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https://www.readbyqxmd.com/read/28797230/use-of-biological-priors-enhances-understanding-of-genetic-architecture-and-genomic-prediction-of-complex-traits-within-and-between-dairy-cattle-breeds
#1
Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
BACKGROUND: A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28797229/odg-omics-database-generator-a-tool-for-generating-querying-and-analyzing-multi-omics-comparative-databases-to-facilitate-biological-understanding
#2
Joseph Guhlin, Kevin A T Silverstein, Peng Zhou, Peter Tiffin, Nevin D Young
BACKGROUND: Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28794902/generic-distributed-framework-for-cloud-services-marketplace-based-on-unified-ontology
#3
Samer Hasan, V Valli Kumari
Cloud computing is a pattern for delivering ubiquitous and on demand computing resources based on pay-as-you-use financial model. Typically, cloud providers advertise cloud service descriptions in various formats on the Internet. On the other hand, cloud consumers use available search engines (Google and Yahoo) to explore cloud service descriptions and find the adequate service. Unfortunately, general purpose search engines are not designed to provide a small and complete set of results, which makes the process a big challenge...
November 2017: Journal of Advanced Research
https://www.readbyqxmd.com/read/28794464/expression-changes-in-pelvic-organ-prolapse-a-systematic-review-and-in-silico-study
#4
Maryam B Khadzhieva, Dmitry S Kolobkov, Svetlana V Kamoeva, Lyubov E Salnikova
Pelvic organ prolapse (POP) is a highly disabling condition common for a vast number of women worldwide. To contribute to existing knowledge in POP pathogenesis, we performed a systematic review of expression studies on both specific gene and whole-genome/proteome levels and an in silico analysis of publicly available datasets related to POP development. The most extensively investigated genes in individual studies were related to extracellular matrix (ECM) organization. Three premenopausal and two postmenopausal sets from two Gene Expression Omnibus (GEO) studies (GSE53868 and GSE12852) were analyzed; Gene Ontology (GO) terms related to tissue repair (locomotion, biological adhesion, immune processes and other) were enriched in all five datasets...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28766103/protocol-driven-decision-support-within-e-referral-systems-to-streamline-patient-consultation-triaging-and-referrals-from-primary-care-to-specialist-clinics
#5
Ehsan Maghsoud-Lou, Sean Christie, Samina Raza Abidi, Syed Sibte Raza Abidi
Patient referral is a protocol where the referring primary care physician refers the patient to a specialist for further treatment. The paper-based current referral process at times lead to communication and operational issues, resulting in either an unfulfilled referral request or an unnecessary referral request. Despite the availability of standardized referral protocols they are not readily applied because they are tedious and time-consuming, thus resulting in suboptimal referral requests. We present a semantic-web based Referral Knowledge Modeling and Execution Framework to computerize referral protocols, clinical guidelines and assessment tools in order to develop a computerized e-Referral system that offers protocol-based decision support to streamline and standardize the referral process...
September 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28765438/dental-faculty-members-pedagogic-beliefs-and-curriculum-aims-in-problem-based-learning-an-exploratory-study
#6
HsingChi von Bergmann, Judith Walker, Kirsten R Dalrymple, Charles F Shuler
The aims of this exploratory study were to explore dental faculty members' views and beliefs regarding knowledge, the dental profession, and teaching and learning and to determine how these views related to their problem-based learning (PBL) instructional practices. Prior to a PBL in dental education conference held in 2011, all attendees were invited to complete a survey focused on their pedagogical beliefs and practices in PBL. Out of a possible 55 participants, 28 responded. Additionally, during the conference, a forum was held in which preliminary survey findings were shared and participants contributed to focus group data collection...
August 2017: Journal of Dental Education
https://www.readbyqxmd.com/read/28761781/the-difference-in-expression-of-long-noncoding-rnas-in-rat-semen-induced-by-high-fat-diet-was-associated-with-metabolic-pathways
#7
Tian An, Hui Fan, Yu F Liu, Yan Y Pan, Ying K Liu, Fang F Mo, Yu J Gu, Ya L Sun, Dan D Zhao, Na Yu, Yue Ma, Chen Y Liu, Qiu L Wang, Zheng Y Li, Fei Teng, Si Hua Gao, Guang J Jiang
BACKGROUND: Obesity, a common metabolic disease, is a known cause of male infertility due to its associated health risk. Long noncoding RNAs (lncRNAs) have also been reported to be associated with male reproductive diseases; however, their role in the association between high-fat diet-induced obesity (DIO) and male reproduction remains unclear. METHODS: We used microarray analysis to compare the expression levels of lncRNAs and mRNAs in the spermatozoa of rats with DIO and normal rats...
2017: PeerJ
https://www.readbyqxmd.com/read/28758431/prodige-prediction-models-in-prostate-cancer-for-personalized-medicine-challenge
#8
A R Alitto, R Gatta, Bgl Vanneste, M Vallati, E Meldolesi, A Damiani, V Lanzotti, G C Mattiucci, V Frascino, C Masciocchi, F Catucci, A Dekker, P Lambin, V Valentini, G Mantini
AIM: Identifying the best care for a patient can be extremely challenging. To support the creation of multifactorial Decision Support Systems (DSSs), we propose an Umbrella Protocol, focusing on prostate cancer. MATERIALS & METHODS: The PRODIGE project consisted of a workflow for standardizing data, and procedures, to create a consistent dataset useful to elaborate DSSs. Techniques from classical statistics and machine learning will be adopted. The general protocol accepted by our Ethical Committee can be downloaded from cancerdata...
July 31, 2017: Future Oncology
https://www.readbyqxmd.com/read/28750648/towards-a-more-molecular-taxonomy-of-disease
#9
Jisoo Park, Benjamin J Hescott, Donna K Slonim
BACKGROUND: Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. RESULTS: We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data...
July 27, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28733112/distinctions-in-gene-specific-changes-in-dna-methylation-in-response-to-folic-acid-supplementation-between-women-with-normal-weight-and-obesity
#10
Hea Jin Park, Lynn B Bailey, Deanna C Shade, Dorothy B Hausman, Natalie M Hohos, Richard B Meagher, Gail Pa Kauwell, Richard D Lewis, Alicia K Smith
BACKGROUND/OBJECTIVES: Obesity and maternal folate deficiency are associated with increased risk for neural tube defects (NTDs). Limited knowledge exists on the impact of folate status or obesity on DNA methylation of genes related to NTD risk and folate metabolism. SUBJECTS/METHODS: Women (18-35y) with normal weight (NW; BMI 18.5-24.9kg/m(2); n=12) and obesity (OB; BMI >30kg/m(2); n=6) were provided FA (800μg/d) for 8-weeks. Serum folate concentration and changes in DNA methylation across 2098 CpG sites in 91 genes related to NTD risk and folate metabolism were examined...
July 18, 2017: Obesity Research & Clinical Practice
https://www.readbyqxmd.com/read/28731430/neuroimaging-feature-terminology-a-controlled-terminology-for-the-annotation-of-brain-imaging-features
#11
Anandhi Iyappan, Erfan Younesi, Alberto Redolfi, Henri Vrooman, Shashank Khanna, Giovanni B Frisoni, Martin Hofmann-Apitius
Ontologies and terminologies are used for interoperability of knowledge and data in a standard manner among interdisciplinary research groups. Existing imaging ontologies capture general aspects of the imaging domain as a whole such as methodological concepts or calibrations of imaging instruments. However, none of the existing ontologies covers the diagnostic features measured by imaging technologies in the context of neurodegenerative diseases. Therefore, the Neuro-Imaging Feature Terminology (NIFT) was developed to organize the knowledge domain of measured brain features in association with neurodegenerative diseases by imaging technologies...
July 18, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28728979/ploc-mvirus-predict-subcellular-localization-of-multi-location-virus-proteins-via-incorporating-the-optimal-go-information-into-general-pseaac
#12
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. 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...
July 17, 2017: Gene
https://www.readbyqxmd.com/read/28723579/elucidating-high-dimensional-cancer-hallmark-annotation-via-enriched-ontology
#13
Shankai Yan, Ka-Chun Wong
MOTIVATION: Cancer hallmark annotation is a promising technique that could discover novel knowledge about cancer from the biomedical literature. The automated annotation of cancer hallmarks could reveal relevant cancer transformation processes in the literature or extract the articles that correspond to the cancer hallmark of interest. It acts as a complementary approach that can retrieve knowledge from massive text information, advancing numerous focused studies in cancer research. Nonetheless, the high-dimensional nature of cancer hallmark annotation imposes a unique challenge...
July 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28710028/gene-expression-profiles-of-fin-regeneration-in-loach-paramisgurnus-dabryanu
#14
Li Li, Jingya He, Linlin Wang, Weihua Chen, Zhongjie Chang
Teleost fins can regenerate accurate position-matched structure and function after amputation. However, we still lack systematic transcriptional profiling and methodologies to understand the molecular basis of fin regeneration. After histological analysis, we established a suppression subtraction hybridization library containing 418 distinct sequences expressed differentially during the process of blastema formation and differentiation in caudal fin regeneration. Genome ontology and comparative analysis of differential distribution of our data and the reference zebrafish genome showed notable subcategories, including multi-organism processes, response to stimuli, extracellular matrix, antioxidant activity, and cell junction function...
July 18, 2017: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/28708537/a-proteomic-study-of-mesenchymal-stem-cells-from-equine-umbilical-cord
#15
Leandro Maia, Carolina Nogueira de Moraes, Marianne Camargos Dias, Julia Bauzá Martinez, Antonia Odena Caballol, Giorgia Testoni, Carla Martins de Queiroz, Ramón Díaz Peña, Fernanda C Landim-Alvarenga, Eliandre de Oliveira
To the best of our knowledge, this is the first study describing the proteome of equine umbilical cord intervascular matrix mesenchymal stem cells (UCIM-MSCs) in a global and functional manner. The aim of this work was to analyze the proteome of previously characterized UCIM-MSCs to determine protein abundance and classify the identified proteins according to Gene Ontology (GO) terms. Protein classification analysis according to biological process, molecular function and cellular component was performed using the PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System, which revealed enrichment for 42 biological processes, 23 molecular functions and 18 cellular components...
May 24, 2017: Theriogenology
https://www.readbyqxmd.com/read/28708456/mosquito-borne-diseases-and-omics-tissue-restricted-expression-and-alternative-splicing-revealed-by-transcriptome-profiling-of-anopheles-stephensi
#16
Sreelakshmi K Sreenivasamurthy, Anil K Madugundu, Arun H Patil, Gourav Dey, Ajeet Kumar Mohanty, Manish Kumar, Krishna Patel, Charles Wang, Ashwani Kumar, Akhilesh Pandey, Thottethodi Subrahmanya Keshava Prasad
Malaria is one of the most debilitating mosquito-borne diseases with high global health burdens. While much of the research on malaria and mosquito-borne diseases is focused on Africa, Southeast Asia accounts for a sizable portion of the global burden of malaria. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. A promising development in this context is that the completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, including the progress in deciphering the vectorial ability of this mosquito species at a molecular level...
July 14, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28700989/doritool-a-bioinformatics-integrative-tool-for-post-association-functional-annotation
#17
Isabel Martín-Antoniano, Lola Alonso, Miguel Madrid, Evangelina López de Maturana, Núria Malats
The emergence of high-throughput data in biology has increased the need for functional in silico analysis and prompted the development of integrative bioinformatics tools to facilitate the obtainment of biologically meaningful data. In this paper, we present DoriTool, a comprehensive, easy, and friendly pipeline integrating biological data from different functional tools. The tool was designed with the aim to maximize reproducibility and reduce the working time of the researchers, especially of those with limited bioinformatics skills, and to help them with the interpretation of the results...
July 13, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28699547/lightweight-predicate-extraction-for-patient-level-cancer-information-and-ontology-development
#18
Muhammad Amith, Hsing-Yi Song, Yaoyun Zhang, Hua Xu, Cui Tao
BACKGROUND: Knowledge engineering for ontological knowledgebases is resource and time intensive. To alleviate these issues, especially for novices, automated tools from the natural language domain can assist in the development process of ontologies. We focus towards the development of ontologies for the public health domain and use patient-centric sources from MedlinePlus related to HPV-causing cancers. METHODS: This paper demonstrates the use of a lightweight open information extraction (OIE) tool to derive accurate knowledge triples that can lead to the seeding of an ontological knowledgebase...
July 5, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28692419/long-term-cigarette-smoke-exposure-and-changes-in-mirna-expression-and-proteome-in-non-small-cell-lung-cancer
#19
Jayshree Advani, Yashwanth Subbannayya, Krishna Patel, Aafaque Ahmad Khan, Arun H Patil, Ankit P Jain, Hitendra S Solanki, Aneesha Radhakrishnan, Sneha M Pinto, Nandini A Sahasrabuddhe, Joji K Thomas, Premendu P Mathur, Bipin G Nair, Xiaofei Chang, T S Keshava Prasad, David Sidransky, Harsha Gowda, Aditi Chatterjee
Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis...
July 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28679876/pitfalls-of-ontology-in-medicine
#20
Bakheet Aldosari, Abdullah Alanazi, Mowafa Househ
Much research has been done in the last few decades in clinical research, medicine, life sciences, etc. leading to an exponential increase in the generation of data. Managing this vast information not only requires integration of the data, but also a means to analyze, relate, and retrieve it. Ontology, in the field of medicine, describes the concepts of medical terminologies and the relation between them, thus, enabling the sharing of medical knowledge. Ontology-based analyses are associated with a risk that errors in modeling may deteriorate the results' quality...
2017: Studies in Health Technology and Informatics
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