Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

The interface between oral and systemic health: the need for more collaboration.

The focus of this review is to highlight the need for improved communication between medical and dental professionals in order to deliver more effective care to patients. The need for communication is increasingly required to capitalise on recent advances in the biological sciences and in medicine for the management of patients with chronic diseases. Improvements in longevity have resulted in populations with increasing special oral-care needs, including those who have cancer of the head and neck, those who are immunocompromised due to HIV/AIDS, advanced age, residence in long-term care facilities or the presence of life-long conditions, and those who are receiving long-term prescription medications for chronic conditions (e.g., anti-hypertensives, anticoagulants, immunosuppressants, antidepressants). These medications can cause adverse reactions in the oral cavity, such as xerostomia and ulceration. Patients with xerostomia are at increased risk of tooth decay, periodontal disease and infection. The ideal management of such individuals should involve the collaborative efforts of physicians, nurses, dentists and dental hygienists, thus optimising treatment and minimising secondary complications deriving from the oral cavity.

Ordonnance de sortie d'hôpital: un défi pour la continuité des soins et la collaboration interprofessionnelle [Hospital's discharge prescription: a challenge for continuity of care and the interprofessional collaboration].

The transition between hospital and community is an interface at high risk for medication. "The Association of Family Doctors" committee in the canton of Vaud (MFVaud), together with community pharmacists' and Homecare representatives, have begun to consider the following improvements: fast and co-ordinated care providers' information; arrangements for family doctors appointments as soon as possible; awareness and education for interprofessional collaboration; more secured preparation of pill boxes; development of interprofessional means such as medication use reviews and reconciliations. In the opinion of all the experts, there is an urgent public health need to act in an interprofessional manner, even if the solutions required (especially change in professional culture and technologies) are not immediate.

The Impact of Industry Collaboration on Academic Research Output: A Dynamic Panel Data Analysis

The aim of this paper is to analyse the impact of university knowledge and technology transfer activities on academic research output. Specifically, we study whether researchers with collaborative links with the private sector publish less than their peers without such links, once controlling for other sources of heterogeneity. We report findings from a longitudinal dataset on researchers from two engineering departments in the UK between 1985 until 2006. Our results indicate that researchers with industrial links publish significantly more than their peers. Academic productivity, though, is higher for low levels of industry involvement as compared to high levels.

Sistema Distribuído de Monitorização de Tráfego com uma Arquitectura Peer-to-Peer

As características do tráfego na Internet são cada vez mais complexas devido à crescente diversidade de aplicações, à existência de diferenças drásticas no comportamento de utilizadores, à mobilidade de utilizadores e equipamentos, à complexidade dos mecanismos de geração e controlo de tráfego, e à crescente diversidade dos tipos de acesso e respectivas capacidades. Neste cenário é inevitável que a gestão da rede seja cada vez mais baseada em medições de tráfego em tempo real. Devido à elevada quantidade de informação que é necessário processar e armazenar, é também cada vez maior a necessidade das plataformas de medição de tráfego assumirem uma arquitectura distribuída, permitindo o armazenamento distribuído, replicação e pesquisa dos dados medidos de forma eficiente, possivelmente imitando o paradigma Peer-to-Peer (P2P). Esta dissertação descreve a especificação, implementação e teste de um sistema de medição de tráfego com uma arquitectura distribuída do tipo P2P, que fornece aos gestores de rede uma ferramenta para configurar remotamente sistemas de monitorização instalados em diversos pontos da rede para a realização de medições de tráfego. O sistema pode também ser usado em redes orientadas à comunidade onde os utilizadores podem partilhar recursos das suas máquinas para permitir que outros realizem medições e partilhem os dados obtidos. O sistema é baseado numa rede de overlay com uma estrutura hierárquica organizada em áreas de medição. A rede de overlay é composta por dois tipos de nós, denominados de probes e super-probes, que realizam as medições e armazenam os resultados das mesmas. As superprobes têm ainda a função de garantir a ligação entre áreas de medição e gerir a troca de mensagens entre a rede e as probes a elas conectadas. A topologia da rede de overlay pode mudar dinamicamente, com a inserção de novos nós e a remoção de outros, e com a promoção de probes a super-probes e viceversa, em resposta a alterações dos recursos disponíveis. Os nós armazenam dois tipos de resultados de medições: Light Data Files (LDFs) e Heavy Data Files (HDFs). Os LDFs guardam informação relativa ao atraso médio de ida-evolta de cada super-probe para todos os elementos a ela ligados e são replicados em todas as super-probes, fornecendo uma visão simples mas facilmente acessível do estado da rede. Os HDFs guardam os resultados detalhados das medições efectuadas a nível do pacote ou do fluxo e podem ser replicados em alguns nós da rede. As réplicas são distribuídas pela rede tendo em consideração os recursos disponíveis nos nós, de forma a garantir resistência a falhas. Os utilizadores podem configurar medições e pesquisar os resultados através do elemento denominado de cliente. Foram realizados diversos testes de avaliação do sistema que demonstraram estar o mesmo a operar correctamente e de forma eficiente.