115 research outputs found
Modeling a description logic vocabulary for cancer research
AbstractThe National Cancer Institute has developed the NCI Thesaurus, a biomedical vocabulary for cancer research, covering terminology across a wide range of cancer research domains. A major design goal of the NCI Thesaurus is to facilitate translational research. We describe: the features of Ontylog, a description logic used to build NCI Thesaurus; our methodology for enhancing the terminology through collaboration between ontologists and domain experts, and for addressing certain real world challenges arising in modeling the Thesaurus; and finally, we describe the conversion of NCI Thesaurus from Ontylog into Web Ontology Language Lite. Ontylog has proven well suited for constructing big biomedical vocabularies. We have capitalized on the Ontylog constructs Kind and Role in the collaboration process described in this paper to facilitate communication between ontologists and domain experts. The artifacts and processes developed by NCI for collaboration may be useful in other biomedical terminology development efforts
Development of FuGO: An ontology for functional genomics investigations
The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data
sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans
Overview and Utilization of the NCI Thesaurus
The NCI Thesaurus is a reference terminology covering areas of basic and clinical
science, built with the goal of facilitating translational research in cancer. It contains
nearly 110 000 terms in approximately 36000 concepts, partitioned in 20 subdomains,
which include diseases, drugs, anatomy, genes, gene products, techniques,
and biological processes, among others, all with a cancer-centric focus in content, and
originally designed to support coding activities across the National Cancer Institute.
Each concept represents a unit of meaning and contains a number of annotations, such
as synonyms and preferred name, as well as annotations such as textual definitions
and optional references to external authorities. In addition, concepts are modelled
with description logic (DL) and defined by their relationships to other concepts;
there are currently approximately 90 types of named relations declared in the
terminology. The NCI Thesaurus is produced by the Enterprise Vocabulary Services
project, a collaborative effort between the NCI Center for Bioinformatics and the
NCI Office of Communications, and is part of the caCORE infrastructure stack
(http://ncicb.nci.nih.gov/NCICB/core). It can be accessed programmatically through
the open caBIO API and browsed via the web (http://nciterms.nci.nih.gov). A history
of editing changes is also accessible through the API. In addition, the Thesaurus is
available for download in various file formats, including OWL, the web ontology
language, to facilitate its utilization by others
Guías de diseño para generar flujo de trabajo en proceso de compras (Design lines to generateworkflow in purchasing process)
La gestión de compras puede responder a las demandas cambiantes del entorno y resultar en un incremento en los beneficios para las empresas. Específicamente las compras en instituciones de salud, cada vez adquieren mayor relevancia, ya que tienen el reto de atender con calidad, brindar respuestas oportunas, contar con seguridad en sus compras, actuar con eficiencia y estar en constante innovación, teniendo en cuenta el contexto de demanda creciente y exigente, una rápida evolución tecnológica, con recursos económicos y financieros generalmente limitados. El sistema flujo de trabajo es una herramienta de gran apoyo para la gestión de cualquier proceso, consiste en enfocarse en el procedimiento de cada actividad de trabajo asignando recursos y tareas, logrando que el trabajo sea más eficiente a través de la mejora de los procedimientos. Es por ello que el presente documento mediante la metodología PADM (Process Analysis Design Methodology) y un análisis de herramientas que se encuentran en el mercado propone una guía de diseño para implementar un flujo de trabajo en el proceso de compras de clínicas privadas
The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services
BACKGROUND: Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. RESULTS: The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. CONCLUSION: The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development
Catechol-O-methyltransferase gene haplotypes in Mexican and Spanish patients with fibromyalgia
Autonomic dysfunction is frequent in patients with fibromyalgia (FM). Heart rate variability analyses have demonstrated signs of ongoing sympathetic hyperactivity. Catecholamines are sympathetic neurotransmitters. Catechol-O-methyltransferase (COMT), an enzyme, is the major catecholamine-clearing pathway. There are several single-nucleotide polymorphisms (SNPs) in the COMT gene associated with the different catecholamine-clearing abilities of the COMT enzyme. These SNPs are in linkage disequilibrium and segregate as 'haplotypes'. Healthy females with a particular COMT gene haplotype (ACCG) producing a defective enzyme are more sensitive to painful stimuli. The objective of our study was to define whether women with FM, from two different countries (Mexico and Spain), have the COMT gene haplotypes that have been previously associated with greater sensitivity to pain. All the individuals in the study were female. Fifty-seven Mexican patients and 78 Spanish patients were compared with their respective healthy control groups. All participants filled out the Fibromyalgia Impact Questionnaire (FIQ). Six COMT SNPs (rs2097903, rs6269, rs4633, rs4818, rs4680, and rs165599) were genotyped from peripheral blood DNA. In Spanish patients, there was a significant association between three SNPs (rs6269, rs4818, and rs4680) and the presence of FM when compared with healthy controls. Moreover, in Spanish patients with the 'high pain sensitivity' haplotype (ACCG), the disease, as assessed by the FIQ, was more severe. By contrast, Mexican patients displayed only a weak association between rs6269 and rs165599, and some FIQ subscales. In our group of Spanish patients, there was an association between FM and the COMT haplotype previously associated with high pain sensitivity. This association was not observed in Mexican patients. Studies with a larger sample size are needed in order to verify or amend these preliminary results
ELANE rs17223045C/T and rs3761007G/A variants: Protective factors against COVID-19
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for causing coronavirus disease 2019 (COVID-19). The development and severity of this infectious disease is influenced by a combination of environmental and genetic factors. Angiotensin-converting enzyme 2 (ACE2) facilitates SARS-CoV-2 entry into human cells, with transmembrane serine protease 2 (TMPRSS2) playing a crucial role in S protein priming. Other proteases, such as cathepsin L and elastase, neutrophil-expressed (ELANE), have the capability to prime the S protein and contribute to SARS-CoV-2 infection. ELANE variants have not been previously examined in COVID-19 patients. We aimed to assess the association of single nucleotide variants (SNVs) within ELANE with COVID-19 and biochemical markers. The study included 319 SARS-CoV-2-infected patients and 288 controls. Genotyping of ELANE rs17216663C/T (Pro257Leu), rs17223045C/T (As1n30Asn), and rs3761007G/A was conducted using a 5'-nuclease allelic discrimination assay (TaqMan assay). Our findings indicate that ELANE rs17223045C/T (C vs T: odds ratio [OR] 0.08, P = 0.005, and CC vs CT: OR 0.08, P = 0.005) and rs3761007G/A (G vs A: OR 0.38, P = 0.009, and GG vs GA: OR 0.40, P = 0.008) confer protection against COVID-19. However, these variants were not associated with biochemical markers. In conclusion, our data suggests that ELANE rs17223045C/T and rs3761007G/A SNVs may play a protective role against COVID-19
Consumo de álcool entre estudantes de uma escola pública da cidade de Cajazeiras, PB
El objetivo de este trabajo fue identificar el uso de bebidas alcohólicas por parte de estudiantes de la mayor escuela pública de la ciudad de Cajazeiras-PB. Se realizó un estudio descriptivo transversal con abordaje cuantitativo, sobre muestra de 300 alumnos de una escuela pública de la ciudad. Se verificó que 71% ya había consumido alcohol; 66,4% experimentó con drogas entre los 13-17 años; 21,3% tuvieron experiencias en bares/discotecas; 39,4% bebieron con mayor frecuencia en bares/discobares/discotecas. Se constató que hay alto consumo de alcohol entre adolescentes, haciéndose necesaria la implementación de acciones educativas, apuntando a la disminución del consumo.O objetivo deste trabalho foi identificar o uso de bebidas alcoólicas pelos estudantes da maior escola pública da cidade de Cajazeiras, PB. Realizou-se estudo descritivo transversal, com abordagem quantitativa, e a amostra ficou composta por 300 alunos de uma escola pública da cidade. Verificou-se que 71% já tinham usado álcool, 66,4% fizeram experimentação da droga entre 13-17 anos, 69,4% usaram por diversão, 59,5% já se embriagaram ao consumir álcool, 21,3% experimentam em bares/boates e 39,4% beberam com maior frequência em bares/danceterias/boates. Constatou-se que há alto consumo de álcool entre adolescentes, sendo necessária a implementação de ações educativas, visando a diminuição do consumo.The objective of this study was to identify the use of alcohol among students of the largest public school in Cajazeiras, Pernambuco. This cross-sectional descriptive study was performed with a sample of 300 students. It was found that 71% had drunk alcohol before; 66.4% had their first drink when they were between 13-17 years old; 69.4% drank for fun; 59.5% have already gotten drink from consuming alcohol; 21.3% had their first drink at bars/night clubs; 39.4% usually drank at bars/dance clubs/night clubs. It was found that alcohol use is high among adolescents, thus there is a need to implement educational actions, aiming at reducing alcohol use
Effects of hecogenin and its possible mechanism of action on experimental models of gastric ulcer in mice
This study investigates the gastroprotective effects of hecogenin, a steroid saponin isolated from Agave sisalana, on experimental models of gastric ulcer. Male Swiss mice were used in the models of ethanol-and indometacin-induced gastric ulcer. To clarify the hecogenin mechanism of action, the roles of nitric oxide (NO), sulfhydryls (GSH), K-ATP(+) channels and prostaglandins were also investigated, and measurements of lipid peroxidation (TBARS assay) and nitrite levels in the stomach of hecogenin-treated and untreated animals were performed. Furthermore, the effects of hecogenin on myeloperoxidase (MPO) release from human neutrophils were assessed in vitro. Our results showed that hecogenin (3.1, 7.5, 15, 30, 60 and 90 mg/kg, p.o.) acutely administered, before ethanol or indomethacin, exhibited a potent gastroprotective effect. Although the pretreatments with L-NAME, an iNOS inhibitor, and capsazepine, a TRPV1 receptor agonist, were not able to reverse the hecogenin effect, this was reversed by glibenclamide, a K-ATP(+) blocker, and indomethacin in the model of ethanol-induced gastric lesions. the hecogenin pretreatment normalized GSH levels and significantly reduced lipid peroxidation and nitrite levels in the stomach, as evaluated by the ethanol-induced gastric lesion model. the drug alone increased COX-2 expression and this effect was further enhanced in the presence of ethanol. It also decreased MPO release and significantly protected the gastric mucosa. in conclusion, we showed that hecogenin presents a significant gastroprotective effect that seems to be mediated by K-ATP(+) channels opening and the COX-2/PG pathway. in addition, its antioxidant and anti-inflammatory properties may play a role in the gastroprotective drug effect. (C) 2012 Elsevier B. V. All rights reserved.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Fed Ceara, Dept Physiol & Pharmacol, BR-60431270 Fortaleza, Ceara, BrazilUniv Fed Ceara, Dept Pharm, BR-60431270 Fortaleza, Ceara, BrazilUniv Fed Paraiba, Dept Pharmaceut Sci, BR-58100000 Joao Pessoa, Paraiba, BrazilUniv Fed Ceara, Dept Morphol, BR-60431270 Fortaleza, Ceara, BrazilUniversidade Federal de São Paulo, Dept Pharmacol, BR-04044020 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Pharmacol, BR-04044020 São Paulo, BrazilWeb of Scienc
ABO gene polymorphisms are associated with acute coronary syndrome and with plasma concentration of HDL-cholesterol and triglycerides
The role of ABO gene polymorphisms in acute coronary syndrome (ACS) and lipid metabolism is increasingly recognized. We investigated whether ABO gene polymorphisms are significantly associated with ACS and the plasma lipid profile. Six ABO gene polymorphisms (rs651007 T/C, rs579459 T/C, rs495928 T/C, rs8176746 T/G, rs8176740 A/T, and rs512770 T/C) were determined by 5’exonuclease TaqMan assays in 611 patients with ACS and 676 healthy controls. The results demonstrated that the rs8176746 T allele was associated with a lower risk of ACS under the co-dominant, dominant, recessive, over-dominant, and additive models (P = 0.0004, P = 0.0002, P = 0.039, P = 0.0009, and P = 0.0001, respectively). Furthermore, under co-dominant, dominant, and additive models, the rs8176740 A allele was associated with a lower risk of ACS (P = 0.041, P = 0.022, and P = 0.039, respectively). On the other hand, the rs579459 C allele was associated with a lower risk of ACS under the dominant, over-dominant, and additive models (P = 0.025, P = 0.035, and P = 0.037, respectively). In a subanalysis performed with the control group, rs8176746 T and rs8176740 A alleles were associated with low systolic blood pressure and with both high high-density lipoprotein-cholesterol (HDL-C) and low triglyceride plasma concentrations, respectively. In conclusion, ABO gene polymorphisms were associated with a lower risk of ACS, and lower systolic blood pressure and plasma lipid levels, suggesting a causal relationship between ABO blood groups and the incidence of ACS
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