Estudo clínico randomizado e duplo cego comparando dois métodos de escleroterapia para veias reticulares e telangiectasias em membros inferiores

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Helping End-Users “Engineer” Dependable Web Applications

End-user programmers are increasingly relying on web authoring environments to create web applications. Although often consisting primarily of web pages, such applications are increasingly going further, harnessing the content available on the web through “programs” that query other web applications for information to drive other tasks. Unfortunately, errors can be pervasive in web applications, impacting their dependability. This paper reports the results of an exploratory study of end-user web application developers, performed with the aim of exposing prevalent classes of errors. The results suggest that end-users struggle the most with the identification and manipulation of variables when structuring requests to obtain data from other web sites. To address this problem, we present a family of techniques that help end user programmers perform this task, reducing possible sources of error. The techniques focus on simplification and characterization of the data that end-users must analyze while developing their web applications. We report the results of an empirical study in which these techniques are applied to several popular web sites. Our results reveal several potential benefits for end-users who wish to “engineer” dependable web applications.

ENHANCEMENT OF THE FAA’s ON-LINE WILDLIFE AIRCRAFT STRIKE DATABASE WITH AN INTERACTIVE GRAPHICS CAPABILITY

Embry-Riddle Aeronautical University (Prescott, AZ, USA) was awarded a grant from the William J. Hughes FAA Technical Center in October 1999 to develop and maintain a web site dealing with a wide variety of airport safety wildlife concerns. Initially, the web site enabled users to access related topics such as wildlife management (at/near airports), bird identification information, FAA wildlife management guidelines, education, pictures, current news, upcoming meetings and training, available jobs and discussion/forum sections. In April 2001, the web site was augmented with an on-line wildlife strike report (FAA Form 5200-7). Upon submittal on-line, “quick look” email notifications are sent to concerned government personnel. The distribution of these emails varies as to whether there was damage, human injuries/fatalities, and whether feather remains were collected and will be sent to the Smithsonian Institution for identification. In July 2002, a real-time on-line query system was incorporated to allow federal and local government agencies, airport and operator personnel, and USDA and airport wildlife biologists to access this database (which as of June 2005 contains 68,288 researched strike reports added to at a rate of approximately 500 strike reports/month) to formulate strategies to reduce the hazards wildlife present to aviation. To date (June 2005), over 15,000 on-line real-time queries were processed. In June 2004, ERAU was authorized to develop a graphical interface to this on-line query system. Current capabilities include mapping strikes (by species) on the US map, each of the contiguous 48 state maps (with AK and HI being added), and airport diagrams of the major metropolitan airports as well as the next 46 airports with the most reported strikes The latter capability depicts strikes by runway in plan as well as in elevation view. Currently under development is the ability to view time-sequenced strikes on the US map. This extensive graphical interface will give analysts the ability to view strike patterns with a wide variety of variables including species, seasons, migration patterns, etc. on US and state maps and airport diagrams.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of SIS, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that SIS has overall better performance. Conclusions: SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of SIS in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.

Seeing beyond reading: a survey on visual text analytics

We review recent visualization techniques aimed at supporting tasks that require the analysis of text documents, from approaches targeted at visually summarizing the relevant content of a single document to those aimed at assisting exploratory investigation of whole collections of documents.Techniques are organized considering their target input materialeither single texts or collections of textsand their focus, which may be at displaying content, emphasizing relevant relationships, highlighting the temporal evolution of a document or collection, or helping users to handle results from a query posed to a search engine.We describe the approaches adopted by distinct techniques and briefly review the strategies they employ to obtain meaningful text models, discuss how they extract the information required to produce representative visualizations, the tasks they intend to support and the interaction issues involved, and strengths and limitations. Finally, we show a summary of techniques, highlighting their goals and distinguishing characteristics. We also briefly discuss some open problems and research directions in the fields of visual text mining and text analytics.

The SB-index and the HSB-index: efficient indices for spatial data warehouses

Spatial data warehouses (SDWs) allow for spatial analysis together with analytical multidimensional queries over huge volumes of data. The challenge is to retrieve data related to ad hoc spatial query windows according to spatial predicates, avoiding the high cost of joining large tables. Therefore, mechanisms to provide efficient query processing over SDWs are essential. In this paper, we propose two efficient indices for SDW: the SB-index and the HSB-index. The proposed indices share the following characteristics. They enable multidimensional queries with spatial predicate for SDW and also support predefined spatial hierarchies. Furthermore, they compute the spatial predicate and transform it into a conventional one, which can be evaluated together with other conventional predicates by accessing a star-join Bitmap index. While the SB-index has a sequential data structure, the HSB-index uses a hierarchical data structure to enable spatial objects clustering and a specialized buffer-pool to decrease the number of disk accesses. The advantages of the SB-index and the HSB-index over the DBMS resources for SDW indexing (i.e. star-join computation and materialized views) were investigated through performance tests, which issued roll-up operations extended with containment and intersection range queries. The performance results showed that improvements ranged from 68% up to 99% over both the star-join computation and the materialized view. Furthermore, the proposed indices proved to be very compact, adding only less than 1% to the storage requirements. Therefore, both the SB-index and the HSB-index are excellent choices for SDW indexing. Choosing between the SB-index and the HSB-index mainly depends on the query selectivity of spatial predicates. While low query selectivity benefits the HSB-index, the SB-index provides better performance for higher query selectivity.

Proteomic profiling of the rat hypothalamus

Background: The hypothalamus plays a pivotal role in numerous mechanisms highly relevant to the maintenance of body homeostasis, such as the control of food intake and energy expenditure. Impairment of these mechanisms has been associated with the metabolic disturbances involved in the pathogenesis of obesity. Since rodent species constitute important models for metabolism studies and the rat hypothalamus is poorly characterized by proteomic strategies, we performed experiments aimed at constructing a two-dimensional gel electrophoresis (2-DE) profile of rat hypothalamus proteins. Results: As a first step, we established the best conditions for tissue collection and protein extraction, quantification and separation. The extraction buffer composition selected for proteome characterization of rat hypothalamus was urea 7 M, thiourea 2 M, CHAPS 4%, Triton X-100 0.5%, followed by a precipitation step with chloroform/methanol. Two-dimensional (2-D) gels of hypothalamic extracts from four-month-old rats were analyzed; the protein spots were digested and identified by using tandem mass spectrometry and database query using the protein search engine MASCOT. Eighty-six hypothalamic proteins were identified, the majority of which were classified as participating in metabolic processes, consistent with the finding of a large number of proteins with catalytic activity. Genes encoding proteins identified in this study have been related to obesity development. Conclusion: The present results indicate that the 2-DE technique will be useful for nutritional studies focusing on hypothalamic proteins. The data presented herein will serve as a reference database for studies testing the effects of dietary manipulations on hypothalamic proteome. We trust that these experiments will lead to important knowledge on protein targets of nutritional variables potentially able to affect the complex central nervous system control of energy homeostasis.

Analytical Processing Over XML and XLink

Current commercial and academic OLAP tools do not process XML data that contains XLink. Aiming at overcoming this issue, this paper proposes an analytical system composed by LMDQL, an analytical query language. Also, the XLDM metamodel is given to model cubes of XML documents with XLink and to deal with syntactic, semantic and structural heterogeneities commonly found in XML documents. As current W3C query languages for navigating in XML documents do not support XLink, XLPath is discussed in this article to provide features for the LMDQL query processing. A prototype system enabling the analytical processing of XML documents that use XLink is also detailed. This prototype includes a driver, named sql2xquery, which performs the mapping of SQL queries into XQuery. To validate the proposed system, a case study and its performance evaluation are presented to analyze the impact of analytical processing over XML/XLink documents.

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Abstract Background MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. Results In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots. Conclusions Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.

Dental caries associated factors in 12 year-old schoolchildren from a municipality in the state of São Paulo, Brazil

Objective To analyze the possible association between dental caries, fluorosis and the need for treatment in 12 year-old schoolchildren and the socioeconomic conditions of parents/guardians in the city of Franca, in the state of São Paulo. Methods A random sample of schoolchildren aged 12 was obtained from the school records in Franca, using a systematic random technique. The epidemiological survey was carried out by a single calibrated examiner, on 258 public and private schoolchildren in order to obtain the prevalence of dental caries, the need for treatment and the severity of dental fluorosis. Parents/guardians were also interviewed to assess their socioeconomic conditions (education and per capita income). We used multiple correlation analysis to investigate associations between category variables. Results It was possible to identify two distinct groups, with associations between the variables: the first group, represented by schoolchildren with average prevalence of caries, need for treatment, low level of parental education and income; and a second group represented by schoolchildren with low prevalence of caries, no need for treatment, high parental education and income. The two dimensions explained approximately 35% of total inertia. The factors within each group are related. Conclusion High income and parental education are associated with the low prevalence of dental caries but there is no association with dental fluorosis.

PRoSPer: perceptual similarity queries in medical CBIR systems through user profiles

In this paper, we present a novel approach to perform similarity queries over medical images, maintaining the semantics of a given query posted by the user. Content-based image retrieval systems relying on relevance feedback techniques usually request the users to label relevant/irrelevant images. Thus, we present a highly effective strategy to survey user profiles, taking advantage of such labeling to implicitly gather the user perceptual similarity. The profiles maintain the settings desired for each user, allowing tuning of the similarity assessment, which encompasses the dynamic change of the distance function employed through an interactive process. Experiments on medical images show that the method is effective and can improve the decision making process during analysis.

O ciclo da comunicação científica na semiosfera

Este ensaio apresenta a construção de um objeto de pesquisa com base na teoria da semiótica da cultura. São feitas reflexões sobre os sistemas modelizantes envolvidos no ciclo da comunicação científica em grupo de pesquisa de universidade, desde a busca da informação até a publicação dos resultados dos estudos. As linguagens naturais (idiomas) e artificiais (linguagem de busca em computadores e vocabulários controlados) são identificadas. A partir disso, o objeto se delineia como o conjunto de textos da cultura e a própria semiosfera, representada pelos diálogos dos sujeitos da cultura e o processo de comunicação envolvido. Alguns desafios se apresentam, como: a necessidade de aprofundamento na teoria da semiótica da cultura, a participação do pesquisador também como sujeito da pesquisa e o trabalho com a interdisciplinaridade para estudar um objeto com as vertentes da ciência da informação, biomedicina, semiótica e outras disciplinas a elas relacionadas.

QuMinS: fast and scalable querying, mining and summarizing multi-modal databases

Given a large image set, in which very few images have labels, how to guess labels for the remaining majority? How to spot images that need brand new labels different from the predefined ones? How to summarize these data to route the user’s attention to what really matters? Here we answer all these questions. Specifically, we propose QuMinS, a fast, scalable solution to two problems: (i) Low-labor labeling (LLL) – given an image set, very few images have labels, find the most appropriate labels for the rest; and (ii) Mining and attention routing – in the same setting, find clusters, the top-'N IND.O' outlier images, and the 'N IND.R' images that best represent the data. Experiments on satellite images spanning up to 2.25 GB show that, contrasting to the state-of-the-art labeling techniques, QuMinS scales linearly on the data size, being up to 40 times faster than top competitors (GCap), still achieving better or equal accuracy, it spots images that potentially require unpredicted labels, and it works even with tiny initial label sets, i.e., nearly five examples. We also report a case study of our method’s practical usage to show that QuMinS is a viable tool for automatic coffee crop detection from remote sensing images.

Skeletal muscle mitochondrial DNA content in exercising humans

[EN] Several weeks of intense endurance training enhances mitochondrial biogenesis in humans. Whether a single bout of exercise alters skeletal muscle mitochondrial DNA (mtDNA) content remains unexplored. Double-stranded mtDNA, estimated by slot-blot hybridization and real time PCR and expressed as mtDNA-to-nuclear DNA ratio (mtDNA/nDNA) was obtained from the vastus lateralis muscle of healthy human subjects to investigate whether skeletal muscle mtDNA changes during fatiguing and nonfatiguing prolonged moderate intensity [2.0-2.5 h; approximately 60% maximal oxygen consumption (Vo(2 max))] and short repeated high-intensity exercise (5-8 min; approximately 110% Vo(2 max)). In control resting and light exercise (2 h; approximately 25% Vo(2 max)) studies, mtDNA/nDNA did not change. Conversely, mtDNA/nDNA declined after prolonged fatiguing exercise (0.863 +/- 0.061 vs. 1.101 +/- 0.067 at baseline; n = 14; P = 0.005), remained lower after 24 h of recovery, and was restored after 1 wk. After nonfatiguing prolonged exercise, mtDNA/nDNA tended to decline (n = 10; P = 0.083) but was reduced after three repeated high-intensity exercise bouts (0.900 +/- 0.049 vs. 1.067 +/- 0.071 at baseline; n = 7; P = 0.013). Our findings indicate that prolonged and short repeated intense exercise can lead to significant reductions in human skeletal muscle mtDNA content, which might function as a signal stimulating mitochondrial biogenesis with exercise training.

Muscular development and physical activity as major determinants of femoral bone mass acquisition during growth

[EN] OBJECTIVES: To investigate to what extent bone mass accrual is determined by physical activity and changes in lean, fat, and total body mass during growth. METHODS: Twenty six physically active and 16 age matched control boys were followed up for three years. All subjects were prepubertal at the start of the survey (mean (SEM) age 9.4 (0.3) years). The weekly physical activity of the active boys included compulsory physical education sessions (80-90 minutes a week), three hours a week of extracurricular sports participation, and occasional sports competitions at weekends. The physical activity of the control group was limited to the compulsory physical education curriculum. Bone mineral content (BMC) and areal density (BMD), lean mass, and fat mass were measured by dual energy x ray absorptiometry. RESULTS: The effect of sports participation on femoral bone mass accrual was remarkable. Femoral BMC and BMD increased twice as much in the active group as in the controls over the three year period (p < 0.05). The greatest correlation was found between the increment in femoral bone mass and the increment in lean mass (BMC r = 0.67 and BMD r = 0.69, both p < 0.001). Multiple regression analysis revealed enhancement in lean mass as the best predictor of the increment in femoral bone BMC (R = 0.65) and BMD (R = 0.69). CONCLUSIONS: Long term sports participation during early adolescence results in greater accrual of bone mass. Enhancement of lean mass seems to be the best predictor of this bone mass accumulation. However, for a given muscle mass, a greater level of physical activity is associated with greater bone mass and density in peripubertal boys.