Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.

Ontology driven integration platform for clinical and translational research

Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a dynamic and distributed environment. Components of the semantic solution and its overall architecture are described.

SAMPLING METHODOLOGY FOR AIRBORNE SEMIVOLATILE ORGANIC POLLUTANTS USING POLYURETHANE FOAMS (COLLECTION, PESTICIDES, VOLATILE)

Indoor and ambient air organic pollutants have been gaining attention because they have been measured at levels with possible health effects. Studies have shown that most airborne polychlorinated biphenyls (PCBs), pesticides and many polycyclic aromatic hydrocarbons (PAHs) are present in the free vapor state. The purpose of this research was to extend recent investigative work with polyurethane foam (PUF) as a collection medium for semivolatile compounds. Open-porous flexible PUFs with different chemical makeup and physical properties were evaluated as to their collection affinities/efficiencies for various classes of compounds and the degree of sample recovery. Filtered air samples were pulled through plugs of PUF spiked with various semivolatiles under different simulated environmental conditions (temperature and humidity), and sampling parameters (flow rate and sample volume) in order to measure their effects on sample breakthrough volume (V(,B)). PUF was also evaluated in the passive mode using organo-phosphorus pesticides. Another major goal was to improve the overall analytical methodology; PUF is inexpensive, easy to handle in the field and has excellent airflow characteristics (low pressure drop). It was confirmed that the PUF collection apparatus behaves as if it were a gas-solid chromatographic system, in that, (V(,B)) was related to temperature and sample volume. Breakthrough volumes were essentially the same using both polyether and polyester type PUF. Also, little change was observed in the V(,B)s after coating PUF with common chromatographic liquid phases. Open cell (reticulated) foams gave better recoveries than closed cell foams. There was a slight increase in (V(,B)) with an increase in the number of cells/pores per inch. The high-density polyester PUF was found to be an excellent passive and active collection adsorbent. Good recoveries could be obtained using just solvent elution. A gas chromatograph equipped with a photoionization detector gave excellent sensitivities and selectivities for the various classes of compounds investigated. ^

Hepatitis B and C infections in U.S. incarcerated populations: Prevalence and related mortality

Published reports have consistently indicated high prevalence of serologic markers for hepatitis B (HBV) and hepatitis C (HCV) infection in U.S. incarcerated populations. Quantifying the current and projected burden of HBV and HCV infection and hepatitis-related sequelae in correctional healthcare systems with even modest precision remains elusive, however, because the prevalence and sequelae of HBV and HCV in U.S. incarcerated populations are not well-studied. This dissertation contributes to the assessment of the burden of HBV and HCV infections in U.S. incarcerated populations by addressing some of the deficiencies and gaps in previous research. ^ Objectives of the three dissertation studies were: (1) To investigate selected study-level factors as potential sources of heterogeneity in published HBV seroprevalence estimates in U.S. adult incarcerated populations (1975-2005), using meta-regression techniques; (2) To quantify the potential influence of suboptimal sensitivity of screening tests for antibodies to hepatitis C virus (anti-HCV) on previously reported anti-HCV prevalence estimates in U.S. incarcerated populations (1990-2005), by comparing these estimates to error-adjusted anti-HCV prevalence estimates in these populations; (3) To estimate death rates due to HBV, HCV, chronic liver disease (CLD/cirrhosis), and liver cancer from 1984 through 2003 in male prisoners in custody of the Texas Department of Criminal Justice (TDCJ) and to quantify the proportion of CLD/cirrhosis and liver cancer prisoner deaths attributable to HBV and/or HCV. ^ Results were as follows. Although meta-regression analyses were limited by the small body of literature, mean population age and serum collection year appeared to be sources of heterogeneity, respectively, in prevalence estimates of antibodies to HBV antigen (HBsAg+) and any positive HBV marker. Other population characteristics and study methods could not be ruled out as sources of heterogeneity. Anti-HCV prevalence is likely somewhat higher in male and female U.S. incarcerated populations than previously estimated in studies using anti-HCV screening tests alone without the benefit of repeat or additional testing. Death rates due to HBV, HCV, CLD/cirrhosis, and liver cancer from 1984 through 2003 in TDCJ male prisoners exceeded state and national rates. HCV rates appeared to be increasing and disproportionately affecting Hispanics. HCV was implicated in nearly one-third of liver cancer deaths. ^