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https://www.readbyqxmd.com/read/28710028/gene-expression-profiles-of-fin-regeneration-in-loach-paramisgurnus-dabryanu
#1
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 11, 2017: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/28708537/a-proteomic-study-of-mesenchymal-stem-cells-from-equine-umbilical-cord
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28676255/an-ontology-based-approach-to-patient-follow-up-assessment-for-continuous-and-personalized-chronic-disease-management
#8
Yi-Fan Zhang, Ling Gou, Tian-Shu Zhou, De-Nan Lin, Jing Zheng, Ye Li, Jing-Song Li
OBJECTIVE: Chronic diseases are complex and persistent clinical conditions that require close collaboration among patients and health care providers in the implementation of long-term and integrated care programs. However, current solutions focus partially on intensive interventions at hospitals rather than on continuous and personalized chronic disease management. This study aims to fill this gap by providing computerized clinical decision support during follow-up assessments of chronically ill patients at home...
July 1, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28664394/discover-mouse-gene-coexpression-landscapes-using-dictionary-learning-and-sparse-coding
#9
Yujie Li, Hanbo Chen, Xi Jiang, Xiang Li, Jinglei Lv, Hanchuan Peng, Joe Z Tsien, Tianming Liu
Gene coexpression patterns carry rich information regarding enormously complex brain structures and functions. Characterization of these patterns in an unbiased, integrated, and anatomically comprehensive manner will illuminate the higher-order transcriptome organization and offer genetic foundations of functional circuitry. Here using dictionary learning and sparse coding, we derived coexpression networks from the space-resolved anatomical comprehensive in situ hybridization data from Allen Mouse Brain Atlas dataset...
June 29, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28664200/an-ontology-enabled-natural-language-processing-pipeline-for-provenance-metadata-extraction-from-biomedical-text-short-paper
#10
Joshua Valdez, Michael Rueschman, Matthew Kim, Susan Redline, Satya S Sahoo
Extraction of structured information from biomedical literature is a complex and challenging problem due to the complexity of biomedical domain and lack of appropriate natural language processing (NLP) techniques. High quality domain ontologies model both data and metadata information at a fine level of granularity, which can be effectively used to accurately extract structured information from biomedical text. Extraction of provenance metadata, which describes the history or source of information, from published articles is an important task to support scientific reproducibility...
October 2016: On Move Meaningful Internet Syst
https://www.readbyqxmd.com/read/28663072/automatic-prediction-of-coronary-artery-disease-from-clinical-narratives
#11
Kevin Buchan, Michele Filannino, Özlem Uzuner
Coronary Artery Disease (CAD) is not only the most common form of heart disease, but also the leading cause of death in both men and women[1]. We present a system that is able to automatically predict whether patients develop coronary artery disease based on their narrative medical histories, i.e., clinical free text. Although the free text in medical records has been used in several studies for identifying risk factors of coronary artery disease, to the best of our knowledge our work marks the first attempt at automatically predicting development of CAD...
June 26, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28661440/online-recognition-of-daily-activities-by-color-depth-sensing-and-knowledge-models
#12
Carlos Fernando Crispim-Junior, Alvaro Gómez Uría, Carola Strumia, Michal Koperski, Alexandra König, Farhood Negin, Serhan Cosar, Anh Tuan Nghiem, Duc Phu Chau, Guillaume Charpiat, Francois Bremond
Visual activity recognition plays a fundamental role in several research fields as a way to extract semantic meaning of images and videos. Prior work has mostly focused on classification tasks, where a label is given for a video clip. However, real life scenarios require a method to browse a continuous video flow, automatically identify relevant temporal segments and classify them accordingly to target activities. This paper proposes a knowledge-driven event recognition framework to address this problem. The novelty of the method lies in the combination of a constraint-based ontology language for event modeling with robust algorithms to detect, track and re-identify people using color-depth sensing (Kinect(®) sensor)...
June 29, 2017: Sensors
https://www.readbyqxmd.com/read/28651821/sequencing-based-network-analysis-provides-a-core-set-of-gene-resource-for-understanding-kidney-immune-response-against-edwardsiella-tarda-infection-in-japanese-flounder
#13
Xiumei Liu, Zan Li, Wenzhao Wu, Yuxiang Liu, Jinxiang Liu, Yan He, Xubo Wang, Zhigang Wang, Jie Qi, Haiyang Yu, Quanqi Zhang
Marine organisms are under a frequent threat from various pathogens. Edwardsiella tarda is one of the major fish pathogens infecting both cultured and wild fish species. It can also infect a variety of other vertebrates, including amphibians, reptiles, and mammals, and bacteremia caused by E. tarda can be fatal in humans. The kidney is the largest lymphoid organ in fish, and generating kidney transcriptomic information under different stresses is crucial for understanding molecular mechanisms underlying the immune responses in the kidneys...
August 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28651634/data-and-expert-driven-rule-induction-and-filtering-framework-for-functional-interpretation-and-description-of-gene-sets
#14
Aleksandra Gruca, Marek Sikora
BACKGROUND: High-throughput methods in molecular biology provided researchers with abundance of experimental data that need to be interpreted in order to understand the experimental results. Manual methods of functional gene/protein group interpretation are expensive and time-consuming; therefore, there is a need to develop new efficient data mining methods and bioinformatics tools that could support the expert in the process of functional analysis of experimental results. RESULTS: In this study, we propose a comprehensive framework for the induction of logical rules in the form of combinations of Gene Ontology (GO) terms for functional interpretation of gene sets...
June 26, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28651575/ontological-interpretation-of-biomedical-database-content
#15
Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz
BACKGROUND: Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. METHODS: By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology...
June 26, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#16
Barbara B Raddatz, Ingo Spitzbarth, Katja A Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28632751/owl2-benchmarking-for-the-evaluation-of-knowledge-based-systems
#17
Sher Afgun Khan, Muhammad Abdul Qadir, Muhammad Azeem Abbas, Muhammad Tanvir Afzal
OWL2 semantics are becoming increasingly popular for the real domain applications like Gene engineering and health MIS. The present work identifies the research gap that negligible attention has been paid to the performance evaluation of Knowledge Base Systems (KBS) using OWL2 semantics. To fulfil this identified research gap, an OWL2 benchmark for the evaluation of KBS is proposed. The proposed benchmark addresses the foundational blocks of an ontology benchmark i.e. data schema, workload and performance metrics...
2017: PloS One
https://www.readbyqxmd.com/read/28629436/disease-compass-a-navigation-system-for-disease-knowledge-based-on-ontology-and-linked-data-techniques
#18
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
BACKGROUND: Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts...
June 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28625714/proteomic-analysis-of-seminal-plasma-from-locally-adapted-curraleiro-p%C3%A3-duro-bulls-bos-taurus-identifying-biomarkers-involved-in-sperm-physiology-in-endangered-animals-for-conservation-of-biodiversity
#19
E B Menezes, R V de Oliveira, M F van Tilburg, E A Barbosa, N V Nascimento, A L M C S Velho, F B Moreno, R A Moreira, A C O Monteiro-Moreira, G M C Carvalho, A F Ramos, E Memili, A A Moura
The present study was aimed at evaluating the seminal plasma proteins and sperm parameters of Curraleiro Pé-Duro bulls. Semen was collected from 10 bulls by electroejaculation, and sperm parameters were evaluated in fresh and frozen-thawed semen. Seminal plasma proteins were analyzed by 2-D SDS-PAGE and mass spectrophotometry. Tools in computational biology were used to generate bioinformatic knowledge and evaluate gene ontology, protein-protein interactions, phylogenetic trees and multiple sequence alignments...
May 29, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/28622634/type-of-gonadotropin-used-during-controlled-ovarian-stimulation-induces-differential-gene-expression-in-human-cumulus-cells-a-randomized-study
#20
María Cruz, Antonio Requena, David Agudo, Juan Antonio García-Velasco
BACKGROUND: The cumulus-oocyte complex plays a central role in the regulation of folliculogenesis where it is important for the maturation, reprogramming, and fertilization of oocytes. Consequently, cumulus cell gene expression profiling is being explored as a promising method for assessing oocyte competence in the near future. Through DNA microarray technology, we analyzed the potential differences in the gene expression profiles of cumulus cells from preovulatory follicles after controlled ovarian stimulation using different types of gonadotropins...
June 8, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
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