Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum

Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of gene expression levels and their underlying sequence polymorphisms continue to pose many challenges. Methods are limited in their ability to illuminate the full structure of the eQTL data. Most rely on an exhaustive, genome scale search that considers all possible locus–gene pairs and tests the linkage between each locus and gene

Is there an association between ACTN3 R577X polymorphism and muscle power phenotypes in young, non-athletic adults?

We investigated the association between ACTN3 R577X polymorphism and jumping (vertical squat and counter-movement jump tests) and sprint ability (30 m dash) in non-athletic, healthy young adults [N=284 (217 male), mean (SD) age: 21 (2) years]. We analyzed the differences in the study phenotypes among ACTN3 R577X genotypes by one-way analysis of covariance before and after adjusting for sex, age, weight and height (confounders). We also compared the genotype and allele frequencies between those with the best and worst results in the aforementioned tests (≥90th vs 0.05). In summary, α-actinin-3 deficiency does not negatively influence the ability to generate explosive leg muscle power in a young non-athletic population

ACTN3 R577X Polymorphism does not Influence Explosive Leg Muscle Power in Elite Volleyball Players

We examined the association of R577X polymorphism (rs1815739) in the α-actinin-3 (ACTN3) gene with “explosive” leg muscle power performance in a group of male and female elite volleyball players (n=66, 31 men, 35 women) and in a group of non-athletic male and female young adults (n=334, 243 men, 91 women). We assessed power performance by means of the vertical squat and counter-movement jump tests. We also determined whether the genotypic frequencies of the ACTN3 R577X genotypes differed between groups. We did not observe any effect of the ACTN3 R577X polymorphism on study phenotypes in both groups, regardless of gender (all P>0.05). Genotype frequencies were similar between volleyball and control groups (P=0.095). Moreover, we did not find an association between the ACTN3 R577X polymorphism and the likelihood of being an elite volleyball player using the dominant (RR vs RX+XX) and the recessive model (RR+RX vs XX). In summary, these findings suggest that the ACTN3 R577X polymorphism does not influence explosive leg muscle power in elite volleyball players

Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.

Genetical genomics: spotlight on QTL hotspots

No abstract available

Effects of dipole position, orientation and noise on the accuracy of EEG source localization

BACKGROUND: The electroencephalogram (EEG) reflects the electrical activity in the brain on the surface of scalp. A major challenge in this field is the localization of sources in the brain responsible for eliciting the EEG signal measured at the scalp. In order to estimate the location of these sources, one must correctly model the sources, i.e., dipoles, as well as the volume conductor in which the resulting currents flow. In this study, we investigate the effects of dipole depth and orientation on source localization with varying sets of simulated random noise in 4 realistic head models. METHODS: Dipole simulations were performed using realistic head models and using the boundary element method (BEM). In all, 92 dipole locations placed in temporal and parietal regions of the head with varying depth and orientation were investigated along with 6 different levels of simulated random noise. Localization errors due to dipole depth, orientation and noise were investigated. RESULTS: The results indicate that there are no significant differences in localization error due tangential and radial dipoles. With high levels of simulated Gaussian noise, localization errors are depth-dependant. For low levels of added noise, errors are similar for both deep and superficial sources. CONCLUSION: It was found that if the signal-to-noise ratio is above a certain threshold, localization errors in realistic head models are, on average the same for deep and superficial sources. As the noise increases, localization errors increase, particularly for deep sources

Characterization of the LIGO detectors during their sixth science run

31 pages, 13 figures - See paper for full list of authorsInternational audienceIn 2009-2010, the Laser Interferometer Gravitational-wave Observatory (LIGO) operated together with international partners Virgo and GEO600 as a network to search for gravitational waves of astrophysical origin. The sensitiv- ity of these detectors was limited by a combination of noise sources inherent to the instrumental design and its environment, often localized in time or frequency, that couple into the gravitational-wave readout. Here we review the performance of the LIGO instruments during this epoch, the work done to characterize the de- tectors and their data, and the effect that transient and continuous noise artefacts have on the sensitivity of LIGO to a variety of astrophysical sources

Improved functional prediction of proteins by learning kernel combinations in multilabel settings

Background We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. Results Explicit modeling of multilabels significantly improves the capability of learning protein function from multiple kernels. The performance and the interpretability of the inference model are further improved by simultaneously predicting the subcellular localization of proteins and by combining pairwise classifiers to consistent class membership estimates. Conclusion For the purpose of functional prediction of proteins, multilabels provide valuable information that should be included adequately in the training process of classifiers. Learning of functional categories gains from co-prediction of subcellular localization. Pairwise separation rules allow very detailed insights into the relevance of different measurements like sequence, structure, interaction data, or expression data. A preliminary version of the software can be downloaded from http://www.inf.ethz.ch/personal/vroth/KernelHMM/.ISSN:1471-210

Searching for stochastic gravitational waves using data from the two co-located LIGO Hanford detectors

21 pages, 10 figures, 5 tables, see paper for full list of authorsInternational audienceSearches for a stochastic gravitational-wave background (SGWB) using terrestrial detectors typically involve cross-correlating data from pairs of detectors. The sensitivity of such cross-correlation analyses depends, among other things, on the separation between the two detectors: the smaller the separation, the better the sensitivity. Hence, a co-located detector pair is more sensitive to a gravitational-wave background than a non-co-located detector pair. However, co-located detectors are also expected to suffer from correlated noise from instrumental and environmental effects that could contaminate the measurement of the background. Hence, methods to identify and mitigate the effects of correlated noise are necessary to achieve the potential increase in sensitivity of co-located detectors. Here we report on the first SGWB analysis using the two LIGO Hanford detectors and address the complications arising from correlated environmental noise. We apply correlated noise identification and mitigation techniques to data taken by the two LIGO Hanford detectors, H1 and H2, during LIGO's fifth science run. At low frequencies, 40 - 460 Hz, we are unable to sufficiently mitigate the correlated noise to a level where we may confidently measure or bound the stochastic gravitational-wave signal. However, at high frequencies, 460-1000 Hz, these techniques are sufficient to set a 95% confidence level (C.L.) upper limit on the gravitational-wave energy density of \Omega(f)<7.7 x 10^{-4} (f/ 900 Hz)^3, which improves on the previous upper limit by a factor of ∼180. In doing so, we demonstrate techniques that will be useful for future searches using advanced detectors, where correlated noise (e.g., from global magnetic fields) may affect even widely separated detectors

Analyse des signaux pour un dispositif de mesure et de stimulation du système nerveux central

- Un des enjeux actuels en Neurosciences est de pouvoir enregistrer simultanément les activités d'un grand nombre de cellules au sein de grands réseaux de neurones, et de pouvoir stimuler de manière dynamique ces réseaux afin d'en contrôler les activités. Le but du projet Neurocom est de réaliser un système multiélectrode haute densité intégré sur silicium, permettant d'enregistrer et de stimuler de grands réseaux de neurones in vitro. Ce dispositif sera constitué d'une microstructure d'électrodes stérilisable hybridée sur un circuit analogique intégré (préamplification, filtrage, multiplexage, stimulation), lui-même interfacé via une carte numérique de commande et acquisition reliée à un PC. Afin de pouvoir mieux appréhender les phénomènes bioélectriques et électrochimiques à l'interface capteur et donc mieux spécifier le cahier des charges et l'architecture du système, la maquette de test NEUROCOM1 a été conçue en électronique discrète et est actuellement utilisée pour conduire différents tests