Estimating and evaluating the statistics of gapped local-alignment scores

We present a novel maximum-likelihood-based algorithm for estimating the distribution of alignment scores from the scores of unrelated sequences in a database search. Using a new method for measuring the accuracy of p-values, we show that our maximum-likelihood-based algorithm is more accurate than existing regression-based and lookup table methods. We explore a more sophisticated way of modeling and estimating the score distributions (using a two-component mixture model and expectation maximization), but conclude that this does not improve significantly over simply ignoring scores with small E-values during estimation. Finally, we measure the classification accuracy of p-values estimated in different ways and observe that inaccurate p-values can, somewhat paradoxically, lead to higher classification accuracy. We explain this paradox and argue that statistical accuracy, not classification accuracy, should be the primary criterion in comparisons of similarity search methods that return p-values that adjust for target sequence length.

Taxonomic theory and the ICF: Foundations for a unified disability athletics classification

Development of a unified classification system to replace four of the systems currently used in disability athletics (i.e., track and field) has been widely advocated. The definition and purpose of classification, underpinned by taxonomic principles and collectively endorsed by relevant disability sport organizations, have not been developed but are required for successful implementation of a unified system. It is posited that the International classification of functioning. disability, and health (ICF), published by the World Health Organization (2001), and current disability athletics systems are, fundamentally, classifications of the functioning and disability associated with health conditions and are highly interrelated. A rationale for basing a unified disability athletics system on ICF is established. Following taxonomic analysis of the current systems, the definition and purpose of a unified disability athletics classification are proposed and discussed. The proposed taxonomic framework and definitions have implications for other disability sport classification systems.

Phylogeny and classification of the Digenea (Platyhelminthes : Trematoda)

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history. (C) 2003 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

Effect of changing data collection parameters on statistical motor unit number estimates

The effect of number of samples and selection of data for analysis on the calculation of surface motor unit potential (SMUP) size in the statistical method of motor unit number estimates (MUNE) was determined in 10 normal subjects and 10 with amyotrophic lateral sclerosis (ALS). We recorded 500 sequential compound muscle action potentials (CMAPs) at three different stable stimulus intensities (10–50% of maximal CMAP). Estimated mean SMUP sizes were calculated using Poisson statistical assumptions from the variance of 500 sequential CMAP obtained at each stimulus intensity. The results with the 500 data points were compared with smaller subsets from the same data set. The results using a range of 50–80% of the 500 data points were compared with the full 500. The effect of restricting analysis to data between 5–20% of the CMAP and to standard deviation limits was also assessed. No differences in mean SMUP size were found with stimulus intensity or use of different ranges of data. Consistency was improved with a greater sample number. Data within 5% of CMAP size gave both increased consistency and reduced mean SMUP size in many subjects, but excluded valid responses present at that stimulus intensity. These changes were more prominent in ALS patients in whom the presence of isolated SMUP responses was a striking difference from normal subjects. Noise, spurious data, and large SMUP limited the Poisson assumptions. When these factors are considered, consistent statistical MUNE can be calculated from a continuous sequence of data points. A 2 to 2.5 SD or 10% window are reasonable methods of limiting data for analysis. Muscle Nerve 27: 320–331, 2003

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

We have developed a computational strategy to identify the set of soluble proteins secreted into the extracellular environment of a cell. Within the protein sequences predominantly derived from the RIKEN representative transcript and protein set, we identified 2033 unique soluble proteins that are potentially secreted from the cell. These proteins contain a signal peptide required for entry into the secretory pathway and lack any transmembrane domains or intracellular localization signals. This class of proteins, which we have termed the mouse secretome, included >500 novel proteins and 92 proteins

Indicadores para diagn??stico, monitoramento e avalia????o de programas sociais no Brasil

O objetivo do texto ?? discutir as potencialidades e limita????es do uso das informa????es estat??sticas produzidas pelo IBGE e os registros administrativos de ??rg??os p??blicos para a constru????o de indicadores para diagn??stico, monitoramento e avalia????o de programas sociais no Brasil. Inicia-se com uma apresenta????o sobre os aspectos conceituais b??sicos acerca dos indicadores sociais, suas propriedades e formas de classifica????o. Depois, discute-se uma proposta de estrutura????o de um sistema de indicadores para subsidiar o processo de formula????o e avalia????o de pol??ticas e programas p??blicos no Pa??s. Conclui-se o texto advogando-se a necessidade de estruturar sistemas de indicadores que se ap??iem na busca de informa????es j?? existentes em fontes secund??rias e na produ????o de dados no ??mbito dos pr??prios programas.

Avaliação assistida informatizada : indicadores do potencial cognitivo de crianças com deficiência

A identificação e a avaliação de crianças com desenvolvimento atípico configuram um processo muito importante para subsidiar as estratégias de ensino voltadas para a promoção do potencial de aprendizagem. O interesse em relação ao prognóstico de crianças com deficiência tem impulsionado o desenvolvimento de novas tecnologias e pesquisas relacionadas à avaliação, prevenção e intervenção. Nesse contexto, torna-se relevante verificar com instrumentos adequados indicadores linguísticos, cognitivos e comportamentais, para assim traçar metas a partir daquilo que as crianças podem aprender. Dessa forma, esta pesquisa teve por objetivo verificar se a avaliação assistida informatizada se apresenta como uma modalidade de diagnóstico mais prescritivo do desenvolvimento cognitivo, quando comparada à avaliação psicométrica, na aplicação em crianças com deficiência. Na modalidade assistida há ajuda do examinador para conduzir a criança a um melhor nível de desempenho cognitivo. Participaram 11 crianças que frequentam uma instituição de atendimento clínico, em saúde, para crianças com deficiência, na Grande Vitória. Na avaliação psicométrica foram utilizados a Escala de Maturidade Mental Colúmbia computadorizada – Colúmbiacomp e o Teste de Vocabulário por Imagens Peabody - TVIPcomp. Na avaliação assistida informatizada foram aplicadas três provas voltadas para as habilidades de classificação e raciocínio analógico: Exclusão de Objetos, Exclusão de Figuras Geométricas e Jogo de Analogia de Figuras, no ambiente informatizado SINDAPSI. Protocolos de registro de fatores afetivo-motivacionais e de operações cognitivas foram utilizados durante as tarefas assistidas. Na avaliação do comportamento, o Child Behavior Checklist – CBCL foi respondido pelas mães. Dados documentais e dos instrumentos foram submetidos à análise estatística descritiva para verificar o desempenho das crianças nas duas formas de avaliação informatizada (psicométrica e assistida). Nos testes psicométricos, 64% das crianças alcançaram índice “abaixo da média” no TVIPcomp, e 55% “médio-inferior” no Colúmbiacomp. Em relação ao perfil de desempenho cognitivo, na Prova de Exclusão de Objetos computadorizada 55% das crianças foram avaliadas como “não-mantenedoras”. Na Prova de Exclusão de Figuras Geométricas computadorizada 55% da amostra foi classificada no perfil “alto-escore”, e no Jogo de Analogias de Figuras computadorizado 45% apresentou o perfil “ganhador”. A amostra demonstrou níveis de dificuldade na realização dos testes,tanto na modalidade psicométrica quanto assistida. Contudo, o desempenho nos testes assistidos foi relativamente melhor, evidenciando que o grupo se beneficiou da mediação,implementada na fase de assistência, para melhorar as habilidades cognitivas. Além disso, a apresentação informatizada dos testes apresentou-se como fator motivador para a realização e persistência nas tarefas.

Estudo da evolução da paisagem da área do município de Linhares (ES) nos anos de 1985 e de 2013/2014, por meio das métricas

Trata a presente pesquisa sobre o estudo da evolução da área da paisagem que compõe o município de Linhares (ES), nos anos de 1985 e 2013/2014, que constitui o maior município do Estado do Espírito Santo. Foi realizada, por meio de processamento digital de imagens de satélites LANDSAT 5 e 8, a classificação de uso e ocupação da terra da área em estudo. Além disso usou-se as imagens do satélite RapdEye para acurácia da classificação digital das imagens. A partir dos resultados levantados de uso e ocupação foram definidas as matrizes da paisagem para 1985 e 2013/2014, bem como avaliadas as manchas que compõem a matriz. Foram aplicadas as métricas da paisagem utilizando a ferramenta de estatística Fragstats, possibilitando o cálculo dos Índices de Paisagem afim de avaliar a evolução qualitativa e quantitativa da paisagem do município de Linhares.

Using different satellite imagery and classification techniques to assess the contribution of trees outside forests in the municipality of Maringá, Brazil

Forest cover of the Maringá municipality, located in northern Parana State, was mapped in this study. Mapping was carried out by using high-resolution HRC sensor imagery and medium resolution CCD sensor imagery from the CBERS satellite. Images were georeferenced and forest vegetation patches (TOFs - trees outside forests) were classified using two methods of digital classification: reflectance-based or the digital number of each pixel, and object-oriented. The areas of each polygon were calculated, which allowed each polygon to be segregated into size classes. Thematic maps were built from the resulting polygon size classes and summary statistics generated from each size class for each area. It was found that most forest fragments in Maringá were smaller than 500 m². There was also a difference of 58.44% in the amount of vegetation between the high-resolution imagery and medium resolution imagery due to the distinct spatial resolution of the sensors. It was concluded that high-resolution geotechnology is essential to provide reliable information on urban greens and forest cover under highly human-perturbed landscapes.

Comparison of methods for classification of the coefficient of variation in papaya

ABSTRACT The objective of this work was to study the distribution of values of the coefficient of variation (CV) in the experiments of papaya crop (Carica papaya L.) by proposing ranges to guide researchers in their evaluation for different characters in the field. The data used in this study were obtained by bibliographical review in Brazilian journals, dissertations and thesis. This study considered the following characters: diameter of the stalk, insertion height of the first fruit, plant height, number of fruits per plant, fruit biomass, fruit length, equatorial diameter of the fruit, pulp thickness, fruit firmness, soluble solids and internal cavity diameter, from which, value ranges were obtained for the CV values for each character, based on the methodology proposed by Garcia, Costa and by the standard classification of Pimentel-Gomes. The results obtained in this study indicated that ranges of CV values were different among various characters, presenting a large variation, which justifies the necessity of using specific evaluation range for each character. In addition, the use of classification ranges obtained from methodology of Costa is recommended.

Multi-attribute classification of housing conservation status in urban regeneration actions

Urban regeneration is more and more a “universal issue” and a crucial factor in the new trends of urban planning. It is no longer only an area of study and research; it became part of new urban and housing policies. Urban regeneration involves complex decisions as a consequence of the multiple dimensions of the problems that include special technical requirements, safety concerns, socio-economic, environmental, aesthetic, and political impacts, among others. This multi-dimensional nature of urban regeneration projects and their large capital investments justify the development and use of state-of-the-art decision support methodologies to assist decision makers. This research focuses on the development of a multi-attribute approach for the evaluation of building conservation status in urban regeneration projects, thus supporting decision makers in their analysis of the problem and in the definition of strategies and priorities of intervention. The methods presented can be embedded into a Geographical Information System for visualization of results. A real-world case study was used to test the methodology, whose results are also presented.

Risk factors for basal cell carcinoma: a case-control study

A controlled trial was performed with the purpose of investigating which factors could be considered of significant risk for the development of basal cell carcinoma. A total of 259 cases of basal cell carcinoma diagnosed from July 1991 to July 1992 were compared with 518 controls matched for age and sex. All subjects in both groups were white. Protocol data were submitted to statistical analysis by the chi-square test and by multiple conditional logistic regression analysis and the following conclusions were reached: 1) light skin color (types I and II of the Fitzpatrick classification), odds ratio of 2.8; outdoor work under constant sunlight, odds ratio of 5.0; the presence of actinic lesions due to exposure to the sun, odds ratio of 4.9, are risk factors perse. 2) Type III skin in the Fitzpatrick classification only represents a risk factor when the patient reports a history of intense sunburns, but not in the absence of such a history. 3) Sunburns per se do not represent a risk factor althorig the point made in item 2 of these conclusions is valid. 4) Other suspected risk factors whose significance was not confirmed by multiple conditioned logistic regression analysis were: residence in rural areas, light eyes and blond hair color, extent of the awareness of the "sun x skin cancer" relationship, familial occurrence of skin cancer, excessive exposure to the sun, and freckles appearing in childhood.