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...

Magnetic shape memory alloys (MSM alloys), a new kind of smart materials, have become a potential candidate in many engineering fields. MSMs have the advantage of bearing a huge strain, much larger than other materials. In addition, they also have fast response. These characteristics make MSM a good choice in micro engineering. However, MSMs display the obvious hysteresis phenomenon of nonlinea...

In a series of papers, Robins and colleagues describe inverse probability of treatment weighted (IPTW) estimation in marginal structural models (MSMs), a method of causal analysis of longitudinal data based on counterfactual principles. This family of statistical techniques is similar in concept to weighting of survey data, except that the weights are estimated using study data rather than defi...

We consider time-continuous, reversible Markov processes on large or continuous state space. For a practical analysis of such processes it is often necessary to construct low dimensional approximations, like Markov State Models (MSM). MSM have been used for this purpose in several applications, particularly in molecular dynamics, see [16] for an example. One of the main goals of MSMs is the cor...

AIM After in utero exposure to tricyclic antidepressants, neonatal withdrawal symptoms have been reported with an estimated incidence between 20 and 50%; however, few data are available for clomipramine. This could also be the case for neonatal pharmacokinetic clomipramine parameters and so this study was set up. METHODS Babies exposed to clomipramine in utero were included in an observationa...