wide range of other chronic diseases. On the other hand, access to health information activates patient participation, and improve their health outcomes. However, existing online information on obesity and its relationship to cancer is heterogeneous ranging from pre-clinical models and case studies to mere hypothesis-based scientific arguments. A formal knowledge representation (i.e., a semantic knowledge base) would help better organizing and delivering quality health information related to obesity and cancer that consumers need...
December 2016: Proceedings
https://www.readbyqxmd.com/read/28500765/developing-bayesian-networks-from-a-dependency-layered-ontology-a-proof-of-concept-in-radiation-oncology
#12
Alan M Kalet, Jason N Doctor, John H Gennari, Mark H Phillips
PURPOSE: Bayesian networks (BNs) are graphical representations of probabilistic knowledge that offer normative reasoning under uncertainty and are well suited for use in medical domains. Traditional knowledge-based network development of BN topology requires that modeling experts establish relevant dependency links between domain concepts by searching and translating published literature, querying domain experts, or applying machine learning algorithms on data. For initial development these methods are time-intensive and this cost hinders the growth of BN applications in medical decision making...
May 13, 2017: Medical Physics
https://www.readbyqxmd.com/read/28499848/understanding-obesity-in-the-context-of-an-indigenous-population-a-qualitative-study
#13
Ricky Bell, Catherine Smith, Leigh Hale, Geoffrey Kira, Steve Tumilty
BACKGROUND: Obesity is a progressive global phenomenon that is disparately prevalent amongst Indigenous populations. While there is a growing body of literature investigating the extrinsic contributors to obesity, there is a lack of evidence to elucidate intrinsic drivers in the context of an Indigenous population. METHODS: Qualitative research theory, inclusive of Indigenous knowledge systems, was applied to the narratives of 15 Indigenous (Māori) people aged between 18 and 65 to contextualise their understandings of obesity...
May 9, 2017: Obesity Research & Clinical Practice
https://www.readbyqxmd.com/read/28494922/analysis-of-jak-stat-signaling-pathway-genes-and-their-micrornas-in-the-intestinal-mucosa-of-genetically-disparate-chicken-lines-induced-with-necrotic-enteritis
#14
Anh Duc Truong, Deivendran Rengaraj, Yeojin Hong, Cong Thanh Hoang, Yeong Ho Hong, Hyun S Lillehoj
The JAK-STAT signaling pathway plays a key role in cytokine and growth factor activation and is involved in several cellular functions and diseases. The main objective of this study was to investigate the expression of candidate JAK-STAT pathway genes and their regulators and interactors in the intestinal mucosal layer of two genetically disparate chicken lines [Marek's disease (MD)-resistant line 6.3 and MD-susceptible line 7.2] induced with necrotic enteritis (NE). Through RNA-sequencing, we investigated 116 JAK-STAT signaling pathway-related genes that were significant and differentially expressed between the intestinal mucosa of the two lines compared with respective uninfected controls...
May 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28479537/requirements-and-solutions-for-personalized-health-systems
#15
Bernd Blobel, Pekka Ruotsalainen, Diego M Lopez, Frank Oemig
Organizational, methodological and technological paradigm changes enable a precise, personalized, predictive, preventive and participative approach to health and social services supported by multiple actors from different domains at diverse level of knowledge and skills. Interoperability has to advance beyond Information and Communication Technologies (ICT) concerns, including the real world business domains and their processes, but also the individual context of all actors involved. The paper introduces and compares personalized health definitions, summarizes requirements and principles for pHealth systems, and considers intelligent interoperability...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28470264/reconstruction-and-analysis-of-the-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-reveal-functional-lncrnas-in-rheumatoid-arthritis
#16
Hui Jiang, Rong Ma, Shubiao Zou, Yongzhong Wang, Zhuqing Li, Weiping Li
Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28469412/use-of-biomedical-ontologies-for-integration-of-biological-knowledge-for-learning-and-prediction-of-adverse-drug-reactions
#17
REVIEW
Shadia Zaman, Sirarat Sarntivijai, Darrell R Abernethy
Drug-induced toxicity is a major public health concern that leads to patient morbidity and mortality. To address this problem, the Food and Drug Administration is working on the PredicTox initiative, a pilot research program on tyrosine kinase inhibitors, to build mechanistic and predictive models for drug-induced toxicity. This program involves integrating data acquired during preclinical studies and clinical trials within pharmaceutical company development programs that they have agreed to put in the public domain and in publicly available biological, pharmacological, and chemical databases...
2017: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28453300/psychiatry-sex-and-science-the-making-of-adolescent-motherhood-in-southern-brazil
#18
Dominique P Béhague
Research linking teen motherhood to psychoneurodevelopmental causes and pathologies has proliferated in the past two decades. In Brazil, a psychodevelopmental project of teen motherhood has gained traction despite many experts' long-standing commitment to psychodynamic psychiatry and social epidemiology, generating epistemic tension rather than substitution. Drawing on historical ethnography conducted in Southern Brazil, I explore how this project materialized through the co-production of epistemic struggles, remedial interventions, and ontological politics...
April 28, 2017: Medical Anthropology
https://www.readbyqxmd.com/read/28452593/the-relationship-between-geographical-and-social-space-and-approaches-to-care-among-rural-and-urban-caregivers-caring-for-a-family-member-with-dementia-a-qualitative-study
#19
Kethy Ehrlich, Azita Emami, Kristiina Heikkilä
Knowledge about family caregivers in rural areas remains sparse. No studies to date have addressed the sociocultural aspects in caregiving, thus neglecting potentially significant data. This study aimed to explore and better understand family caregivers' experiences in rural and urban areas and the sociocultural spheres that these two areas represent. How do family caregivers approach their caregiving situation? A hermeneutical approach was chosen to uncover the underlying meanings of experiences. Open-ended in-depth interviews were conducted...
January 17, 2017: International Journal of Qualitative Studies on Health and Well-being
https://www.readbyqxmd.com/read/28450823/proteomic-profiling-of-human-intraschisis-cavity-fluid
#20
Dhandayuthapani Sudha, Mahdokht Kohansal-Nodehi, Purnima Kovuri, Srikanth Srinivas Manda, Srividya Neriyanuri, Lingam Gopal, Pramod Bhende, Subbulakshmi Chidambaram, Jayamuruga Pandian Arunachalam
BACKGROUND: X-linked retinoschisis (XLRS) is a vitreoretinal degenerative disorder causing vision deterioration, due to structural defects in retina. The hallmark of this disease includes radial streaks arising from the fovea and splitting of inner retinal layers (schisis). Although these retinal changes are attributed to mutations in the retinoschisin gene, schisis is also observed in patients who do not carry mutations. In addition, the origin of intraschisis fluid, the triggering point of schisis formation and its progression are largely unknown still...
2017: Clinical Proteomics
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