BACKGROUND Plasma Citrulline concentration has been correlated to functional enterocyte mass. Dried blood spot (DBS) analysis using LC-MSMS reduces sample amount needed. We optimized DBS elution to increase precision and accuracy of DBS LC-MSMS analysis. METHOD DBS control samples were eluted in varying pH (2.2-7.0) and for varying times (15-75 min) and Cit, Arg and Orn were analyzed using LC...

Markov state models (MSMs) have proven to be useful tools in simulating large and slowly-relaxing biological systems like proteins. MSMs model proteins through dynamics on a discrete-state energy landscape, allowing molecules to effectively sample large regions of phase space. In this work, we use aspects of MSMs to ask: is protein folding mechanistically robust? We first provide a definition o...

Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguis...

Marginal structural models (MSMs) are becoming increasingly popular as a tool to make causal inference from longitudinal data. Unlike standard regression models, MSMs can adjust for time-dependent observed confounders while avoiding the bias due to the adjustment for covariates affected by the treatment. Despite their theoretical appeal, a main practical difficulty of MSMs is the required estim...

Magnetic soft materials (MSMs) and magnetic shape memory polymers (MSMPs) have been some of the most intensely investigated newly developed material types in last decade, thanks to great versatile potential their innovative characteristic behaviors such as remote nearly heatless transformation case MSMs. With regard a number properties recovery ratio, manufacturability, cost or programming pote...

Objective To evaluate the root and root canal morphology of the maxillary second molars (MSMs) in a native Chinese population by cone-beam computed tomography. Methods Cone-beam computed tomography images of 2412 MSMs from 1294 Chinese patients were analyzed to determine the number and morphology of the roots, the root canal morphology, the bilateral symmetry, and the correlations of these para...

Lysine-specific chemical crosslinking in combination with mass spectrometry is emerging as a tool for the structural characterization of protein complexes and protein-protein interactions. After tryptic digestion of crosslinked proteins there are thousands of peptides amenable to MSMS, of which only very few are crosslinked peptides of interest. Here we describe how the advantage offered by off...

BACKGROUND Peptide-based analysis of whole blood using electrospray tandem mass spectrometry (MSMS) in multiple reaction monitoring (MRM) mode enables rapid detection and sequence confirmation of clinically significant hemoglobin (Hb) variants. We applied a similar, quantitative approach to the measurement of delta:beta-globin peptide ratios as potential surrogate markers of HbA(2), a biomarker...

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pullin...

SUMMARY Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding dynamics. MSMExplorer is a visualization application purpose-built to visualize these MSMs with an aim to increase the efficacy and reach of MSM science. AVAILABILITY MSMExplorer is available for download from https://simtk.org/home/msmexplorer...