Biomedical subjects

David Hsu

Publications and source records attributed to David Hsu.

10 recordsLinked to original sources

PubMed2006

A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk.

Parameter estimation is a critical problem in modeling biological pathways. It is difficult because of the large number of parameters to be estimated and the limited experimental data available. In this paper, we propose a decompositional approach to parameter estimation. It exploits the structure of a large pathway model to break it into smaller components, whose parameters can then be estimated independently. This leads to significant improvements in computational efficiency. We present our approach in the context of Hybrid Functional Petri Net modeling and evolutionary search for parameter value estimation. However, the approach can be easily extended to other modeling frameworks and is independent of the search method used. We have tested our approach on a detailed model of the Akt and MAPK pathways with two known and one hypothesized crosstalk mechanisms. The entire model contains 84 unknown parameters. Our simulation results exhibit good correlation with experimental data, and they yield positive evidence in support of the hypothesized crosstalk between the two pathways.

Algorithms↗

PubMed2006

A robust approach for the quantitation of viral concentration in an adenoviral vector-based human immunodeficiency virus vaccine by real-time quantitative polymerase chain reaction.

A real-time quantitative polymerase chain reaction (PCR)-based method was developed to measure the concentration of recombinant adenoviral vector genomes in purified virus bulks and final container samples of monovalent and multivalent human immunodeficiency virus (HIV) adenoviral vector vaccine candidates. This method, referred to as the genome quantitation assay (GQA), was optimized through a rigorous approach for evaluating PCR detection chemistries, designing a robust assay format, and establishing a properly calibrated reference standard. In addition, the use of a simplified lysis procedure, automated liquid transfer system, and parallel-line data analysis contribute to an accurate, precise, reliable, and high-throughput assay procedure that can be used for process monitoring, final formulation, and release of vaccine products. A variance component analysis study indicated that the GQA typically produces results with an interassay precision of less than 10% relative standard deviation (RSD), allowing generation of final results (average of three runs) with associated interassay precision of 6% RSD or less. The precision, accuracy, specificity, and robustness of the GQA demonstrate its utility for analytical characterization of a wide variety of viral vector- and DNA plasmid- based vaccines or gene therapy products. In addition, we also evaluated the Adenovirus Reference Standard generated by the Adenovirus Reference Material Working Group in the GQA to provide a common point-of-reference for our analytical method.

AIDS Vaccines↗

PubMed2005

Nonpharmacological treatment options for epilepsy.

Approximately one third of children with epilepsy have persistent seizures despite trials of multiple antiepileptic medications. For some of these patients, epilepsy surgery may provide freedom from seizures. However, in many cases, epilepsy surgery is not a viable treatment option. Nonpharmacological approaches are a useful adjunct to help manage seizures in these children. This review examines the role of vagus nerve stimulation, the ketogenic diet, and various forms of EEG biofeedback therapy in children with intractable epilepsy. Although the mechanism of action is not known precisely for any of these adjunctive therapies, they add an important and evolving dimension to the management of difficult to control epilepsy in children. In addition, pyridoxine-dependent seizures are discussed as an example of an etiology of refractory seizures that responds well to replacement therapy.

Allylamine↗

PubMed2004

Thermal inactivation of adenovirus type 5.

Adenovirus-based products are being developed for human use as vaccine constructs and gene therapy vehicles. In order to operate by cGMP guidelines and to address biosafety concerns, it is imperative to ensure that adequate decontamination procedures are implemented in adenovirus manufacturing facilities. Liquid decontamination procedures based on heat treatment are relatively easy to employ in a manufacturing setting. In this study, we have conducted small-scale experiments to determine the effectiveness of thermal inactivation procedures on adenovirus type 5. We have determined the robustness of the assays used to measure sample potency with regard to different sample matrices and adenovirus constructs. Greater than eight logs of reduction in adenovirus type 5 potency may be obtained upon exposure of the sample to temperatures greater than 70 degrees C and times longer than 20 min.

Adenoviruses, Human↗

PubMed2004

Frontal lobe seizures and uveitis associated with acute human parvovirus B19 infection.

We report a 5-year-old girl who developed repeated episodes of behavioral alterations shortly after human parvovirus B19 infection and uveitis. Video-electroencephalographic study demonstrated that these brief episodes were frontal lobe seizures. Seizures responded promptly to antiepilepsy medications. Further diagnostic testing did not reveal any rheumatologic disorders. Human parvovirus B19 infections in children are more commonly associated with febrile seizures and meningoencephalitis. Our case demonstrates that, rarely, it may be associated with the development of partial epilepsy.

Acute Disease↗

PubMed2003

A family of ductile intermetallic compounds.

Stoichiometric intermetallic compounds have always been touted for their attractive chemical, physical, electrical, magnetic and mechanical properties, but few practical uses have materialized because they are brittle at room temperature. Here we report on a large family of fully ordered, stoichiometric binary rare-earth intermetallic compounds with high ductility at room temperature. Although conventional wisdom calls for special conditions, such as non-stoichiometry, metastable disorder or doping to achieve some ductility in intermetallic compounds at room temperature, none of these is required in these unique B2 rare-earth compounds. Ab initio calculations of YAg, YCu and NiAl crystal defect energies support the observed deformation modes of these intermetallics.

Anisotropy↗

PubMed2003

Gremlin is the BMP antagonist required for maintenance of Shh and Fgf signals during limb patterning.

During limb outgrowth, signaling by bone morphogenetic proteins (BMPs) must be moderated to maintain the signaling loop between the zone of polarizing activity (ZPA) and the apical ectodermal ridge (AER). Gremlin, an extracellular Bmp antagonist, has been proposed to fulfill this function and therefore be important in limb patterning. We tested this model directly by mutating the mouse gene encoding gremlin (Cktsf1b1, herein called gremlin). In the mutant limb, the feedback loop between the ZPA and the AER is interrupted, resulting in abnormal skeletal pattern. We also show that the gremlin mutation is allelic to the limb deformity mutation (ld). Although Bmps and their antagonists have multiple roles in limb development, these experiments show that gremlin is the principal BMP antagonist required for early limb outgrowth and patterning.

Animals↗

PubMed2003

Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion.

Classic molecular motion simulation techniques, such as Monte Carlo (MC) simulation, generate motion pathways one at a time and spend most of their time in the local minima of the energy landscape defined over a molecular conformation space. Their high computational cost prevents them from being used to compute ensemble properties (properties requiring the analysis of many pathways). This paper introduces stochastic roadmap simulation (SRS) as a new computational approach for exploring the kinetics of molecular motion by simultaneously examining multiple pathways. These pathways are compactly encoded in a graph, which is constructed by sampling a molecular conformation space at random. This computation, which does not trace any particular pathway explicitly, circumvents the local-minima problem. Each edge in the graph represents a potential transition of the molecule and is associated with a probability indicating the likelihood of this transition. By viewing the graph as a Markov chain, ensemble properties can be efficiently computed over the entire molecular energy landscape. Furthermore, SRS converges to the same distribution as MC simulation. SRS is applied to two biological problems: computing the probability of folding, an important order parameter that measures the "kinetic distance" of a protein's conformation from its native state; and estimating the expected time to escape from a ligand-protein binding site. Comparison with MC simulations on protein folding shows that SRS produces arguably more accurate results, while reducing computation time by several orders of magnitude. Computational studies on ligand-protein binding also demonstrate SRS as a promising approach to study ligand-protein interactions.

Algorithms↗

PubMed2002

Using robotics to fold proteins and dock ligands.

The problems of protein folding and ligand docking have been explored largely using molecular dynamics or Monte Carlo methods. These methods are very compute intensive because they often explore a much wider range of energies, conformations and time than necessary. In addition, Monte Carlo methods often get trapped in local minima. We initially showed that robotic motion planning permitted one to determine the energy of binding and dissociation of ligands from protein binding sites (Singh et al., 1999). The robotic motion planning method maps complicated three-dimensional conformational states into a much simpler, but higher dimensional space in which conformational rearrangements can be represented as linear paths. The dimensionality of the conformation space is of the same order as the number of degrees of conformational freedom in three-dimensional space. We were able to determine the relative energy of association and dissociation of a ligand to a protein by calculating the energetics of interaction for a few thousand conformational states in the vicinity of the protein and choosing the best path from the roadmap. More recently, we have applied roadmap planning to the problem of protein folding (Apaydin et al., 2002a). We represented multiple conformations of a protein as nodes in a compact graph with the edges representing the probability of moving between neighboring states. Instead of using Monte Carlo simulation to simulate thousands of possible paths through various conformational states, we were able to use Markov methods to calculate the steady state occupancy of each conformation, needing to calculate the energy of each conformation only once. We referred to this Markov method of representing multiple conformations and transitions as stochastic roadmap simulation or SRS. We demonstrated that the distribution of conformational states calculated with exhaustive Monte Carlo simulations asymptotically approached the Markov steady state if the same Boltzman energy distribution was used in both methods. SRS permits one to calculate contributions from all possible paths simultaneously with far fewer energy calculations than Monte Carlo or molecular dynamics methods. The SRS method also permits one to represent multiple unfolded starting states and multiple, near-native, folded states and all possible paths between them simultaneously. The SRS method is also independent of the function used to calculate the energy of the various conformational states. In a paper to be presented at this conference (Apaydin et al., 2002b) we have also applied SRS to ligand docking in which we calculate the dynamics of ligand-protein association and dissociation in the region of various binding sites on a number of proteins. SRS permits us to determine the relative times of association to and dissociation from various catalytic and non-catalytic binding sites on protein surfaces. Instead of just following the best path in a roadmap, we can calculate the contribution of all the possible binding or dissociation paths and their relative probabilities and energies simultaneously.

Algorithms↗

PubMedDate not supplied

Inactivation of adenovirus type 5 by caustics.

Adenovirus shows significant promise as a vehicle for transfer of therapeutic genes into humans. Based on the importance of this viral vector, it is critical that adequate decontamination procedures are implemented during its large-scale production in multiproduct manufacturing facilities to prevent cross-product contamination and to reduce the risk of personnel exposure. Liquid decontamination procedures based on caustics are easily implemented in a manufacturing setting and are not corrosive to stainless steel surfaces at the concentrations found to inactivate viral proteins and nucleic acids. In this study, we have conducted small-scale experiments to determine the effectiveness of caustic inactivation procedures on adenovirus type 5 and have evaluated the robustness of the process to different sample matrices and adenovirus constructs. We find that the pH of a sample post-addition of caustic solution is a more accurate indicator of the effectiveness of the caustic than its concentration. We have demonstrated that a greater than 6 log reduction in the potency of adenovirus type 5 may be obtained upon exposure of the sample to sodium hydroxide and CIP-100 at concentrations greater than 0.09 M and 0.9%, respectively, at times greater than 10 min.

Adenoviridae↗