Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

Análisis de usabilidad y diseño de un supermercado online

En este trabajo se realiza un estudio de usabilidad para la elaboración óptima de una Web de un supermercado de alimentación online. Para tal fin, se sigue la filosofía del Diseño Centrado en el Usuario. En primer lugar, se presenta un análisis del problema de cara a identificar los requisitos básicos de usabilidad que necesita una Web de esta tipología: se estudia la literatura previa sobre el tema, se consulta a los usuarios y se realiza un análisis comparativo de las principales Webs de supermercados online de ámbito nacional. En segundo lugar, se procede a la elaboración de un prototipo basado en la información recogida en la fase de análisis, y teniendo en cuenta la estructura mental de los usuarios en cuanto a la organización de los productos, obtenida mediante la técnica del card sorting. Finalmente, se procede a evaluar la calidad del prototipo elaborado con una evaluación heurística llevada a cabo por expertos. De todo ello se obtienen una serie de recomendaciones que todo sitio Web de comercio electrónico (en especial supermercados de alimentación) debería cumplir si quiere ofrecer una Web adaptada a las necesidades del usuario.

The policy-making structure of European regulatory networks and the domestic adoption of standards

European regulatory networks (ERNs) constitute the main governance instrument for the informal co-ordination of public regulation at the European Union (EU) level. They are in charge of co-ordinating national regulators and ensuring the implementation of harmonized regulatory policies across the EU, while also offering sector-specific expertise to the Commission. To this aim, ERNs develop 'best practices' and benchmarking procedures in the form of standards, norms and guidelines to be adopted in member states. In this paper, we focus on the Committee of European Securities Regulators and examine the consequences of the policy-making structure of ERNs on the domestic adoption of standards. We find that the regulators of countries with larger financial industries tend to occupy more central positions in the network, especially among newer member states. In turn, network centrality is associated with a more prompt domestic adoption of standards.

What is the most relevant standard of success in assisted reproduction?: The cumulated singleton/twin delivery rates per oocyte pick-up: the CUSIDERA and CUTWIDERA.

National and international registries are essential tools for establishing new standards and comparing success rates, but they do not take into account the total pregnancy/delivery rate per oocyte recovery. In Switzerland and Germany, because of legal constraints, a maximum of three two-pronuclear zygotes are allocated for transfer whereas all the supernumerary pronuclear zygotes are immediately cryopreserved, preventing selection of the transferred embryos. We report on a 10 years' experience (1993-2002) of our centre which performs transfers of unselected embryos and cryopreservation at the two-pronuclear zygote stage. As approximately 30% of all deliveries are from cryo cycles, it is essential to take into account the contribution of the cryo transfers, and we propose therefore to evaluate, as a measure of IVF performance, the cumulated delivery rate per oocyte pick-up. This delivery rate is broken down further into the cumulated singleton delivery rate (CUSIDERA) and the cumulated twin delivery rate (CUTWIDERA). The sum (S) of these two rates is a measure of efficacy while the ratio CUTWIDERA/S as a percentage is a measure of safety of IVF treatments. Using these new indexes, the average 10 year efficacy and safety of our IVF programme were 26 and 19%, respectively. Both CUSIDERA and CUTWIDERA can be calculated easily in any clinical situation and yield useful parameters for patient counselling and internal/external benchmarking purposes.

Estudi de comparació de rendiment de Benchmark multicore i multithreading amb OpenMP 2.5 i OpenMP 3.0

Estudi comparatiu amb benchmark del rendiment en dues plataformes multicore multithreading de diferents modalitats de paral·lelització de multiplicacions de matrius de nombres enters i de nombres en coma flotant mitjançant el model de memòria compartida OpenMP versió 2.5 i OpenMP versió 3.0.

The development of the Quality Indicator for Rehabilitative Care (QuIRC): a measure of best practice for facilities for people with longer term mental health problems

BACKGROUND: Despite the progress over recent decades in developing community mental health services internationally, many people still receive treatment and care in institutional settings. Those most likely to reside longest in these facilities have the most complex mental health problems and are at most risk of potential abuses of care and exploitation. This study aimed to develop an international, standardised toolkit to assess the quality of care in longer term hospital and community based mental health units, including the degree to which human rights, social inclusion and autonomy are promoted. METHOD: The domains of care included in the toolkit were identified from a systematic literature review, international expert Delphi exercise, and review of care standards in ten European countries. The draft toolkit comprised 154 questions for unit managers. Inter-rater reliability was tested in 202 units across ten countries at different stages of deinstitutionalisation and development of community mental health services. Exploratory factor analysis was used to corroborate the allocation of items to domains. Feedback from those using the toolkit was collected about its usefulness and ease of completion. RESULTS: The toolkit had excellent inter-rater reliability and few items with narrow spread of response. Unit managers found the content highly relevant and were able to complete it in around 90 minutes. Minimal refinement was required and the final version comprised 145 questions assessing seven domains of care. CONCLUSIONS: Triangulation of qualitative and quantitative evidence directed the development of a robust and comprehensive international quality assessment toolkit for units in highly variable socioeconomic and political contexts

Desarrollo de un listado de comprobación de buenas prácticas en las inspecciones para autorización de centros y establecimientos sanitarios

Comunicación oral

Sensitivity of genome-wide-association signals to phenotyping strategy: the PROP-TAS2R38 taste association as a benchmark.

Natural genetic variation can have a pronounced influence on human taste perception, which in turn may influence food preference and dietary choice. Genome-wide association studies represent a powerful tool to understand this influence. To help optimize the design of future genome-wide-association studies on human taste perception we have used the well-known TAS2R38-PROP association as a tool to determine the relative power and efficiency of different phenotyping and data-analysis strategies. The results show that the choice of both data collection and data processing schemes can have a very substantial impact on the power to detect genotypic variation that affects chemosensory perception. Based on these results we provide practical guidelines for the design of future GWAS studies on chemosensory phenotypes. Moreover, in addition to the TAS2R38 gene past studies have implicated a number of other genetic loci to affect taste sensitivity to PROP and the related bitter compound PTC. None of these other locations showed genome-wide significant associations in our study. To facilitate further, target-gene driven, studies on PROP taste perception we provide the genome-wide list of p-values for all SNPs genotyped in the current study.

Sorting out measures and definitions of screening participation to improve comparability : the example of colorectal cancer.

Participation is a key indicator of the potential effectiveness of any population-based intervention. Defining, measuring and reporting participation in cancer screening programmes has become more heterogeneous as the number and diversity of interventions have increased, and the purposes of this benchmarking parameter have broadened. This study, centred on colorectal cancer, addresses current issues that affect the increasingly complex task of comparing screening participation across settings. Reports from programmes with a defined target population and active invitation scheme, published between 2005 and 2012, were reviewed. Differences in defining and measuring participation were identified and quantified, and participation indicators were grouped by aims of measure and temporal dimensions. We found that consistent terminology, clear and complete reporting of participation definition and systematic documentation of coverage by invitation were lacking. Further, adherence to definitions proposed in the 2010 European Guidelines for Quality Assurance in Colorectal Cancer Screening was suboptimal. Ineligible individuals represented 1% to 15% of invitations, and variable criteria for ineligibility yielded differences in participation estimates that could obscure the interpretation of colorectal cancer screening participation internationally. Excluding ineligible individuals from the reference population enhances comparability of participation measures. Standardised measures of cumulative participation to compare screening protocols with different intervals and inclusion of time since invitation in definitions are urgently needed to improve international comparability of colorectal cancer screening participation. Recommendations to improve comparability of participation indicators in cancer screening interventions are made.

"Publish or perish!" : la fabrique du chercheur-entrepreneur

La course effrénée à la publication, « publish or perish », participe au renforcement d'une (nouvelle) norme scientifique : la compétitivité. Celle-ci s'est institutionnalisée lors de réformes néolibérales, tant au niveau des systèmes nationaux de recherche et d'enseignement que des instances européennes et internationales. En partant de ce contexte politique, nous avons problématisé la «fabrique» d'un sujet néolibéral, celle du chercheur-entrepreneur, sous l'angle des techniques de gouvernement à distance (benchmarking, systèmes de classement, grilles d'évaluation, etc.) compris comme des «techniques de soi» pouvant amener les enseignants-chercheurs à s'identifier et à agir comme des chercheurs-entrepreneurs. De cette perspective foucaldienne de la «fabrique» du chercheur-entrepreneur, nous distinguons, in fine, une double posture herméneutique possible: un «souci de soi» a-critique, d'ordre gestionnaire, confiant dans les règles méritocratiques et un «souci de soi» critique, d'ordre intellectuel, inquiet de voir s'installer la compétitivité comme norme dominante du champ scientifique.

Evaluation of free libraries for visual recognition of art imagery on mobile devices

This paper describes a systematic research about free software solutions and techniques for art imagery computer recognition problem.

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.

Ilmanvaihtokoneen ohjauksen taloudellisuusvaikutukset

Tämän insinöörityön tarkoituksena oli luoda Insinööritoimisto Olof Granlund Oy:lle malliprojekti ilmanvaihtokoneen ohjauksen mahdollisesta sähköenergian säästöpotentiaalista. Insinöörityötä voidaan myöhemmin käyttää referenssinä tarjottaessa yrityksen palvelua asiakkaille energiakatselmointityössä kiinteistöihin, joissa on suuria ilmanvaihtokone-yksiköitä. Ensin työssä esitellään käytössä olevat, tutkittavat ilmanvaihtokoneet ja niiden toiminta. Sitten selvitetään ilmanvaihtolaitteiden ja niiden ohjauksen eri osien toiminta, sekä ohjausinformaatio, joka välittyy eri laitteiden välillä. Seuraavaksi työssä tutkitaan rakennusautomaation osuutta, sen hyötyä ja rakennetta kiinteistössä. Tämän jälkeen selvitetään hankkeen viranomaismääräykset. Sitten selvitetään, mistä koostuvat kustannukset ilmanvaihtokoneen ohjauksen uusimisessa. Lopuksi vielä tutkitaan, kuinka pitkä on tehtävän investoinnin takaisinmaksuaika, sekä mitkä ovat saneerauksen hiilidioksidi-päästövaikutukset. insinöörityön Lopputuloksena syntyi yrityksen sisäinen kansio. Kansion esimerkkilaskelmia ja laskentamenetelmiä on tarkoitus käyttää jatkossa referenssinä kiinteistönpito-osastolla sähkö- ja lvi-ryhmissä, niiden henkilöiden käytössä, jotka ovat tekemisissä energiakatselmointien kanssa.

Ei jengii ilman svengii : lasten jousiorkesteriopas

Opinnäytetyömme koostuu kahdesta osasta, lasten jousiorkesterioppaasta ja opinnäytetyön sisältöä selittävästä raportista. Ei jengii ilman svengii on opas nuorille jousisoittajille, jotka ovat aloittamassa tai jo aloittaneet orkesterisoiton. Opas sisältää aloittelijaa auttavia vinkkejä sekä hyödyllistä tietoa kaikesta orkesteriin liittyvästä. Oppaan kymmenessä luvussa esitellään mm. mikä orkesteri on, orkesterin sisäinen hierarkia, ergonominen istuminen, mitä treeneissä tehdään, tavallisimmat nuottimerkinnät ja esiintymiseen liittyvät asiat. Oppaan lopussa on lisäksi sanasto mahdollisista oudoista sanoista ja orkesterin kultaiset säännöt, jotka tiivistävät oppaan opit kymmenessä iskulauseessa. Opas sisältää tekstin lisäksi havainnollista kuva-aineistoa. Raportissa esittelemme oppaan tekemisen prosessin. Kerromme miten oppaan aihe kiteytyi ja kenelle oppaamme on tarkoitettu. Arvioimme työprosessia ja työn aineistoa. Lisäksi raportoimme projektin, jossa esittelimme oppaan sisältöä lapsille. Opas on tarkoitettu lapsille luettavaksi mielellään vanhempien tai opettajan kanssa. Opasta voi myös hyödyntää orkesteriopetuksessa. Sen avulla orkesterityöskentelyn aloittaminen on helpompaa sekä ohjaajalle että lapsille. Tuloksena on nuoria orkesterietiketin tuntevia soittajia.