Aesthetics in a Mathematics for Liberal Arts Project

We present and assess a project and its rubric developed and assigned in Mathematics for Liberal Arts, a general education course for non-science and non-business majors, to incorporate different skills including aesthetic design, written and oral communication, and mathematical analysis to tackle a common optimization problem with an aesthetic slant: construct a beverage can (i.e., right circular cylinder) of a given volume while taking into account the cost of materials (i.e., surface area) and aesthetic qualities (e.g., the golden ratio)

Computational discovery of metal-organic frameworks for separations of organic molecules

The separation of para-xylene from a stream of mixed xylenes and ethylbenzene is critical for the large-scale production of plastics in the petrochemical industry. Several groups have identified metal-organic frameworks (MOFs) as having desirable characteristics for this separation. In this thesis, we demonstrate that molecular simulations can be used to efficiently screen large databases of MOFs to identify promising materials for this separation. We validated our approach in conjunction with our experimental collaborators and discovered that two of the top-performing materials from our screening procedure have similar performance to the zeolites used in industrial practice for xylene separations. We also developed a classical force field parameterization approach for refining the interactions between C8 alkyl aromatic hydrocarbons and MOFs using Density Functional Theory (DFT) calculations. We demonstrate that our DFT-based force field gives better predictions of some adsorption properties than generic force fields. A major technological hurdle to using small alcohols as biofuels is in their separation from aqueous fermentation broths. To address this issue, we developed classical models to identify hydrophobic MOFs capable of efficiently performing this separation. We were then able to use our models in a different context to understand the factors governing the thermodynamic stability and structural flexibility of MOFs. The methods developed in this thesis provide unique insight into chemical separations and material properties that would be challenging to obtain from experiments and promote the development of MOFs for industrial applications.Ph.D

Validation of plaster endocast morphology through 3D CT image analysis

A crucial component of research on brain evolution has been the comparison of fossil endocranial surfaces with modern human and primate endocrania. The latter have generally been obtained by creating endocasts out of rubber latex shells filled with plaster. The extent to which the method of production introduces errors in endocast replicas is unknown. We demonstrate a powerful method of comparing complex shapes in 3-dimensions (3D) that is broadly applicable to a wide range of paleoanthropological questions. Pairs of virtual endocasts (VEs) created from high-resolution CT scans of corresponding latex/plaster endocasts and their associated crania were rigidly registered (aligned) in 3D space for two Homo sapiens and two Pan troglodytes specimens. Distances between each cranial VE and its corresponding latex/plaster VE were then mapped on a voxel-by-voxel basis. The results show that between 79.7% and 91.0% of the voxels in the four latex/plaster VEs are within 2 mm of their corresponding cranial VEs surfaces. The average error is relatively small, and variation in the pattern of error across the surfaces appears to be generally random overall. However, inferior areas around the cranial base and the temporal poles were somewhat overestimated in both human and chimpanzee specimens, and the area overlaying Broca's area in humans was somewhat underestimated. This study gives an idea of the size of possible error inherent in latex/plaster endocasts, indicating the level of confidence we can have with studies relying on comparisons between them and, e.g., hominid fossil endocasts. Am J Phys Anthropol, 2007. © 2006 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55857/1/20499_ftp.pd

Vadose Zone Contaminant Fate and Transport Analysis for the 216-B-26 Trench

The BC Cribs and Trenches, part of the 200 TW 1 OU waste sites, received about 30 Mgal of scavenged tank waste, with possibly the largest inventory of 99Tc ever disposed to the soil at Hanford and site remediation is being accelerated. The purpose of this work was to develop a conceptual model for contaminant fate and transport at the 216-B-26 Trench site to support identification and development and evaluation of remediation alternatives. Large concentrations of 99Tc high above the water table implicated stratigraphy in the control of the downward migration. The current conceptual model accounts for small-scale stratigraphy; site-specific changes soil properties; tilted layers; and lateral spreading. It assumes the layers are spatially continuous causing water and solutes to move laterally across the boundary if conditions permit. Water influx at the surface is assumed to be steady. Model parameters were generated with pedotransfer functions; these were coupled high resolution neutron moisture logs that provided information on the underlying heterogeneity on a scale of 3 inches. Two approaches were used to evaluate the impact of remedial options on transport. In the first, a 1-D convolution solution to the convective-dispersive equation was used, assuming steady flow. This model was used to predict future movement of the existing plume using the mean and depth dependent moisture content. In the second approach, the STOMP model was used to first predict the current plume distribution followed by its future migration. Redistribution of the 99Tc plume was simulated for the no-action alternative and on-site capping. Hypothetical caps limiting recharge to 1.0, 0.5, and 0.1 mm yr-1 were considered and assumed not to degrade in the long term. Results show that arrival time of the MCLs, the peak arrival time, and the arrival time of the center of mass increased with decreasing recharge rate. The 1-D convolution model is easy to apply and can easily accommodate initial contaminant inventory and water content depth distributions of any complexity. However, the results are somewhat conservative in that the model does not take credit for stratification and its dimensionality effects. Transient analysis shows transport to be controlled by small-scale stratification that resulted in laterally movement of contaminants and their failure to reach the ground water. Multiple discharges quickly merged into a single plume that migrated beyond the domain boundaries. However, it appears that this very feature that was effective in mitigating deep transport of the contaminants for almost 50 years now functions to confound expected barrier effects. Simulations suggest that a barrier provides no additional protection above the no-action alternative. Although continuous layers are assumed, in reality, there may be discontinuities that could lead to vertical movement. Episodic recharge events could also be conducive to downward movement. As more data becomes available, the conceptual model will be revised. Based on the analyses, capping appears to be no better than the no-action alternative. Projected 99Tc concentrations reaching the groundwater suggest that alternate source control actions may be necessary to reach soil screening levels. The benefits of active remediation are therefore readily apparent. Because none of the alternatives reduce soil concentrations, they effect no active reduction in the groundwater concentrations therefore the residual risk will remain high

Vadose Zone Transport Field Study: FY 2002 Status Report

This work reported here is part of the U. S. Department of Energy’s Science and Technology Initiative to develop improved conceptual models of flow and transport in the vadose zone, particularly for the Hanford Site, Washington. The National Academy of Sciences has identified significant knowledge gaps in conceptual model development as one reason for discovery of subsurface contamination in unexpected places. Inadequate conceptualizations limits, not only the understanding of long-term fate and transport, but also the selection and design of remediation technologies. Current conceptual models are limited partly because they do not account for the random heterogeneity that occurs under the extremes of very nonlinear flow behavior typical of the Hanford vadose zone. A major improvement in conceptual modeling of the Hanford vadose zone includes a better understanding and description of soil anisotropy, a property that appears to control much of the subsurface flow and transport in layered sediments at the Hanford Site

RecA and RadA Proteins of Brucella abortus Do Not Perform Overlapping Protective DNA Repair Functions following Oxidative Burst

Very little is known about the role of DNA repair networks in Brucella abortus and its role in pathogenesis. We investigated the roles of RecA protein, DNA repair, and SOS regulation in B. abortus. While recA mutants in most bacterial species are hypersensitive to UV damage, surprisingly a B. abortus recA null mutant conferred only modest sensitivity. We considered the presence of a second RecA protein to account for this modest UV sensitivity. Analyses of the Brucella spp. genomes and our molecular studies documented the presence of only one recA gene, suggesting a RecA-independent repair process. Searches of the available Brucella genomes revealed some homology between RecA and RadA, a protein implicated in E. coli DNA repair. We considered the possibility that B. abortus RadA might be compensating for the loss of RecA by promoting similar repair activities. We present functional analyses that demonstrated that B. abortus RadA complements a radA defect in E. coli but could not act in place of the B. abortus RecA. We show that RecA but not RadA was required for survival in macrophages. We also discovered that recA was expressed at high constitutive levels, due to constitutive LexA cleavage by RecA, with little induction following DNA damage. Higher basal levels of RecA and its SOS-regulated gene products might protect against DNA damage experienced following the oxidative burst within macrophages. Originally published Journal of Bacteriology, Vol. 188, No. 14, July 200

MicroRNA expression profile identifies high grade, non-muscle-invasive bladder tumors at elevated risk to progress to an invasive phenotype

Abstract: The objective of this study was to identify a panel of microRNAs (miRNAs) differentially expressed in high-grade non-muscle invasive (NMI; TaG3–T1G3) urothelial carcinoma that progress to muscle-invasive disease compared to those that remain non-muscle invasive, whether recurrence happens or not. Eighty-nine high-grade NMI urothelial carcinoma lesions were identified and total RNA was extracted from paraffin-embedded tissue. Patients were categorized as either having a non-muscle invasive lesion with no evidence of progression over a 3-year period or as having a similar lesion showing progression to muscle invasion over the same period. In addition, comparison of miRNA expression levels between patients with and without prior intravesical therapy was performed. Total RNA was pooled for microarray analysis in each group (non-progressors and progressors), and qRT-PCR of individual samples validated differential expression between non-progressive and progressive lesions. MiR-32-5p, -224-5p, and -412-3p were associated with cancer-specific survival. Downregulation of miR-203a-3p and miR-205-5p were significantly linked to progression in non-muscle invasive bladder tumors. These miRNAs include those implicated in epithelial mesenchymal transition, previously identified as members of a panel characterizing transition from the non-invasive to invasive phenotype in bladder tumors. Furthermore, we were able to identify specific miRNAs that are linked to postoperative outcome in patients with high grade NMI urothelial carcinoma of the bladder (UCB) that progressed to muscle-invasive (MI) disease

Imaging 3D Chemistry at 1 nm Resolution with Fused Multi-Modal Electron Tomography

Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment completes. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one nanometer resolution in a Au-Fe$_3$O$_4$ metamaterial, Co$_3$O$_4$ - Mn$_3$O$_4$ core-shell nanocrystals, and ZnS-Cu$_{0.64}$S$_{0.36}$ nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99\% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX / EELS) signals. Now sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials

Public engagement with marine climate change issues: (Re)framings, understandings and responses

Climate change impacts on marine environments have been somewhat neglected in climate change research, particularly with regard to their social dimensions and implications. This paper contributes to addressing this gap through presenting a UK focused mixed-method study of how publics frame, understand and respond to marine climate change-related issues. It draws on data from a large national survey of UK publics (N = 1,001), undertaken in January 2011 as part of a wider European survey, in conjunction with in-depth qualitative insights from a citizens’ panel with participants from the East Anglia region, UK. This reveals that discrete marine climate change impacts, as often framed in technical or institutional terms, were not the most immediate or significant issues for most respondents. Study participants tended to view these climate impacts ‘in context’, in situated ways, and as entangled with other issues relating to marine environments and their everyday lives. Whilst making connections with scientific knowledge on the subject, public understandings of marine climate impacts were mainly shaped by personal experience, the visibility and proximity of impacts, sense of personal risk and moral or equity-based arguments. In terms of responses, study participants prioritised climate change mitigation measures over adaptation, even in high-risk areas. We consider the implications of these insights for research and practices of public engagement on marine climate impacts specifically, and climate change more generally