MOTIVATION We have implemented a coalescent simulation program for a structured population with selection at a single diploid locus. The program includes the functionality of the simulator ms to model population structure and demography, but adds a model for deme- and time-dependent selection using forward simulations. The program can be used, e.g. to study hard and soft selective sweeps in str...

Robins introduced Marginal Structural Models (MSMs), a general class of counterfactual models for the joint effects time-varying treatment regimes in complex longitudinal studies subject to confounding. In his work, identification MSM parameters is established under Sequential Randomization Assumption (SRA), which rules out unmeasured confounding assignment over time. We consider sufficient con...

Protein stabilization is fundamental to enzyme function and evolution, yet understanding the determinants of a protein's stability remains a challenge. This is largely due to a shortage of atomically detailed models for the ensemble of relevant protein conformations and their relative populations. For example, the M182T substitution in TEM β-lactamase, an enzyme that confers antibiotic resistan...

Ensemble/Legacy is a toolkit extension of the Object Technology Framework (OTF) that exposes an object oriented interface for accessing and manipulating ensembles (collections of molecular conformations that share a common chemical topology) and driving Legacy programs (such as MSMS, AMBER, X-PLOR, CORMA/MARDIGRAS, Dials and Windows, and CURVES). Ensemble/Legacy provides a natural programming i...

Deep eutectic solvents (DES) are potential ecofriendly surfactants for the preparation of materials. In this study, both molecularly imprinted polymers (MIPs) and mesoporous siliceous materials (MSMs) were modified by betaine-based DES. Six materials were employed as solid phase extraction (SPE) adsorbents for the rapid purification of levofloxacin. The DES-based materials showed better selecti...

We propose an approach to design mobile agent applications for content-based multimedia information retrieval or electronic commerce on the Internet. The specific mobile agents of interest are called adlets, which are mobile agents carrying the metadata of various kinds of multimedia documents. Adlets autonomously travel from site to site on the Internet, advertising its contents and interactin...

Tandem mass spectrometry has emerged to be one of the most powerful high-throughput techniques for protein identification. Tandem mass spectrometry selects and fragments peptides of interest into N-terminal ions and C-terminal ions, and it measures the mass/charge ratios of these ions. The de novo peptide sequencing problem is to derive the peptide sequences from given tandem mass spectral data...

Submit Manuscript | http://medcraveonline.com Abbreviations: AIDS: Acquired Immune Deficiency Syndrome; BCBL: Body Cavity Based Lymphoma Cell Line; CSWS: Commercial Sex Workers; DNA: Deoxyribonucleic Acid; EIA: Enzyme Immune Assays; ELISA: Enzyme Linked Immunosorbent Assays; FSWS: Female Sex Workers; HBV: Hepatitis B Virus; HCV: Hepatitis C Virus; HHV-8: Human Herpes Virus Type 8; HIV: Human Im...

We present a maximum-caliber method for inferring transition rates of a Markov state model (MSM) with perturbed equilibrium populations given estimates of state populations and rates for an unperturbed MSM. It is similar in spirit to previous approaches, but given the inclusion of prior information, it is more robust and simple to implement. We examine its performance in simple biased diffusion...

A simple, rapid and robust high-throughput assay for the quantitative analysis of metformin in plasma from different species using laser diode thermal desorption interfaced with atmospheric chemical pressure ionization tandem mass spectrometry (LDTD-APCI-MSMS) was developed for use in a pharmaceutical discovery environment. In order to minimize sample preparation a generic protein precipitation...