The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015 : a systematic analysis for the Global Burden of Disease Study 2015

Background Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures. Methods We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER). Findings Globally, life expectancy from birth increased from 61.7 years (95% uncertainty interval 61.4-61.9) in 1980 to 71.8 years (71.5-72.2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11.3 years (3.7-17.4), to 62.6 years (56.5-70.2). Total deaths increased by 4.1% (2.6-5.6) from 2005 to 2015, rising to 55.8 million (54.9 million to 56.6 million) in 2015, but age-standardised death rates fell by 17.0% (15.8-18.1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14.1% (12.6-16.0) to 39.8 million (39.2 million to 40.5 million) in 2015, whereas age-standardised rates decreased by 13.1% (11.9-14.3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42.1%, 39.1-44.6), malaria (43.1%, 34.7-51.8), neonatal preterm birth complications (29.8%, 24.8-34.9), and maternal disorders (29.1%, 19.3-37.1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death. Interpretation At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems. Copyright (C) The Author(s). Published by Elsevier Ltd.Peer reviewe

Etude de salubrité des marais du Mes (Loire-Atlantique). Deuxième partie : Secteur Quimiac/Kercabellec- Mesquer (1992-1993)

Les marais salants de Quimiac et de Kercabellec, siège d'une petite activité d'affinage d'huîtres et d'élevage de palourdes en claires, sont situés dans un environnement fortement urbanisé du fait de l'importance de la vocation touristique et résidentielle de la commune de Mesquer. Les eaux marines remontent librement dans les étiers, qui se vident presque totalement à chaque marée basse, en toute saison. Les petits ruisseaux du bassin versant, ainsi que les fossés entourant les marais, ne sont réellement alimentés qu'en période de pluie. Malgré un réseau d'assainissement couvrant la quasi-totalité du secteur étudié, la surveillance des rejets en mer, exercée par la DDASS et la Cellule Qualité des Eaux Littorales, montre parfois de fortes contaminations bactériologiques des eaux de ces étiers. Les résultats bactériologiques  mesurés dans les coquillages déposés sur le fond des étiers montrent que ceux-ci sont fortement contaminés sur la totalité de leur cours, quelle que soit la saison. Le pic annuel de pollution fait suite au pic d'affluence touristique centré sur la première quinzaine d'août. Les marées de vives-eaux, qui induisent la remise en suspension des sédiments fins contaminés, ont une influence significative sur les fortes concentrations en coliformes fécaux. Par contre, l'influence des précipitations n'a pu être mise en évidence statistiquement en raison d'une faible pluviométrie les jours précédents les prélèvements. Les étiers de Quimiac et de Kercabellec étant fortement et fréquemment pollués sur le plan bactériologique, les auteurs recommandent d'exiger des conditions très strictes à l'octroi des autorisations de prises d'eau destinées à un usage conchylicole. Les résultats obtenus devraient conduire au classement insalubre de ces étiers suivant les normes fixées par l'arrêté ministériel du 12 octobre 1976

The role of the synthetic chromophore of GFP in generating polymorphism-dependent on/off photoluminescence

International audiencePolymorphism, i.e. the ability of a solid material to exist in more than one crystal form, gives unique opportunity to study the correlation between the solid-state molecular arrangement and the photoluminescence properties, and allows optimizing the performances of materials with reduced synthesis effort. Compound 1, which results from the combination of 2phenylbenzoxazole (PBO) and benzylideneimidazolinone (BDI), was known to be weakl

In situ control of oxygen partial pressure in a buffered UO2 fuel: A manufacturing process

An innovative laboratory process making use of the specific properties of solid redox buffers was developed for producing O2 self-regulated UO2 fuel samples. The method was optimized using Molybdenum and Niobium oxide buffers. The starting materials were first mixed with the UO2 powder, then pressed into pellets and finally sintered in a quasi-closed vessel at 1670 °C under strictly controlled oxygen potential using appropriate solid redox buffers. Speciation of Mo and Nb was characterized using Scanning Electron Microscopy (SEM) combined with Energy Dispersive X-ray spectroscopy (EDX) as well as X-ray Diffraction (XRD). Using this optimized procedure, both oxido-reducing forms of the O2 buffer incorporated into the UO2 specimens were preserved during sintering, allowing an in situ control of the O2 partial pressure inside the material. The processing methodology, the laboratory experimental set-up, the sintering procedure and the characteristics of the final oxygen buffered UO2 fuel are described. This work opens the path to representative laboratory studies related to the redox dependent behavior of irradiated fuels in reactor

A defect model for UO2+x based on electrical conductivity and deviation from stoichiometry measurements

International audienceElectrical conductivity of UO2+x shows a strong dependence upon oxygen partial pressure and temperature which may be interpreted in terms of prevailing point defects. A simulation of this property along with deviation from stoichiometry is carried out based on a model that takes into account the presence of impurities, oxygen interstitials, oxygen vacancies, holes, electrons and clusters of oxygen atoms. The equilibrium constants for each defect reaction are determined to reproduce the experimental data. An estimate of defect concentrations and their dependence upon oxygen partial pressure can then be determined. The simulations carried out for 8 different temperatures (973–1673 K) over a wide range of oxygen partial pressures are discussed and resulting defect equilibrium constants are plotted in an Arrhenius diagram. This provides an estimate of defect formation energies which may further be compared to other experimental data or ab-initio and empirical potential calculations

Thermodynamic modelling of advanced oxide and carbide nuclear fuels: description of the U-Pu-O-C system

In the present work a thermodynamic model is derived for the (U,Pu)O2 oxide, the (U,Pu)C carbide fuels using the Calphad method to describe consistently both phase diagrams and thermodynamic data of the phase involved in the U-Pu_O_C system. All the available thermodynamic and phase diagram data of the binary and ternary sub-systems are very well reproduced by our model. For the quaternary system, the calculated phase equilibria in the U0.3PU0.7-C-O region are in good agreement with the experimental data. Keywords: Nuclear fuels, uranium dioxide, mixed oxide of uranium and plutonium, uranium carbide, plutonium carbide, mixed carbide of uranium and plutoinium, uranium oxycarbide, plutonium oxycarbide, mixed oxycarbide of uranium and plutonium, thermodynamics, phase diagrams, calphadJRC.E.3-Materials researc