Pre-processing for noise detection in gene expression classification data

Due to the imprecise nature of biological experiments, biological data is often characterized by the presence of redundant and noisy data. This may be due to errors that occurred during data collection, such as contaminations in laboratorial samples. It is the case of gene expression data, where the equipments and tools currently used frequently produce noisy biological data. Machine Learning algorithms have been successfully used in gene expression data analysis. Although many Machine Learning algorithms can deal with noise, detecting and removing noisy instances from the training data set can help the induction of the target hypothesis. This paper evaluates the use of distance-based pre-processing techniques for noise detection in gene expression data classification problems. This evaluation analyzes the effectiveness of the techniques investigated in removing noisy data, measured by the accuracy obtained by different Machine Learning classifiers over the pre-processed data.

Spatial analysis of urban violence based on emergency room data

OBJECTIVE: To estimate the spatial intensity of urban violence events using wavelet-based methods and emergency room data. METHODS: Information on victims attended at the emergency room of a public hospital in the city of São Paulo, Southeastern Brazil, from January 1, 2002 to January 11, 2003 were obtained from hospital records. The spatial distribution of 3,540 events was recorded and a uniform random procedure was used to allocate records with incomplete addresses. Point processes and wavelet analysis technique were used to estimate the spatial intensity, defined as the expected number of events by unit area. RESULTS: Of all georeferenced points, 59% were accidents and 40% were assaults. There is a non-homogeneous spatial distribution of the events with high concentration in two districts and three large avenues in the southern area of the city of São Paulo. CONCLUSIONS: Hospital records combined with methodological tools to estimate intensity of events are useful to study urban violence. The wavelet analysis is useful in the computation of the expected number of events and their respective confidence bands for any sub-region and, consequently, in the specification of risk estimates that could be used in decision-making processes for public policies.

Study of C- and O-glycosylflavones in sugarcane extracts using liquid chromatography: exact mass measurement mass spectrometry

The flavonoids present in sugarcane (Saccharum officinarum) extracts were analyzed by liquid chromatography - mass spectrometry (LC-MS), and a study of the fragmentation patterns of selected flavonoids was conducted using orthogonal acceleration time-of-flight electrospray ionization mass spectrometry (ESI-oa-ToF MS). Seven C- and O-glycosylflavones were identified in the extracts, namely, schaftoside, isoschaftoside, luteolin-8-C-(rhamnosylglucoside), vitexin, orientin, tricin-7-O-neohesperidoside and tricin-7-O-glucoside. Of these, five were identified in the absence of direct comparison with their respective standards. The described method also permitted the differentiation of the 6-C and 8-C isomeric flavones, schaftoside and isoschaftoside. The combination of fragmentation data and exact mass measurement showed to be complimentary to the HPLC-UV-MS techniques previously utilized for isomers discrimination in sugarcane studies.

New data on the natural history and description of the immatures of Fulgeochlizus bruchi, a bioluminescent beetle from Central Brazil (Elateridae, Pyrophorini)

The mature larva and pupa of Fulgeochlizus bruchi (Candèze, 1896) are described and illustrated. Bioluminescent patterns are also given. Comments, new data on the first instar larva and natural history data are presented. The first instar larvae differ from the mature larvae mainly in their chaetotaxy, which is sparse and more symmetrically distributed.

Efetividade de programa de suplementação alimentar no ganho ponderal de crianças

OBJETIVO: Avaliar a efetividade de programa governamental de suplementação alimentar no ganho ponderal de crianças. MÉTODOS: Estudo de coorte com dados secundários de 25.433 crianças de baixa renda com idade entre seis e 24 meses que ingressaram em programa de distribuição de leite fortificado Projeto Vivaleite, realizado no Estado de São Paulo de 2003 a 2008. O ganho ponderal foi medido por meio dos valores de escores z de peso para idade, calculados pelo padrão da Organização Mundial da Saúde (2007), obtidos, na rotina do programa, ao ingressar e a cada quatro meses durante a permanência. As crianças foram divididas em três grupos de escore z ao entrar: sem comprometimento de peso (z > -1); risco de baixo peso (-2 < z < -1) e baixo peso (z < -2). Utilizou-se regressão linear multinível (modelo misto), permitindo a comparação, em cada idade, das médias ajustadas do escore z dos ingressantes e participantes há pelo menos quatro meses, ajustadas para correlação entre medidas repetidas. RESULTADOS: Verificou-se efeito positivo do programa no ganho de peso das crianças, variando em função do estado nutricional ao ingressar; para as que entraram sem comprometimento de peso, o ganho médio ajustado foi 0,183 escore z;entre as que entraram com risco de baixo peso, foi 0,566; e entre as ingressantes com baixo peso, foi 1,005 escore z. CONCLUSÕES: O programa é efetivo para o ganho ponderal de crianças menores de dois anos, com efeito mais pronunciado entre as crianças que entram no programa em condições menos favoráveis de peso.

Calibration of the dietary data obtained from the Brazilian center of the Natural History of HPV Infection in Men study: the HIM Study

The objective of this study was to estimate the regressions calibration for the dietary data that were measured using the quantitative food frequency questionnaire (QFFQ) in the Natural History of HPV Infection in Men: the HIM Study in Brazil. A sample of 98 individuals from the HIM study answered one QFFQ and three 24-hour recalls (24HR) at interviews. The calibration was performed using linear regression analysis in which the 24HR was the dependent variable and the QFFQ was the independent variable. Age, body mass index, physical activity, income and schooling were used as adjustment variables in the models. The geometric means between the 24HR and the calibration-corrected QFFQ were statistically equal. The dispersion graphs between the instruments demonstrate increased correlation after making the correction, although there is greater dispersion of the points with worse explanatory power of the models. Identification of the regressions calibration for the dietary data of the HIM study will make it possible to estimate the effect of the diet on HPV infection, corrected for the measurement error of the QFFQ.

Discrepancies among ecological, household, and individual data on fruits and vegetables consumption in Brazil

Information on fruits and vegetables consumption in Brazil in the three levels of dietary data was analyzed and compared. Data about national supply came from Food Balance Sheets compiled by the FAO; household availability information was obtained from the Brazilian National Household Budget Survey (HBS); and actual intake information came from a large individual dietary intake survey that was representative of the adult population of São Paulo city. All sources of information were collected between 2002 and 2003. A subset of the HBS, representative of São Paulo city, was used in our analysis in order to improve the quality of the comparison with actual intake data. The ratio of national supply to household availability of fruits and vegetables was 2.6 while the ratio of national supply to actual intake was 4.0. The discrepancy ratio in the comparison between household availability and actual intake was smaller, 1.6. While the use of supply and availability data has advantages, as lower cost, must be taken into account that these sources tend to overestimate actual intake of fruits and vegetables.

Queimadas de cana-de-açúcar: Avaliação de efeitos na qualidade do ar e na saúde respiratória de crianças

Pesquisa em Espírito Santo do Turvo (SP) analisou poluição atmosférica causada por queima de cana-de-açúcar e saúde respiratória de crianças. Realizaram-se medições de PM10, PTS e NO2, durante safra, em 2004 e 2005, em pátio de escola, e aplicou-se questionário para avaliar morbidade respiratória referida dos alunos. No município, há cultivo de cana, queimada no pré-corte e usina próxima à área urbana. Resultados dos questionários foram comparados àqueles obtidos em Juquitiba (SP) previamente. As medições de poluentes, realizadas em dias em que havia queima de cana, estiveram abaixo dos padrões de qualidade do ar. Entretanto, foram indicadas altas prevalências de sintomas e doenças respiratórias.

Novas curvas de crescimento da Organização Mundial da Saúde: comparação com valores de crescimento de crianças pré-escolares das cidades de Taubaté e Santo André, São Paulo

OBJETIVO: Em 2007, a Organização Mundial da Saúde (OMS) propôs um referencial de crescimento de cinco a 19 anos, a ser utilizado em continuidade ao referencial de menores de cinco anos (de 2006), que, entre outras características, aos cinco anos de idade mostra um bom ajuste com a curva de 2006. Este estudo visa comparar os referenciais da OMS com o crescimento observado em pré-escolares brasileiros. MÉTODOS: A partir dos dados antropométricos de 2.830 crianças com idade entre três e seis anos de duas amostras das cidades de Taubaté e Santo André, em São Paulo, foram calculados os valores dos percentis (P) 5, 50 e 95 de peso, estatura e índice de massa corpórea (IMC). Os valores dos novos referenciais da OMS foram comparados a esses resultados de acordo com o sexo e a faixa etária. RESULTADOS: Nos percentis de estatura, o referencial apresentou valores próximos ou pouco superiores aos dos pré-escolares até os cinco anos. Nessa idade, a tendência se inverte, obtendo-se valores progressivamente inferiores até os sete anos. Para peso e IMC, em todas as idades consideradas, o P5 e 50 dos referenciais são pouco menores que os das crianças, mas o P95 indica uma tendência de crescimento progressivamente menor, fazendo com que, próximo aos sete anos, o P95 de IMC dos pré-escolares da amostra seja cerca de 4kg/m² maior. CONCLUSÕES: Os referenciais da OMS apontam uma prevalência menor de magreza (desnutrição) e baixa estatura entre cinco e sete anos e, ao mesmo tempo, uma elevação importante da prevalência de obesidade entre três e sete anos de idade.

Body Mass Index, Cigarette Smoking, and Alcohol Consumption and Cancers of the Oral Cavity, Pharynx, and Larynx: Modeling Odds Ratios in Pooled Case-Control Data

study-specific results, their findings should be interpreted with caution

Narrowing socioeconomic inequality in child stunting: the Brazilian experience, 1974–2007

Objective To assess trends in the prevalence and social distribution of child stunting in Brazil to evaluate the effect of income and basic service redistribution policies implemented in that country in the recent past. Methods The prevalence of stunting (height-for-age z score below \22122 using the Child Growth Standards of the World Health Organization) among children aged less than 5 years was estimated from data collected during national household surveys carried out in Brazil in 1974\201375 (n = 34 409), 1989 (n = 7374), 1996 (n = 4149) and 2006\201307 (n = 4414). Absolute and relative socioeconomic inequality in stunting was measured by means of the slope index and the concentration index of inequality, respectively. Findings Over a 33-year period, we documented a steady decline in the national prevalence of stunting from 37.1 per cent to 7.1 per cent. Prevalence dropped from 59.0 per cent to 11.2 per cent in the poorest quintile and from 12.1 per cent to 3.3 per cent among the wealthiest quintile. The decline was particularly steep in the last 10 years of the period (1996 to 2007), when the gaps between poor and wealthy families with children under 5 were also reduced in terms of purchasing power; access to education, health care and water and sanitation services; and reproductive health indicators.Conclusion In Brazil, socioeconomic development coupled with equity-oriented public policies have been accompanied by marked improvements in living conditions and a substantial decline in child undernutrition, as well as a reduction of the gap in nutritional status between children in the highest and lowest socioeconomic quintiles. Future studies will show whether these gains will be maintained under the current global economic crisis

Comércio varejista de alimentos no município de São Paulo: a evolução da legislação sanitária

O código Sanitário Municipal de Alimentos, Decreto Municipal nº 25.544, de 14 de março de 1988, regulamentou a fiscalização sanitária de g~eneros alimentícios no varejo até 26 de novembro de 2002, data em que entrou em vigor a Lei Estadual nC 10.083, de 23 de setembro de 1998, Código Sanitário do estado de São Paulo, utilizado pelos serviços municipais de vigilância, em caráter temporário, até a promulgação do atual Código Sanitário do Município de São Paulo nº 13.735, em 9 de janeiro de 2004. Este código regulamenta todos os serviços e produtos de interesse da saúde, inclusive a produção e distribuição de alimentos e água para consumo humano. Por meio do estudo dos diferentes códigos vigentes no município e de legislações esparsas, foi possível identificar as nmudanças ocorridas na legislação e nos procedimentos administrativos da vigilância sanitária do varejo de alimentos no Município de São Paulo. Concluiu-se que o Código Sanitário do Município de São Paulo é uma legislação completa e atualizada, com previsão legal de utilização de regulamentos técnicos modernos de forma combinada, especialmente os que tratam da produção e distribuição de alimentos, com ênfase nas Boas Práticas de Fabricação (BPFs)

Assessing influence in survival data with a cure fraction and covariates

Diagnostic methods have been an important tool in regression analysis to detect anomalies, such as departures from error assumptions and the presence of outliers and influential observations with the fitted models. Assuming censored data, we considered a classical analysis and Bayesian analysis assuming no informative priors for the parameters of the model with a cure fraction. A Bayesian approach was considered by using Markov Chain Monte Carlo Methods with Metropolis-Hasting algorithms steps to obtain the posterior summaries of interest. Some influence methods, such as the local influence, total local influence of an individual, local influence on predictions and generalized leverage were derived, analyzed and discussed in survival data with a cure fraction and covariates. The relevance of the approach was illustrated with a real data set, where it is shown that, by removing the most influential observations, the decision about which model best fits the data is changed.

Data collapse, scaling functions, and analytical solutions of generalized growth models

We consider a nontrivial one-species population dynamics model with finite and infinite carrying capacities. Time-dependent intrinsic and extrinsic growth rates are considered in these models. Through the model per capita growth rate we obtain a heuristic general procedure to generate scaling functions to collapse data into a simple linear behavior even if an extrinsic growth rate is included. With this data collapse, all the models studied become independent from the parameters and initial condition. Analytical solutions are found when time-dependent coefficients are considered. These solutions allow us to perceive nontrivial transitions between species extinction and survival and to calculate the transition's critical exponents. Considering an extrinsic growth rate as a cancer treatment, we show that the relevant quantity depends not only on the intensity of the treatment, but also on when the cancerous cell growth is maximum.

Qualitative Analysis of the Interdisciplinary Interaction between Data Analysis Specialists and Novice Clinical Researchers

Background: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. Methods/Principal Findings: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of ""what if'' situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. Conclusion/Significance: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.