A Method for Reducing the Severity of Epidemics by Allocating Vaccines According to Centrality

One long-standing question in epidemiological research is how best to allocate limited amounts of vaccine or similar preventative measures in order to minimize the severity of an epidemic. Much of the literature on the problem of vaccine allocation has focused on influenza epidemics and used mathematical models of epidemic spread to determine the effectiveness of proposed methods. Our work applies computational models of epidemics to the problem of geographically allocating a limited number of vaccines within several Texas counties. We developed a graph-based, stochastic model for epidemics that is based on the SEIR model, and tested vaccine allocation methods based on multiple centrality measures. This approach provides an alternative method for addressing the vaccine allocation problem, which can be combined with more conventional approaches to yield more effective epidemic suppression strategies. We found that allocation methods based on in-degree and inverse betweenness centralities tended to be the most effective at containing epidemics.Comment: 10 pages, accepted to ACM BCB 201

A Global Stochastic Modeling Framework to Simulate and Visualize Epidemics

Epidemics have caused major human and monetary losses through the course of human civilization. It is very important that epidemiologists and public health personnel are prepared to handle an impending infectious disease outbreak. the ever-changing demographics, evolving infrastructural resources of geographic regions, emerging and re-emerging diseases, compel the use of simulation to predict disease dynamics. By the means of simulation, public health personnel and epidemiologists can predict the disease dynamics, population groups at risk and their geographic locations beforehand, so that they are prepared to respond in case of an epidemic outbreak. As a consequence of the large numbers of individuals and inter-personal interactions involved in simulating infectious disease spread in a region such as a county, sizeable amounts of data may be produced that have to be analyzed. Methods to visualize this data would be effective in facilitating people from diverse disciplines understand and analyze the simulation. This thesis proposes a framework to simulate and visualize the spread of an infectious disease in a population of a region such as a county. As real-world populations have a non-homogeneous demographic and spatial distribution, this framework models the spread of an infectious disease based on population of and geographic distance between census blocks; social behavioral parameters for demographic groups. the population is stratified into demographic groups in individual census blocks using census data. Infection spread is modeled by means of local and global contacts generated between groups of population in census blocks. the strength and likelihood of the contacts are based on population, geographic distance and social behavioral parameters of the groups involved. the disease dynamics are represented on a geographic map of the region using a heat map representation, where the intensity of infection is mapped to a color scale. This framework provides a tool for public health personnel and epidemiologists to run what-if analyses on disease spread in specific populations and plan for epidemic response. By the means of demographic stratification of population and incorporation of geographic distance and social behavioral parameters into the modeling of the outbreak, this framework takes into account non-homogeneity in demographic mix and spatial distribution of the population. Generation of contacts per population group instead of individuals contributes to lowering computational overhead. Heat map representation of the intensity of infection provides an intuitive way to visualize the disease dynamics

The degradation of MgB2 under ambient environment

The superconductivities of samples prepared by several procedures were found to degrade under ambient environment. The degradation mechanism was studied by measuring the change of surface chemical composition of dense MgB2 pellets (prepared by hot isostatic pressure, HIPed) under atmospheric exposure using X-ray Photoelectron Spectroscopy (XPS). Results showed that samples with poor connectivity between grains and with smaller grain sizes degrade with time when exposed to ambient conditions. In these samples, the Tc did not change with time, but the superconducting transition became broader and the Meissner fraction decreased. In contrast, our well-sintered and the HIPed samples remained stable for several months under ambient condition. The degradation was found to be related to surface decomposition as observed by XPS. We observed the formation of oxidized Mg, primarily in the form of a Mg hydroxide, the increase of C and O contents, and the reduction of B concentration in the surface layer of MgB2 samples.Comment: 15 pages, 3 figure

Improved superconducting properties of MgB2

We present electrical transport, magnetization, and specific heat measurements on bulk MgB2 samples (T_{c} = 38.5 K) synthesized under 200 MPa pressure using a process based on hot isostatic pressing with cooling under pressure. The samples are fully dense and display excellent superconducting properties, including a narrow superconducting transition width (\Delta T_{c} = 0.75 K), a high upper critical field H_{c2} (H_{c2}(0) ~ 155 kOe), and a critical current density J_{c} that is the largest yet measured for bulk samples of MgB2 (J_{c}(0) ~ 1.4 MA/cm^{2}). Specific heat measurements yielded a jump \Delta C at T_{c} of 92 mJ/mol K. These superconducting properties are comparable to those obtained with techniques that are not so well suited to industrial scale fabrication.Comment: 7 text pages, 5 figures, submitted to Physica

Microstructure and superconducting properties of hot isostatically pressed MgB2

Bulk samples of MgB2 have been formed by hot isostatic pressing (HIPping) of commercial powder at 100MPa and 950=B0C. The resulting material is 100% dense with a sharp superconducting transition at 37.5K. Microstructural studies have indicated the presence of small amounts of second phases within the material, namely MgO and B rich compositions, probably MgB4. Magnetisation measurements performed at 20K have revealed values of Jc=1.3 x 106A/cm2 at zero field, and 9.3 x 105A/cm2 at 1T. Magneto optical (MO) studies have shown direct evidence for the superconducting homogeneity and strong intergranular current flow in the material.Comment: 3 pages, 6 figures, text updated, new references included and discussed. Submitted to Superconductor Science and Technolog

tRNA epitranscriptomics and biased codon are linked to proteome expression in

Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.Singapore. National Research FoundationSingapore-MIT Alliance (Graduate Fellowship

Global Stochastic Field Simulator

This poster was featured at the 2013 Perot Museum of Nature and Science's 'Social Science' exhibit. It discusses the Global Stochastic Field Simulator, conceived in the summer of 2011

A Framework to Simulate and Visualize Epidemics

This poster was featured at the 2013 Perot Museum of Nature and Science's 'Social Science' exhibit. The poster discusses a framework to simulate and visualize epidemics