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https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28611940/involvement-of-chromatin-remodeling-genes-and-the-rho-gtpases-rhob-and-cdc42-in-ovarian-clear-cell-carcinoma
#6
Nicolai Skovbjerg Arildsen, Jenny-Maria Jönsson, Katarina Bartuma, Anna Ebbesson, Sofia Westbom-Fremer, Anna Måsbäck, Susanne Malander, Mef Nilbert, Ingrid A Hedenfalk
OBJECTIVE: Ovarian clear cell carcinomas (OCCCs) constitute a rare ovarian cancer subtype with distinct clinical features, but may nonetheless be difficult to distinguish morphologically from other subtypes. There is limited knowledge of genetic events driving OCCC tumorigenesis beyond ARID1A, which is reportedly mutated in 30-50% of OCCCs. We aimed to further characterize OCCCs by combined global transcriptional profiling and targeted deep sequencing of a panel of well-established cancer genes...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28587674/navise-superenhancer-navigator-integrating-epigenomics-signal-algebra
#7
Alex M Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J Araúzo-Bravo
BACKGROUND: Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers...
June 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28585481/novel-approaches-to-develop-community-built-biological-network-models-for-potential-drug-discovery
#8
Marja Talikka, Natalia Bukharov, William S Hayes, Martin Hofmann-Apitius, Leonidas Alexopoulos, Manuel C Peitsch, Julia Hoeng
Hundreds of thousands of data points are now routinely generated in clinical trials by molecular profiling and NGS technologies. A true translation of this data into knowledge is not possible without analysis and interpretation in a well-defined biology context. Currently, there are many public and commercial pathway tools and network models that can facilitate such analysis. At the same time, insights and knowledge that can be gained is highly dependent on the underlying biological content of these resources...
June 6, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28560380/sorafenib-induces-variations-of-the-dna-methylome-in-ha22t-vgh-human-hepatocellular-carcinoma-derived-cells
#9
Edoardo Abeni, Alessandro Salvi, Eleonora Marchina, Michele Traversa, Bruna Arici, Giuseppina De Petro
Sorafenib is currently used to treat advanced and/or unresectable hepatocellular carcinoma (HCC), but the increase of the median survival was only 3 months. Moreover, sorafenib has severe side effects and patients develop resistance quickly. Epigenetic alterations such as DNA methylation play a decisive role in the development and progression of HCC. To our knowledge, there are no studies that analysed the global DNA methylation changes in HCC cells treated with sorafenib. Using MeDip-chip technologies, we found 1230 differentially methylated genes in HA22T/VGH cells treated with sorafenib compared to untreated cells...
May 24, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28545254/bacterial-virus-ontology-coordinating-across-databases
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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