Attention performance among Brazilian truck drivers and its association with amphetamine use: pilot study

The aim of this article was to describe the attention functioning of twenty-two truck drivers and its relationship with amphetamine use. Those drivers who reported using amphetamines in the twelve months previous to the interview had the best performance in a test evaluating sustained attention functioning. Although amphetamine use may initially seem advantageous to the drivers, it may actually impair safe driving. The findings suggest the importance of monitoring the laws regarding amphetamine use in this country.

Influence of dual-task on sit-to-stand-to-sit postural control in Parkinson's disease

Postural control deficits are the most disabling aspects of Parkinson's disease (PD), resulting in decreased mobility and functional independence. The aim of this study was to assess the postural control stability, revealed by variables based on the centre of pressure (CoP), in individuals with PD while performing a sit-to-stand-to-sit sequence under single- and dual-task conditions. An observational, analytical and cross-sectional study was performed. The sample consisted of 9 individuals with PD and 9 healthy controls. A force platform was used to measure the CoP displacement and velocity during the sit-to-stand-to-sit sequence. The results were statistically analysed. Individuals with PD required greater durations for the sit-to-stand-to-sit sequence than the controls (p < 0.05). The anteroposterior and mediolateral CoP displacement were higher in the individuals with PD (p < 0.05). However, only the anteroposterior CoP velocity in the stand-to-sit phase (p = 0.006) was lower in the same individuals. Comparing the single- and dual-task conditions in both groups, the duration, the anteroposterior CoP displacement and velocity were higher in the dual-task condition (p < 0.05). The individuals with PD presented reduced postural control stability during the sit-to-stand-to-sit sequence, especially when under the dual-task condition. These individuals have deficits not only in motor performance, but also in cognitive performance when performing the sit-to-stand-to-sit sequence in their daily life tasks. Moreover, both deficits tend to be intensified when two tasks are performed simultaneously.

Hemispheric asymmetry and theory of mind: Is there an association?

Introduction. In autism and schizophrenia attenuated/atypical functional hemispheric asymmetry and theory of mind impairments have been reported, suggesting common underlying neuroscientific correlates. We here investigated whether impaired theory of mind performance is associated with attenuated/atypical hemispheric asymmetry. An association may explain the co-occurrence of both dysfunctions in psychiatric populations. Methods. Healthy participants (n 129) performed a left hemisphere (lateralised lexical decision task) and right hemisphere (lateralised face decision task) dominant task as well as a visual cartoon task to assess theory of mind performance. Results. Linear regression analyses revealed inconsistent associations between theory of mind performance and functional hemisphere asymmetry: enhanced theory of mind performance was only associated with (1) faster right hemisphere language processing, and (2) reduced right hemisphere dominance for face processing (men only). Conclusions. The majority of non-significant findings suggest that theory of mind and functional hemispheric asymmetry are unrelated. Instead of ''overinterpreting'' the two significant results, discrepancies in the previous literature relating to the problem of the theory of mind concept, the variety of tasks, and the lack of normative data are discussed. We also suggest how future studies could explore a possible link between hemispheric asymmetry and theory of mind.

Using qualia information to identify lexical semantic classes in an unsupervised clustering task

Acquiring lexical information is a complex problem, typically approached by relying on a number of contexts to contribute information for classification. One of the first issues to address in this domain is the determination of such contexts. The work presented here proposes the use of automatically obtained FORMAL role descriptors as features used to draw nouns from the same lexical semantic class together in an unsupervised clustering task. We have dealt with three lexical semantic classes (HUMAN, LOCATION and EVENT) in English. The results obtained show that it is possible to discriminate between elements from different lexical semantic classes using only FORMAL role information, hence validating our initial hypothesis. Also, iterating our method accurately accounts for fine-grained distinctions within lexical classes, namely distinctions involving ambiguous expressions. Moreover, a filtering and bootstrapping strategy employed in extracting FORMAL role descriptors proved to minimize effects of sparse data and noise in our task.

Computational analysis of the genetic and environmental contributions to disease-related human phenotypes: From predicting adverse lipid response of HIV patients receiving antiretroviral therapy to genome-wide association studies of cardiovascular and lipid related disorders

Genetic variants influence the risk to develop certain diseases or give rise to differences in drug response. Recent progresses in cost-effective, high-throughput genome-wide techniques, such as microarrays measuring Single Nucleotide Polymorphisms (SNPs), have facilitated genotyping of large clinical and population cohorts. Combining the massive genotypic data with measurements of phenotypic traits allows for the determination of genetic differences that explain, at least in part, the phenotypic variations within a population. So far, models combining the most significant variants can only explain a small fraction of the variance, indicating the limitations of current models. In particular, researchers have only begun to address the possibility of interactions between genotypes and the environment. Elucidating the contributions of such interactions is a difficult task because of the large number of genetic as well as possible environmental factors.In this thesis, I worked on several projects within this context. My first and main project was the identification of possible SNP-environment interactions, where the phenotypes were serum lipid levels of patients from the Swiss HIV Cohort Study (SHCS) treated with antiretroviral therapy. Here the genotypes consisted of a limited set of SNPs in candidate genes relevant for lipid transport and metabolism. The environmental variables were the specific combinations of drugs given to each patient over the treatment period. My work explored bioinformatic and statistical approaches to relate patients' lipid responses to these SNPs, drugs and, importantly, their interactions. The goal of this project was to improve our understanding and to explore the possibility of predicting dyslipidemia, a well-known adverse drug reaction of antiretroviral therapy. Specifically, I quantified how much of the variance in lipid profiles could be explained by the host genetic variants, the administered drugs and SNP-drug interactions and assessed the predictive power of these features on lipid responses. Using cross-validation stratified by patients, we could not validate our hypothesis that models that select a subset of SNP-drug interactions in a principled way have better predictive power than the control models using "random" subsets. Nevertheless, all models tested containing SNP and/or drug terms, exhibited significant predictive power (as compared to a random predictor) and explained a sizable proportion of variance, in the patient stratified cross-validation context. Importantly, the model containing stepwise selected SNP terms showed higher capacity to predict triglyceride levels than a model containing randomly selected SNPs. Dyslipidemia is a complex trait for which many factors remain to be discovered, thus missing from the data, and possibly explaining the limitations of our analysis. In particular, the interactions of drugs with SNPs selected from the set of candidate genes likely have small effect sizes which we were unable to detect in a sample of the present size (<800 patients).In the second part of my thesis, I performed genome-wide association studies within the Cohorte Lausannoise (CoLaus). I have been involved in several international projects to identify SNPs that are associated with various traits, such as serum calcium, body mass index, two-hour glucose levels, as well as metabolic syndrome and its components. These phenotypes are all related to major human health issues, such as cardiovascular disease. I applied statistical methods to detect new variants associated with these phenotypes, contributing to the identification of new genetic loci that may lead to new insights into the genetic basis of these traits. This kind of research will lead to a better understanding of the mechanisms underlying these pathologies, a better evaluation of disease risk, the identification of new therapeutic leads and may ultimately lead to the realization of "personalized" medicine.

Polymorphisms in candidate genes and their association with carcass traits and meat quality in Nellore cattle

The objective of this work was to estimate the allele polymorphism frequencies of genes in Nellore cattle and associate them with meat quality and carcass traits. Six hundred males were genotyped for the following polymorphisms: DGAT1 (VNTR with 18 nucleotides at the promoter region); ANK1, a new polymorphism, identified and mapped here at the gene regulatory region NW_001494427.3; TCAP (AY428575.1:g.346G>A); and MYOG (NW_001501985:g.511G>C). In the association study, phenotype data of hot carcass weight, ribeye area, backfat thickness, percentage of intramuscular fat, shear force, myofibrillar fragmentation index, meat color (L*, a*, b*), and cooking losses were used. Allele B from the ANK1 gene was associated with greater redness (a*). Alleles 5R, 6R, and 7R from the DGAT1 VNTR gene were associated with increased intramuscular fat, reduced cooking losses and increased ribeye area, respectively. The single nucleotide polymorphism (SNP) of the TCAP gene was not polymorphic, and MYOG alleles were not associated with any of the evaluated characteristics. These results indicate that ANK1 and DGAT1 genes can be used in the selection of Nellore cattle for carcass and meat quality.

National Library and Library Network in Finland - Cooperation Being the Driving Force of Success

Kristiina Hormia-Poutasen esitys Danish Research Association -tapahtumassa Tanskassa 15.9.2011

Novel force control methods in a teleoperation system of a hydraulic slider

The objective of the this research project is to develop a novel force control scheme for the teleoperation of a hydraulically driven manipulator, and to implement an ideal transparent mapping between human and machine interaction, and machine and task environment interaction. This master‘s thesis provides a preparatory study for the present research project. The research is limited into a single degree of freedom hydraulic slider with 6-DOF Phantom haptic device. The key contribution of the thesis is to set up the experimental rig including electromechanical haptic device, hydraulic servo and 6-DOF force sensor. The slider is firstly tested as a position servo by using previously developed intelligent switching control algorithm. Subsequently the teleoperated system is set up and the preliminary experiments are carried out. In addition to development of the single DOF experimental set up, methods such as passivity control in teleoperation are reviewed. The thesis also contains review of modeling of the servo slider in particular reference to the servo valve. Markov Chain Monte Carlo method is utilized in developing the robustness of the model in presence of noise.

Scalable Feature Selection Applications for Genome-Wide Association Studies of Complex Diseases

Personalized medicine will revolutionize our capabilities to combat disease. Working toward this goal, a fundamental task is the deciphering of geneticvariants that are predictive of complex diseases. Modern studies, in the formof genome-wide association studies (GWAS) have afforded researchers with the opportunity to reveal new genotype-phenotype relationships through the extensive scanning of genetic variants. These studies typically contain over half a million genetic features for thousands of individuals. Examining this with methods other than univariate statistics is a challenging task requiring advanced algorithms that are scalable to the genome-wide level. In the future, next-generation sequencing studies (NGS) will contain an even larger number of common and rare variants. Machine learning-based feature selection algorithms have been shown to have the ability to effectively create predictive models for various genotype-phenotype relationships. This work explores the problem of selecting genetic variant subsets that are the most predictive of complex disease phenotypes through various feature selection methodologies, including filter, wrapper and embedded algorithms. The examined machine learning algorithms were demonstrated to not only be effective at predicting the disease phenotypes, but also doing so efficiently through the use of computational shortcuts. While much of the work was able to be run on high-end desktops, some work was further extended so that it could be implemented on parallel computers helping to assure that they will also scale to the NGS data sets. Further, these studies analyzed the relationships between various feature selection methods and demonstrated the need for careful testing when selecting an algorithm. It was shown that there is no universally optimal algorithm for variant selection in GWAS, but rather methodologies need to be selected based on the desired outcome, such as the number of features to be included in the prediction model. It was also demonstrated that without proper model validation, for example using nested cross-validation, the models can result in overly-optimistic prediction accuracies and decreased generalization ability. It is through the implementation and application of machine learning methods that one can extract predictive genotype–phenotype relationships and biological insights from genetic data sets.

Plant rhizosphere specificity and variability in the insect and plant adhesins, Madl and Mad2, within the genus Metarhizium suggest plant adaptation as an evolutionary force

Metarhizium is a soil-inhabiting fungus currently used as a biological control agent against various insect species, and research efforts are typically focused on its ability to kill insects. In section 1, we tested the hypothesis that species of Metarhizium are not randomly distributed in soils but show plant rhizosphere-specific associations. Results indicated an association of three Metarhizium species (Metarhizium robertsii, M. brunneum and M. guizhouense) with the rhizosphere of certain types of plant species. M. robertsii was the only species that was found associated with grass roots, suggesting a possible exclusion of M. brunneum and M. guizhouense, which was supported by in vitro experiments with grass root exudate. M. guizhouense and M. brunneum only associated with wildflower rhizosphere when co-occurring with M. robertsii. With the exception of these co-occurrences, M. guizhouense was found to associate exclusively with the rhizosphere of tree species, while M. brunneum was found to associate exclusively with the rhizosphere of shrubs and trees. These associations demonstrate that different species of Metarhizium associate with specific plant types. In section 2, we explored the variation in the insect adhesin, Madl, and the plant adhesin, Mad2, in fourteen isolates of Metarhizium representing seven different species. Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions. Phylogenetic analysis of 5' EF-Ia, which is used for species identification, as well as Madl and Mad2 sequences demonstrated that the Mad2 phylogeny is more congruent with 5' EF-1a than Madl. This suggests Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation. While other abiotic and biotic factors cannot be excluded in contributing to divergence, it appears that plant associations have been the driving factor causing divergence among Metarhizium species.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Perception d’effort et de mise en charge et asymétrie motrice lors du passage assis à debout chez le sujet hémiparétique

L’asymétrie de mise en charge (MEC) lors du passage assis à debout (PAD) chez les personnes hémiparétiques est une observation clinique connue mais peu expliquée. Ce projet visait donc le développement de connaissances sur les facteurs explicatifs de l’asymétrie de MEC chez cette clientèle en s’intéressant plus spécifiquement au lien entre la distribution des efforts aux genoux lors du PAD et l’asymétrie de MEC observée ainsi qu’à la perception de ces deux éléments lors de cette tâche. Ainsi, les objectifs généraux étaient de : 1) déterminer si l’exécution spontanée asymétrique du PAD des sujets hémiparétiques est expliquée par une distribution des efforts symétriques aux genoux en quantifiant ces efforts par le Taux d’utilisation musculaire électromyographique (TUMEMG) et, 2) déterminer si les individus hémiparétiques sont conscients des stratégies motrices qu’ils utilisent en évaluant leurs perceptions de MEC et d’efforts aux genoux durant le PAD. La première étude a évalué la capacité des personnes hémiparétiques à percevoir leur distribution de MEC aux membres inférieurs lors du PAD. Par rapport aux participants sains, leur distribution de MEC fut davantage asymétrique et leurs erreurs de perception plus élevées. La deuxième étude a quantifié la distribution des efforts aux genoux chez les sujets sains et hémiparétiques lors du PAD spontané. Les deux groupes ont montré une association entre leur distribution de MEC et leur distribution d’effort. Toutefois, la relation était plus faible chez les patients. Le classement des participants hémiparétiques en sous-groupes selon leur degré d’asymétrie de force maximale des extenseurs des genoux (faible, modéré, sévère) a révélé une similarité des efforts aux genoux parétique et non parétique chez le groupe ayant une atteinte sévère. La troisième étude a déterminé si la perception de la distribution des efforts aux genoux des sujets hémiparétiques était reliée à leur distribution réelle d’effort mesurée lors de PAD exécutés dans différentes positions de pieds. En plus d’être incapables de percevoir les changements de distribution d’effort induits par les différentes positions de pieds, leurs erreurs de perception d’effort furent plus élevées que celles de MEC. Par le biais du test fonctionnel assis-debout de cinq répétitions, la dernière étude a déterminé l’influence du nombre de répétitions du PAD sur les distributions de MEC et d’efforts aux genoux chez les sujets sains et hémiparétiques. Contrairement aux contrôles, les distributions des sujets hémiparétiques furent plus asymétriques à la première répétition du test fonctionnel que lors de l’exécution spontanée unique du PAD. En somme, les résultats de cette thèse ont démontré que la distribution des efforts aux genoux doit être considérée parmi les facteurs explicatifs de l’asymétrie de MEC des individus hémiparétiques lors du PAD et qu’il y a un besoin de mieux documenter la perception des personnes hémiparétiques lorsqu’elles exécutent des tâches fonctionnelles.