Diffuse large B-cell lymphoma is the most common subtype of non-Hodgkin’s lymphoma. It a germinal center (GC)–derived, aggressive, and heterogeneous disease. Several transcription factors signaling pathways that play central role in progression GC reaction differentiation have been shown to an oncogenic diffuse 6 (BCL6) transcriptional repressor induces phenotype blocks plasma cell (PC) differe...

We thank Robins et al. (1) for their thoughtful commentary on our article (2). Before responding, we wish to point out that they altered our notation slightly, using m rather than j to refer to the baseline time point. Robins et al. distinguish between two types of historyadjusted marginal structural models (HA-MSMs), those that consider an outcome at a fixed time point (‘‘group 1,’’ or those w...

BACKGROUND Dating apps play a major role in connecting men who are interested in meeting other men for sex. Besides finding a partner, these tools are also exploited for other activities such as encouraging people to get involved in the habit of illicit drug consumption (substance use). METHODS This study evaluated the overall usage of dating apps among Thai men who have sex with men (MSMs), ...

Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be com...

Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge in molecular biophysics. Network models, such as Markov state models (MSMs), are one potential solution to this problem. MSMs have recently yielded quantitative agreement with experimentally derived structures and folding rates for specific systems, leaving them positioned to potentially provide a d...

Molecular dynamics simulations of biomolecules produce a very high dimensional time-series dataset. Performing analysis necessarily involves projection onto a lower dimensional space. A priori selection of projection coordinates requires (perhaps unavailable) prior information or intuition about the system. At best, such a projection can only confirm the intuition. At worst, a poor projection c...

Markov state models (MSMs)--or discrete-time master equation models--are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative connection with experiments (often tens of thousands of states even for small systems) are generally too complicated to understand. Here, I present a bayesian ag...

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...