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https://www.readbyqxmd.com/read/28344915/from-the-evaluation-of-existing-solutions-to-an-all-inclusive-package-for-biobanks
#1
Heimo Müller, Nicolas Malservet, Philip Quinlan, Robert Reihs, Matthieu Penicaud, Antoine Chami, Kurt Zatloukal, George Dagher
The domain of biobanking has gone through many stages and as a result there are a wide range of commercial and open source software solutions available. The utilization of these software tools requires different levels of domain and technical skills for installation, configuration and ultimate us of these biobank software tools. To compound this complexity the biobanking community are required to work together in order to share knowledge and jointly build solutions to underpin the research infrastructure. We have evaluated the available tools, described them in a catalogue (BiobankApps) and made a selection of tools available to biobanks in a reference toolbox (BIBBOX) that are use-case driven...
2017: Health and Technology
https://www.readbyqxmd.com/read/28344914/automatic-classification-of-histopathological-diagnoses-for-building-a-large-scale-tissue-catalogue
#2
Robert Reihs, Heimo Müller, Stefan Sauer, Kurt Zatloukal
In this paper an automatic classification system for pathological findings is presented. The starting point in our undertaking was a pathologic tissue collection with about 1.4 million tissue samples described by free text records over 23 years. Exploring knowledge out of this "big data" pool is a challenging task, especially when dealing with unstructured data spanning over many years. The classification is based on an ontology-based term extraction and decision tree build with a manually curated classification system...
2017: Health and Technology
https://www.readbyqxmd.com/read/28339073/identification-of-proteins-in-the-aqueous-humor-associated-with-cataract-development-using-itraq-methodology
#3
Minhong Xiang, Xingru Zhang, Qingsong Li, Hanmin Wang, Zhenyong Zhang, Zhumei Han, Meiqing Ke, Xingxing Chen
Proteins in the aqueous humor (AH) are important in the induction of cataract development. The identification of cataract-associated proteins assists in identifying patients and predisposed to the condition and improve treatment efficacy. Proteomics analysis has previously been used for identifying protein markers associated with eye diseases; however, few studies have examined the proteomic alterations in cataract development due to high myopia, glaucoma and diabetes. The present study, using the isobaric tagging for relative and absolute protein quantification methodology, aimed to examine cataract-associated proteins in the AH from patients with high myopia, glaucoma or diabetes, and controls...
March 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28337675/an-ontology-based-search-engine-for-digital-reconstructions-of-neuronal-morphology
#4
Sridevi Polavaram, Giorgio A Ascoli
Neuronal morphology is extremely diverse across and within animal species, developmental stages, brain regions, and cell types. This diversity is functionally important because neuronal structure strongly affects synaptic integration, spiking dynamics, and network connectivity. Digital reconstructions of axonal and dendritic arbors are thus essential to quantify and model information processing in the nervous system. NeuroMorpho.Org is an established repository containing tens of thousands of digitally reconstructed neurons shared by several hundred laboratories worldwide...
March 23, 2017: Brain Informatics
https://www.readbyqxmd.com/read/28326913/reflecting-on-the-learning-opportunities-of-presenting-at-a-conference
#5
Beverly Joshua
Background Research productivity is a major indicator of higher educational institutions' (HEI) academic performance. The increasing focus on research productivity is resulting in an expectation that academics publish their research initiatives, ideas and developments in their scope of work or area of interest. It can influence academic status and compel nursing academics to undertake higher degrees, including PhDs or other doctoral studies. Aim To articulate a nurse academic's reflection on presenting her doctoral thesis at an international conference and to encourage students to embrace the dissemination of research...
March 22, 2017: Nurse Researcher
https://www.readbyqxmd.com/read/28324254/pilot-testing-model-to-uncover-industrial-symbiosis-in-brazilian-industrial-clusters
#6
Adriana Valélia Saraceni, Luis Mauricio Resende, Pedro Paulo de Andrade Júnior, Joseane Pontes
The main objective of this study was to create a pilot model to uncover industrial symbiosis practices in Brazilian industrial clusters. For this purpose, a systematic revision was conducted in journals selected from two categories of the ISI Web of Knowledge: Engineering, Environmental and Engineering, Industrial. After an in-depth revision of literature, results allowed the creation of an analysis structure. A methodology based on fuzzy logic was applied and used to attribute the weights of industrial symbiosis variables...
March 21, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28302519/using-ontology-based-semantic-similarity-to-facilitate-the-article-screening-process-for-systematic-reviews
#7
Xiaonan Ji, Alan Ritter, Po-Yin Yen
OBJECTIVE: Systematic Reviews (SRs) are utilized to summarize evidence from high quality studies and are considered the preferred source of evidence-based practice (EBP). However, conducting SRs can be time and labor intensive due to the high cost of article screening. In previous studies, we demonstrated utilizing established (lexical) article relationships to facilitate the identification of relevant articles in an efficient and effective manner. Here we propose to enhance article relationships with background semantic knowledge derived from Unified Medical Language System (UMLS) concepts and ontologies...
March 13, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28302059/correspondence-of-d-melanogaster-and-c-elegans-developmental-stages-revealed-by-alternative-splicing-characteristics-of-conserved-exons
#8
Ruiqi Gao, Jingyi Jessica Li
BACKGROUND: We report a statistical study to find correspondence of D. melanogaster and C. elegans developmental stages based on alternative splicing (AS) characteristics of conserved cassette exons using modENCODE RNA-seq data. We identify "stage-associated exons" to capture the AS characteristics of each stage and use these exons to map pairwise stages within and between the two species by an overlap test. RESULTS: Within fly and worm, adjacent developmental stages are mapped to each other, i...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28298238/biofed-federated-query-processing-over-life-sciences-linked-open-data
#9
Ali Hasnain, Qaiser Mehmood, Syeda Sana E Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
BACKGROUND: Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints...
March 15, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28290293/comparative-proteomic-analysis-of-milk-derived-exosomes-in-human-and-bovine-colostrum-and-mature-milk-samples-by-itraq-coupled-lc-ms-ms
#10
Mei Yang, Dahe Song, Xueyan Cao, Rina Wu, Biao Liu, Wenhui Ye, Junrui Wu, Xiqing Yue
Exosomes are membranous vesicles found in biological fluids with important functions. However, milk-derived exosome proteins from humans and bovines have not been studied in detail. The advanced iTRAQ proteomic approach was used to analyze milk-derived exosomes in human and bovine colostrum and mature milk samples. A total of 920 milk exosome proteins were identified and quantified. Among these, 575 differentially expressed exosome proteins (P<0.05) were found. Multivariate analysis, gene ontology (GO) annotation and the KEGG pathway were used to interpret the identified proteins...
February 2017: Food Research International
https://www.readbyqxmd.com/read/28282143/proteome-analysis-of-human-perilymph-using-an-intraoperative-sampling-method
#11
Heike Andrea Schmitt, Andreas Pich, Anke Schröder, Verena Scheper, Giorgio Lilli, Günter Reuter, Thomas Lenarz
The knowledge about the etiology and pathophysiology of sensorineural hearing loss (SNHL) is still very limited. The project aims at the improvement of understanding different types of SNHL by proteome analysis of human perilymph. Sampling of perilymph has been established during inner ear surgeries (cochlear implant and vestibular schwannoma surgeries) and safety of the sampling method was determined by pure tone audiometry. An in-depth shot-gun proteomics approach was performed to identify cochlear proteins and individual proteome in perilymph of patients...
March 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28274758/gfd-net-a-novel-semantic-similarity-methodology-for-the-analysis-of-gene-networks
#12
Juan J Díaz-Montaña, Norberto Díaz-Díaz, Francisco Gómez-Vela
Since the popularization of biological network inference methods, it has become crucial to create methods to validate the resulting models. Here we present GFD-Net, the first methodology that applies the concept of semantic similarity to gene network analysis. GFD-Net combines the concept of semantic similarity with the use of gene network topology to analyze the functional dissimilarity of gene networks based on Gene Ontology (GO). The main innovation of GFD-Net lies in the way that semantic similarity is used to analyze gene networks taking into account the network topology...
March 5, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28265120/a-genome-wide-gene-by-trauma-interaction-study-of-alcohol-misuse-in-two-independent-cohorts-identifies-prkg1-as-a-risk-locus
#13
R Polimanti, J Kaufman, H Zhao, H R Kranzler, R J Ursano, R C Kessler, J Gelernter, M B Stein
Traumatic life experiences are associated with alcohol use problems, an association that is likely to be moderated by genetic predisposition. To understand these interactions, we conducted a gene-by-environment genome-wide interaction study (GEWIS) of alcohol use problems in two independent samples, the Army STARRS (STARRS, N=16 361) and the Yale-Penn (N=8084) cohorts. Because the two cohorts were assessed using different instruments, we derived separate dimensional alcohol misuse scales and applied a proxy-phenotype study design...
March 7, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28263989/extracting-microrna-gene-relations-from-biomedical-literature-using-distant-supervision
#14
Andre Lamurias, Luka A Clarke, Francisco M Couto
Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text...
2017: PloS One
https://www.readbyqxmd.com/read/28250238/a-study-on-regional-differences-in-decidualization-of-the-mouse-uterus
#15
Miao Zhao, Wen-Qian Zhang, Ji-Long Liu
Although regional differences in mouse decidualization have been recognized for decades, the molecular mechanisms remain under-studied. In the present study, by using RNA-seq, we compared transcriptomic differences between the anti-mesometrial (AM) region and the mesometrial (M) region of mouse uterus on day 8 of pregnancy. A total of 1423 differentially expressed genes were identified, of which 811 genes were up-regulated and 612 genes were down-regulated in the AM region compared to the M region. Gene ontology analysis showed that up-regulated genes were generally involved in cell metabolism and differentiation, whereas down-regulated genes were associated with lymphocyte themes and immune response...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28244549/relating-complexity-and-error-rates-of-ontology-concepts-more-complex-ncit-concepts-have-more-errors
#16
Hua Min, Ling Zheng, Yehoshua Perl, Michael Halper, Sherri De Coronado, Christopher Ochs
OBJECTIVES: Ontologies are knowledge structures that lend support to many health-information systems. A study is carried out to assess the quality of ontological concepts based on a measure of their complexity. The results show a relation between complexity of concepts and error rates of concepts. METHODS: A measure of lateral complexity defined as the number of exhibited role types is used to distinguish between more complex and simpler concepts. Using a framework called an area taxonomy, a kind of abstraction network that summarizes the structural organization of an ontology, concepts are divided into two groups along these lines...
February 28, 2017: Methods of Information in Medicine
https://www.readbyqxmd.com/read/28243197/computer-aided-experiment-planning-toward-causal-discovery-in-neuroscience
#17
Nicholas J Matiasz, Justin Wood, Wei Wang, Alcino J Silva, William Hsu
Computers help neuroscientists to analyze experimental results by automating the application of statistics; however, computer-aided experiment planning is far less common, due to a lack of similar quantitative formalisms for systematically assessing evidence and uncertainty. While ontologies and other Semantic Web resources help neuroscientists to assimilate required domain knowledge, experiment planning requires not only ontological but also epistemological (e.g., methodological) information regarding how knowledge was obtained...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28241430/the-importance-of-endophenotypes-to-evaluate-the-relationship-between-genotype-and-external-phenotype
#18
REVIEW
Marinus F W Te Pas, Ole Madsen, Mario P L Calus, Mari A Smits
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment...
February 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28237357/integrating-social-context-into-comprehensive-shared-care-plans-a-scoping-review
#19
Suzanne S Sullivan, Francine Mistretta, Sabrina Casucci, Sharon Hewner
BACKGROUND: Failure to address social determinants of health (SDH) may contribute to the problem of readmissions in high-risk individuals. Comprehensive shared care plans (CSCP) may improve care continuity and health outcomes by communicating SDH risk factors across settings. PURPOSE: The purpose of this study to evaluate the state of knowledge for integrating SDH into a CSCP. Our scoping review of the literature considered 13,886 articles, of which seven met inclusion criteria...
February 3, 2017: Nursing Outlook
https://www.readbyqxmd.com/read/28230725/towards-a-semantic-web-of-things-a-hybrid-semantic-annotation-extraction-and-reasoning-framework-for-cyber-physical-system
#20
Zhenyu Wu, Yuan Xu, Yunong Yang, Chunhong Zhang, Xinning Zhu, Yang Ji
Web of Things (WoT) facilitates the discovery and interoperability of Internet of Things (IoT) devices in a cyber-physical system (CPS). Moreover, a uniform knowledge representation of physical resources is quite necessary for further composition, collaboration, and decision-making process in CPS. Though several efforts have integrated semantics with WoT, such as knowledge engineering methods based on semantic sensor networks (SSN), it still could not represent the complex relationships between devices when dynamic composition and collaboration occur, and it totally depends on manual construction of a knowledge base with low scalability...
February 20, 2017: Sensors
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