MOTIVATION Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. Thi...

Abstract Marginal structural models (MSMs) can be used to estimate the causal effect of a potentially time-varying treatment in presence time-dependent confounding via weighted regression. The standard approach using inverse probability weighting (IPTW) sensitive model misspecification and lead high-variance estimates due extreme weights. Various methods have been proposed partially address thi...

Urethral gonorrhoea (UG) dramatically decreased in Paris between 1986 and 1997 as a consequence of safer sexual behaviour. Thus, only 43 cases of gonorrhoea have been collected in our clinic in 1997, the lowest number since the early 1970s. Since 1998, an increase has been observed, as in other STD clinics in France and in the Renago laboratory network. 1–3 Men who have sex with men (MSMs) repr...

BACKGROUND Retrospective studies of haemodialysis patients from large dialysis organizations in the United States have indicated that intravenous vitamin D may be associated with a survival benefit. However, patients prescribed vitamin D are generally healthier than those who are not, suggesting that treatment by indication may have biased previous findings. Additionally, no survival benefit as...

In order to reduce practice variations and offer cancer patients the best treatments according to reference guidelines, therapeutic decisions have to be taken, in France, by "multidisciplinary staff meetings'' (MSMs) as patient-specific care plans which are then implemented by cancer specialists. OncoDoc2 is a CDSS implementing CancerEst guidelines, a "local reference guideline'', on breast can...

The Defence Conceptual Modelling Framework (DCMF) is the Swedish Defence Research Agency’s (FOI) proposal to deal with conceptual modelling in the military domain. The vision of the DCMF is to enable composability, interoperability and reuse of knowledge for modelling and simulation. The final products, the conceptual models, are called Mission Space Models (MSMs), following the original CMMS p...

The study of folding and conformational changes of macromolecules by molecular dynamics simulations often requires the generation of large amounts of simulation data that are difficult to analyze. Markov (state) models (MSMs) address this challenge by providing a systematic way to decompose the state space of the molecular system into substates and to estimate a transition matrix containing the...

Molecular recognition, the process by which biological macromolecules selectively bind, plays an important role in many biological processes. Molecular simulations hold great potential to reveal the chemical details of molecular recognition and to complement experiments. However, it is challenging to reconstruct the binding process for two-body systems like protein-ligand complexes because the ...

Background. Several studies have used phylogenetics to investigate Human Immunodeficiency Virus (HIV) transmission among Men who have Sex with Men (MSMs) in Montreal, Quebec, Canada, revealing many transmission clusters. The Quebec HIV genotyping program sequence database now includes viral sequences from close to 4, 000 HIV-positive individuals classified as MSMs. In this paper, we investigate...

Even in the absence of unmeasured confounding factors or model misspecification, standard methods for estimating the causal effect of a time-varying treatment on the mean of a repeated measures outcome (for example, GEE regression) may be biased when there are time-dependent variables that are simultaneously confounders of the effect of interest and are predicted by previous treatment. In contr...