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

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

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

MRE11A Polymorphisms Are Associated With Subclinical Atherosclerosis and Cardiovascular Risk Factors. A Case-Control Study of the GEA Mexican Project

DNA damage and subsequent repair pathways have been involved in the initiation and progression of atherosclerosis. Meiotic recombination 11 homolog A (MRE11A) gene polymorphisms have been associated with the presence of myocardial infarction. We analyzed five MRE11A gene polymorphisms in 386 individuals with subclinical atherosclerosis and 1093 healthy controls. Under different models, the rs13447720 (Odds ratio = 0.646, Padditive = 0.009; Odds ratio = 0.636, Pdominant = 0.012; Odds ratio = 0.664, Pover–dominant = 0.025; Odds ratio = 0.655, Pcodominant1 = 0.021) and rs499952 (Odds ratio = 0.807, Padditive = 0.032; Odds ratio = 0.643, Pcodominant2 = 0.034) polymorphisms were associated with a lower risk of subclinical atherosclerosis. On the other hand, the rs2155209 polymorphism was associated with a reduced risk of having a coronary artery calcification score ≥ 100 Agatston units. The rs13447720, rs499952, and rs2155209 polymorphisms, as well as the haplotypes that included the five studied polymorphisms were associated with some clinical and metabolic parameters in both subclinical atherosclerosis and healthy individuals. Our results suggest that the rs13447720 and rs499952 polymorphisms are associated with a decreased risk of developing subclinical atherosclerosis, whereas the rs2155209 is associated with a lower subclinical atherosclerosis severity (coronary artery calcification < 100 Agatston units). MRE11A polymorphisms and haplotypes were associated with clinical and metabolic parameters

A SCN9A gene-encoded dorsal root ganglia sodium channel polymorphism associated with severe fibromyalgia

<p>Abstract</p> <p>Background</p> <p>A consistent line of investigation suggests that autonomic nervous system dysfunction may explain the multi-system features of fibromyalgia (FM); and that FM is a sympathetically maintained neuropathic pain syndrome. Dorsal root ganglia (DRG) are key sympathetic-nociceptive short-circuit sites. Sodium channels located in DRG (particularly Nav1.7) act as molecular gatekeepers for pain detection. Nav1.7 is encoded in gene SCN9A of chromosome 2q24.3 and is predominantly expressed in the DRG pain-sensing neurons and sympathetic ganglia neurons. Several SCN9A sodium channelopathies have been recognized as the cause of rare painful dysautonomic syndromes such as paroxysmal extreme pain disorder and primary erythromelalgia. The aim of this study was to search for an association between fibromyalgia and several SCN9A sodium channels gene polymorphisms.</p> <p>Methods</p> <p>We studied 73 Mexican women suffering from FM and 48 age-matched women who considered themselves healthy. All participants filled out the Fibromyalgia Impact Questionnaire (FIQ). Genomic DNA from whole blood containing EDTA was extracted by standard techniques. The following SCN9A single-nucleotide polymorphisms (SNP) were determined by 5' exonuclease TaqMan assays: rs4371369; rs4387806; rs4453709; rs4597545; rs6746030; rs6754031; rs7607967; rs12620053; rs12994338; and rs13017637.</p> <p>Results</p> <p>The frequency of the rs6754031 polymorphism was significantly different in both groups (<it>P </it>= 0.036) mostly due to an absence of the GG genotype in controls. Interestingly; patients with this rs6754031 GG genotype had higher FIQ scores (median = 80; percentile 25/75 = 69/88) than patients with the GT genotype (median = 63; percentile 25/75 = 58/73; <it>P </it>= 0.002) and the TT genotype (median = 71; percentile 25/75 = 64/77; <it>P </it>= 0.001).</p> <p>Conclusion</p> <p>In this ethnic group; a disabling form of FM is associated to a particular SCN9A sodium channel gene variant. These preliminary results raise the possibility that some patients with severe FM may have a dorsal root ganglia sodium channelopathy.</p