Open-target sparse sensing of biological agents using DNA microarray.

Background: Current biosensors are designed to target and react to specific nucleic acid sequences or structural epitopes. These 'target-specific' platforms require creation of new physical capture reagents when new organisms are targeted. An 'open-target' approach to DNA microarray biosensing is proposed and substantiated using laboratory generated data.

VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results.

Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown.

Empirical evidence for synchrony in the evolution of TB cases and HIV+ contacts among the San Francisco homeless.

The re-emergence of tuberculosis (TB) in the mid-1980s in many parts of the world, including the United States, is often attributed to the emergence and rapid spread of human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS). Although it is well established that TB transmission is particularly amplified in populations with high HIV prevalence, the epidemiology of interaction between TB and HIV is not well understood. This is partly due to the scarcity of HIV-related data, a consequence of the voluntary nature of HIV status reporting and testing, and partly due to current practices of screening high risk populations through separate surveillance programs for HIV and TB.

Early detection of tuberculosis outbreaks among the San Francisco homeless: trade-offs between spatial resolution and temporal scale.

Background: San Francisco has the highest rate of tuberculosis (TB) in the U.S. with recurrent outbreaks among the homeless and marginally housed.

Multi-syndrome analysis of time series using PCA: a new concept for outbreak investigation.

To date, despite widespread availability of time series data on multiple syndromes, multivariate analysis of syndromic data remains under-explored. We present a non-parametric multivariate framework for early detection of temporal anomalies based on principal components analysis of historical data on multiple syndromes. We introduce simulated outbreaks of different shapes and magnitudes into the historical data, and compare the detection sensitivity and timeliness of the multi-syndrome detection method with those of uni-syndrome.