Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental variation, phylogeographic history, and population demographic processes all contribute to spatially structured genetic variation, however few current models attempt to separate these confounding effects. To illustrate the benefits of using a spatially-explicit model for identifying potentially adaptive loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi-scale spatial variation present in a data set, were incorporated into a landscape genetic approach relating AFLP frequencies with 23 environmental variables. Four major findings emerged. 1) Fifteen loci were significantly correlated with at least one predictor variable (R (adj) (2) > 0.5). 2) Models including PCNM variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major environmental factors driving potentially adaptive genetic variation in G. nivalis. Techniques presented in this paper offer an efficient method for identifying potentially adaptive genetic variation and associated environmental forces of selection, providing an important step forward for the conservation of non-model species under global change.

Some solutions to obtain very efficient separations in isocratic and gradient modes using small particles size and ultra-high pressure.

The UHPLC strategy which combines sub-2 microm porous particles and ultra-high pressure (>1000 bar) was investigated considering very high resolution criteria in both isocratic and gradient modes, with mobile phase temperatures between 30 and 90 degrees C. In isocratic mode, experimental conditions to reach the maximal efficiency were determined using the kinetic plot representation for DeltaP(max)=1000 bar. It has been first confirmed that the molecular weight of the compounds (MW) was a critical parameter which should be considered in the construction of such curves. With a MW around 1000 g mol(-1), efficiencies as high as 300,000 plates could be theoretically attained using UHPLC at 30 degrees C. By limiting the column length to 450 mm, the maximal plate count was around 100,000. In gradient mode, the longest column does not provide the maximal peak capacity for a given analysis time in UHPLC. This was attributed to the fact that peak capacity is not only related to the plate number but also to column dead time. Therefore, a compromise should be found and a 150 mm column should be preferentially selected for gradient lengths up to 60 min at 30 degrees C, while the columns coupled in series (3x 150 mm) were attractive only for t(grad)>250 min. Compared to 30 degrees C, peak capacities were increased by about 20-30% for a constant gradient length at 90 degrees C and gradient time decreased by 2-fold for an identical peak capacity.

An efficient use of virtualization in grid/cloud environments

Grid is a hardware and software infrastructure that provides dependable, consistent, pervasive, and inexpensive access to high-end computational resources. Grid enables access to the resources but it does not guarantee any quality of service. Moreover, Grid does not provide performance isolation; job of one user can influence the performance of other user’s job. The other problem with Grid is that the users of Grid belong to scientific community and the jobs require specific and customized software environment. Providing the perfect environment to the user is very difficult in Grid for its dispersed and heterogeneous nature. Though, Cloud computing provide full customization and control, but there is no simple procedure available to submit user jobs as in Grid. The Grid computing can provide customized resources and performance to the user using virtualization. A virtual machine can join the Grid as an execution node. The virtual machine can also be submitted as a job with user jobs inside. Where the first method gives quality of service and performance isolation, the second method also provides customization and administration in addition. In this thesis, a solution is proposed to enable virtual machine reuse which will provide performance isolation with customization and administration. The same virtual machine can be used for several jobs. In the proposed solution customized virtual machines join the Grid pool on user request. Proposed solution describes two scenarios to achieve this goal. In first scenario, user submits their customized virtual machine as a job. The virtual machine joins the Grid pool when it is powered on. In the second scenario, user customized virtual machines are preconfigured in the execution system. These virtual machines join the Grid pool on user request. Condor and VMware server is used to deploy and test the scenarios. Condor supports virtual machine jobs. The scenario 1 is deployed using Condor VM universe. The second scenario uses VMware-VIX API for scripting powering on and powering off of the remote virtual machines. The experimental results shows that as scenario 2 does not need to transfer the virtual machine image, the virtual machine image becomes live on pool more faster. In scenario 1, the virtual machine runs as a condor job, so it easy to administrate the virtual machine. The only pitfall in scenario 1 is the network traffic.

El comportamiento penalmente relevante en el delito de defraudación tributaria: una propuesta político-criminal

El sistema tributario es fundamental en el Estado social y democrático de Derecho, pues el ejercicio y efectivo disfrute de muchos derechos fundamentales depende del correcto funcionamiento de la actividad tributaria. Además de esto, la situación económica actual demanda una adecuada política en contra del fraude tributario, lo que necesariamente implica analizar si el modelo penal vigente es el más adecuado para enfrentar el fraude fiscal. Teniendo en cuenta que muchas de las características de la criminalidad tributaria no son exclusivas de un país, pues ésta trasciende habitualmente las fronteras de los países por medio del recurso a empresas multinacionales o la localización de empresas en “paraísos fiscales”, el análisis del fraude tributario no debe limitarse al examen jurídico del modelo legislativo español, debiendo trascender a un estudio de política criminal que vincula consideraciones criminológicas y jurídicas. En consecuencia, en esta investigación se propone un análisis que no se reduce a los debates exclusivamente jurídicos. Se busca, además, efectuar un examen que tenga por fundamento una perspectiva criminológica y de Law in action a fin de evaluar críticamente la respuesta a la criminalidad tributaria por parte del modelo de regulación penal vigente en España. Esta orientación permitirá una más amplia comprensión del fenómeno de la criminalidad tributaria, así como de las categorías jurídicas adecuadas político criminalmente para su prevención. Este estudio interdisciplinario nos conducirá, al final de la investigación, tanto a proponer la interpretación del modelo de legislación penal vigente, como una reforma al mismo que pretenda solucionar algunos de los problemas de prevención que a lo largo de la investigación se señalan.

International consensus conference on PFAPA syndrome: evaluation of a new set of classification criteria

INTRODUCTION: PFAPA syndrome is characterized by periodic fever, associated with pharyngitis, cervical adenitis and/or aphthous stomatitis and belongs to the auto-inflammatory diseases. Diagnostic criteria are based on clinical features and the exclusion of other periodic fever syndromes. An analysis of a large cohort of patients has shown weaknesses for these criteria and there is a lack of international consensus. An International Conference was held in Morges in November 2008 to propose a new set of classification criteria based on a consensus among experts in the field.OBJECTIVE: We aimed to verify the applicability of the new set of classification criteria.PATIENTS & METHODS: 80 patients diagnosed with PFAPA syndrome from 3 centers (Genoa, Lausanne and Geneva) for pediatric rheumatology were included in the study. A detailed description of the clinical and laboratory features was obtained. The new classification criteria and the actual diagnostic criteria were applied to the patients.RESULTS: Only 40/80 patients (50%) fulfilled all criteria of the new classification. 31 patients were excluded because they didn't meet one of the 7 diagnostic criteria, 7 because of 2 criteria, and one because of 3 criteria. When we applied the current criteria to the same patients, 11/80 patients (13.7%) needed to be excluded. 8/80 patients (10%) were excluded from both sets. Exclusion was related only to some of the criteria. Number of patients for each not fulfilled criterion (new set of criteria/actual criteria): age (1/6), symptoms between episodes (2/2), delayed growth (4/1), main symptoms (21/0), periodicity, length of fever, interval between episodes, and length of disease (20/0). The application of some of the new criteria was not easy, as they were both very restrictive and needed precise information from the patients.CONCLUSION: Our work has shown that the new set of classification criteria can be applied to patients suspected for PFAPA syndrome, but it seems to be more restrictive than the actual diagnostic criteria. A further work of validation needs to be done in order to determine if this new set of classification criteria allow a good discrimination between PFAPA patients and other causes of recurrent fever syndromes.

The peroxisomal Acyl-CoA thioesterase Pte1p from Saccharomyces cerevisiae is required for efficient degradation of short straight chain and branched chain fatty acids.

The role of the Saccharomyces cerevisae peroxisomal acyl-coenzyme A (acyl-CoA) thioesterase (Pte1p) in fatty acid beta-oxidation was studied by analyzing the in vitro kinetic activity of the purified protein as well as by measuring the carbon flux through the beta-oxidation cycle in vivo using the synthesis of peroxisomal polyhydroxyalkanoate (PHA) from the polymerization of the 3-hydroxyacyl-CoAs as a marker. The amount of PHA synthesized from the degradation of 10-cis-heptadecenoic, tridecanoic, undecanoic, or nonanoic acids was equivalent or slightly reduced in the pte1Delta strain compared with wild type. In contrast, a strong reduction in PHA synthesized from heptanoic acid and 8-methyl-nonanoic acid was observed for the pte1Delta strain compared with wild type. The poor catabolism of 8-methyl-nonanoic acid via beta-oxidation in pte1Delta negatively impacted the degradation of 10-cis-heptadecenoic acid and reduced the ability of the cells to efficiently grow in medium containing such fatty acids. An increase in the proportion of the short chain 3-hydroxyacid monomers was observed in PHA synthesized in pte1Delta cells grown on a variety of fatty acids, indicating a reduction in the metabolism of short chain acyl-CoAs in these cells. A purified histidine-tagged Pte1p showed high activity toward short and medium chain length acyl-CoAs, including butyryl-CoA, decanoyl-CoA and 8-methyl-nonanoyl-CoA. The kinetic parameters measured for the purified Pte1p fit well with the implication of this enzyme in the efficient metabolism of short straight and branched chain fatty acyl-CoAs by the beta-oxidation cycle.

Report of Working Group set up by the Tanaiste in March 2006 to examine the nature and extent of Haemochromatosis in Ireland and to advise her on the action necessary to address the problems caused by Haemochromatosis

It was agreed at a meeting on 15th February, 2006, between Ms Mary Harney, TD, Tanaiste and Minister for Health and Children and Dr Maurice Manning that a Working Group would be set up to examine all of the issues relating to haemochromatosis in Ireland and to advise her on the actions necessary to address these issues. Read the Report (PDF, 709kb)  

Segimon Comas : importància i contextualització històrica d'un universitari i acadèmic del set-cents

Contextualització històrica dels inicis de l'Acadèmia de Bones Lletres al segle XVIII, i un dels seus artífexs, Segimon Comas.

Ultra-high pressure liquid chromatography-mass spectrometry for plant metabolomics: a systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers.

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

ARCHITECTING USER-CENTRIC PRIVACY-AS-A-SET-OF-SERVICES: DIGITAL IDENTITY RELATED PRIVACY FRAMEWORK

AbstractDigitalization gives to the Internet the power by allowing several virtual representations of reality, including that of identity. We leave an increasingly digital footprint in cyberspace and this situation puts our identity at high risks. Privacy is a right and fundamental social value that could play a key role as a medium to secure digital identities. Identity functionality is increasingly delivered as sets of services, rather than monolithic applications. So, an identity layer in which identity and privacy management services are loosely coupled, publicly hosted and available to on-demand calls could be more realistic and an acceptable situation. Identity and privacy should be interoperable and distributed through the adoption of service-orientation and implementation based on open standards (technical interoperability). Ihe objective of this project is to provide a way to implement interoperable user-centric digital identity-related privacy to respond to the need of distributed nature of federated identity systems. It is recognized that technical initiatives, emerging standards and protocols are not enough to guarantee resolution for the concerns surrounding a multi-facets and complex issue of identity and privacy. For this reason they should be apprehended within a global perspective through an integrated and a multidisciplinary approach. The approach dictates that privacy law, policies, regulations and technologies are to be crafted together from the start, rather than attaching it to digital identity after the fact. Thus, we draw Digital Identity-Related Privacy (DigldeRP) requirements from global, domestic and business-specific privacy policies. The requirements take shape of business interoperability. We suggest a layered implementation framework (DigldeRP framework) in accordance to model-driven architecture (MDA) approach that would help organizations' security team to turn business interoperability into technical interoperability in the form of a set of services that could accommodate Service-Oriented Architecture (SOA): Privacy-as-a-set-of- services (PaaSS) system. DigldeRP Framework will serve as a basis for vital understanding between business management and technical managers on digital identity related privacy initiatives. The layered DigldeRP framework presents five practical layers as an ordered sequence as a basis of DigldeRP project roadmap, however, in practice, there is an iterative process to assure that each layer supports effectively and enforces requirements of the adjacent ones. Each layer is composed by a set of blocks, which determine a roadmap that security team could follow to successfully implement PaaSS. Several blocks' descriptions are based on OMG SoaML modeling language and BPMN processes description. We identified, designed and implemented seven services that form PaaSS and described their consumption. PaaSS Java QEE project), WSDL, and XSD codes are given and explained.

COMMIT: Convex Optimization Modeling for Microstructure Informed Tractography.

Tractography is a class of algorithms aiming at in vivo mapping the major neuronal pathways in the white matter from diffusion magnetic resonance imaging (MRI) data. These techniques offer a powerful tool to noninvasively investigate at the macroscopic scale the architecture of the neuronal connections of the brain. However, unfortunately, the reconstructions recovered with existing tractography algorithms are not really quantitative even though diffusion MRI is a quantitative modality by nature. As a matter of fact, several techniques have been proposed in recent years to estimate, at the voxel level, intrinsic microstructural features of the tissue, such as axonal density and diameter, by using multicompartment models. In this paper, we present a novel framework to reestablish the link between tractography and tissue microstructure. Starting from an input set of candidate fiber-tracts, which are estimated from the data using standard fiber-tracking techniques, we model the diffusion MRI signal in each voxel of the image as a linear combination of the restricted and hindered contributions generated in every location of the brain by these candidate tracts. Then, we seek for the global weight of each of them, i.e., the effective contribution or volume, such that they globally fit the measured signal at best. We demonstrate that these weights can be easily recovered by solving a global convex optimization problem and using efficient algorithms. The effectiveness of our approach has been evaluated both on a realistic phantom with known ground-truth and in vivo brain data. Results clearly demonstrate the benefits of the proposed formulation, opening new perspectives for a more quantitative and biologically plausible assessment of the structural connectivity of the brain.

How to set and monitor goals for prevalence of child obesity: guidance for Primary Care Trusts (PCTs) and local authorities

This guidance follows on from the publication of the Government's obesity strategy Healthy Weight, Healthy Lives: A Cross-Government strategy for England. The guidance provides advice to PCTs and local authorities on how to set child obesity goals as part of the Vital Signs and the National Indicator Set. This will be followed shortly with full guidance on developing local plans.

Consultation on Personal and Public Involvement strategy

Personal and Public Involvement (PPI) is an integral element of effective commissioning and is underpinned by a core set of values and principles - involving and listening to people in order to help us make services better.It brings about a number of recognised benefits if fully embraced into our culture and practice, these include:Use of service user knowledge and expertise;Better priority setting and decision making;More responsive, appropriate, efficient and tailored services;Transformation and reduction of complaints;Increased levels of service satisfaction;Increased dignity and self worth.The Public Health Agency (PHA) and Health and Social Care Board (HSCB) have now developed a joint Personal and Public Involvement (PPI) Strategy after extensive engagement and discussion. The Strategy has been approved by both organisations and is now being formally consulted on during the period 23rd June 2011 to 15th September 2011.The Strategy is now available for your consideration. We have developed the following documents (please see attachments below):Valuing People, Valuing Their Participation. Involving You and Listening to You Consultation Document.Valuing People, Valuing Their Participation, Involving You and Listening to You. [An Easy Read version of the Personal and Public Involvement Strategy].Valuing People, Valuing Their Participation. [An Equality and Human Rights Screening of the Strategy].Key Questions to guide consideration of the Personal and Public Involvement Strategy.People are encouraged to read the Strategy and to let us have your views.� There is a set of Key Questions, but any comments, ideas and or suggestions that you may have, that could support us in our efforts to embed Personal and Public Involvement into our culture and practice, would be most welcome.Responses should be returned by 4.00pm on Thursday 15th September 2011 to:By post:Martin QuinnRegional PPI LeadPublic Health AgencyGransha Park House15 Gransha ParkLondonderryBT47 6FNBy email: siobhan.carlin@hscni.net By telephone: (028) 7186 0086A more detailed version of the consultation document is avalable by clicking here or contacting Siobhan Carlin, email: siobhan.carlin@hscni.net, Tel: (028) 7186 0086.If you require any of these documents in an alternative format such as Braille, larger print or in another language if you are not fluent in English, please do not hesitate to contact us.A report of feedback received as part of this consultation can be made available upon request.Please be aware that the PHA and HSCB are also currently consulting on the Community Development Strategy.You are invited to consider responding to this consultation as well if appropriate.

Construcció i explotació d'un magatzem de dades per a l'anàlisi estadístic dels resultats del Campionat de Fórmula 1

En els darrers anys les organitzacions han anat agafant consciència de la importància de la gestió de la seva informació. D'aquesta necessitat d'organitzar les pròpies dades d'una forma coherent i eficient per al seu anàlisi sorgeixen els magatzems de dades. El projecte "Construcció i explotació d'un magatzem de dades per a l'anàlisi estadístic dels resultats del Campionat de Fórmula 1" s'emmarca dins aquest context i te com a objectiu el disseny d'un magatzem de dades per a cobrir les necessitats del Institut Català d'Esports de Motor (ICEM) en la gestió de les seves dades referents a la Fórmula 1. En aquest projecte s'han executat les diferents fases necessàries per a la creació d'un nou magatzem. En primer lloc s'ha fet l'anàlisi de requeriments i de les dades disponibles. A continuació s'ha fet el disseny i la implementació física del magatzem de dades. Seguidament s'ha procedit amb l'extracció, transformació i càrrega de dades originals (ETL) i per finalitzar s'han creat els informes. Com a resultat s'han obtingut una sèrie d'informes per a ser consumits de manera immediata pels usuaris del ICEM. Aquests informes han de permetre l'anàlisi de les dades d'una forma senzilla i àgil. A més s'ha implementat un sistema d'actualització automàtic de les dades que per al manteniment de la informació del magatzem.La implementació del magatzem de dades s'ha fet sobre una base de dades Oracle 10g Express Edition i els informes s'ha dissenyat amb l'eina Oracle Discoverer. Per a l'automatització de les dades s'ha fet servir a més visual basic script i l'eina de càrrega SQL*Loader.