Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Background: The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies.Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models ( e. g. relational), they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles.Results: We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file databases. First, annotationTools contains a specialized set of functions for mining this widely used database format in a systematic manner. It thus offers a straightforward solution for annotating microarray experiments. Second, building on these basic functions and relying on the combination of information from several databases, it provides tools to easily perform cross-species analyses of gene expression data.Here, we present two example applications of annotationTools that are of direct relevance for the analysis of heterogeneous gene expression profiles, namely a cross-platform mapping of probes and a cross-species mapping of orthologous probes using different orthology databases. We also show how to perform an explorative comparison of disease-related transcriptional changes in human patients and in a genetic mouse model.Conclusion: The R package annotationTools provides a simple solution to handle microarray annotation and orthology tables, as well as other flat molecular biology databases. Thereby, it allows easy integration and analysis of heterogeneous microarray experiments across different technological platforms or species.

A convex optimization framework for global tractography

In this article we present a novel approach for diffusion MRI global tractography. Our formulation models the signal in each voxel as a linear combination of fiber-tract basis func- tions, which consist of a comprehensive set of plausible fiber tracts that are locally compatible with the measured MR signal. This large dictionary of candidate fibers is directly estimated from the data and, subsequently, efficient convex optimization techniques are used for recovering the smallest subset globally best fitting the measured signal. Experimen- tal results conducted on a realistic phantom demonstrate that our approach significantly reduces the computational cost of global tractography while still attaining a reconstruction quality at least as good as the state-of-the-art global methods.

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont.

? The arbuscular mycorrhizal symbiosis is arguably the most ecologically important eukaryotic symbiosis, yet it is poorly understood at the molecular level. To provide novel insights into the molecular basis of symbiosis-associated traits, we report the first genome-wide analysis of the transcriptome from Glomus intraradices DAOM 197198. ? We generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. NRVTs were used to construct an oligoarray for investigating gene expression. ? We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis. Induced expression of genes encoding membrane transporters and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides, are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens. ? Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, advancing future research on these agriculturally and ecologically important symbionts.

Is human lactation a particularly efficient process?

The recommended dietary allowances of many expert committees (UK DHSS 1979, FAO/WHO/UNU 1985, USA NRC 1989) have set out the extra energy requirements necessary to support lactation on the basis of an efficiency of 80 per cent for human milk production. The metabolic efficiency of milk synthesis can be derived from the measurements of resting energy expenditure in lactating women and in a matched control group of non-pregnant non-lactating women. The results of the present study in Gambian women, as well as a review of human studies on energy expenditure during lactation performed in different countries, suggest an efficiency of human milk synthesis greater than the value currently used by expert committees. We propose that an average figure of 95 per cent would be more appropriate to calculate the energy cost of human lactation.

Monitoring of illicit pill distribution networks using an image collection exploration framework

This paper proposes a novel approach for the analysis of illicit tablets based on their visual characteristics. In particular, the paper concentrates on the problem of ecstasy pill seizure profiling and monitoring. The presented method extracts the visual information from pill images and builds a representation of it, i.e. it builds a pill profile based on the pill visual appearance. Different visual features are used to build different image similarity measures, which are the basis for a pill monitoring strategy based on both discriminative and clustering models. The discriminative model permits to infer whether two pills come from the same seizure, while the clustering models groups of pills that share similar visual characteristics. The resulting clustering structure allows to perform a visual identification of the relationships between different seizures. The proposed approach was evaluated using a data set of 621 Ecstasy pill pictures. The results demonstrate that this is a feasible and cost effective method for performing pill profiling and monitoring.

Metabolic intervention on lipid synthesis converging pathways abrogates prostate cancer growth.

One of the most conserved features of all cancers is a profound reprogramming of cellular metabolism, favoring biosynthetic processes and limiting catalytic processes. With the acquired knowledge of some of these important changes, we have designed a combination therapy in order to force cancer cells to use a particular metabolic pathway that ultimately results in the accumulation of toxic products. This innovative approach consists of blocking lipid synthesis, at the same time that we force the cell, through the inhibition of AMP-activated kinase, to accumulate toxic intermediates, such as malonyl-coenzyme A (malonyl-CoA) or nicotinamide adenine dinucleotide phosphate. This results in excess of oxidative stress and cancer cell death. Our new therapeutic strategy, based on the manipulation of metabolic pathways, will certainly set up the basis for new upcoming studies defining a new paradigm of cancer treatment.

Analysis of fatty acids in ecstasy tablets

Fatty acids are the basis of so-called stearates which are frequently used as lubricants in the production of ecstasy tablets. Being a product added at the initial tablet production step its composition does not change once the compression is performed. The analysis of fatty acids can therefore provide useful information for a drug intelligence purpose. In this context an appropriate analytical method was developed to improve results already obtained by routine analyses. Considering the small quantity of such fatty acids in ecstasy tablets (not, vert, similar3%) the research focussed on their extraction and concentration. Two different procedures were tested: (1) liquid/liquid extraction using dichloromethane followed by derivatisation and (2) in situ transesterification using bortrifluoride. Analyses were performed by GC-MS. The two procedures were optimized and applied to eight ecstasy seizures, in order to choose one of the procedures for its application to a large ecstasy sample set. They were compared by considering the number of peaks detected and sample amount needed, reproducibility and other technical aspects.

A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.

Wer gewinnt die Nationalratswahlen 2007 ? : Möglichkeiten und Grenzen von Wahlvorhersagen auf der Basis von kantonalen Parlamentswahlen

Au centre de cette contribution se pose la question de la mesure dans laquelle des résultats issus des élections cantonales peuvent servir d'instrument de pronostic pour les scores électoraux au niveau du Conseil national. L'analyse des résultats des élections tenues au cours des trente dernières années montre que les données cantonales (pondérées avec le nombre d'électeurs potentiels et la participation au vote) prédisent, dans environ neuf cas sur dix, la tendance réelle au niveau national. Si cela se vérifiait encore aux prochaines élections, alors les Verts peuvent s'attendre à des gains importants en termes de nouveaux électeurs et électrices. De même, mais dans une moindre mesure, l'UDC peux compter sur une augmentation de ses votants. Par contre, tant le PRD que le PS seront perdants et le PDC ne s'en sortira pas beaucoup mieux. En ce qui concerne la marge d'erreur de ces pronostics, elle se trouve au-dessous des 1 pourcents dans 73% des cas et pour 91% des cas elle ne dépasse pas les 2 pourcents.

Limits on the validity of infinite length assumptions for modelling shallow landslides

The infinite slope method is widely used as the geotechnical component of geomorphic and landscape evolution models. Its assumption that shallow landslides are infinitely long (in a downslope direction) is usually considered valid for natural landslides on the basis that they are generally long relative to their depth. However, this is rarely justified, because the critical length/depth (L/H) ratio below which edge effects become important is unknown. We establish this critical L/H ratio by benchmarking infinite slope stability predictions against finite element predictions for a set of synthetic two-dimensional slopes, assuming that the difference between the predictions is due to error in the infinite slope method. We test the infinite slope method for six different L/H ratios to find the critical ratio at which its predictions fall within 5% of those from the finite element method. We repeat these tests for 5000 synthetic slopes with a range of failure plane depths, pore water pressures, friction angles, soil cohesions, soil unit weights and slope angles characteristic of natural slopes. We find that: (1) infinite slope stability predictions are consistently too conservative for small L/H ratios; (2) the predictions always converge to within 5% of the finite element benchmarks by a L/H ratio of 25 (i.e. the infinite slope assumption is reasonable for landslides 25 times longer than they are deep); but (3) they can converge at much lower ratios depending on slope properties, particularly for low cohesion soils. The implication for catchment scale stability models is that the infinite length assumption is reasonable if their grid resolution is coarse (e.g. >25?m). However, it may also be valid even at much finer grid resolutions (e.g. 1?m), because spatial organization in the predicted pore water pressure field reduces the probability of short landslides and minimizes the risk that predicted landslides will have L/H ratios less than 25. Copyright (c) 2012 John Wiley & Sons, Ltd.

Molecular basis for changes in behavioral state in ant social behaviors.

A hallmark of behavior is that animals respond to environmental change by switching from one behavioral state to another. However, information on the molecular underpinnings of these behavioral shifts and how they are mediated by the environment is lacking. The ant Pheidole pallidula with its morphologically and behaviorally distinct major and minor workers is an ideal system to investigate behavioral shifts. The physically larger majors are predisposed to defend the ant nest, whereas the smaller minors are the foragers. Despite this predisposition, majors are able to shift to foraging according to the needs of the colony. We show that the ant foraging (ppfor) gene, which encodes a cGMP-dependent protein kinase (PKG), mediates this shift. Majors have higher brain PKG activities than minors, and the spatial distribution of the PPFOR protein differs in these workers. Specifically, majors express the PPFOR protein in 5 cells in the anterior face of the ant brain, whereas minors do not. Environmental manipulations show that PKG is lower in the presence of a foraging stimulus and higher when defense is required. Finally, pharmacological activation of PKG increases defense and reduces foraging behavior. Thus, PKG signaling plays a critical role in P. pallidula behavioral shifts.