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.

A susceptible-infected model of early detection of respiratory infection outbreaks on a background of influenza.

The threat of biological warfare and the emergence of new infectious agents spreading at a global scale have highlighted the need for major enhancements to the public health infrastructure. Early detection of epidemics of infectious diseases requires both real-time data and real-time interpretation of data. Despite moderate advancements in data acquisition, the state of the practice for real-time analysis of data remains inadequate.

Evolution of indirect reciprocity by social information: the role of trust and reputation in evolution of altruism.

The complexity of human's cooperative behavior cannot be fully explained by theories of kin selection and group selection. If reciprocal altruism is to provide an explanation for altruistic behavior, it would have to depart from direct reciprocity, which requires dyads of individuals to interact repeatedly. For indirect reciprocity to rationalize cooperation among genetically unrelated or even culturally dissimilar individuals, information about the reputation of individuals must be assessed and propagated in a population.

Qualitative analysis of the all-cause black-white mortality crossover.

To date, despite decades of investigations and the relative abundance of mortality data, our understanding of the phenomenon of 'mortality crossover' remains inadequate. We propose a methodology for transforming mortality data from the 'age-domain' to the 'time-domain'. We then introduce a model of selection partially offset by mobility, to simulate the dynamics of vulnerability in a population cohort that is heterogeneous in health and death.