Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Voice Feature Characteristic in Morbid Obese Population

Morbid obesity is highly prevalent in the Western World, and its consequences present a real public health challenge. Voice alterations can represent one of these consequences and represent an opportunity for interference with therapeutic methods. This particularly features of the individual`s voice was the goal of the present study. A group of 45 adult volunteers of both sexes with a BMI greater than 35 Kg/m(2) was selected among patients of the Obesity Ambulatory of the Digestive Surgery Division. The control group consisted of volunteers matched by sex, age (+/- 1 year), and smoking habits, but with a BMI bellow 30 Kg/m(2). All subjects were submitted to laryngoscopic examination, audio perceptive analysis, and voice acoustics determination. Examinations were always performed by the same doctor, and diagnoses were provided by two different physician specialists in laryngology and voice. Obese individuals exhibit the following modifications in voice feature: hoarseness, murmuring, vocal instability, altered jitter and shimmer, and reduced maximum phonation times as well the presence of voice strangulation at the end of emission. The voices of individuals with morbid obesity are different of the voice of nonobese people and demonstrate significant changes in vocal characteristics.

Claudin-7 down-regulation is an important feature in oral squamous cell carcinoma

Aims: Claudins, a large family of essential tight junction (TJ) proteins, are abnormally regulated in human carcinomas, especially claudin-7. The aim of this study was to investigate claudin-7 expression and alterations in oral squamous cell carcinoma (OSCC). Methods and results: Expression of claudin-7 was analysed in 132 cases of OSCC organized in a tissue microarray. Claudin-7 mRNA transcript was evaluated using real-time polymerase chain reaction and the methylation status of the promoter was also assessed. Claudin-7 was negative in 58.3% of the cases. Loss of claudin-7 protein expression was associated with recurrence (P = 0.019), tumour size (P = 0.014), clinical stage of OSCC (P = 0.055) and disease-free survival (P = 0.015). Down-regulation of the claudin-7 mRNA transcripts was observed in 78% of the cases, in accordance with immunoexpression. Analysis of the methylation status of the promoter region of claudin-7 revealed that treatment of O28 cells (that did not express claudin-7 mRNA transcripts) with 5-Aza-2`-Deoxycytidine (5-Aza-dC) led to the re-expression of claudin-7 mRNA transcript. Conclusion: Loss of claudin-7 expression is associated with important subcellular processes in OSCC with impact on clinical parameters.

Towards improving cluster-based feature selection with a simplified silhouette filter

This paper proposes a filter-based algorithm for feature selection. The filter is based on the partitioning of the set of features into clusters. The number of clusters, and consequently the cardinality of the subset of selected features, is automatically estimated from data. The computational complexity of the proposed algorithm is also investigated. A variant of this filter that considers feature-class correlations is also proposed for classification problems. Empirical results involving ten datasets illustrate the performance of the developed algorithm, which in general has obtained competitive results in terms of classification accuracy when compared to state of the art algorithms that find clusters of features. We show that, if computational efficiency is an important issue, then the proposed filter May be preferred over their counterparts, thus becoming eligible to join a pool of feature selection algorithms to be used in practice. As an additional contribution of this work, a theoretical framework is used to formally analyze some properties of feature selection methods that rely on finding clusters of features. (C) 2011 Elsevier Inc. All rights reserved.

An investigation into feature construction to assist word sense disambiguation

Identifying the correct sense of a word in context is crucial for many tasks in natural language processing (machine translation is an example). State-of-the art methods for Word Sense Disambiguation (WSD) build models using hand-crafted features that usually capturing shallow linguistic information. Complex background knowledge, such as semantic relationships, are typically either not used, or used in specialised manner, due to the limitations of the feature-based modelling techniques used. On the other hand, empirical results from the use of Inductive Logic Programming (ILP) systems have repeatedly shown that they can use diverse sources of background knowledge when constructing models. In this paper, we investigate whether this ability of ILP systems could be used to improve the predictive accuracy of models for WSD. Specifically, we examine the use of a general-purpose ILP system as a method to construct a set of features using semantic, syntactic and lexical information. This feature-set is then used by a common modelling technique in the field (a support vector machine) to construct a classifier for predicting the sense of a word. In our investigation we examine one-shot and incremental approaches to feature-set construction applied to monolingual and bilingual WSD tasks. The monolingual tasks use 32 verbs and 85 verbs and nouns (in English) from the SENSEVAL-3 and SemEval-2007 benchmarks; while the bilingual WSD task consists of 7 highly ambiguous verbs in translating from English to Portuguese. The results are encouraging: the ILP-assisted models show substantial improvements over those that simply use shallow features. In addition, incremental feature-set construction appears to identify smaller and better sets of features. Taken together, the results suggest that the use of ILP with diverse sources of background knowledge provide a way for making substantial progress in the field of WSD.

Interactive Vector Field Feature Identification

We introduce a flexible technique for interactive exploration of vector field data through classification derived from user-specified feature templates. Our method is founded on the observation that, while similar features within the vector field may be spatially disparate, they share similar neighborhood characteristics. Users generate feature-based visualizations by interactively highlighting well-accepted and domain specific representative feature points. Feature exploration begins with the computation of attributes that describe the neighborhood of each sample within the input vector field. Compilation of these attributes forms a representation of the vector field samples in the attribute space. We project the attribute points onto the canonical 2D plane to enable interactive exploration of the vector field using a painting interface. The projection encodes the similarities between vector field points within the distances computed between their associated attribute points. The proposed method is performed at interactive rates for enhanced user experience and is completely flexible as showcased by the simultaneous identification of diverse feature types.

A Parallel Hardware Architecture for Scale and Rotation Invariant Feature Detection

This paper proposes a parallel hardware architecture for image feature detection based on the Scale Invariant Feature Transform algorithm and applied to the Simultaneous Localization And Mapping problem. The work also proposes specific hardware optimizations considered fundamental to embed such a robotic control system on-a-chip. The proposed architecture is completely stand-alone; it reads the input data directly from a CMOS image sensor and provides the results via a field-programmable gate array coupled to an embedded processor. The results may either be used directly in an on-chip application or accessed through an Ethernet connection. The system is able to detect features up to 30 frames per second (320 x 240 pixels) and has accuracy similar to a PC-based implementation. The achieved system performance is at least one order of magnitude better than a PC-based solution, a result achieved by investigating the impact of several hardware-orientated optimizations oil performance, area and accuracy.

U-curve: A branch-and-bound optimization algorithm for U-shaped cost functions on Boolean lattices applied to the feature selection problem

This paper presents the formulation of a combinatorial optimization problem with the following characteristics: (i) the search space is the power set of a finite set structured as a Boolean lattice; (ii) the cost function forms a U-shaped curve when applied to any lattice chain. This formulation applies for feature selection in the context of pattern recognition. The known approaches for this problem are branch-and-bound algorithms and heuristics that explore partially the search space. Branch-and-bound algorithms are equivalent to the full search, while heuristics are not. This paper presents a branch-and-bound algorithm that differs from the others known by exploring the lattice structure and the U-shaped chain curves of the search space. The main contribution of this paper is the architecture of this algorithm that is based on the representation and exploration of the search space by new lattice properties proven here. Several experiments, with well known public data, indicate the superiority of the proposed method to the sequential floating forward selection (SFFS), which is a popular heuristic that gives good results in very short computational time. In all experiments, the proposed method got better or equal results in similar or even smaller computational time. (C) 2009 Elsevier Ltd. All rights reserved.

Desmistificando os braquetes autoligáveis

Atualmente, os braquetes autoligáveis têm sido associados a tratamentos mais rápidos e eficazes, o que desperta a curiosidade em compará-los ao sistema convencional. Ao contrário dos braquetes tradicionais, os autoligáveis não necessitam de ligaduras, sejam elásticas ou metálicas. A literatura é farta em concluir que essa característica diminui, ostensivamente, a resistência do atrito durante as mecânicas de deslize. Além disso, existem alegações sobre a dimimuição da necessidade de extrações e de expansão maxilar com o uso desses acessórios. Portanto, o objetivo dessa revisão de literatura foi buscar os mais novos estudos a respeito dos aparelhos autoligáveis atualmente utilizados nos tratamentos ortodônticos, confirmando ou retificando as especulações vigentes.

Anatomia foliar de Eugenia florida DC. (Myrtaceae)

Foi feito o estudo anatômico da folha de Eugenia florida DC., espécie arbórea da família Myrtaceae, coletada no Campus da Fundação Oswaldo Cruz, Rio de Janeiro, RJ. A espécie apresenta importantes propriedades farmacológicas, incluindo-se atividade antiviral. O presente estudo teve como objetivo fornecer dados, revelados através da microscopia óptica e da microscopia eletrônica de varredura, que possam contribuir para o conhecimento da espécie e, conseqüentemente, para a segurança em sua identificação. Anatomicamente, a folha é hipostomática, com organização dorsiventral do mesofilo. Apresenta tricomas simples apenas sobre a nervura mediana da face adaxial. As células epidérmicas apresentam contorno sinuoso em vista frontal e cutícula estriada. O parênquima paliçádico destaca-se pela grande quantidade de cristais prismáticos de oxalato de cálcio. Em posição subepidérmica ocorrem cavidades secretoras de óleos essenciais, pouco numerosas, nas duas faces da lâmina foliar. As células epidérmicas situadas sobre as estruturas secretoras constituem característica de valor diagnóstico e são reconhecíveis pela célula de topo, que é reniforme, circundada pelas adjacentes, que apresentam disposição radiada. A comparação entre folhas de sol e de sombra revela que, nas primeiras, as estruturas secretoras são completamente diferenciadas, ao contrário das folhas de sombra, além de apresentarem maior concentração de compostos ergásticos.

A new species of Neotropical freshwater stingray of the genus Potamotrygon Garman, 1877 from the Río Madrede Díos, Peru (Chondrichthyes: Potamotrygonidae)

Potamotrygon tatianae sp. nov., is described from Río Madre de Díos, Peru, upper Rio Madeira basin. The new species is distinguished from all congeners by a unique combination of characters, including its dorsal color pattern formed by a relatively slender, highly convoluted, beige to dark brown vermicular pattern, a single row of dorsal tail spines, and a relatively longer tail posterior to caudal stings. Potamotrygon tatianae sp. nov., occurs sympatrically with other species of Potamotrygon (P. falkneri, P. orbignyi and P. motoro). From the similar species P. falkneri, P. tatianae sp. nov., is further distinguished by the absence of circular, reniform, and oval spots, by its proportionally much longer tail, by having dorsal tail spines in one irregular row, and by features of the ventral lateral-line canal, dermal denticles and neurocranium. From P. orbignyi, the new species is distinct by lacking a reticulate pattern on dorsal disc and by the presence of two angular cartilages. From P. motoro, P. tatianae sp. nov., is further separated by the lack of ocelli formed by strong black concentric rings, by the more flattened aspect of its head and disc, and by having smaller and more numerous teeth. The discovery of a new species that so closely resembles a congeneric form in color pattern, a feature highly variable within the latter, highlights the importance of examining large series of individuals and of detailed morphological analyses in revealing the potentially highly cryptic nature of the diversity within the family.

Caracterização de feições oceanográficas na plataforma de Santa Catarina através de imagens orbitais

Este trabalho tem por objetivo identificar e caracterizar as feições oceanográficas de pequena e mesoescala que ocorrem na plataforma continental de Santa Catarina (SC). Foram empregadas imagens de temperatura e concentração de clorofila da superfície do mar (TSM e CSM), obtidas pelo sensor MODIS. Foi selecionada uma imagem diária para cada mês do ano de 2003, excetuando dezembro, onde procurou-se avaliar efeitos sazonais. As feições oceanográficas foram observadas através da aplicação de diferentes níveis de contraste e paletas de cores para realce. Foram identificadas feições como vórtices, meandros, cogumelos, plumas, filamentos, frentes e áreas de ressurgências. Os resultados indicam que no verão a distribuição superficial em mesoescala da temperatura é mais homogênea, levando a um número menor de feições observáveis. O fenômeno de ressurgência costeira em escala localizada ao sul da Ilha de SC e junto à costa foi observado nos meses de novembro, janeiro e fevereiro. Durante o outono e o inverno as imagens apresentaram maior grau de complexidade, principalmente devido à presença da frente costeira do Prata, com características de menor temperatura e maiores valores de clorofila.

Description of a new species of the genus Leporinus Spix (Characiformes: Anostomidae) from the rio Araguaia, Brazil, with comments on the taxonomy and distribution of L. parae and L. lacustris

A new species of the genus Leporinus is described from the rio Araguaia, in Mato Grosso and Goiás states, Brazil. The new species has the dental formula 4/3, a unique feature within the genus; all other species of Leporinus have dental formulae 3/3, 3/4 or 4/4. In addition, the new species can also be distinguished by the following combination of characters: 36 to 37 scales in the lateral line, 4/4.5 or 4/5 series of scales in the transversal line, 16 circumpeduncular scale series, anal fin surpassing base of lower caudal-fin rays and three blotches along the lateral line. The new species shares with L. parae and L. lacustris a rather deep body, terminal mouth, long anal fin, three small dark blotches on the lateral line, the latter two, particularly the last one, usually fading, and preference for lentic habitats. Comments on the taxonomy and distribution of the species L. parae and L. lacustris are provided.

A regulação assistencial e a produção do cuidado: um arranjo potente para qualificar a atenção

A produção do cuidado integral e a eqüidade são desafios na gestão do SUS. Analisou-se um arranjo da gestão municipal para a produção do cuidado implantado por meio da regulação assistencial com o objetivo de enriquecer as reflexões sobre o tema. Foi realizado estudo de caso em que os dados foram obtidos mediante observação, entrevistas, narrativas escritas e análise documental. Os sujeitos da pesquisa foram gestores e trabalhadores da Secretaria de Saúde. Como resultado destaca-se um conceito de rede viva, produzida ativamente pela construção de relações entre os trabalhadores dos diferentes serviços. Destacam-se as ações de apoio ao cuidado produzido pelas equipes, com base na regulação assistencial e na gestão dos processos de trabalho. Os resultados foram expressivos na qualificação do cuidado, na redução das filas às especialidades e na satisfação dos profissionais. Como marca do processo, evidencia-se a necessidade de enriquecer, em ato, os saberes técnicos com as tecnologias leves e os saberes produzidos em movimentos ativos da gestão para a produção do cuidado.

Ventilation behavior in trained and untrained men during incremental test: evidence of one metabolic transition point

This study aimed to describe and compare the ventilation behavior during an incremental test utilizing three mathematical models and to compare the feature of ventilation curve fitted by the best mathematical model between aerobically trained (TR) and untrained ( UT) men. Thirty five subjects underwent a treadmill test with 1 km.h(-1) increases every minute until exhaustion. Ventilation averages of 20 seconds were plotted against time and fitted by: bi-segmental regression model (2SRM); three-segmental regression model (3SRM); and growth exponential model (GEM). Residual sum of squares (RSS) and mean square error (MSE) were calculated for each model. The correlations between peak VO2 (VO2PEAK), peak speed (Speed(PEAK)), ventilatory threshold identified by the best model (VT2SRM) and the first derivative calculated for workloads below (moderate intensity) and above (heavy intensity) VT2SRM were calculated. The RSS and MSE for GEM were significantly higher (p < 0.01) than for 2SRM and 3SRM in pooled data and in UT, but no significant difference was observed among the mathematical models in TR. In the pooled data, the first derivative of moderate intensities showed significant negative correlations with VT2SRM (r = -0.58; p < 0.01) and Speed(PEAK) (r = -0.46; p < 0.05) while the first derivative of heavy intensities showed significant negative correlation with VT2SRM (r = -0.43; p < 0.05). In UT group the first derivative of moderate intensities showed significant negative correlations with VT2SRM (r = -0.65; p < 0.05) and Speed(PEAK) (r = -0.61; p < 0.05), while the first derivative of heavy intensities showed significant negative correlation with VT2SRM (r= -0.73; p < 0.01), Speed(PEAK) (r = -0.73; p < 0.01) and VO2PEAK (r = -0.61; p < 0.05) in TR group. The ventilation behavior during incremental treadmill test tends to show only one threshold. UT subjects showed a slower ventilation increase during moderate intensities while TR subjects showed a slower ventilation increase during heavy intensities.