BIGNASim: A NoSQL database structure and analysis portal for nucleic acids simulation data

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120s of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined metatrajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/

Madrid 2020, ahora o nunca

Tutora: Montse QuesadaTreball de fi de grau en Periodisme. Curs 2012-2013Aquest treball té la voluntat de ser un reportatge d’investigació sobre la cursa olímpica de Madrid, des de la candidatura de 2012 fins la de 2020. Els defensors dels Jocs Olímpics a la capital espanyola justifiquen el seu tercer intent consecutiu en el fet de tenir el 80% de les infraestructures necessàries construïdes. En canvi, l’oposició ha trobat en la crisi econòmica el millor motiu per posicionar-se en contra de la celebració dels JJOO./nHem realitzat una sèrie de 15 entrevistes amb tota mena d’experts i personalitats de l’àmbit, intentant albergar sempre tots els possible punts de vista que hagin sorgit al respecte. El resultat ha sigut un article de llarga extensió que fa un repàs a tota la història olímpica de Madrid fins a dia d’avui i intenta interpretar tots els esdeveniments ocorreguts fins ara.Este trabajo tiene la voluntad de ser un reportaje de investigación sobre la carrera olímpica de Madrid, desde la candidatura de 2012 hasta la de 2020. Los defensores de los Juegos Olímpicos en la capital española justifican su tercer intento consecutivo en tener el 80% de las infraestructuras necesarias construidas. En cambio, la oposición ha encontrado en la crisis económica el mejor motivo para posicionarse en contra de la celebración de los JJOO./nHemos realizado un total de 15 entrevistas a expertos y personalidades del ámbito, intentando albergar todos los puntos de vista que existen al respecto. El resultado ha sido un artículo de larga extensión que es un repaso de toda la historia olímpica de Madrid hasta el día de hoy, e intenta interpretar todos los acontecimientos ocurridos hasta ahora.This survey’s aim is to create a journalistic investigation report about Madrid´s Olympic race since their first candidature in 2012 until the current 2020 candidature. People for Madrid’s Olympic Games justify the necessity of the third candidature in a row by saying that 80% of the infrastructure is already done. Those against the Games believe that the economic crisis in Spain is concerning enough to postpone this candidature./nWe have done 15 interviews with all kind of experts and personalities involved with the topic, always trying to reach the many different visions about it. The result is an extensive article which goes thorough the history of Madrid’s Olympic candidatures until today trying to explain the different relevant events

Madrid 2020, ahora o nunca

Tutora: Montse QuesadaTreball de fi de grau en Periodisme. Curs 2012-2013Aquest treball té la voluntat de ser un reportatge d’investigació sobre la cursa olímpica de Madrid, des de la candidatura de 2012 fins la de 2020. Els defensors dels Jocs Olímpics a la capital espanyola justifiquen el seu tercer intent consecutiu en el fet de tenir el 80% de les infraestructures necessàries construïdes. En canvi, l’oposició ha trobat en la crisi econòmica el millor motiu per posicionar-se en contra de la celebració dels JJOO./nHem realitzat una sèrie de 15 entrevistes amb tota mena d’experts i personalitats de l’àmbit, intentant albergar sempre tots els possible punts de vista que hagin sorgit al respecte. El resultat ha sigut un article de llarga extensió que fa un repàs a tota la història olímpica de Madrid fins a dia d’avui i intenta interpretar tots els esdeveniments ocorreguts fins ara.Este trabajo tiene la voluntad de ser un reportaje de investigación sobre la carrera olímpica de Madrid, desde la candidatura de 2012 hasta la de 2020. Los defensores de los Juegos Olímpicos en la capital española justifican su tercer intento consecutivo en tener el 80% de las infraestructuras necesarias construidas. En cambio, la oposición ha encontrado en la crisis económica el mejor motivo para posicionarse en contra de la celebración de los JJOO./nHemos realizado un total de 15 entrevistas a expertos y personalidades del ámbito, intentando albergar todos los puntos de vista que existen al respecto. El resultado ha sido un artículo de larga extensión que es un repaso de toda la historia olímpica de Madrid hasta el día de hoy, e intenta interpretar todos los acontecimientos ocurridos hasta ahora.This survey’s aim is to create a journalistic investigation report about Madrid´s Olympic race since their first candidature in 2012 until the current 2020 candidature. People for Madrid’s Olympic Games justify the necessity of the third candidature in a row by saying that 80% of the infrastructure is already done. Those against the Games believe that the economic crisis in Spain is concerning enough to postpone this candidature./nWe have done 15 interviews with all kind of experts and personalities involved with the topic, always trying to reach the many different visions about it. The result is an extensive article which goes thorough the history of Madrid’s Olympic candidatures until today trying to explain the different relevant events

Novel methodology for the optimization of the retrofitting

This paper aims to present a novel methodology that permits to determine the optimal retrofitting actions to be implemented in a given building of the tertiary sector, based on its architectonic characteristics (e.g. volume, useful area, orientation, walls thermal transmittance, etc.), climatic conditions (i.e. solar radiation, temperature) and operation profiles. The proposed methodology has been developed by the technological centers "Eurecat" and "Fundació CTM Centre Tecnològic", in the framework of two national research projects. The proposed methodology is based on the combination of mathematical models that characterize the annual energy demand vectors of a given building based on its characteristics, and the use of an evolutionary-based optimization algorithms to evaluate the different (available) retrofitting actions for both the passive and active part of the building, with objective to determine the optimal ones in terms of energy efficiency, investment and maintenance cost and GHG emissions reduction. The proposed methodology has been developed as a beta software tool for windows-based operating systems, which through a simplified graphic user interface permits the customization of the databased, the configuration of the building's characteristics, as well as the evaluation and optimization of different retrofitting actions in both the passive and active parts of a given building. Finally, it presents graphically and numerically the obtained results.Peer ReviewedPostprint (published version

Novel methodology for the optimization of the retrofitting

This paper aims to present a novel methodology that permits to determine the optimal retrofitting actions to be implemented in a given building of the tertiary sector, based on its architectonic characteristics (e.g. volume, useful area, orientation, walls thermal transmittance, etc.), climatic conditions (i.e. solar radiation, temperature) and operation profiles. The proposed methodology has been developed by the technological centers "Eurecat" and "Fundació CTM Centre Tecnològic", in the framework of two national research projects. The proposed methodology is based on the combination of mathematical models that characterize the annual energy demand vectors of a given building based on its characteristics, and the use of an evolutionary-based optimization algorithms to evaluate the different (available) retrofitting actions for both the passive and active part of the building, with objective to determine the optimal ones in terms of energy efficiency, investment and maintenance cost and GHG emissions reduction. The proposed methodology has been developed as a beta software tool for windows-based operating systems, which through a simplified graphic user interface permits the customization of the databased, the configuration of the building's characteristics, as well as the evaluation and optimization of different retrofitting actions in both the passive and active parts of a given building. Finally, it presents graphically and numerically the obtained results.Peer Reviewe

Novel methodology for the optimization of the retrofitting

This paper aims to present a novel methodology that permits to determine the optimal retrofitting actions to be implemented in a given building of the tertiary sector, based on its architectonic characteristics (e.g. volume, useful area, orientation, walls thermal transmittance, etc.), climatic conditions (i.e. solar radiation, temperature) and operation profiles. The proposed methodology has been developed by the technological centers "Eurecat" and "Fundació CTM Centre Tecnològic", in the framework of two national research projects. The proposed methodology is based on the combination of mathematical models that characterize the annual energy demand vectors of a given building based on its characteristics, and the use of an evolutionary-based optimization algorithms to evaluate the different (available) retrofitting actions for both the passive and active part of the building, with objective to determine the optimal ones in terms of energy efficiency, investment and maintenance cost and GHG emissions reduction. The proposed methodology has been developed as a beta software tool for windows-based operating systems, which through a simplified graphic user interface permits the customization of the databased, the configuration of the building's characteristics, as well as the evaluation and optimization of different retrofitting actions in both the passive and active parts of a given building. Finally, it presents graphically and numerically the obtained results.Peer Reviewe

Readmissions and complications in breast ductal carcinoma in situ: A retrospective study comparing screen- and non-screen-detected patients

Objective: Population-wide mammographic screening programs aim to reduce breast cancer mortality. However, a broad view of the harms and benefits of these programs is necessary to favor informed decisions, especially in the earliest stages of the disease. Here, we compare the outcomes of patients diagnosed with breast ductal carcinoma in situ in participants and non-participants of a population-based mammographic screening program. Methods: A retrospective cohort study of all patients diagnosed with breast ductal carcinoma in situ between 2000 and 2010 within a single hospital. A total of 211 patients were included, and the median follow-up was 8.4 years. The effect of detection mode (screen-detected and non-screen-detected) on breast cancer recurrences, readmissions, and complications was evaluated through multivariate logistic regression analysis. Results: In the majority of women, breast ductal carcinoma in situ was screen-detected (63.5%). Screen-detected breast ductal carcinoma in situ was smaller in size compared to those non-screen-detected (57.53% < 20 mm versus 78.03%, p = 0.002). Overall, breast-conserving surgery was the most frequent surgery (86.26%); however, mastectomy was higher in non-screen-detected breast ductal carcinoma in situ (20.78% versus 9.7%, p = 0.024). Readmissions for mastectomy were more frequent in non-screen-detected breast ductal carcinoma in situ. Psychological complications, such as fatigue, anxiety, and depression, had a prevalence of 15% within our cohort. Risk of readmissions and complications was higher within the non-screen-detected group, as evidenced by an odds ratio = 6.25 (95% confidence interval = 1.95-19.99) for readmissions and an odds ratio = 2.41 (95% confidence interval = 1.95-4.86) for complications. Conclusions: Our findings indicate that women with breast ductal carcinoma in situ breast cancer diagnosed through population-based breast cancer screening program experience a lower risk of readmissions and complications than those diagnosed outside these programs. These findings can help aid women and health professionals make informed decisions regarding screening

Readmissions and complications in breast ductal carcinoma in situ : A retrospective study comparing screen- and non-screen-detected patients

Population-wide mammographic screening programs aim to reduce breast cancer mortality. However, a broad view of the harms and benefits of these programs is necessary to favor informed decisions, especially in the earliest stages of the disease. Here, we compare the outcomes of patients diagnosed with breast ductal carcinoma in situ in participants and non-participants of a population-based mammographic screening program. A retrospective cohort study of all patients diagnosed with breast ductal carcinoma in situ between 2000 and 2010 within a single hospital. A total of 211 patients were included, and the median follow-up was 8.4 years. The effect of detection mode (screen-detected and non-screen-detected) on breast cancer recurrences, readmissions, and complications was evaluated through multivariate logistic regression analysis. In the majority of women, breast ductal carcinoma in situ was screen-detected (63.5%). Screen-detected breast ductal carcinoma in situ was smaller in size compared to those non-screen-detected (57.53% < 20 mm versus 78.03%, p = 0.002). Overall, breast-conserving surgery was the most frequent surgery (86.26%); however, mastectomy was higher in non-screen-detected breast ductal carcinoma in situ (20.78% versus 9.7%, p = 0.024). Readmissions for mastectomy were more frequent in non-screen-detected breast ductal carcinoma in situ. Psychological complications, such as fatigue, anxiety, and depression, had a prevalence of 15% within our cohort. Risk of readmissions and complications was higher within the non-screen-detected group, as evidenced by an odds ratio = 6.25 (95% confidence interval = 1.95-19.99) for readmissions and an odds ratio = 2.41 (95% confidence interval = 1.95-4.86) for complications. Our findings indicate that women with breast ductal carcinoma in situ breast cancer diagnosed through population-based breast cancer screening program experience a lower risk of readmissions and complications than those diagnosed outside these programs. These findings can help aid women and health professionals make informed decisions regarding screening

Prevalence of persistent pain after breast cancer treatment by detection mode among participants in population-based screening programs.

BACKGROUND: To date, the study of the risks and benefits of breast cancer screening has not included the onset of persistent pain after breast cancer treatment within the context of population-based screening programs. Our purpose was to investigate the prevalence of persistent pain and associated factors in women diagnosed with breast cancer (screening or interval) in the context of a population-based breast cancer screening program in Spain. METHODS: A total of 1,057 women participating in a population-based breast cancer screening program were diagnosed with breast cancer between 2000 and 2008. The women were treated surgically and followed-up to 2013. The risk of developing persistent pain was estimated through multivariate logistic regression analysis. RESULTS: Breast cancer was detected during routine screening in 732 women (69.3 %) and emerged as an interval cancer between two screening rounds in 325 (30.7 %). Persistent pain was present in 118 women (11.3 %). Women diagnosed through routine screening reported a higher prevalence of persistent pain (12.9 %) than those with interval cancers (7.8 %)(P  =2 (Odds Ratio [OR]: 4.5 95 % Confidence Interval [CI]: 2.1-9.5) versus no comorbidities, and having undergone an axillary lymph node dissection (OR: 2.0 95 % CI: 1.0-4.0) versus sentinel lymph node biopsy. CONCLUSIONS: The prevalence of persistent pain was relatively low. The detection mode was not related to the onset of persistent pain. The factors associated with persistent pain were a Charlson index > =2 and the performance of axillary lymph node dissection. Women treated for breast cancer are at risk for developing persistent pain regardless of the detection mode, especially those with comorbidities and those who have undergone axillary lymph node dissection.This study was supported by grants from Instituto de Salud Carlos III FEDER (grant numbers: PS09/01153, PI12/00387, PI11/01296 and PI15/00098) and by the Research Network on Health Services in Chronic Diseases (REDISSEC: RD12/0001/0015)