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Novikova, Daria D., Pavel A. Cherenkov, Yana G. Sizentsova und Victoria V. Mironova. „metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming“. Genes 11, Nr. 6 (09.06.2020): 634. http://dx.doi.org/10.3390/genes11060634.
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At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.
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Goll, Johannes, Douglas B. Rusch, David M. Tanenbaum, Mathangi Thiagarajan, Kelvin Li, Barbara A. Methé und Shibu Yooseph. „METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics“. Bioinformatics 26, Nr. 20 (26.08.2010): 2631–32. http://dx.doi.org/10.1093/bioinformatics/btq455.
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Goll, Johannes, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph und Barbara A. Methé. „A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)“. PLoS ONE 7, Nr. 6 (13.06.2012): e29044. http://dx.doi.org/10.1371/journal.pone.0029044.
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Huang, Katherine, Arthur Brady, Anup Mahurkar, Owen White, Dirk Gevers, Curtis Huttenhower und Nicola Segata. „MetaRef: a pan-genomic database for comparative and community microbial genomics“. Nucleic Acids Research 42, Nr. D1 (06.11.2013): D617—D624. http://dx.doi.org/10.1093/nar/gkt1078.
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Blondé, Ward, Erick Antezana, Vladimir Mironov, Stefan Schulz, Martin Kuiper und Bernard De Baets. „Using the relation ontology Metarel for modelling Linked Data as multi-digraphs“. Semantic Web 5, Nr. 2 (2014): 115–26. http://dx.doi.org/10.3233/sw-130096.
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Ulitsky, Igor, Irit Gat-Viks und Ron Shamir. „MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data“. Genome Biology 9, Nr. 1 (2008): R1. http://dx.doi.org/10.1186/gb-2008-9-1-r1.
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France, Lydéric, und Christian Nicollet. „MetaRep, an extended CMAS 3D program to visualize mafic (CMAS, ACF-S, ACF-N) and pelitic (AFM-K, AFM-S, AKF-S) projections“. Computers & Geosciences 36, Nr. 6 (Juni 2010): 786–91. http://dx.doi.org/10.1016/j.cageo.2010.01.001.
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Pastusiak, Tadeusz. „Consistency of data presented on modern maps of ice cover in the Arctic“. Polish Cartographical Review 48, Nr. 2 (01.07.2016): 55–66. http://dx.doi.org/10.1515/pcr-2016-0005.
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Abstract Information about the condition of ice cover on surface of the water, which are the content of map, are important for carrying out safe navigation and efficient economic activity in the polar regions. Methods of mapping can be fully automated on the basis of developed through years of experience algorithms or additionally supported by experienced professionals. The content of some of those now commonly encountered maps is compiled on the basis of mixed methods. In this work geographic positions of ice maps content are analyzed taking into consideration their usefulness for planning ship’s voyage in ice. The results of this work allow using the contents of studied maps for determining the ship’s route in ice and voyage planning of the ship in ice according to her hull strengthening. The ice maps often have boundary lines for different values of reference. The maximum width of the strips of each boundary line within the Marginal Ice Zone is 100 km. The mean square error of position of the analyzed maps is +/− 2.0 km. Average locations of boundaries are consistent except for GRIB type maps of the OSI SAF and NIS, which seem to indicate much lower value of ice floe concentration. The NIC MIZ maps and S-411 standard maps are consistent for the 13% and 81% concentration. The 40% limits on MASIE maps and 46% limits of concentration on S-411 standard maps are also consistent. The course of ice edge issued by the NIS for the GMDSS METAREA, 19 region visualizes well the boundaries of the area where the ship might encounter any form of ice. Information of the GMDSS METAREA 20 region issued by the AARI represents the average of the limits 1 to 46% of all sources of information, and on average the 13% limit of ice concentration. The one-year old ice limit with thickness of 0.10 to 0.30 meters on the AARI map is consistent with course and average location of boundaries of 81% ice concentration on the NIC MIZ map and S-411 standard map. The multi-year old ice limit of thickness from 0.30 to 2.00 meters on the AARI map is coincident with the 79% limit of concentration displayed on the NIS map.
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Shim, Sung Ryul, Seong-Jang Kim und Jonghoo Lee. „Diagnostic test accuracy: application and practice using R software“. Epidemiology and Health 41 (28.03.2019): e2019007. http://dx.doi.org/10.4178/epih.e2019007.
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The objective of this paper is to describe general approaches of diagnostic test accuracy (DTA) that are available for the quantitative synthesis of data using R software. We conduct a DTA that summarizes statistics for univariate analysis and bivariate analysis. The package commands of R software were “metaprop” and “metabin” for sensitivity, specificity, and diagnostic odds ratio; forest for forest plot; reitsma of “mada” for a summarized receiver-operating characteristic (ROC) curve; and “metareg” for meta-regression analysis. The estimated total effect sizes, test for heterogeneity and moderator effect, and a summarized ROC curve are reported using R software. In particular, we focus on how to calculate the effect sizes of target studies in DTA. This study focuses on the practical methods of DTA rather than theoretical concepts for researchers whose fields of study were non-statistics related. By performing this study, we hope that many researchers will use R software to determine the DTA more easily, and that there will be greater interest in related research.
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Tanajura, Clemente Augusto Souza, Filipe Bitencourt Costa, Renato Ramos da Silva, Giovanni Abdelnur Ruggiero und Victor Bastos Daher. „ASSIMILATION OF SEA SURFACE HEIGHT ANOMALIES INTO HYCOM WITH AN OPTIMAL INTERPOLATION SCHEME OVER THE ATLANTIC OCEAN METAREA V“. Revista Brasileira de Geofísica 31, Nr. 2 (01.06.2013): 257. http://dx.doi.org/10.22564/rbgf.v31i2.293.
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ABSTRACT. Along-track sea surface height anomaly (SSHA) data from the Jason-1 and Jason-2 satellites were assimilated into the ocean model HYCOM from July 1, 2009 until December 31, 2009. A new and simple approach to overcome the bias between the model and observed SSHA was proposed. It focuses on the meso-scale differences between the data and the model along each satellite track. An optimal interpolation method and the Cooper & Haines (1996) scheme (C&H) were employed to produce a SSHA analysis field and to adjust model layer thicknesses over the Atlantic METAREA V. The corrected model state was used as initial condition for the next assimilation cycle. SSHA data with a 7-day window were assimilated in 3-day intervals centered in the SSHA data window and the C&H scheme was applied taking the SSHA analysis. A control run without assimilation was also performed. The results showed that the model SSHA was completely reorganized by the end of the experiment. The modifications of SSHA were compared to the American Navy HYCOM+NCODA system and AVISO data. Maximum error was reduced from 0.7 m to 0.2 m by assimilation. Comparisons were also made with the Argo temperature and salinity vertical profiles. Improvements in the currents and volume transport were also produced by assimilation. The impact in temperature was in general positive, but there was no substantial modification in salinity. Keywords: ocean data assimilation, Jason-1 and Jason-2 satellites, Argo. RESUMO. Dados de anomalia da altura da superfície do mar (AASM) dos satellites Jason-1 e Jason-2 foram assimilados no modelo oceânico HYCOM de 1 de julho de 2009 a 31 de dezembro de 2009. Um nova e simples abordagem foi proposta para superar o viés entre os dados observados de AASM e o campo do modelo. Ela enfoca as diferenças entre o modelo e as observações na mesoescala ao longo de cada trilha dos satélites. Um método de interpolação estatística e o esquema de Cooper & Haines (1996) (C&H) foram empregados para produzir um campo de análise de AASM e ajustes nas espessuras das camadas do modelo sobre a METAREA V do Atlântico. O estado corrigido do modelo foi usado como condição inicial para o próximo ciclo de assimilação. Dados de AASM em uma janela de 7 dias foram assimilados a cada 3 dias em data centrada na janela de dados e o método de C&H foi aplicado com a análise de AASM. Os resultados mostraram que a AASM do modelo foi completamente reorganizada no final do experimento. As modificações de AASM foram comparadas com análises globais do sistema Americano HYCOM+NCODA e com dados do AVISO. Erros máximos foram reduzidos de 0,7 m para 0,2 m com a assimilação. Comparações foram também feitas com perfis verticais de temperatura e salinidade do Argo. Melhorias nas correntes e no transporte de volume foram produzidas em relação à rodada de controle. O impacto na temperatura foi em geral positivo, mas não houve modificação substancial na salinidade. Palavras-chave: assimilação de dados oceanográficos, satélites Jason-1 e Jason-2, Argo.
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Shim, Sung Ryul, und Seong-Jang Kim. „Intervention meta-analysis: application and practice using R software“. Epidemiology and Health 41 (28.03.2019): e2019008. http://dx.doi.org/10.4178/epih.e2019008.
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The objective of this study was to describe general approaches for intervention meta-analysis available for quantitative data synthesis using the R software. We conducted an intervention meta-analysis using two types of data, continuous and binary, characterized by mean difference and odds ratio, respectively. The package commands for the R software were “metacont”, “metabin”, and “metagen” for the overall effect size, “forest” for forest plot, “metareg” for meta-regression analysis, and “funnel” and “metabias” for the publication bias. The estimated overall effect sizes, test for heterogeneity and moderator effect, and the publication bias were reported using the R software. In particular, the authors indicated methods for calculating the effect sizes of the target studies in intervention meta-analysis. This study focused on the practical methods of intervention meta-analysis, rather than the theoretical concepts, for researchers with no major in statistics. Through this study, the authors hope that many researchers will use the R software to more readily perform the intervention meta-analysis and that this will in turn generate further related research.
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Lima, Jose Antonio Moreira. „EDITORIAL“. Revista Brasileira de Geofísica 31, Nr. 2 (01.06.2013): 207. http://dx.doi.org/10.22564/rbgf.v31i2.299.
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This issue presents a set of papers related to the development of ocean forecasting models with data assimilation skills for the South Atlantic Ocean, more specifically for the Metarea V maritime region whose western border is delimited by the Brazilian shelf. This work has been done with the collaboration of many Brazilian researchers under the Oceanographic Modeling and Observation Network (REMO) research group. The evolution from an early stage of running ocean models with mean climatological forcings aiming at the study of specific oceanographic processes to the present stage of running operational ocean forecast models with synoptic forcings and data assimilation had a strong contribution from researchers with a meteorological background, who brought their expertise on numerical weather forecasting.The papers present distinct topics associated with an ocean forecasting system, such as a detailed description of network design and implementation of the ocean circulation models, a proposed approach of nesting distinct models starting from a large scale Atlantic Ocean grid to regional high-resolution local grids, data assimilation methods, synoptic sea surface fields obtained from remote sensing, surface heat fluxes, and planning observational measurement programs for assimilation and model evaluation.We hope that these papers contribute towards developing this specific area of operational oceanic forecasting within the Brazilian scientific and ocean technology communities. We still have a steady way to follow in order to consolidate and improve the propo-sed initiatives, but the first steps were already given and sound results are now available. In the near future, we foresee continuous improvement of oceanic models and data assimilation methods as well as collaboration with interested researchers from Brazilian and foreign institutions. Jose Antonio Moreira LimaInvited Editor Este volume apresenta um conjunto de artigos relacionados com o tema previsão oceânica de curto prazo para o Oceano Atlântico Sul, mais especificamente para a região marítima Metarea V, através de modelos numéricos de circulação com assimilação de dados observacionais. Este trabalho está sendo desenvolvido a partir da cooperação de diversos pesquisadores brasileiros colaboradores da Rede de Modelagem e Observação Oceanográfica (REMO). No estudo dos processos oceanográficos, a evolução do estágio de rodar modelos oceânicos utilizando forçantes climatológicas médias para o estágio atual de rodar modelos operacionais com forçantes sinóticas e assimilação de dados teve uma forte contribuição de pesquisadores oriundos da área de meteorologia, que trouxeram seu conhecimento aplicado dos modelos de previsão do tempo.Os artigos abordam diversos tópicos associados com um sistema de previsão oceânica, tais como uma descrição detalhada do projeto e implementação dos modelos de circulação oceânica; aninhamento escalonado de modelos com escalas distintas, a partir de malha computacional do Oceano Atlântico, para malhas regionais com alta resolução espacial; métodos de assimilação de campos e dados observados; campos sinóticos da superfície do mar através sensoriamento remoto; fluxos de calor de superfície; e planejamento de observações para assimilação e avaliação dos modelos.Desejamos que estes artigos contribuam para desenvolvimento desta área específica de previsão oceânica operacional junto às comunidades científica e de tecnologia oceânica brasileira. Temos ainda um extenso caminho pela frente para consolidar e aperfeiçoar as iniciativas propostas, mas os primeiros passos foram dados e bons resultados já estão disponíveis. Para o futuro, vislumbramos aprimoramento contínuo dos modelos oceânicos e métodos de assimilação de dados, assim como a colaboração com pesquisadores interessados de instituições brasileiras ou estrangeiras. Jose Antonio Moreira LimaEditor Convidado
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Lima, Leonardo Nascimento, und Clemente Augusto Souza Tanajura. „A STUDY OF THE IMPACT OF ALTIMETRY DATA ASSIMILATION ON SHORT-TERM PREDICTABILITY OF THE HYCOM OCEAN MODEL IN REGIONS OF THE TROPICAL AND SOUTH ATLANTIC OCEAN“. Revista Brasileira de Geofísica 31, Nr. 2 (01.06.2013): 271. http://dx.doi.org/10.22564/rbgf.v31i2.302.
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ABSTRACT. In this study, assimilation of Jason-1 and Jason-2 along-track sea level anomaly (SLA) data was conducted in a region of the tropical and South Atlantic (7◦N-36◦S, 20◦W up to the Brazilian coast) using an optimal interpolation method and the HYCOM (Hybrid Coordinate Ocean Model). Four 24 h-forecast experiments were performed daily from January 1 until March 31, 2011 considering different SLA assimilation data windows (1 day and 2 days) and different coefficients in the parameterization of the SLA covariance matrix model. The model horizontal resolution was 1/12◦ and the number of vertical layers was 21. The SLA analyses added to the mean sea surface height were projected to the subsurface with the Cooper & Haines (1996) scheme. The results showed that the experiment with 2-day window of along-track data and with specific parameterizations of the model SLA covariance error for sub-regions of the METAREA V was the most accurate. It completely reconstructed the model sea surface height and important improvements in the circulation were produced. For instance, there was a substantial improvement in the representation of the Brazil Current and North Brazil Undercurrent. However, since no assimilation of vertical profiles of temperature and salinity and of sea surface temperature was performed, the methodology employed here should be considered only as a step towards a high quality analysis for operational forecasting systems. Keywords: data assimilation, optimal interpolation, Cooper & Haines scheme, altimetry data. RESUMO. Neste estudo, a assimilação de dados de anomalia da altura da superfície do mar (AASM) ao longo da trilha dos satélites Jason-1 e Jason-2 foi conduzida em uma região do Atlântico tropical e Sul (7◦N-36◦S, 20◦W até a costa do Brasil) com o método de interpolação ótima e o modelo oceânico HYCOM (Hybrid Coordinate Ocean Model). Foram realizados quatro experimentos de previsão de 24 h entre 1 de janeiro e 31 de março de 2011, considerando diferentes janelas de assimilação de AASM (1 dia e 2 dias) e diferentes coeficientes na parametrização da matriz de covariância dos erros de AASM do modelo. A resolução horizontal empregada no HYCOM foi 1/12◦ para 21 camadas verticais. As correções de altura da superfície do mar devido à assimilação de AASM foram projetadas abaixo da camada de mistura através da técnica de Cooper & Haines (1996). Os resultados mostraram que o experimento com assimilação de dados ao longo da trilha dos satélites com a janela de 2 dias e com parametrizações da matriz de covariância específicas para sub-regiões da METAREA V foi o mais acurado. Ele reconstruiu completamente a altura da superfície do mar e também proporcionou melhorias na circulação oceânica reproduzida pelo modelo. Por exemplo, houve substancial melhoria da representação nos campos da Corrente do Brasil e Subcorrente Norte do Brasil. Entretanto, tendo em vista que não foi realizada a assimilação de perfis verticais de temperatura e de salinidade e da temperatura da superfície do mar, a metodologia apresentada deve ser considerada apenas como um passo na conquista de uma análise oceânica e de um sistema previsor de qualidade para fins operacionais. Palavras-chave: assimilação de dados, interpolação ótima, técnica de Cooper & Haines, dados de altimetria.
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Gabioux, Mariela Gabioux, Vladimir Santos Da Costa, João Marcos Azevedo Correia de Souza, Bruna Faria de Oliveira und Afonso De Moraes Paiva. „MODELING THE SOUTH ATLANTIC OCEAN FROM MEDIUM TO HIGH-RESOLUTION“. Revista Brasileira de Geofísica 31, Nr. 2 (01.06.2013): 229. http://dx.doi.org/10.22564/rbgf.v31i2.291.
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ABSTRACT. The standard REMO (a Brazilian approach towards operational oceanography) model configuration is tested, and results of two numerical simulations with HYCOM are presented and discussed. This configuration consists basically of a high-resolution eddy-resolving, 1/12 degree model for the Metarea V (latitudes from 7◦N to 35◦50’S, and longitudes between 20◦W and the Brazilian coast), nested in a medium-resolution eddy-permitting, 1/4 degree model of the Atlantic Ocean. These simulations aim for: a) creating a basic set-up for implementation of assimilation techniques leading to ocean prediction; b) the development of hydrodynamic bases for environmental studies; and c) providing boundary conditions for regional domains with increased resolution. This is the first time HYCOM is applied in high-resolution and particularly tailored for this region of the ocean. The 1/4 degree simulation was able to simulate realistic Equatorial and South Atlantic large scale circulation, both the wind-driven and the thermohaline components. The high-resolution introduces realistic mesoscale activity, in particular that associated with the dynamics of western boundary currents, and captures also both the continental shelf and the upper-ocean modes of variability associated with atmospheric synoptic forcing. Important issues for the simulation of the South Atlantic with high-resolution are discussed, like the ideal place for boundaries, improvements in the bathymetric representation, and the control of SST bias by the introduction of surface relaxation. In order to make a preliminary assessment of the model behavior when submitted to data assimilation, the Cooper & Haines (1996) method was used to extrapolate SSH anomalies fields to deeper layers every 7 days, with encouraging results.Keywords: numerical simulation, nesting, southwest Atlantic, Brazil Current. RESUMO. Neste trabalho são apresentados e discutidos resultados de duas simulações numéricas realizadas com o model HYCOM e que representam a configuração padrão do projeto REMO (Rede de Modelagem e Observação Oceanográfica), uma abordagem brasileira para a oceanografia operacional. Esta configuração consiste em um modelo em alta resolução (1/12 de grau, que resolve a mesoescala) da região denominada de Metarea V (latitudes de 7◦N a 35◦50’S e longitudes desde 20◦W até a costa brasileira), aninhado em um modelo em média-resolução (1/4 de grau, que resolve apenas parcialmente a mesoescala) do oceano Atlântico. Estas simulações tem como objetivos: a) a geração de um set-up básico para implementação de técnicas de assimilação visando a previsão oceânica; b) o desenvolvimento de bases hidrodinâmicas para estudos ambientais; e c) a geração de condições de contorno para domínios regionais com maior resolução. Esta é a primeira vez que o HYCOM é aplicado em alta resolução e especialmente configurado para esta região do oceano. A simulação em 1/4 de grau simulou de forma realista a circulação de larga escala no Atlântico Sul e Equatorial, tanto a componente eólica quanto a termohalina. A simulação em alta resolução foi capaz de introduzir também de forma realista a mesoescala, em particular aquela associada à dinâmica das correntes de contorno oeste, e de capturar a variabilidade da porção superior do oceano e da plataforma continental associada à forçante atmosférica em escala sinótica. Aspectos importantes para a simulação do Atlântico Sul em alta resolução são discutidos, como o posicionamento dos contornos, a representação da batimetria e o controle de possíveis tendências na TSM pela introdução de um termo de relaxamento para climatologia em superfície. Uma avaliação preliminar do comportamento do modelo submetido à assimilação de dados foi realizada com o método de Cooper & Haines (1996), capaz de extrapolar campos de anomalias de elevação da superfície para camadas mais profundas a cada 7 dias, com resultados promissores.Palavras-chave: simulação numérica, aninhamento, Atlântico sudoeste, Corrente do Brasil.
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Pop-Vicas, Aurora E., Cybele Lara R. Abad, Fay Osman, Kelsey Baubie und Nasia Safdar. „1245. Does Complexity of Infection Prevention Bundles Matter in Colorectal Surgery? A Systematic Review and Meta-Analysis“. Open Forum Infectious Diseases 6, Supplement_2 (Oktober 2019): S448. http://dx.doi.org/10.1093/ofid/ofz360.1108.
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Abstract Background Surgical site infection (SSI) prevention bundles in colorectal surgery are common. The optimal bundle composition and impact of increasingly complex and resource-intensive bundled interventions on SSI remain unclear. Methods (1) A systematic review and meta-analysis of randomized and observational trials with pre-post implementation data for colorectal SSI prevention bundles to study their effect on superficial, deep, and organ-space SSI. (2) A meta-regression to determine whether the bundle size (number of different bundle elements) affects SSI. (3) A correlation analysis to identify individual bundle elements with greatest SSI reduction. We used the METAN, METAEFF, and METAREG packages in STATA SE 15 for analysis. Results We included 38 studies in the systematic review, and 29 studies (49,589 patients) in the meta-analysis. Bundle composition was highly variable, ranging from 3 – 13 guideline-recommended elements per bundle. Meta-analyses showed bundles to be associated with relative risk reductions of 43% for any SSI (RR 0.57 [95% CI 0.48–0.67]; 44% for superficial SSI (RR 0.56 [95% CI 0.42–0.75]; 33% for deep SSI (RR 0.67 [95% CI 0.45–0.98], and 37% for organ/space SSI (RR 0.63 [95% CI 0.49 – 0.81]). On meta-regression, bundle size, especially ≥10 elements, was significantly associated with SSI reduction for any SSI (P = 0.04) and for superficial SSI (P = 0.005). Individual bundle elements correlated with strongest SSI reductions were mechanical bowel prep combined with oral antibiotics (R = −0.68, P = 0.0028) and pre-operative chlorhexidine showers (R = −0.49, P = 0.04) for organ/space SSI. Protocols including separate instrument trays and glove ± gown change prior to surgical wound closure (R = −0.55, P = 0.009), and standardized postoperative wound dressing change at 48 hours (R = −30.59, P = 0.005) correlated with highest superficial SSI reductions. Conclusion Complex colorectal bundles with ≥10 clinical guideline-recommended prevention elements are associated with higher reductions in any SSI and in superficial SSI. Further research should evaluate how complex SSI prevention colorectal bundles can be implemented and sustained with high fidelity in the clinical setting in a cost-effective manner. Disclosures All authors: No reported disclosures.
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Schneider-Thoma, Johannes, Irene Bighelli, Spyridon Siafis und Stefan Leucht. „M201. MODERATORS OF WEIGHT GAIN IN RANDOMIZED CONTROLLED TRIALS OF SCHIZOPHRENIA – A META-REGRESSION ANALYSIS“. Schizophrenia Bulletin 46, Supplement_1 (April 2020): S212—S213. http://dx.doi.org/10.1093/schbul/sbaa030.513.
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Abstract Background Weight gain is an important side effect of antipsychotics. Meta-analyses of randomized controlled trials indicate differences between the multiple antipsychotics in propensity to cause weight gain. However, antipsychotic-associated weight gain, in randomized controlled trials as well as in real life situations, might also depend on population characteristics and treatment-related factors. As a preparatory work for a systematic review and network-meta-analysis on metabolic side effects of antipsychotics (presented in another poster at this conference), we conducted a meta-regression analysis of potential moderators of weight gain. Methods We selected acute phase short-term, acute phase long-term as well as relapse prevention studies (all found by systematic reviews conducted by our group in the past) from our database of randomized controlled trials of antipsychotics in schizophrenia. We conducted We examined the moderators baseline weight, study duration, percentage women, and publication year. We conducted the analyses for all drugs pooled, placebo and per individual drug. For presentation of the results we focus on the drugs aripiprazole, haloperidol, quetiapine, olanzapine, and risperidone, because these are popular drugs in clinical practice, they differ in their receptor-binding profiles and multiple studies are available for these drugs. We conducted the analysis in R using the commands metacont, metagen and metareg from the package meta. Results The dataset comprises 603 randomized controlled trials with 141 584 patients that examined 40 different antipsychotics. Trial duration varied between 3 and 156 weeks (median 8 weeks). 168 studies with 49 670 patients reported on change in body weight. We found no effect of baseline weight on antipsychotic-associated weight gain, however on placebo, lower baseline weight was associated with more weight loss. Moreover, on antipsychotics, higher percentage of women was associated with less weight gain, and, on placebo, higher percentage of women was associated with more weight loss. Longer study duration was not associated with increased weight gain. On placebo, longer studies were associated with more weight loss. There was no effect of publication year. Discussion Surprisingly, we found no moderating effect of baseline weight and study duration on weight gain. However, our data suggests that men and women could have different risk of weight gain. Moreover, weight loss after switching to placebo might be higher in women and patients with less baseline weight. For interpretation, it must be noted that meta-regressions are observational evidence and thus prone to confounding. In addition, the scatter plots, presented on the poster, need to be considered to judge the robustness and magnitude of the moderated effects. Additional meta-regressions (planned to present on the poster) should address further potential moderators, such as antipsychotic dose, ethnicity, previous antipsychotic exposure and dropout rates.
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Fremin, Brayon J., Hila Sberro und Ami S. Bhatt. „MetaRibo-Seq measures translation in microbiomes“. Nature Communications 11, Nr. 1 (29.06.2020). http://dx.doi.org/10.1038/s41467-020-17081-z.
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Mello, Raquel Leite, João Bosco Rodrigues Alvarenga, Ana Cristina Neves de Freitas, Clemente Tanajura, Lucimara Russo und Jean Felix de Oliveira. „Previsões Oceânicas no Atlântico Sudoeste (METAREA V) Utilizando“. Revista Brasileira de Geofísica 31, Nr. 2 (16.04.2014). http://dx.doi.org/10.22564/rbgf.v31i2.20.
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Neste trabalho foi utilizado o modelo hidrodinâmico HYCOM (HYbrid Coordinate Ocean Model) em duas grades aninhadas. Uma grade para todo o Oceano Atlântico (1/4º) aninhada a outra com para a Metarea V (1/12º). O objetivo é avaliar qual a fonte de dados de ASM (Altura da Superfície do Mar) imposta no modelo é mais adequada para a previsão numérica da área de interesse. Foram realizados três experimentos com diferentes campos de ASM impostos na condição inicial com o esquema de Cooper & Haines (1996) e um experimento controle no qual não foi imposta fonte de ASM externa. De maneira geral, os resultados obtidos através das simulações do HYCOM apresentam-se satisfatórios quando comparados aos dados observacionais de temperatura e salinidade de derivadores Argo. O experimento NRL com ASM total obtido dos resultados do HYCOM+NCODA (Navy Coupled Ocean Data Assimilation) GLOBAL 1/12º obtidos no NRL (Naval Research Laboratory) foi o que melhor representou o perfil médio de temperatura e salinidade observado. No Diagrama de Taylor, este mesmo experimento mostrou maior correlação (0,99), menor erro quadrático médio (0,99ºC) e desvio padrão (8,76ºC) muito próximo dos dados observados (8,67ºC).
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Gabioux, Mariela, Vladimir Santos da Costa, Joao Marcos Azevedo Correia de Souza, Bruna Faria de Oliveira und Afonso De Moraes Paiva. „MODELING THE SOUTH ATLANTIC OCEAN FROM MEDIUM TO HIGH RESOLUTION“. Revista Brasileira de Geofísica 31, Nr. 2 (16.04.2014). http://dx.doi.org/10.22564/rbgf.v31i2.27.
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Results of the basic model configuration of the REMO project, a Brazilian approach towards operational oceanography, are discussed. This configuration consists basically of a high-resolution eddy-resolving, 1/12 degree model for the Metarea V, nested in a medium-resolution eddy-permitting, 1/4 degree model of the Atlantic Ocean. These simulations performed with HYCOM model, aim for: a) creating a basic set-up for implementation of assimilation techniques leading to ocean prediction; b) the development of hydrodynamics bases for environmental studies; c) providing boundary conditions for regional domains with increased resolution. The 1/4 degree simulation was able to simulate realistic equatorial and south Atlantic large scale circulation, both the wind-driven and the thermohaline components. The high resolution simulation was able to generate mesoscale and represent well the variability pattern within the Metarea V domain. The BC mean transport values were well represented in the southwestern region (between Vitória-Trinidade sea mount and 29S), in contrast to higher latitudes (higher than 30S) where it was slightly underestimated. Important issues for the simulation of the South Atlantic with high resolution are discussed, like the ideal place for boundaries, improvements in the bathymetric representation and the control of bias SST, by the introducing of a small surface relaxation. In order to make a preliminary assessment of the model behavior when submitted to data assimilation, the Cooper & Haines (1996) method was used to extrapolate SSH anomalies fields to deeper layers every 7 days, with encouraging results.
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Blondé, Ward. „Metarel: An Ontology to Support the Inferencing of Semantic Web Relations within Biomedical Ontologies“. Nature Precedings, 27.07.2009. http://dx.doi.org/10.1038/npre.2009.3463.1.
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Blondé, Ward, Erick Antezana, Bernard De Baets, Vladimir Mironov und Martin Kuiper. „Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies“. Nature Precedings, 06.08.2009. http://dx.doi.org/10.1038/npre.2009.3562.1.
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„MetaRE: search for cis-regulatory elements via meta-analysis of transcriptomic data“. 11-ая Международная конференция по биоинформатике регуляции и структуры геномов и системной биологии, 01.08.2018, 179. http://dx.doi.org/10.18699/bgrssb-2018-150.
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Lima, Leonardo Nascimento, und Clemente Augusto Souza Tanajura. „ESTUDO DO IMPACTO DA ASSIMILAÇÃO DE DADOS ALTIMÉTRICOS NA PREVISIBILIDADE DE CURTO-PRAZO DO MODELO OCEÂNICO HYCOM SOBRE A METAREA V DO OCEANO ATLÂNTICO“. Revista Brasileira de Geofísica 31, Nr. 2 (16.04.2014). http://dx.doi.org/10.22564/rbgf.v31i2.25.
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Neste estudo, assimilação de dados de anomalia da altura da superfície do mar (AASM) ao longo da trilha dos satélites Jason-1 e Jason-2 foi conduzida na METAREA V do Atlântico Sul (7ºN-36ºS, 20ºW até a costa do Brasil) com o método de interpolação ótima e o modelo oceânico HYCOM. Foram realizados quatro experimentos de previsão de 24 h durante os dias de 1 de janeiro a 31 de março de 2011 considerando diferentes janelas de assimilação de AASM (1 dia e 2 dias) e diferentes coeficientes na parametrização da matriz de co-variância dos erros de AASM do modelo. A resolução horizontal empregada no HYCOM foi 1/12º para 21 camadas verticais. As correções de altura da superfície do mar devido à assimilação de AASM foram projetadas abaixo da camada de mistura através da técnica de Cooper & Haines (1996). Os resultados mostraram que o experimento com assimilação de dados ao longo da trilha dos satélites com a janela de 2 dias e com parametrizações da matriz de co-variância específicas para sub-regiões da METAREA V foi o mais acurado. Ele reconstruiu completamente o campo de altura da superfície do mar do modelo e que importantes melhorias na circulação foram obtidas. Por exemplo, houve substancial melhoria da representação nos campos da Corrente do Brasil e Sub-corrente Norte do Brasil. Entretanto, tendo em vista que não foi realizada assimilação de perfis verticais de temperatura e de salinidade e da temperatura da superfície do mar, a metodologia apresentada deve ser considerada apenas como um passo na conquista da uma análise oceânica e um sistema previsor de qualidade para fins operacionais.
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Tanajura, Clemente Augusto Souza, Filipe Bitencourt Costa, Renato Ramos da Silva, Giovanni Abdelnur Ruggiero und Victor Bastos Daher. „ASSIMILATION OF SEA SURFACE HEIGHT ANOMALIES INTO HYCOM WITH AN OPTIMAL INTERPOLATION SCHEME OVER THE ATLANTIC OCEAN METAREA V“. Revista Brasileira de Geofísica 31, Nr. 2 (16.04.2014). http://dx.doi.org/10.22564/rbgf.v31i2.28.
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Along-track sea surface height anomaly (SSHA) data from the Jason-1 and Jason-2 satellites were assimilated into the ocean model HYCOM from July 1, 2009 until December 31, 2009. A new and simple approach to overcome the bias between the model and observed SSHA was proposed. It focuses on the meso-scale differences between the data and the model along each satellite track. An optimal interpolation method and the Cooper and Haines (1996) scheme (C&H) were employed to produce a SSHA analysis field and to adjust model layer thicknesses over the Atlantic METAREA V. The corrected model state was used as initial condition for the next assimilation cycle. SSHA data with a 7-day window were assimilated in 3-day intervals centered in the SSHA data window and the C&H scheme was applied taking the SSHA analysis. A control run without assimilation was also performed. The results showed that the model SSHA was completely reorganized by the end of the experiment. The modifications of SSHA were compared to the American Navy HYCOM+NCODA system and AVISO data. Maximum error was reduced from 0.7 m to 0.2 m by assimilation. Comparisons were also made with the Argo temperature and salinity vertical profiles. Improvements in the currents and volume transport were also produced by assimilation. The impact in temperature was in general positive, but there was no substantial modification in salinity.
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Ghiasvand, Hesam, Katherine M. Waye, Mehdi Noroozi, Gholamreza Ghaedamini Harouni, Bahram Armoon und Azadeh Bayani. „Clinical determinants associated with quality of life for people who live with HIV/AIDS: a Meta-analysis“. BMC Health Services Research 19, Nr. 1 (29.10.2019). http://dx.doi.org/10.1186/s12913-019-4659-z.
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Abstract Background During recent years, Quality of Life (QoL) is a significant assessment factor in clinical trials and epidemiological researches due to the advent of Antiretroviral Therapy (ART), Human Immunodeficiency Virus (HIV) has become a manageable,chronic disease. With regards, more attention must be paid to the QoL of infected patients. Limited evidence exists on the impact of ART on QoL among HIV infected patients. Due to lacking of a systematic approach to summarizing the available evidence on the clinical determinants of People Who Live with HIV/AIDS (PWLHs’) QoL, this study aimed to analyze the impact of clinical determinants (ART experience, CD4 count < 200, co-morbidities, time diagnosis and accessibility to cares) on QoL among PWLHs’. Methods This study was designed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). PubMed, Science Direct, Web of Science, and Cochrane electronic databases were searched in February 2017 to identify all past studies that discussed social and behavioral characteristics of QoL in PLWHA. To recognize effective factors on social and behavioral QoL, a meta-analysis was conducted. Polled Odds Ratios (ORs) were utilized at a 95% confidence level. Since sampling methods differed between articles in the systematic review, we evaluated pooled estimates using a random effect model. Metan, metareg, metacum, and metabias commands in STATA version 13.0 were applied to analyze the data. Results Our findings indicated that ART has a positive impact on QoL, with a pooled effect size at approximately 1.04 with a confidence interval between 0.42 to 1.66 which indicates this impact is not very considerable and may be relatively neutral. The pooled effect size for CD4 count on QoL was .29 (95%CI = .22–.35), indicating that there is a negative associate between CD4 count and QoL. The co-morbidity as a negative determinant for QoL among HIV/AIDS infected people. The pooled effect size implies on a relative neutral association, although the confidence interval is wide and ranges between 0.32 to 1.58. The pooled effect size is about 1.82 with confidence interval 1.27 to 2.37 which indicates a considerable positive association with lowest level of heterogeneity. Conclusions The results illustrated that time diagnosing and availability to hospital services had significant relationship with a higher QoL and CD4 < 200 was associated with a lower QoL. In conclusion, policy makers should set an agenda setting to provide a suitable diagnostic and therapeutic facilities to early detecting and continues monitoring the health status of People Who Live with HIV/AIDS (PWLHs’).