Evidence of a cancer type-specific distribution for consecutive somatic mutation distances

Specific molecular mechanisms may affect the pattern of mutation in particular regions, and therefore leaving a footprint or signature in the DNA of their activity. The common approach to identify these signatures is studying the frequency of substitutions. However, such an analysis ignores the important spatial information, which is important with regards to the mutation occurrence statistics. In this work, we propose that the study of the distribution of distances between consecutive mutations along the DNA molecule can provide information about the types of somatic mutational processes. In particular, we have found that specific cancer types show a power-law in interoccurrence distances, instead of the expected exponential distribution dictated with the Poisson assumption commonly made in the literature. Cancer genomes exhibiting power-law interoccurrence distances were enriched in cancer types where the main mutational process is described to be the activity of the APOBEC protein family, which produces a particular pattern of mutations called Kataegis. Therefore, the observation of a power-law in interoccurence distances could be used to identify cancer genomes with Kataegis

Tuberculosis and airflow obstruction: evidence from the PLATINO study in Latin America

The aim of the present study was to evaluate the association between history of tuberculosis and airflow obstruction.A population-based, multicentre study was carried out and included 5,571 subjects aged >= 40 yrs living in one of five Latin American metropolitan areas: São Paulo (Brazil); Montevideo (Uruguay); Mexico City (Mexico); Santiago (Chile); and Caracas (Venezuela). Subjects performed pre- and post-bronchodilator spirometry and were asked whether they had ever been diagnosed with tuberculosis by a physician.The overall prevalence of airflow obstruction (forced expiratory volume in one second/forced vital capacity post-bronchodilator < 0.7) was 30.7% among those with a history of tuberculosis, compared with 13.9% among those without a history. Males with a medical history of tuberculosis were 4.1 times more likely to present airflow obstruction than those without such a diagnosis. This remained unchanged after adjustment for confounding by age, sex, schooling, ethnicity, smoking, exposure to dust and smoke, respiratory morbidity in childhood and current morbidity. Among females, the unadjusted and adjusted odds ratios were 2.3 and 1.7, respectively.In conclusion, history of tuberculosis is associated with airflow obstruction in Latin American middle-aged and older adults.Univ Fed Pelotas, BR-96020220 Pelotas, BrazilUniversidade Federal de São Paulo, São Paulo, BrazilNatl Inst Resp Dis, Mexico City, DF, MexicoUniv Republica, Montevideo, UruguayCatholic Univ Chile, Santiago, ChileCent Univ Venezuela, Caracas, VenezuelaUniversidade Federal de São Paulo, São Paulo, BrazilWeb of Scienc

Health status perception and airflow obstruction in five Latin American cities: the PLATINO study

Background: COPD is a highly prevalent disease but underdiagnosed, undertreated and possibly under-recognized by patients. Limited information exists regarding patients' perception of COPD severity. We compared patients' general, health status perception, degree of breathlessness and physical activity limitation with the severity of their respiratory condition measured by airway obstruction, in a population-based sample.Methods: We used postbronchodilator FEV(1)/FVC < 0.70 to define COPD. Patients' perception of their general. health status was derived from the question in general, you would say that your health is: excellent, very good, good, fair or poor?Results: Spirometry was performed in 5314 subjects: an FEV(1)/FVC ratio below 0.70 was found in 759 subjects. in persons with COPD, general. health status decreased with increasing GOLD stages. Over one-half of subjects with stage 2 and one third of those with stages 3 and 4 reported their health status as good to excellent. There was also a disparity between airway obstruction severity and breathlessness intensity. Although the more severe COPD stages were frequently associated with significant compromise of work and everyday activities, patients often tended to provide an optimistic self evaluation of their health status.Conclusions: the discrepancy observed between general health status, dyspnea severity, physical activity limitation and airway obstruction most likely reflect patients' underperception of disease severity, emphasizing the need for improving case-finding measures and multi-component evaluation of COPD subjects. (C) 2009 Elsevier B.V. All rights reserved.Boehringer Ingelheim GmbHCent Univ Venezuela, Hosp Univ Caracas, Serv Neumonol, Caracas 1030, VenezuelaUniv Calif Los Angeles, Sch Publ Hlth, Los Angeles, CA 90066 USAInst Resp Dis, Mexico City 14080, DF, MexicoUniv Republica, Hosp Maciel, Montevideo, UruguayUniversidade Federal de São Paulo, BR-04021070 São Paulo, BrazilPontificia Univ Catolica Chile, Dept Salud Publ, Santiago, ChilePontificia Univ Catolica Chile, Catedra Neumol, Santiago, ChileUniv Fed Pelotas, Fac Med, BR-96030002 Pelotas, RS, BrazilUniversidade Federal de São Paulo, BR-04021070 São Paulo, BrazilWeb of Scienc

Chronic obstructive pulmonary disease and body mass index in five Latin America cities: the PLATINO study

Background: the body mass index (BMI) is a prognostic factor for chronic obstructive pulmonary disease (COPD). Despite its importance, little information is available regarding BMI alteration in COPD from a population-based study. We examined characteristics by BMI categories in the total and COPD populations in five Latin-American cities, and explored the factors influencing BMI in COPD.Methods: COPD was defined as a postbronchodilator forced expiratory volume in the first second/forced vital capacity (FEV(1)/FVC)= 30.0 kg/m(2)).Results: Interviews were completed in 5571 subjects from 6711 eligible individuals, and spirometry was performed in 5314 subjects. There were 759 subjects with COPD and 4555 without COPD. Compared with the non-COPD group, there was a higher proportion of COPD subjects in the underweight and normal weight categories, and a lower proportion in the obese category. Over one-half COPD subjects had BMI over 25 kg/m(2). No differences in BMI strata among countries were found in COPD subjects. Factors associated with lower BMI in mates with COPD were aging, current smoking, and global initiative for chronic obstructive lung disease (GOLD) stages III - IV, whereas wheeze and residing in Santiago and Montevideo were associated with higher BMI. in females with COPD, current smoking, lower education, and GOLD stages II - IV were associated with lower BMI, while dyspnea and wheeze were associated with higher BMI.Conclusions: BMI alterations are common in COPD with no significant differences among countries. Current smoking, age, GOLD stages, education level, residing in Santiago and Montevideo, dyspnea and wheeze were independently associated with BMI in COPD. (c) 2008 Elsevier B.V. All rights reserved.Cent Univ Venezuela, Fac Med, Hosp Univ Caracas, Serv Neumonol, Caracas 1030, VenezuelaInst Resp Dis, Mexico City 14080, DF, MexicoUniversidade Federal de São Paulo, BR-04021070 São Paulo, BrazilUniv Republica, Hosp Maciel, Fac Med, Montevideo 2610, UruguayPontificia Univ Catolica Chile, Fac Med, Dept Salud Publ, Santiago, ChileUniv Calif Los Angeles, Sch Publ Hlth, Los Angeles, CA 90066 USAUniv Fed Pelotas Duque Caxias, Fac Med, Pelotas, RS, BrazilUniversidade Federal de São Paulo, BR-04021070 São Paulo, BrazilWeb of Scienc

Triggering events with GPUs at ATLAS

The growing complexity of events produced in LHC collisions demands increasing computing power both for the online selection and for the offline reconstruction of events. In recent years there have been significant advances in the performance of Graphics Processing Units (GPUs) both in terms of increased compute power and reduced power consumption that make GPUs extremely attractive for use in a complex particle physics experiments such as ATLAS. A small scale prototype of the full ATLAS High Level Trigger has been implemented that exploits reconstruction algorithms optimized for this new massively parallel paradigm. We discuss the integration procedure followed for this prototype and present the performance achieved and the prospects for the future.Peer Reviewe

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011