ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

COOP/WONCA Charts as a Screen for Mental Disorders in Primary Care

PURPOSE most people with mental disorders receive treatment in primary care. The charts developed by the Dartmouth Primary Care Cooperative Research Network (COOP) and the World Organization of National Colleges, Academies, and Academic Associations of General Practitioners/Family Physicians (WONCA) have not yet been evaluated as a screen for these disorders, using a structured psychiatric interview by an expert or considering diagnoses other than depression. We evaluated the validity and feasibility of the COOP/WONCA Charts as a mental disorders screen by comparing them both with other questionnaires previously validated and with the assessment of a mental health specialist using a structured diagnostic interview. METHODS We trained community health workers and nurse assistants working in a collaborative mental health care model to administer the COOP/WONCA Charts, the 20-item Self-Reporting Questionnaire (SRQ-20), and the World Health Organization Five Well-Being Index (WHO-5) to 120 primary care patients. A psychiatrist blinded to the patients' results on these questionnaires administered the SCID, or Structured Clinical Interview for the DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition). RESULTS The area under the receiver operating characteristic curve was at least 0.80 for single items, a 3-item combination, and the total score of the COOP/WONCA Charts, as well as for the SRQ-20 and the WHO-5, for screening both for all mental disorders and for depressive disorders. The accuracy, sensitivity, specificity, and positive and negative predictive values of these measures ranged between 0.77 and 0.92. Community health workers and nurse assistants rated the understandability, ease of use, and clinical relevance of all 3 questionnaires as satisfactory. CONCLUSIONS One-time assessment of patients with the COOP/WONCA Charts is a valid and feasible option for screening for mental disorders by primary care teams.

Monte Carlo investigation of the critical behavior of Stavskaya's probabilistic cellular automaton

Stavskaya's model is a one-dimensional probabilistic cellular automaton (PCA) introduced in the end of the 1960s as an example of a model displaying a nonequilibrium phase transition. Although its absorbing state phase transition is well understood nowadays, the model never received a full numerical treatment to investigate its critical behavior. In this Brief Report we characterize the critical behavior of Stavskaya's PCA by means of Monte Carlo simulations and finite-size scaling analysis. The critical exponents of the model are calculated and indicate that its phase transition belongs to the directed percolation universality class of critical behavior, as would be expected on the basis of the directed percolation conjecture. We also explicitly establish the relationship of the model with the Domany-Kinzel PCA on its directed site percolation line, a connection that seems to have gone unnoticed in the literature so far.

Coupled reliability and boundary element model for probabilistic fatigue life assessment in mixed mode crack propagation

Fatigue and crack propagation are phenomena affected by high uncertainties, where deterministic methods fail to predict accurately the structural life. The present work aims at coupling reliability analysis with boundary element method. The latter has been recognized as an accurate and efficient numerical technique to deal with mixed mode propagation, which is very interesting for reliability analysis. The coupled procedure allows us to consider uncertainties during the crack growth process. In addition, it computes the probability of fatigue failure for complex structural geometry and loading. Two coupling procedures are considered: direct coupling of reliability and mechanical solvers and indirect coupling by the response surface method. Numerical applications show the performance of the proposed models in lifetime assessment under uncertainties, where the direct method has shown faster convergence than response surface method. (C) 2010 Elsevier Ltd. All rights reserved.

Assembling a consistent set of sentences in relational probabilistic logic with stochastic independence

We examine the representation of judgements of stochastic independence in probabilistic logics. We focus on a relational logic where (i) judgements of stochastic independence are encoded by directed acyclic graphs, and (ii) probabilistic assessments are flexible in the sense that they are not required to specify a single probability measure. We discuss issues of knowledge representation and inference that arise from our particular combination of graphs, stochastic independence, logical formulas and probabilistic assessments. (C) 2007 Elsevier B.V. All rights reserved.

Probabilistic logic with independence

This paper investigates probabilistic logics endowed with independence relations. We review propositional probabilistic languages without and with independence. We then consider graph-theoretic representations for propositional probabilistic logic with independence; complexity is analyzed, algorithms are derived, and examples are discussed. Finally, we examine a restricted first-order probabilistic logic that generalizes relational Bayesian networks. (c) 2007 Elsevier Inc. All rights reserved.

Control charts for individual observations of a bivariate Poisson process

In this paper, three single-control charts are proposed to monitor individual observations of a bivariate Poisson process. The specified false-alarm risk, their control limits, and ARLs were determined to compare their performances for different types and sizes of shifts. In most of the cases, the single charts presented better performance rather than two separate control charts ( one for each quality characteristic). A numerical example illustrates the proposed control charts.

Economic design of an X chart for short-run production

The aim of this paper is to present an economical design of an X chart for a short-run production. The process mean starts equal to mu(0) (in-control, State I) and in a random time it shifts to mu(1) > mu(0) (out-of-control, State II). The monitoring procedure consists of inspecting a single item at every m produced ones. If the measurement of the quality characteristic does not meet the control limits, the process is stopped, adjusted, and additional (r - 1) items are inspected retrospectively. The probabilistic model was developed considering only shifts in the process mean. A direct search technique is applied to find the optimum parameters which minimizes the expected cost function. Numerical examples illustrate the proposed procedure. (C) 2009 Elsevier B.V. All rights reserved.

An extinction-survival-type phase transition in the probabilistic cellular automaton p182-q200

We investigate the critical behaviour of a probabilistic mixture of cellular automata (CA) rules 182 and 200 (in Wolfram`s enumeration scheme) by mean-field analysis and Monte Carlo simulations. We found that as we switch off one CA and switch on the other by the variation of the single parameter of the model, the probabilistic CA (PCA) goes through an extinction-survival-type phase transition, and the numerical data indicate that it belongs to the directed percolation universality class of critical behaviour. The PCA displays a characteristic stationary density profile and a slow, diffusive dynamics close to the pure CA 200 point that we discuss briefly. Remarks on an interesting related stochastic lattice gas are addressed in the conclusions.

Critical applications of SW 846 US EPA methods to evaluation of marine samples quality

Technical evaluation of analytical data is of extreme relevance considering it can be used for comparisons with environmental quality standards and decision-making as related to the management of disposal of dredged sediments and the evaluation of salt and brackish water quality in accordance with CONAMA 357/05 Resolution. It is, therefore, essential that the project manager discusses the environmental agency's technical requirements with the laboratory contracted for the follow-up of the analysis underway and even with a view to possible re-analysis when anomalous data are identified. The main technical requirements are: (1) method quantitation limits (QLs) should fall below environmental standards; (2) analyses should be carried out in laboratories whose analytical scope is accredited by the National Institute of Metrology (INMETRO) or qualified or accepted by a licensing agency; (3) chain of custody should be provided in order to ensure sample traceability; (4) control charts should be provided to prove method performance; (5) certified reference material analysis or, if that is not available, matrix spike analysis, should be undertaken and (6) chromatograms should be included in the analytical report. Within this context and with a view to helping environmental managers in analytical report evaluation, this work has as objectives the discussion of the limitations of the application of SW 846 US EPA methods to marine samples, the consequences of having data based on method detection limits (MDL) and not sample quantitation limits (SQL), and present possible modifications of the principal method applied by laboratories in order to comply with environmental quality standards.

Análise comportamental de recém-nascidos pré-termos incluídos em um programa de estimulação tátil-cinestésica durante a internação hospitalar

OBJETIVO: Avaliar o efeito da estimulação tátil-cinestésica na evolução do padrão comportamental e clínico de recém-nascidos pré-termos (RNPT) durante o período de internação hospitalar. MÉTODOS: Trinta e dois RNPT, com peso ao nascimento inferior a 2.500 gramas, clinicamente estáveis e destituídos de asfixia perinatal importante foram divididos em 16 bebês do grupo controle (GC) e 16 do experimental (GE). Foram coletados dados da evolução clínica a partir dos registros hospitalares e da avaliação comportamental por meio de filmagens semanais de oito minutos, desde a inclusão do RNPT na amostra até a alta hospitalar. RESULTADOS: Tendência a redução do tempo de internação hospitalar, aumento do ganho de peso diário e predominância de comportamentos auto-organizados (respiração regular, estado de alerta, tônus equilibrado, posturas mistas, movimentação coordenada, movimentos de mão na face, sucção, preensão, apoio) para os RNPT do GE. A análise comparativa das idades pós-conceptuais divididas em intervalos (I - 31 a 33 semanas 6/7; II - 34 a 36 semanas 6/7; e III - 37 a 39 semanas 6/7) ressaltou, no aspecto motor, um tônus equilibrado e movimentação voluntária coordenada para os três períodos, maior permanência em posturas mistas (intervalo I) ou em flexão (intervalo II) e a obtenção de respiração mais regular na faixa etária I do GE. CONCLUSÃO: Destaque da estimulação tátil-cinestésica como método de intervenção durante o período de internação hospitalar, contribuindo para a auto-organização e regulação comportamental de RNPT. Artigo registrado no Australian New Zealand Clinical Trials Registry (ANZCTR) sob o número ACTRN12610000133033.

Confiabilidade da informação sobre hospitalizações por causas externas de um hospital público em São José dos Campos, São Paulo, Brasil

OBJETIVO: Conhecer a qualidade dos dados de internação por causas externas em São José dos Campos, São Paulo. MÉTODO: Foram estudadas as internações pelo Sistema Único de Saúde por lesões decorrentes de causas externas no primeiro semestre de 2003, no Hospital Municipal, referência para o atendimento ao trauma no Município, por meio da comparação dos dados registrados no Sistema de Informações Hospitalares com os prontuários de 990 internações. A concordância das variáveis relativas à vítima, à internação e ao agravo foi avaliada pela taxa bruta de concordância e pelo coeficiente Kappa. As lesões e as causas externas foram codificadas segundo a 10ª revisão da Classificação Internacional de Doenças, respectivamente, capítulos XIX e XX. RESULTADOS: A taxa de concordância bruta foi de boa qualidade para as variáveis relativas à vítima e à internação, variando de 89,0% a 99,2%. As lesões tiveram concordância ótima, exceto os traumatismos do pescoço (k=0,73), traumatismos múltiplos (k=0,67) e fraturas do tórax (k=0,49). As causas externas tiveram concordância ótima para acidentes de transporte (k=0,90) e quedas (k=0,83). A confiabilidade foi menor para agressões (k=0,50), causas indeterminadas (k=0,37), e complicações da assistência médica (k=0,03). Houve concordância ótima nos acidentes de transporte em pedestres, ciclistas e motociclistas. CONCLUSÃO: A maioria das variáveis de estudo teve boa qualidade no nível de agregação analisado. Algumas variáveis relativas à vítima e alguns tipos de causas externas necessitam de aperfeiçoamento da qualidade dos dados. O perfil da morbidade hospitalar encontrado confirmou os acidentes de transporte como importante causa externa de internação hospitalar no Município.

A new classification of foods based on the extent and purpose of their processing

This paper describes a new food classification which assigns foodstuffs according to the extent and purpose of the industrial processing applied to them. Three main groups are defined: unprocessed or minimally processed foods (group 1), processed culinary and food industry ingredients (group 2), and ultra-processed food products (group 3). The use of this classification is illustrated by applying it to data collected in the Brazilian Household Budget Survey which was conducted in 2002/2003 through a probabilistic sample of 48,470 Brazilian households. The average daily food availability was 1,792 kcal/person being 42.5% from group 1 (mostly rice and beans and meat and milk), 37.5% from group 2 (mostly vegetable oils, sugar, and flours), and 20% from group 3 (mostly breads, biscuits, sweets, soft drinks, and sausages). The share of group 3 foods increased with income, and represented almost one third of all calories in higher income households. The impact of the replacement of group 1 foods and group 2 ingredients by group 3 products on the overall quality of the diet, eating patterns and health is discussed.

Monitoramento por entrevistas telefônicas de fatores de risco para doenças crônicas: experiência de Goiânia, Goiás, Brasil

Este estudo descreve alguns resultados do sistema de monitoramento de fatores de risco para doenças crônicas por entrevistas telefônicas no Município de Goiânia, Goiás, Brasil, 2005. Foi estudada amostra probabilística (n = 2.002) da população adulta servida por linhas telefônicas residenciais fixas. Foram analisadas variáveis comportamentais (consumo alimentar, atividade física, tabagismo e consumo de bebida alcoólica), peso e altura referidos e referência a diagnóstico médico de doenças crônicas. Foram calculadas estimativas de prevalência e valores de qui-quadrado. Observou-se baixo consumo de frutas e hortaliças (47,1%), alta freqüência de inatividade física ocupacional (86,6%), no deslocamento para o trabalho (92,6%) e lazer (61,9%), consumo excessivo de bebidas alcoólicas (23,2%), excesso de peso (36,5%), obesidade (10,6%), hipertensão arterial (22,4%), dislipidemias (18,4%) e diabetes (4,4%). A maioria dos fatores de risco apresentou associação inversa com escolaridade e direta com idade, com diferenças significativas entre sexos (p < 0,05). Observou-se alta prevalência dos fatores de risco de doenças crônicas não transmissíveis e de auto-referidas. Aspectos positivos do sistema: baixo custo operacional, possibilidade de monitorar a carga e a tendência das doenças crônicas não transmissíveis no nível local.

Questionário de freqüência alimentar para adultos com base em estudo populacional

O estudo teve por objetivo desenvolver questionário de freqüência alimentar para cada um dos grupos: para mulheres, homens e ambos os gêneros, baseados nos dados dietéticos obtidos em estudo de base populacional de diferentes faixas de renda. Para elaboração do questionário foram utilizados dados dietéticos de recordatório de 24h para 1.477 indivíduos de amostra probabilística do município de São Paulo, em 2003. Foram selecionados os itens alimentares que contribuíram com pelo menos 90% da ingestão diária de calorias e nutrientes. O período de referência foi o ano anterior à entrevista e a escolha de alimentos pôde ser feita entre quatro tamanhos de porção.