Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

High-throughput prioritization of cancer-causing mutations (drivers) is a key challenge of cancer genome projects, due to the number of somatic variants detected in tumors. One important step in this task is to assess the functional impact of tumor somatic mutations. A number of computational methods have been employed for that purpose, although most were originally developed to distinguish disease-related nonsynonymous single nucleotide variants (nsSNVs) from polymorphisms. Our new method, transformed Functional Impact score for Cancer (transFIC), improves the assessment of the functional impact of tumor nsSNVs by taking into account the baseline tolerance of genes to functional variants.

Londres, terra promesa: l'emigració de joves universitaris titulats catalans a Londres

L’alta taxa d’atur juvenil a Catalunya i la precarització persistent del mercat laboral per als joves, han provocat que molts d’ells es plantegin marxar a l’estranger per a provar sort. Segons l’INE, al 2012 van emigrar 10791 catalans i el 35,7% són joves d’entre 16 i 34 anys. El Regne Unit va ser la tercera destinació preferida, amb 958 catalans emigrants reconeguts. La globalització ha difuminat les fronteres i ha obert els horitzons a empreses i treballadors. Les experiències internacionals són cada cop més necessàries si volem formar part d’aquest món, però tenen les seves contrapartides. La present investigació estudia el cas de 10 joves catalans amb titulacions universitàries que han marxat a Londres a la recerca d’aquesta experiència internacional, tot desitjant assentar les bases d’una carrera professional exitosa. El focus d’estudi és conèixer les motivacions de l’emigració que han trobat a la ciutat anglesa i quines són les expectatives de futur

The EU-ADR Web Platform: delivering advanced pharmacovigilance tools

PURPOSE: Pharmacovigilance methods have advanced greatly during the last decades, making post-market drug assessment an essential drug evaluation component. These methods mainly rely on the use of spontaneous reporting systems and health information databases to collect expertise from huge amounts of real-world reports. The EU-ADR Web Platform was built to further facilitate accessing, monitoring and exploring these data, enabling an in-depth analysis of adverse drug reactions risks.METHODS: The EU-ADR Web Platform exploits the wealth of data collected within a large-scale European initiative, the EU-ADR project. Millions of electronic health records, provided by national health agencies, are mined for specific drug events, which are correlated with literature, protein and pathway data, resulting in a rich drug-event dataset. Next, advanced distributed computing methods are tailored to coordinate the execution of data-mining and statistical analysis tasks. This permits obtaining a ranked drug-event list, removing spurious entries and highlighting relationships with high risk potential.RESULTS: The EU-ADR Web Platform is an open workspace for the integrated analysis of pharmacovigilance datasets. Using this software, researchers can access a variety of tools provided by distinct partners in a single centralized environment. Besides performing standalone drug-event assessments, they can also control the pipeline for an improved batch analysis of custom datasets. Drug-event pairs can be substantiated and statistically analysed within the platform's innovative working environment.CONCLUSIONS: A pioneering workspace that helps in explaining the biological path of adverse drug reactions was developed within the EU-ADR project consortium. This tool, targeted at the pharmacovigilance community, is available online at https://bioinformatics.ua.pt/euadr/. Copyright © 2012 John Wiley & Sons, Ltd.

Noves perspectives en el diagnòstic del deteriorament cognitiu lleu i la malaltia de l'Alzheimer

Els criteris per al diagnòstic clínic de la malaltia d’Alzheimer es van establir el 1984 pel National Institute of Neurological and Communicative Disorders and Stroke (NINCDS) i la Alzheimer’s Disease and Related Disorders Association (ADRDA). D’aplicació continuada fins a l’actualitat, aquests criteris estan quedant obsolets i per tant des de diversos àmbits s’ha abogat per una revisió profunda dels mateixos. Tres grups d’experts formats per reconeguts especialistes del National Institute on Aging (NIA) i la Alzheimer’s Association proposen un conjunt de recomanacions per modificar aquests criteris en l’àmbit de la investigació clínica. Dues diferències remarcables s’inclouen en aquests nous criteris: la incorporació de biomarcadors i la formalització de diferents estadis de la malaltia d’Alzheimer. D’aquesta manera, el deteriorament cognitiu lleu s’incorpora al procés diagnòstic com un estadi més de la patologia. Tanmateix, aquests criteris es troben en revisió i, de moment sols son aplicables en l’àmbit de recerca per tal d’arribar a un consens definitiu que permeti la modificació definitiva dels criteris clínics universals a aplicar. En aquest article es presenten els principals avenços en la investigació referents a la malaltia d’Alzheimer i al Deteriorament Cognitiu lleu per tal d’emmarcar els nous criteris de recerca.

Impact of the Spanish smoking law on exponsure to secondhand smoke in offices and hospitality venues: before-and-after study

BACKGROUND/OBJECTIVES: A smoking law was passed by the Spanish Parliament in December 2005 and was enforced by 1 January 2006. The law bans smoking in all indoor workplaces but only in some hospitality venues, because owners are allowed to establish a smoking zone (venues>100 m2) or to allow smoking without restrictions (venues<100 m2). The objective of the study is to assess the impact of the Spanish smoking law on exposure to secondhand smoke (SHS) in enclosed workplaces, including hospitality venues. MATERIALS AND METHODS: The study design is a before-and-after evaluation. We studied workplaces and hospitality venues from eight different regions of Spain. We took repeated samples of vapor-phase nicotine concentration in 398 premises, including private offices (162), public administration offices (90), university premises (43), bars and restaurants (79), and discotheques and pubs (24). RESULTS: In the follow-up period, SHS levels were markedly reduced in indoor offices. The median decrease in nicotine concentration ranged from 60.0% in public premises to 97.4% in private areas. Nicotine concentrations were also markedly reduced in bars and restaurants that became smoke-free (96.7%) and in the no-smoking zones of venues with separate spaces for smokers (88.9%). We found no significant changes in smoking zones or in premises allowing smoking, including discotheques and pubs. CONCLUSIONS: Overall, this study shows the positive impact of the law on reducing SHS in indoor workplaces. However, SHS was substantially reduced only in bars and restaurants that became smoke-free. Most hospitality workers continue to be exposed to very high levels of SHS. Therefore, a 100% smoke-free policy for all hospitality venues is required.

Prevalencia de la discapacidad en España por comunidades autónomas: el papel de los factores individuales y del entorno geográfico en su variabilidad

Fundamento: La prevalencia de discapacidad en la población general presenta una gran variabilidad geográfica, de manera que identificar aquellos factores que pudieran explicarla será importante para la planificación de políticas sociales. En este trabajo se analiza la variabilidad de la discapacidad por comunidades autónomas desde una doble vertiente, los factores individuales y del entorno. Métodos: Los datos proceden principalmente de la Encuesta de Discapacidad, Deficiencias y Estado de Salud de 1999 y del Inebase, ambas del Instituto Nacional de Estadística (INE). Se calculó la prevalencia de discapacidad simple y ajustada por edad de las CCAA. Se analizan los factores individuales asociados a la discapacidad mediante una regresión logística y los factores individuales y de la comunidad autónoma conjuntamente con una regresión logística de dos niveles. Resultados: La prevalencia de discapacidad muestra una diferencia máxima de 5,75 puntos entre las comunidades autónomas. En la regresión logística la comunidad de residencia fue estadísticamente significativa (OR: 3,35 en la de mayor prevalencia respecto a la de menor) junto con otras variables individuales: edad (OR de 40-64= 1,78 OR de 65-79= 1,87 y OR de >79= 3,34), sexo (OR mujer= 0,66), situación laboral (OR sin trabajo=2,25 OR amas casa/estudiante=1,39 y OR otros=2,03), estado de salud (OR regular= 1,69 OR malo/muy malo= 2,05) y enfermedades crónicas (OR 1-3=1,56 OR4-6=1,82 OR>6=2,59). En la regresión de dos niveles las variables individuales explican poca varianza (s=0,261) y ninguna de las variables relativas a las CCAA mejora el modelo. Conclusiones: Las características individuales no explican suficientemente la variabilidad de la discapacidad entre CCAA y no se han identificado variables del entorno que sean significativas.

Eficacia de la inducción miofascial para el tratamiento de la espasticidad en pacientes con parálisis cerebral espástica: ensayo clínico aleatorizado

¿El tratamiento mediante la inducción miofascial disminuye la espasticidad en los pacientes con Parálisis Cerebral Espástica (PCE) mientras son intervenidos con un tratamiento convencional? Objetivos: Comprobar si la inducción miofascial disminuye la espasticidad en pacientes con parálisis cerebral espástica (PCE) y así mismo prevenir las complicaciones musculoesqueléticas y aumentar el rango de movilidad articular. Metodología: Ensayo controlado clínico aleatorizado que recoge un total de 96 casos de PCE con Grado l, ll y lll de afectación según la Escala de clasificación Gross Motor Function Measure (GMFM). Se asignará de forma aleatoria y equitativamente 48 sujetos al grupo control aplicándose el tratamiento convencional y 48 sujetos al grupo experimental, donde la inducción miofascial se complementará con tratamiento convencional. Durante 3 meses se llevará a cabo el plan de intervención, 2 días a la semana en ambos grupos. Los datos serán analizados a través de las siguientes escalas: el tono muscular (Escala de Ashworth Modificada, Escala de Tardieu, Test pendular Wartenberg) funcionalidad y actividad (Gross Motor Function Classification System, Gross Motor Function Mesurement, Pediatric Evaluation of Disability Inventory), valoración neurológica (National Institute of NEurological Disordes and Stroke Scale) y la satisfacción del paciente (Questionnaire on Pain Caused by Spasticity). Estos datos serán extraidos el primer día, el último y 3 meses más tarde a modo de seguimiento. Durante el plan de intervención también se realizarán valoraciones semanales y mensuales.

Secondhand tobacco smoke exposure in open and semi-open settings: a systematic review

Background: Some countries have recently extended smoke-free policies to particular outdoor settings; however, there is controversy regarding whether this is scientifically and ethically justifiable. Objectives: The objective of the present study was to review research on secondhand smoke (SHS) exposure in outdoor settings. Data sources: We conducted different searches in PubMed for the period prior to September 2012. We checked the references of the identified papers, and conducted a similar search in Google Scholar. Study selection: Our search terms included combinations of"secondhand smoke,""environmental tobacco smoke,""passive smoking" OR"tobacco smoke pollution" AND"outdoors" AND"PM" (particulate matter),"PM2.5" (PM with diameter ≤ 2.5 µm),"respirable suspended particles,""particulate matter,""nicotine,""CO" (carbon monoxide),"cotinine,""marker,""biomarker" OR"airborne marker." In total, 18 articles and reports met the inclusion criteria. Results: Almost all studies used PM2.5 concentration as an SHS marker. Mean PM2.5 concentrations reported for outdoor smoking areas when smokers were present ranged from 8.32 to 124 µg/m3 at hospitality venues, and 4.60 to 17.80 µg/m3 at other locations. Mean PM2.5 concentrations in smoke-free indoor settings near outdoor smoking areas ranged from 4 to 120.51 µg/m3. SHS levels increased when smokers were present, and outdoor and indoor SHS levels were related. Most studies reported a positive association between SHS measures and smoker density, enclosure of outdoor locations, wind conditions, and proximity to smokers. Conclusions: The available evidence indicates high SHS levels at some outdoor smoking areas and at adjacent smoke-free indoor areas. Further research and standardization of methodology is needed to determine whether smoke-free legislation should be extended to outdoor settings.

A state-space approach for measuring regional manufacturing production indices

In this paper we propose a latent variable model, in the spirit of Israilevich and Kuttner (1993), to measure regional manufacturing production. To test the validity of the proposed methodology, we have applied it for those Spanish regions that have a direct quantitative index. The results demonstrate the accuracy of the methodology proposed and show that it can overcome some of the difficulties of the indirect method applied by the INE, the Spanish National Institute of Statistics.

Case-Crossover Analysis of Air Pollution Health Effects: A Systematic Review of Methodology and Application

Case-crossover is one of the most used designs for analyzing the health-related effects of air pollution. Nevertheless, no one has reviewed its application and methodology in this context. Objective: We conducted a systematic review of case-crossover (CCO) designs used to study the relationship between air pollution and morbidity and mortality, from the standpoint of methodology and application.Data sources and extraction: A search was made of the MEDLINE and EMBASE databases.Reports were classified as methodologic or applied. From the latter, the following information was extracted: author, study location, year, type of population (general or patients), dependent variable(s), independent variable(s), type of CCO design, and whether effect modification was analyzed for variables at the individual level. Data synthesis: The review covered 105 reports that fulfilled the inclusion criteria. Of these, 24 addressed methodological aspects, and the remainder involved the design’s application. In the methodological reports, the designs that yielded the best results in simulation were symmetric bidirectional CCO and time-stratified CCO. Furthermore, we observed an increase across time in the use of certain CCO designs, mainly symmetric bidirectional and time-stratified CCO. The dependent variables most frequently analyzed were those relating to hospital morbidity; the pollutants most often studied were those linked to particulate matter. Among the CCO-application reports, 13.6% studied effect modification for variables at the individual level.Conclusions: The use of CCO designs has undergone considerable growth; the most widely used designs were those that yielded better results in simulation studies: symmetric bidirectional and time-stratified CCO. However, the advantages of CCO as a method of analysis of variables at the individual level are put to little use

Association between Long-Term Exposure to Traffic-Related Air Pollution and Subclinical Atherosclerosis: The REGICOR Study

Background: Epidemiological evidence of the effects of long-term exposure to air pollu tion on the chronic processes of athero genesis is limited. Objective: We investigated the association of long-term exposure to traffic-related air pollu tion with subclinical atherosclerosis, measured by carotid intima media thickness (IMT) and ankle–brachial index (ABI). Methods: We performed a cross-sectional analysis using data collected during the reexamination (2007–2010) of 2,780 participants in the REGICOR (Registre Gironí del Cor: the Gerona Heart Register) study, a population-based prospective cohort in Girona, Spain. Long-term exposure across residences was calculated as the last 10 years’ time-weighted average of residential nitrogen dioxide (NO2) estimates (based on a local-scale land-use regression model), traffic intensity in the nearest street, and traffic intensity in a 100 m buffer. Associations with IMT and ABI were estimated using linear regression and multinomial logistic regression, respectively, controlling for sex, age, smoking status, education, marital status, and several other potential confounders or intermediates. Results: Exposure contrasts between the 5th and 95th percentiles for NO2 (25 μg/m), traffic intensity in the nearest street (15,000 vehicles/day), and traffic load within 100 m (7,200,000 vehicle-m/day) were associated with differences of 0.56% (95% CI: –1.5, 2.6%), 2.32% (95% CI: 0.48, 4.17%), and 1.91% (95% CI: –0.24, 4.06) percent difference in IMT, respectively. Exposures were positively associated with an ABI of > 1.3, but not an ABI of < 0.9. Stronger associations were observed among those with a high level of education and in men ≥ 60 years of age. Conclusions: Long-term traffic-related exposures were associated with subclinical markers of atherosclerosis. Prospective studies are needed to confirm associations and further examine differences among population subgroups.key words: ankle–brachial index, average daily traffic, cardiovascular disease, exposure assessment, exposure to tailpipe emissions, intima media thickness, land use regression model, Mediterranean diet, nitrogen dioxide