Selection bias in gene extraction on the basis of microarray gene-expression data

In the context of cancer diagnosis and treatment, we consider the problem of constructing an accurate prediction rule on the basis of a relatively small number of tumor tissue samples of known type containing the expression data on very many (possibly thousands) genes. Recently, results have been presented in the literature suggesting that it is possible to construct a prediction rule from only a few genes such that it has a negligible prediction error rate. However, in these results the test error or the leave-one-out cross-validated error is calculated without allowance for the selection bias. There is no allowance because the rule is either tested on tissue samples that were used in the first instance to select the genes being used in the rule or because the cross-validation of the rule is not external to the selection process; that is, gene selection is not performed in training the rule at each stage of the cross-validation process. We describe how in practice the selection bias can be assessed and corrected for by either performing a cross-validation or applying the bootstrap external to the selection process. We recommend using 10-fold rather than leave-one-out cross-validation, and concerning the bootstrap, we suggest using the so-called. 632+ bootstrap error estimate designed to handle overfitted prediction rules. Using two published data sets, we demonstrate that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.

Are supplier selection criteria going green? Case studies of companies in Brazil

Purpose - The purpose of this paper is to verify if Brazilian companies are adopting environmental requirements in the supplier selection process. Further, this paper intends to analyze whether there is a relation between the level of environmental management maturity and the inclusion of environmental criteria in the companies` selection of suppliers. Design/methodology/approach - A review of mainstream literature on environmental management, traditional criteria in the supplier selection process and the incorporation of environmental requirements in this context. The empirical study`s strategy is based on five Brazilian case studies with industrial companies. Face-to-face interviews and informal conversations are to be held, explanations made by e-mail with representatives from the purchasing, environmental management, logistics and other areas, and observation and the collection of company documents are also employed. Findings - Based on the cases, it is concluded that companies still use traditional criteria to select suppliers, such as quality and cost, and do not adopt environmental requirements in the supplier selection process in a uniform manner. Evidence found shows that the level of environmental management maturity influences the depth with which companies adopt environmental criteria when selecting suppliers. Thus, a company with more advanced environmental management adopts more formal procedures for selecting environmentally appropriate suppliers than others. Originality/value - This is the first known study to verify if Brazilian companies are adopting environmental requirements in the supplier selection process.

Anti-inflammatory effects of red pepper (Capsicum baccatum) on carrageenan- and antigen-induced inflammation

Inflammation is a pivotal component of a variety of diseases, such as atherosclerosis and tumour progression. Various naturally occurring phytochemicals exhibit anti-inflammatory activity and are considered to be potential drug candidates against inflammation-related pathological processes. Capsicum baccatum L. var. pendulum (Willd.) Eshbaugh (Solanaceae) is the most consumed species in Brazil, and its compounds, such as capsaicinoids, have been found to inhibit the inflammatory process. However, the anti-inflammatory effects of C. baccatum have not been characterized. Thus, this study was designed to evaluate the effects of C. baccatum juice in animal models of acute inflammation induced by carrageenan and immune inflammation induced by methylated bovine serum albumin. Pretreatment (30 min) of rats with pepper juice (0.25-2.0 g kg(-1)) significantly decreased leucocyte and neutrophil migration, exudate volume and protein and LDH concentration in pleural exudates of a pleurisy model. This juice also inhibited neutrophil migration and reduced the vascular permeability on carrageenan-induced peritonitis in mice. C. baccatum juice also reduced neutrophil recruitment and exudate levels of pro-inflammatory cytokines TNF-alpha, and IL-1 beta in mouse inflammatory immune peritonitis. Furthermore, we demonstrated that the main constituent of C. baccatum juice, as extracted with chloroform, is capsaicin. In agreement with this, capsaicin was able to inhibit the neutrophil migration towards the inflammatory focus. To our knowledge, this is the first demonstration of the anti-inflammatory effect of C. baccatum juice and our data suggest that this effect may be induced by capsaicin. Moreover, the anti-inflammatory effect induced by red pepper may be by inhibition of pro-inflammatory cytokine production at the inflammatory site.

Phosphoinositide-3 Kinase gamma Activity Contributes to Sepsis and Organ Damage by Altering Neutrophil Recruitment

Rationale Sepsis is a leading cause of death in the intensive care unit, characterized by a systemic inflammatory response (SIRS) and bacterial infection, which can often induce multiorgan damage and failure. Leukocyte recruitment, required to limit bacterial spread, depends on phosphoinositide-3 kinase gamma (PI3K gamma) signaling in vitro; however, the role of this enzyme in polymicrobial sepsis has remained unclear. Objectives: This study aimed to determine the specific role of the kinase activity of PI3K gamma in the pathogenesis of sepsis and multiorgan damage. Methods. PI3K gamma wild-type, knockout, and kinase-dead mice were exposed to cecal ligation and perforation induced sepsis and assessed for survival; pulmonary, hepatic, and cardiovascular damage; coagulation derangements; systemic inflammation; bacterial spread; and neutrophil recruitment. Additionally, wild-type mice were treated either before or after the onset of sepsis with a PI3K gamma inhibitor and assessed for survival, neutrophil recruitment, and bacterial spread. Measurements and Main Results: Both genetic and pharmaceutical PI3K gamma kinase inhibition significantly improved survival, reduced multiorgan damage, and limited bacterial decompartmentalization, while modestly affecting SIRS. Protection resulted from both neutrophil-independent mechanisms, involving improved cardiovascular function, and neutrophil-dependent mechanisms, through reduced susceptibility to neutrophil migration failure during severe sepsis by maintaining neutrophil surface expression of the chemokine receptor, CXCR2. Furthermore, PI3K gamma pharmacological inhibition significantly decreased mortality and improved neutrophil migration and bacterial control, even when administered during established septic shock. Conclusions: This study establishes PI3K gamma as a key molecule in the pathogenesis of septic infection and the transition from SIRS to organ damage and identifies it as a novel possible therapeutic target.

HTLV-I/II and blood donors: determinants associated with seropositivity in a low risk population

OBJECTIVE: Blood donors in Brazil have been routinely screened for HTLV-I/II since 1993. A study was performed to estimate the prevalence of HTLV-I/II infection in a low risk population and to better understand determinants associated with seropositivity. METHODS: HTLV-I/II seropositive (n=135), indeterminate (n=167) and seronegative blood donors (n=116) were enrolled in an open prevalence prospective cohort study. A cross-sectional epidemiological study of positive, indeterminate and seronegative HTLV-I/II subjects was conducted to assess behavioral and environmental risk factors for seropositivity. HTLV-I/II serological status was confirmed using enzyme-linked immunosorbent assay (EIA) and Western blot (WB). RESULTS: The three groups were not homogeneous. HTLV-I/II seropositivity was associated to past blood transfusion and years of schooling, a marker of socioeconomic status, and use of non-intravenous illegal drugs. CONCLUSIONS: The study results reinforce the importance of continuous monitoring and improvement of blood donor selection process.

Processos de regulação da violência escolar: das políticas às práticas

Esta comunicação tem como objetivo analisar como as políticas respeitantes à segurança escolar são reinterpretadas e reorientadas em resultado das estratégias e filosofias de intervenção das direções das escolas e outros agentes educativos. Tendo como premissa que o contexto social não determina linearmente a violência escolar, o estudo centrou-­se na análise das relações entre o contexto social local e organizacional das escolas, procurando identificar os factores relevantes para o processo de regulação da violência. Foram selecionados três clusters de escolas na Área Metropolitana de Lisboa, tendo em conta contrastes intra e inter clusters assim como a sua posição relativa face aos níveis de violência registadas a nível nacional. Foi identificada uma diversidade significativa de respostas à violência, concretizadas na mobilização de diferentes recursos pelos responsáveis das escolas com o duplo objetivo de atingir as metas políticas definidas e os seus próprios interesses estratégicos. Esta apropriação e reorientação das políticas realiza-­se através da estruturação de redes locais de poder, hierarquizando competências e responsabilidades, e no processo, redefinindo os objetivos do processo de prevenção e intervenção. A ocultação das situações de violência, o recrutamento preferencial de estudantes de classe média ou com sucesso educativo elevado, ou ainda as sanções desproporcionais para alunos agressores ou indisciplinados, foram algumas das estratégias identificadas. Isto mostra que os atores têm diferentes possibilidades e capacidades de ação num sistema complexo de regras sociais que, dentro de certos limites, lhes permite reinterpretar e reconstruir regras e, em última instância, contribuir para a alteração do próprio sistema (Mouzelis, 2000;; Burns e Flam, 2000;; Lipsky, 1980).

Contrastive terminology: semitic, anglo-germanic and latin concept building through complex terms. (avoiding one-way method procedures in translation

This paper aims to present a contrastive approach between three different ways of building concepts after proving the similar syntactic possibilities that coexist in terms. However, from the semantic point of view we can see that each language family has a different distribution in meaning. But the most important point we try to show is that the differences found in the psychological process when communicating concepts should guide the translator and the terminologist in the target text production and the terminology planning process. Differences between languages in the information transmission process are due to the different roles the different types of knowledge play. We distinguish here the analytic-descriptive knowledge and the analogical knowledge among others. We also state that none of them is the best when determining the correctness of a term, but there has to be adequacy criteria in the selection process. This concept building or term building success is important when looking at the linguistic map of the information society.

Supplier's selection model based on an empirical study

The problem of selecting suppliers/partners is a crucial and important part in the process of decision making for companies that intend to perform competitively in their area of activity. The selection of supplier/partner is a time and resource-consuming task that involves data collection and a careful analysis of the factors that can positively or negatively influence the choice. Nevertheless it is a critical process that affects significantly the operational performance of each company. In this work, there were identified five broad selection criteria: Quality, Financial, Synergies, Cost, and Production System. Within these criteria, it was also included five sub-criteria. After the identification criteria, a survey was elaborated and companies were contacted in order to understand which factors have more weight in their decisions to choose the partners. Interpreted the results and processed the data, it was adopted a model of linear weighting to reflect the importance of each factor. The model has a hierarchical structure and can be applied with the Analytic Hierarchy Process (AHP) method or Value Analysis. The goal of the paper it's to supply a selection reference model that can represent an orientation/pattern for a decision making on the suppliers/partners selection process

Finding a school technological partner: a multicriteria method for school information system producer selection

The choice of an information systems is a critical factor of success in an organization's performance, since, by involving multiple decision-makers, with often conflicting objectives, several alternatives with aggressive marketing, makes it particularly complex by the scope of a consensus. The main objective of this work is to make the analysis and selection of a information system to support the school management, pedagogical and administrative components, using a multicriteria decision aid system – MMASSITI – Multicriteria Method- ology to Support the Selection of Information Systems/Information Technologies – integrates a multicriteria model that seeks to provide a systematic approach in the process of choice of Information Systems, able to produce sustained recommendations concerning the decision scope. Its application to a case study has identi- fied the relevant factors in the selection process of school educational and management information system and get a solution that allows the decision maker’ to compare the quality of the various alternatives.

Sustainability Improvement of a composite materials’ industry through recycling and re-engineering process approaches

Recent Advances in Mechanics and Materials in Design

People and object tracking for video annotation

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

International partner selection Indian technical textile market

Due to a combination of a vast agricultural industry and a tremendously growing technical textile industry, Ludvig Svensson identified India as target market for possible expansion through domestic production and supply. However, Svensson needed additional information about the industry structure and key players. Therefore, this project focused on a detailed analysis of the technical textile market and its players by following the international partner selection process. Thereby, five key players were identified as potential partners, as well as the need for additional research to determine alternative entry modes, as the market does not currently seem to be receptive for Svensson products.

Yield of essential oil and safrole content based on fresh and dry biomass of long pepper in the Brazilian Amazon

Long pepper (Piper hispidinervum) is an Amazonian species of commercial interest due to the production of safrole. Drying long pepper biomass to extract safrole is a time consuming and costly process that can also result in the contamination of the material by microorganisms. The objective of this study was to analyze the yield of essential oil and safrole content of fresh and dried biomass of long pepper accessions maintained in the Active Germoplasm Bank of Embrapa Acre, in the state of Acre, Brazil, aiming at selecting genotypes with best performance on fresh biomass to recommend to the breeding program of the species. Yield of essential oil and safrole content were assessed in 15 long pepper accessions. The essential oil extraction was performed by hydrodistillation and analyzed by gas chromatography. A joint analysis of experiments was performed and the means of essential oil yield and safrole content for each biomass were compared by Student's t-test. There was variability in the essential oil yield and safrole content. There was no difference between the types of biomass for oil yield; however to the safrole content there was difference. Populations 9, 10, 12 and 15 had values of oil yield between 4.1 and 5.3%, and safrole content between 87.2 and 94.3%. The drying process does not interfere in oil productivity. These populations have potential for selection to the long pepper breeding program using oil extraction in the fresh biomass

Fine time scaling of purifying selection on human nonsynonymous mtDNA mutations based on the worldwide population tree and mother-child pairs

A high-resolution mtDNA phylogenetic tree allowed us to look backward in time to investigate purifying selection. Purifying selection was very strong in the last 2,500 years, continuously eliminating pathogenic mutations back until the end of the Younger Dryas (∼11,000 years ago), when a large population expansion likely relaxed selection pressure. This was preceded by a phase of stable selection until another relaxation occurred in the out-of-Africa migration. Demography and selection are closely related: expansions led to relaxation of selection and higher pathogenicity mutations significantly decreased the growth of descendants. The only detectible positive selection was the recurrence of highly pathogenic nonsynonymous mutations (m.3394T>C-m.3397A>G-m.3398T>C) at interior branches of the tree, preventing the formation of a dinucleotide STR (TATATA) in the MT-ND1 gene. At the most recent time scale in 124 mother-children transmissions, purifying selection was detectable through the loss of mtDNA variants with high predicted pathogenicity. A few haplogroup-defining sites were also heteroplasmic, agreeing with a significant propensity in 349 positions in the phylogenetic tree to revert back to the ancestral variant. This nonrandom mutation property explains the observation of heteroplasmic mutations at some haplogroup-defining sites in sequencing datasets, which may not indicate poor quality as has been claimed.