Predictive gene lists for breast cancer prognosis: a topographic visualisation study

Background: The controversy surrounding the non-uniqueness of predictive gene lists (PGL) of small selected subsets of genes from very large potential candidates as available in DNA microarray experiments is now widely acknowledged 1. Many of these studies have focused on constructing discriminative semi-parametric models and as such are also subject to the issue of random correlations of sparse model selection in high dimensional spaces. In this work we outline a different approach based around an unsupervised patient-specific nonlinear topographic projection in predictive gene lists. Methods: We construct nonlinear topographic projection maps based on inter-patient gene-list relative dissimilarities. The Neuroscale, the Stochastic Neighbor Embedding(SNE) and the Locally Linear Embedding(LLE) techniques have been used to construct two-dimensional projective visualisation plots of 70 dimensional PGLs per patient, classifiers are also constructed to identify the prognosis indicator of each patient using the resulting projections from those visualisation techniques and investigate whether a-posteriori two prognosis groups are separable on the evidence of the gene lists. A literature-proposed predictive gene list for breast cancer is benchmarked against a separate gene list using the above methods. Generalisation ability is investigated by using the mapping capability of Neuroscale to visualise the follow-up study, but based on the projections derived from the original dataset. Results: The results indicate that small subsets of patient-specific PGLs have insufficient prognostic dissimilarity to permit a distinction between two prognosis patients. Uncertainty and diversity across multiple gene expressions prevents unambiguous or even confident patient grouping. Comparative projections across different PGLs provide similar results. Conclusion: The random correlation effect to an arbitrary outcome induced by small subset selection from very high dimensional interrelated gene expression profiles leads to an outcome with associated uncertainty. This continuum and uncertainty precludes any attempts at constructing discriminative classifiers. However a patient's gene expression profile could possibly be used in treatment planning, based on knowledge of other patients' responses. We conclude that many of the patients involved in such medical studies are intrinsically unclassifiable on the basis of provided PGL evidence. This additional category of 'unclassifiable' should be accommodated within medical decision support systems if serious errors and unnecessary adjuvant therapy are to be avoided.

The effects of mailing design characteristics on direct mail campaign performance

Designing effective direct mail pieces is considered a key success factor in direct marketing. However, related published empirical research is scarce while design recommendations are manifold and often conflicting. Compared with prior work, our study aims to provide more elaborate and empirically validated findings for the effects of direct mail design characteristics by analyzing 677 direct mail campaigns from non-profit organizations and financial service providers. We investigate the effects of (1) various envelope characteristics and observable cues on opening rates, and (2) characteristics of the envelope content on the keeping rates of direct mail campaigns. We show that visual design elements on the outer envelope – rather than sender-related details – are the predominant drivers of opening rates. Factors such as letter length, provision of sender information in the letter, and personalization positively influence the keeping rate. We also observe that opening and keeping rates are uncorrelated at the campaign level, implying that opening direct mail pieces is only a necessary condition for responding to offers, but not per se a driver of direct mail response.

Indication strength of coenological similarity patterns based on genus-level taxon lists and prevalence distribution

Several methods and indicators can be used to evaluate the coenological state of a given habitat, the ones which can be created simply, quickly, standardizably and reliably and which can be used to exactly quantify the state of a given habitat in point of numbers can be of outstanding practical importance in ecology. One possible method is the examination of the genera which can be found in a given habitat in great abundance and have little number of species and various ecological characteristics. For this purpose one of the most appropriate groups is that of ground-dwelling oribatid mites (Acari: Oribatida). In our research, joining the bioindication methodological project of the “Adaptation to Climate Change” Research Group of the Hungarian Academy of Sciences, the indication strength of genus-level taxon lists and the effects of the main pattern-generating factors creating similarity patterns were analysed with the help of data series on oribatid mites collected by us and originating from literature. Our aim was to develop a method with the help of which the difference expressed with distance functions between two oribatid mite genus lists originating from any sources can correspond to spatial and temporal scales. Our results prove that these genus lists are able to express the spatial distance of the habitats. With the help of this base of comparison changes in disturbed or transformed habitats can be expressed by means of oribatid mite communities, with spatial and temporal distances.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Centro esportivo virtual : um recurso de informação em educação fisica e esportes na internet

Universidade Estadual de Campinas . Faculdade de Educação Física

Catalogue of " poneromorph" ant type specimens (Hymenoptera, Formicidae) deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil

The present catalogue lists the type specimes of 112 nominal " poneromorph" ant species housed in the Formicidae collection of the Hymenoptera laboratory, Museu de Zoologia da Universidade de São Paulo (MZSP). The catalogue includes types of Amblyoponinae, Ectatomminae, Heteroponerinae, Ponerinae, and Proceratiinae, that is, all poneromorph (sensu Bolton, 2003) but for the monotypic Paraponerinae, of which the collection bears no type specimens. We present here information on type categories (holotype, paratype, syntype, lectotype, and paralectotype), label data, nomenclatural changes since the original description and type specimens conservation status. At last we present indexes for the taxa names presented.

Ichthyofauna of Rio Jurubatuba, Santos, São Paulo: a high diversity refuge in impacted lands

Ichthyofaunistic surveys in the Atlantic Rainforest have been published in relatively few works, in spite of the major biological importance of this once vast biome which is rapidly vanishing due to disordered human population growth and natural resources overexploitation. The present study aimed to access the fish fauna of a relatively well preserved basin between the cities of Santos and Cubatão (SP), an area highly modified by human activities where recent ichthyofaunistic surveys are still missing. Collections were made during three field trips in Rio Jurubatuba, a medium sized costal river, and Riacho Sabão, one of its main tributaries. A total of 2773 specimens were sampled, representing 25 species from 14 families. Six species were primary marine using the upper reaches of Rio Jurubatuba. Twelve of the 19 freshwater species are endemic of the Atlantic Rainforest and four are present in regional lists of endangered species. Only five species occurred in both Rio Jurubatuba and Riacho Sabão. The most diverse family was Characidae, followed by Poeciliidae, Rivulidae and Heptapteridae. Phalloceros caudimaculatus was the most abundant species, followed by Poecilia vivipara and Geophagus brasiliensis. The study area is considered well preserved and due to its critical location, urges for conservation policies to protect its fish diversity.

The type specimens of "dorylomorph" ants (Hymenoptera, Formicidae: Aenictinae, Ecitoninae, Cerapachyinae, Leptanilloidinae) deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil

The present catalogue lists the "dorylomorph" ant types (Aenictinae: Aenictus; Cerapachyinae: Acanthostichus and Cerapachys; Ecitoninae: Eciton, Labidus, Neivamyrmex and Nomamyrmex; and Leptanilloidinae: Asphinctanilloides and Leptanilloides) housed in the Formicidae collection of the Hymenoptera laboratory, Museu de Zoologia da Universidade de São Paulo (MZSP), Brazil. In total, the collection includes types of 141 nominal species, of which 56 are still valid. The majority of types of dorylomorph species in the MZSP collection are syntypes (67 species), but there are as well 13 species represented by holotypes only, 17 by holotypes and paratypes, 43 species by paratypes only, and one species by a paralectotype. We record the label information, condition of the specimens, nomenclatural changes, type status, and provide indexes of the listed taxa.

A catalogue of the Pseudomyrmecinae ants type specimens (Hymenoptera, Formicidae) deposited in the Museu de Zoologia da Universidade de São Paulo, Brazil

This catalogue lists the type specimens of 37 species of Pseudomyrmecinae ants deposited in the Hymenoptera Formicidae collection of the Museu de Zoologia da Universidade de São Paulo, which holds types of the only two genera that occur in the Neotropics, Pseudomyrmex Lund and Myrcidris Ward. We record the label information, condition of the specimens, nomenclatural changes, type status, and provide an index of the listed taxa.

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil. A list with 538 species of butterflies recorded in the Baixada Santista, São Paulo ( SE Brazil) is presented. Standard sampling protocols (i.e. with entomological nets) were followed. Baited traps were installed for fruit feeding species. Data from the literature and entomological collections were also considered in the total estimated species richness. The species richness recorded in the Baixada Santista region represents about 16% of the Brazilian butterfly fauna, and 34% of the known butterfly fauna for the state of São Paulo. The present list contains an appreciably higher number of species in comparison to other lists from similar biomes farther south, such as Blumenau in Santa Catarina, and Maquiné in Rio Grande do Sul.

Listas de alimentos relacionadas ao consumo alimentar de um grupo de idosos: análises e perspectivas

INTRODUÇÃO: A despeito do aumento expressivo da população idosa nos últimos anos, são escassos os estudos brasileiros relacionados ao consumo alimentar desses indivíduos. OBJETIVOS: Propor uma lista de alimentos mais consumidos por idosos residentes na Zona Leste de São Paulo e analisar os alimentos que contribuem para o consumo de nutrientes relevantes ao estado nutricional e, consequentemente, à saúde dos idosos. MÉTODOS: Foram avaliados 100 indivíduos acima de 60 anos, frequentadores de um centro de referência. Para caracterização do estado nutricional foi calculado o Índice de Massa Corporal (IMC). Para elaboração das listas de alimentos foram aplicados dois recordatórios alimentares de 24 horas (RA24h) em duas estações diferentes do ano, que foram analisados quanto à frequência de consumo de cada alimento e quanto à contribuição percentual de energia, macronutrientes, fibras, cálcio e vitamina D. RESULTADOS: Com relação ao estado nutricional, 52% apresentaram o IMC < 28 kg/m²; 15% entre 28 e 30 kg/m²; 26% entre 30 e 35 kg/m² e 7% com IMC > 35 kg/m². O aspecto positivo da dieta foi a preservação de hábitos saudáveis como o consumo de arroz e feijão, e também de vegetais verde-escuros. Como aspecto negativo observou-se que a dieta dos idosos é monótona, pois poucos alimentos contribuem para o consumo de vários nutrientes. Além disso, houve um elevado consumo de carboidratos refinados em detrimento do consumo de alimentos integrais. CONCLUSÕES: As listas de alimentos obtidas, além de permitirem a reflexão sobre intervenções educativas, permitem o desenvolvimento subsequente de um Questionário de Frequência Alimentar específico para esse grupo.

Um enfoque sanitário sobre a demanda judicial de medicamentos

No Brasil, apesar dos avanços da assistência farmacêutica, permanecem falhas na garantia do acesso dos cidadãos aos medicamentos pelo Estado. Nos últimos anos, vem crescendo a reivindicação de medicamentos por parte do cidadão via sistema judiciário. Os objetos dessas solicitações são tanto os medicamentos em falta na rede pública como aqueles ainda não incorporados pelo Sistema Único de Saúde. Este fenômeno pode ser analisado sob diferentes perspectivas, inclusive a sanitária, entendida aqui como os desfechos sobre a saúde dos indivíduos que demandam estes medicamentos. O presente texto busca discutir as principais características das demandas judiciais frente aos seguintes aspectos: o uso racional de medicamentos, o uso de evidências científicas para a indicação terapêutica proposta e o quanto as demandas se justificam diante do conceito de acesso adotado pelo campo da assistência farmacêutica. Ponderações podem ser feitas no sentido de minimizar os riscos à saúde dos demandantes de medicamentos por via judicial, sobretudo quando o objeto da ação são medicamentos não pertencentes às listas de fornecimento público, ou com uso off label, ou desprovidos de registro no país. Considera-se que o Judiciário, a partir do fornecimento de medicamentos, busca garantir a saúde dos demandantes, e assim a dignidade da pessoa humana. Cabe ressaltar que este objetivo só será atingido quando a garantia da saúde estiver associada aos aspectos que certificam a segurança do paciente, inclusive no uso de medicamentos.

Efficacy of sweet solutions for analgesia in infants between 1 and 12 months of age: a systematic review

Objective To compare the efficacy of oral sweet solutions to water or no treatment in infants aged 1-12 months during immunisation. Methods Randomised controlled trials (RCTs) were retrieved through internet searches or manual searches of reference lists. Search terms included newborn, infant, pain, sucrose and alternative names for sweet solutions. Summary estimates with 95% CIs were calculated and included relative risk (RR), risk difference (RD) and number needed to treat to benefit (NNTB) for dichotomous outcomes, and weighted mean differences (WMD) for continuous outcomes. Where pooling of results was not possible, a narrative summary of study results is presented. Results Of the 695 studies identified, 14 RCTs with 1674 injections met the inclusion criteria. Sucrose or glucose, compared to water or no treatment decreased crying during or following immunisation in 13 of the 14 studies. Infants receiving 30% glucose (three trials, 243 infants) had a decreased RR in crying incidence following immunisation (typical RR 0.80, 95% CI 0.69 to 0.93; RD -0.17, 95% CI -0.29 to -0.05; NNTB 6, 95% CI 3 to 20). With sucrose or glucose, there was a 10% WMD reduction in proportion of crying time (95% CI - 18 to - 2) and a 12 s reduction in crying duration (95% CI - 23 to -0.7 s). An optimal dose of sucrose or glucose could not be ascertained due to the varied volumes and concentrations used. Conclusion Infants aged 1-12 months administered sucrose or glucose before immunisation had moderately reduced incidence and duration of crying. Healthcare professionals should consider using sucrose or glucose before and during immunisation.

A recuperação da informação e o conceito de informação: o que é relevante em mediação cultural?

The article presents and discusses issues such as informativeness, offering of directions and information retrieval, and also lists definitions of information and mediation. Based on the topics presented, the possible problems faced by information professionals are discussed while cultural mediators in the context of art museums.

Kinematic parameters and membership probabilities of open clusters in the Bordeaux PM2000 catalogue

Aims. We derive lists of proper-motions and kinematic membership probabilities for 49 open clusters and possible open clusters in the zone of the Bordeaux PM2000 proper motion catalogue (+ 11 degrees <= delta <= + 18 degrees). We test different parametrisations of the proper motion and position distribution functions and select the most successful one. In the light of those results, we analyse some objects individually. Methods. We differenciate between cluster and field member stars, and assign membership probabilities, by applying a new and fully automated method based on both parametrisations of the proper motion and position distribution functions, and genetic algorithm optimization heuristics associated with a derivative-based hill climbing algorithm for the likelihood optimization. Results. We present a catalogue comprising kinematic parameters and associated membership probability lists for 49 open clusters and possible open clusters in the Bordeaux PM2000 catalogue region. We note that this is the first determination of proper motions for five open clusters. We confirm the non-existence of two kinematic populations in the region of 15 previously suspected non-existent objects.