Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.

Punishing the foreigner: implicit discrimination in the Premier League based on oppositional identity

We present the first empirical study to reveal the presence of implicit discrimination in a non-experimental setting. By using a large dataset of in-match data in the English Premier League, we show that white referees award significantly more yellow cards against non-white players of oppositional identity. We argue that this is the result of implicit discrimination by showing that this discriminatory behaviour: (i) increases in how rushed the referee is before making a decision, and (ii) it increases in the level of ambiguity of the decision. The variation in (i) and (ii) cannot be explained by any form of conscious discrimination such as taste-based or statistical discrimination. Moreover, we show that oppositional identity players do not differ in their behaviour from other players along several dimensions related to aggressiveness and style of play providing further evidence that this is not statistical discrimination.

How reliable is internet-based self-reported identity, socio-demographic and obesity measures in European adults?

In e-health intervention studies, there are concerns about the reliability of internet-based, self-reported (SR) data and about the potential for identity fraud. This study introduced and tested a novel procedure for assessing the validity of internet-based, SR identity and validated anthropometric and demographic data via measurements performed face-to-face in a validation study (VS). Participants (n = 140) from seven European countries, participating in the Food4Me intervention study which aimed to test the efficacy of personalised nutrition approaches delivered via the internet, were invited to take part in the VS. Participants visited a research centre in each country within 2 weeks of providing SR data via the internet. Participants received detailed instructions on how to perform each measurement. Individual’s identity was checked visually and by repeated collection and analysis of buccal cell DNA for 33 genetic variants. Validation of identity using genomic information showed perfect concordance between SR and VS. Similar results were found for demographic data (age and sex verification). We observed strong intra-class correlation coefficients between SR and VS for anthropometric data (height 0.990, weight 0.994 and BMI 0.983). However, internet-based SR weight was under-reported (Δ −0.70 kg [−3.6 to 2.1], p < 0.0001) and, therefore, BMI was lower for SR data (Δ −0.29 kg m−2 [−1.5 to 1.0], p < 0.0001). BMI classification was correct in 93 % of cases. We demonstrate the utility of genotype information for detection of possible identity fraud in e-health studies and confirm the reliability of internet-based, SR anthropometric and demographic data collected in the Food4Me study.

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

Investigation of a new GRASP-based clustering algorithm applied to biological data

A large amount of biological data has been produced in the last years. Important knowledge can be extracted from these data by the use of data analysis techniques. Clustering plays an important role in data analysis, by organizing similar objects from a dataset into meaningful groups. Several clustering algorithms have been proposed in the literature. However, each algorithm has its bias, being more adequate for particular datasets. This paper presents a mathematical formulation to support the creation of consistent clusters for biological data. Moreover. it shows a clustering algorithm to solve this formulation that uses GRASP (Greedy Randomized Adaptive Search Procedure). We compared the proposed algorithm with three known other algorithms. The proposed algorithm presented the best clustering results confirmed statistically. (C) 2009 Elsevier Ltd. All rights reserved.

An electrochemical sensor for (L)-dopa based on oxovanadium-salen thin film electrode applied flow injection system

An oxovanadium-salen complex (NAP-ethylene-bis(salicylidenciminato) oxovanadium) thin film deposited on a graphite-polyurethane electrode was investigated with regard to its potential use for detection of L-dopa in flow injection system. The oxovanadium(IV)/oxovanadium(V) redox couple of the modified electrode was found to mediate the L-dopa oxidation before its use in the FIA system. Experimental parameters, such as pH of the carrier solution, flow rate, sample volume injection and probable interferents were investigated. Under the optimized FIA conditions, the amperometric signal was linearly dependent on the L-dopa concentration over the range 1.0 x 10(-1) to 1.0 x 10(-4) mol L-1 (I-anodic, mu A) = 0.01 + 0.25 [L-dopa mu mol L-1]) with a detection limit (S/N = 3) of 8.0 x 10(-7) mol L-1 and a sampling frequency of 90 h(-1) was achieved. For a concentration of 1.0 x 10(-5) mol L-1 L-dopa, the R.S.D. of nine consecutive measurements was 3.7%. (c) 2006 Elsevier B.V. All rights reserved.

Study of the interaction between cardiolipin bilayers and methylene blue in polymer-based Layer-by-Layer and Langmuir films applied as membrane mimetic systems

An increase of the reports involving mimetic systems has been observed. Briefly, these systems use biological phospholipids to exploit specific interactions between membrane-models and drugs. Here, the Layer-by-Layer (LbL) and Langmuir techniques were used to investigate the interaction between cardiolipin (CLP-negative phospholipid) and a cationic-like drug methylene blue (MB). Supported by a cationic polyelectrolyte (PAH), LbL films containing PAH/(CLP + MB) and PAH/(CLP + MB + AgNP) were grown up to 14 bilayers. The optical microscopy analysis revealed a decrease of the CLP vesicle sizes in the presence of MB as a possible consequence of the MB action onto the mechanical properties of the CLP membrane. From FTIR spectra, changes mainly related to peak position and band intensity and shape were observed in the spectra from PAH/CLP when in the presence of MB. The latter supports that the interactions between the phosphate and amine charged groups from CLP and PAH, respectively, established during the LbL film fabrication, besides the CLP hydrocarbon environment, are influenced by the presence of MB. Using the micro-Raman technique, a chemical mapping was build based on MB spectrum by resonance Raman scattering (RRS) and surface-enhanced resonance Raman scattering (SERRS). The later phenomenon was activated by Ag nanoparticles (AgNPs) trapped within the LbL film allowing collecting spectra for a single bilayer of PAH/(CLP + MB + AgNP). A rough estimation showed a SERRS amplification of 10(3) in comparison to RRS spectra. As a complementary approach, Langmuir films of CLP in the presence of co-spread MB were investigated through surface pressure vs mean molecular area (pi-A) isotherms. The results showed that for concentrations of MB below 100 mol%, the drug is expelled to water subphase for high values of surface pressure (condensed phase). For concentration at 100% and higher, the MB keeps bound to CLP floating monolayer. (C) 2010 Elsevier B.V. All rights reserved.

A novel approach based on recurrent neural networks applied to nonlinear systems optimization

This paper presents an efficient approach based on recurrent neural network for solving nonlinear optimization. More specifically, a modified Hopfield network is developed and its internal parameters are computed using the valid subspace technique. These parameters guarantee the convergence of the network to the equilibrium points that represent an optimal feasible solution. The main advantage of the developed network is that it treats optimization and constraint terms in different stages with no interference with each other. Moreover, the proposed approach does not require specification of penalty and weighting parameters for its initialization. A study of the modified Hopfield model is also developed to analyze its stability and convergence. Simulation results are provided to demonstrate the performance of the proposed neural network. (c) 2005 Elsevier B.V. All rights reserved.

A DOE based approach for the design of RBF artificial neural networks applied to prediction of surface roughness in AISI 52100 hardened Steel turning

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Optimization Strategies Based on Sequential Quadratic Programming Applied for a Fermentation Process for Butanol Production

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

Effect of cerium (IV) ions on the anticorrosion properties of siloxane-poly(methyl methacrylate) based film applied on tin coated steel

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

Biocompatibility of resin-based dental materials applied as liners in deep cavities prepared in human teeth

Background: Since only a few data have been published concerning the effects of resinous dental materials on the pulp-dentin complex, the aim of this study was to evaluate the biocompatibility of resin-based materials applied as liners in deep cavities prepared in duman teeth. Methods: After preparing class V cavities, the following dental materials were applied on the axial walls: group 1, Vitrebond™ (VIT; 3M ESPE); group 2, Ultra-Blend® Plus™ (UBP; Untradent); and group 3, Clearfil™ SE Bond (CSEB; Kuraray). In group 4 (control), the hard-setting calcium hydroxide cement Dycal (CH; Caulk/Dentsply) was used. The teeth extracted at 7 days or between 30 and 85 days after the clinical procedures were processed for histological evaluation. Results: For all the experimental and control groups, most of specimens exhibited no pulpal response or slight inflammatory reaction associated with slight tissue disorganization at 7-day period. Moderate inflammatory pulpal response occurred only in one tooth (RDT = 262 μm) of group 3 in which transdentinal diffusion of resin components was observed. Conclusion: The resin-based dental cements VIT and UBP as well as the bonding agent CSEB presented acceptable biocompatibility when applied in deep cavities prepared in sound human teeth. © 2006 Wiley Periodicals, Inc.

Knowledge-based integrated Production Management Model applied to automotive companies

This paper aims to examine the relevance of a production management model, in the shop-floor operations environment, that integrates the dimensions of production organisation (lean and mass production), work organisation (enriched and semi-autonomous groups) and knowledge management. A theoretical model has been applied to automotive companies to verify model adherence. Each of those dimensions has been described by factors. Shop-floor personnel interviews were conducted to confirm the factors relevance to that company. Results have shown that the model represented the reality of those companies concerning the researched dimensions. The factors allow managers to promote a favourable context for knowledge sharing. © 2010 Inderscience Enterprises Ltd.

The contributions of applied anthropology to peasant development

Includes bibliography