The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Reliable selfing rate estimates from imperfect population genetic data.

Genotypic frequencies at codominant marker loci in population samples convey information on mating systems. A classical way to extract this information is to measure heterozygote deficiencies (FIS) and obtain the selfing rate s from FIS = s/(2 - s), assuming inbreeding equilibrium. A major drawback is that heterozygote deficiencies are often present without selfing, owing largely to technical artefacts such as null alleles or partial dominance. We show here that, in the absence of gametic disequilibrium, the multilocus structure can be used to derive estimates of s independent of FIS and free of technical biases. Their statistical power and precision are comparable to those of FIS, although they are sensitive to certain types of gametic disequilibria, a bias shared with progeny-array methods but not FIS. We analyse four real data sets spanning a range of mating systems. In two examples, we obtain s = 0 despite positive FIS, strongly suggesting that the latter are artefactual. In the remaining examples, all estimates are consistent. All the computations have been implemented in a open-access and user-friendly software called rmes (robust multilocus estimate of selfing) available at http://ftp.cefe.cnrs.fr, and can be used on any multilocus data. Being able to extract the reliable information from imperfect data, our method opens the way to make use of the ever-growing number of published population genetic studies, in addition to the more demanding progeny-array approaches, to investigate selfing rates.

Cost Analysis of Long-Term Treatment of Patients with Symptomatic Gastroesophageal Reflux Disease (GERD) with Esomeprazole On-Demand Treatment or Esomeprazole Continuous Treatment: An Open, Randomized, Multicenter Study in Switzerland.

Objectives: To assess the difference in direct medical costs between on-demand (OD) treatment with esomeprazole (E) 20 mg and continuous (C) treatment with E 20 mg q.d. from a clinical practice view in patients with gastroesophageal reflux disease (GERD) symptoms. Methods: This open, randomized study (ONE: on-demand Nexium evaluation) compared two long-term management options with E 20 mg in endoscopically uninvestigated patients seeking primary care for GERD symptoms who demonstrated complete relief of symptoms after an initial treatment of 4 weeks with E 40 mg. Data on consumed quantities of all cost items were collected in the study, while data on prices during the time of study were collected separately. The analysis was done from a societal perspective. Results: Forty-nine percent (484 of 991) of patients randomized to the OD regimen and 46% (420 of 913) of the patients in the C group had at least one contact with the investigator that would have occurred nonprotocol-driven. The difference of the adjusted mean direct medical costs between the treatment groups was CHF 88.72 (95% confidence interval: CHF 41.34-153.95) in favor of the OD treatment strategy (Wilcoxon rank-sum test: P < 0.0001). Adjusted direct nonmedical costs and productivity loss were similar in both groups. Conclusions: The adjusted direct medical costs of a 6-month OD treatment with esomeprazole 20 mg in uninvestigated patients with symptoms of GERD were significantly lower compared with a continuous treatment with E 20 mg once a day. The OD therapy represents a cost-saving alternative to the continuous treatment strategy with E.

The Case for Linking World Law Data

The present paper advocates for the creation of a federated, hybrid database in the cloud, integrating law data from all available public sources in one single open access system - adding, in the process, relevant meta-data to the indexed documents, including the identification of social and semantic entities and the relationships between them, using linked open data techniques and standards such as RDF. Examples of potential benefits and applications of this approach are also provided, including, among others, experiences from of our previous research, in which data integration, graph databases and social and semantic networks analysis were used to identify power relations, litigation dynamics and cross-references patterns both intra and inter-institutionally, covering most of the World international economic courts.

Binary proposal for assessing quality of Open Access Institutional Repositories : the case of Spanish repositories

The reason for this study is to propose a new quantitative approach on how to assess the quality of Open Access University Institutional Repositories. The results of this new approach are tested in the Spanish University Repositories. The assessment method is based in a binary codification of a proposal of features that objectively describes the repositories. The purposes of this method are assessing the quality and an almost automatically system for updating the data of the characteristics. First of all a database was created with the 38 Spanish institutional repositories. The variables of analysis are presented and explained either if they are coming from bibliography or are a set of new variables. Among the characteristics analyzed are the features of the software, the services of the repository, the features of the information system, the Internet visibility and the licenses of use. Results from Spanish universities ARE provided as a practical example of the assessment and for having a picture of the state of the development of the open access movement in Spain.

Maca - a configurable tool to integrate Polish morphological data

There are a number of morphological analysers for Polish. Most of these, however, are non-free resources. What is more, different analysers employ different tagsets and tokenisation strategies. This situation calls for a simpleand universal framework to join different sources of morphological information, including the existing resources as well as user-provided dictionaries. We present such a configurable framework that allows to write simple configuration files that define tokenisation strategies and the behaviour of morphologicalanalysers, including simple tagset conversion.

An Italian to Catalan RBMT system reusing data from existing language pairs

This paper presents an Italian to CatalanRBMT system automatically built bycombining the linguistic data of theexisting pairs Spanish-Catalan andSpanish-Italian. A lightweight manualpostprocessing is carried out in order tofix inconsistencies in the automaticallyderived dictionaries and to add very frequentwords that are missing accordingto a corpus analysis. The system isevaluated on the KDE4 corpus and outperformsGoogle Translate by approximatelyten absolute points in terms ofboth TER and GTM.

Early selection in open-pollinated Eucalyptus families based on competition covariates

The objetive of this work was to evaluate the influence of intergenotypic competition in open-pollinated families of Eucalyptus and its effects on early selection efficiency. Two experiments were carried out, in which the timber volume was evaluated at three ages, in a randomized complete block design. Data from the three years of evaluation (experiment 1, at 2, 4, and 7 years; and experiment 2, at 2, 5, and 7 years) were analyzed using mixed models. The following were estimated: variance components, genetic parameters, selection gains, effective number, early selection efficiency, selection gain per unit time, and coincidence of selection with and without the use of competition covariates. Competition effect was nonsignificant for ages under three years, and adjustment using competition covariates was unnecessary. Early selection for families is effective; families that have a late growth spurt are more vulnerable to competition, which markedly impairs ranking at the end of the cycle. Early selection is efficient according to all adopted criteria, and the age of around three years is the most recommended, given the high efficiency and accuracy rate in the indication of trees and families. The addition of competition covariates at the end of the cycle improves early selection efficiency for almost all studied criteria.

A priori parameterisation of the CERES soil-crop models and tests against several European data sets

Mechanistic soil-crop models have become indispensable tools to investigate the effect of management practices on the productivity or environmental impacts of arable crops. Ideally these models may claim to be universally applicable because they simulate the major processes governing the fate of inputs such as fertiliser nitrogen or pesticides. However, because they deal with complex systems and uncertain phenomena, site-specific calibration is usually a prerequisite to ensure their predictions are realistic. This statement implies that some experimental knowledge on the system to be simulated should be available prior to any modelling attempt, and raises a tremendous limitation to practical applications of models. Because the demand for more general simulation results is high, modellers have nevertheless taken the bold step of extrapolating a model tested within a limited sample of real conditions to a much larger domain. While methodological questions are often disregarded in this extrapolation process, they are specifically addressed in this paper, and in particular the issue of models a priori parameterisation. We thus implemented and tested a standard procedure to parameterize the soil components of a modified version of the CERES models. The procedure converts routinely-available soil properties into functional characteristics by means of pedo-transfer functions. The resulting predictions of soil water and nitrogen dynamics, as well as crop biomass, nitrogen content and leaf area index were compared to observations from trials conducted in five locations across Europe (southern Italy, northern Spain, northern France and northern Germany). In three cases, the model’s performance was judged acceptable when compared to experimental errors on the measurements, based on a test of the model’s root mean squared error (RMSE). Significant deviations between observations and model outputs were however noted in all sites, and could be ascribed to various model routines. In decreasing importance, these were: water balance, the turnover of soil organic matter, and crop N uptake. A better match to field observations could therefore be achieved by visually adjusting related parameters, such as field-capacity water content or the size of soil microbial biomass. As a result, model predictions fell within the measurement errors in all sites for most variables, and the model’s RMSE was within the range of published values for similar tests. We conclude that the proposed a priori method yields acceptable simulations with only a 50% probability, a figure which may be greatly increased through a posteriori calibration. Modellers should thus exercise caution when extrapolating their models to a large sample of pedo-climatic conditions for which they have only limited information.

Estimation of age- and stage-specific Catalan breast cancer survival functions using US and Catalan survival data

Background: During the last part of the 1990s the chance of surviving breast cancer increased. Changes in survival functions reflect a mixture of effects. Both, the introduction of adjuvant treatments and early screening with mammography played a role in the decline in mortality. Evaluating the contribution of these interventions using mathematical models requires survival functions before and after their introduction. Furthermore, required survival functions may be different by age groups and are related to disease stage at diagnosis. Sometimes detailed information is not available, as was the case for the region of Catalonia (Spain). Then one may derive the functions using information from other geographical areas. This work presents the methodology used to estimate age- and stage-specific Catalan breast cancer survival functions from scarce Catalan survival data by adapting the age- and stage-specific US functions. Methods: Cubic splines were used to smooth data and obtain continuous hazard rate functions. After, we fitted a Poisson model to derive hazard ratios. The model included time as a covariate. Then the hazard ratios were applied to US survival functions detailed by age and stage to obtain Catalan estimations. Results: We started estimating the hazard ratios for Catalonia versus the USA before and after the introduction of screening. The hazard ratios were then multiplied by the age- and stage-specific breast cancer hazard rates from the USA to obtain the Catalan hazard rates. We also compared breast cancer survival in Catalonia and the USA in two time periods, before cancer control interventions (USA 1975–79, Catalonia 1980–89) and after (USA and Catalonia 1990–2001). Survival in Catalonia in the 1980–89 period was worse than in the USA during 1975–79, but the differences disappeared in 1990–2001. Conclusion: Our results suggest that access to better treatments and quality of care contributed to large improvements in survival in Catalonia. On the other hand, we obtained detailed breast cancer survival functions that will be used for modeling the effect of screening and adjuvant treatments in Catalonia.

Semantic data integration in a newspaper content management system

A newspaper content management system has to deal with a very heterogeneous information space as the experience in the Diari Segre newspaper has shown us. The greatest problem is to harmonise the different ways the involved users (journalist, archivists...) structure the newspaper information space, i.e. news, topics, headlines, etc. Our approach is based on ontology and differentiated universes of discourse (UoD). Users interact with the system and, from this interaction, integration rules are derived. These rules are based on Description Logic ontological relations for subsumption and equivalence. They relate the different UoD and produce a shared conceptualisation of the newspaper information domain.

SDS open source

Estudi de viabilitat sobre la implantació d'un software-defined storage open source en entorns empresarials. Comparativa entre Gluster, Ceph, OpenAFS, TahoeFS i XtreemFS.

Measurement of a Structured Backflow in an Open Small Channel Induced by Surface-Tension Gradients

We present experiments in which the laterally confined flow of a surfactant film driven by controlled surface tension gradients causes the subtended liquid layer to self-organize into an inner upstream microduct surrounded by the downstream flow. The anomalous interfacial flow profiles and the concomitant backflow are a result of the feedback between two-dimensional and three-dimensional microfluidics realized during flow in open microchannels. Bulk and surface particle image velocimetry data combined with an interfacial hydrodynamics model explain the dependence of the observed phenomena on channel geometry.

ODiSEA: International Registry on Research Data

El artículo revisa los temas principales en la preservación y reuso de los datos de investigación (beneficios, ciclo de vida, proyectos, normativas ) e identifica la falta de un registro mundial de bancos, repositorios y bibliotecas de datos. Expone la creación de una herramienta web que recoja este tipo de depósitos y los clasifique por áreas disciplinares: ODiSEA International Registry on Research Data. Ofrecemos resultados sobre número y tipología temática de este tipo de depósitos a escala mundial. Esta aportación facilita el descubrimiento de nuevos conjuntos de datos cuya recombinación desde una perspectiva multidisciplinar fomentará la innovación y la rentabilidad de la inversión en ciencia.