Hip2Norm: an object-oriented cross-platform program for 3D analysis of hip joint morphology using 2D pelvic radiographs

We developed an object-oriented cross-platform program to perform three-dimensional (3D) analysis of hip joint morphology using two-dimensional (2D) anteroposterior (AP) pelvic radiographs. Landmarks extracted from 2D AP pelvic radiographs and optionally an additional lateral pelvic X-ray were combined with a cone beam projection model to reconstruct 3D hip joints. Since individual pelvic orientation can vary considerably, a method for standardizing pelvic orientation was implemented to determine the absolute tilt/rotation. The evaluation of anatomically morphologic differences was achieved by reconstructing the projected acetabular rim and the measured hip parameters as if obtained in a standardized neutral orientation. The program had been successfully used to interactively objectify acetabular version in hips with femoro-acetabular impingement or developmental dysplasia. Hip(2)Norm is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway) for graphical user interface (GUI) and is transportable to any platform.

Development of a high performance parallel computing platform and its use in the study of nanostructures : clusters, sheets and tubes .

Small clusters of gallium oxide, technologically important high temperature ceramic, together with interaction of nucleic acid bases with graphene and small-diameter carbon nanotube are focus of first principles calculations in this work. A high performance parallel computing platform is also developed to perform these calculations at Michigan Tech. First principles calculations are based on density functional theory employing either local density or gradient-corrected approximation together with plane wave and gaussian basis sets. The bulk Ga2O3 is known to be a very good candidate for fabricating electronic devices that operate at high temperatures. To explore the properties of Ga2O3 at nonoscale, we have performed a systematic theoretical study on the small polyatomic gallium oxide clusters. The calculated results find that all lowest energy isomers of GamOn clusters are dominated by the Ga-O bonds over the metal-metal or the oxygen-oxygen bonds. Analysis of atomic charges suggest the clusters to be highly ionic similar to the case of bulk Ga2O3. In the study of sequential oxidation of these slusters starting from Ga2O, it is found that the most stable isomers display up to four different backbones of constituent atoms. Furthermore, the predicted configuration of the ground state of Ga2O is recently confirmed by the experimental result of Neumark's group. Guided by the results of calculations the study of gallium oxide clusters, performance related challenge of computational simulations, of producing high performance computers/platforms, has been addressed. Several engineering aspects were thoroughly studied during the design, development and implementation of the high performance parallel computing platform, rama, at Michigan Tech. In an attempt to stay true to the principles of Beowulf revolutioni, the rama cluster was extensively customized to make it easy to understand, and use - for administrators as well as end-users. Following the results of benchmark calculations and to keep up with the complexity of systems under study, rama has been expanded to a total of sixty four processors. Interest in the non-covalent intereaction of DNA with carbon nanotubes has steadily increased during past several years. This hybrid system, at the junction of the biological regime and the nanomaterials world, possesses features which make it very attractive for a wide range of applicatioins. Using the in-house computational power available, we have studied details of the interaction between nucleic acid bases with graphene sheet as well as high-curvature small-diameter carbon nanotube. The calculated trend in the binding energies strongly suggests that the polarizability of the base molecules determines the interaction strength of the nucleic acid bases with graphene. When comparing the results obtained here for physisorption on the small diameter nanotube considered with those from the study on graphene, it is observed that the interaction strength of nucleic acid bases is smaller for the tube. Thus, these results show that the effect of introducing curvature is to reduce the binding energy. The binding energies for the two extreme cases of negligible curvature (i.e. flat graphene sheet) and of very high curvature (i.e. small diameter nanotube) may be considered as upper and lower bounds. This finding represents an important step towards a better understanding of experimentally observed sequence-dependent interaction of DNA with Carbon nanotubes.

Development of a wireless platform to generate nitric oxide for implanted biomedical devices

The perturbation of homeostatic mechanisms caused by interactions between any indwelling biomedical device and the biological medium into which it is implanted initiates a dynamic wound healing response from the host which can be rigorous and ongoing. The typical result of this response is a severe degradation in the performance and safety of the device, often to the extent of precluding their clinical use. Nitric oxide (NO) is an endogenously produced biomolecule capable of mediating many of the cellular processes leveraged against implanted devices. The in vivo performance of indwelling devices prepared with NO release coatings has recently been evaluated with very encouraging results. This work developed a platform capable of both generating programmable fluxes of NO and directly evaluating the performance of indwelling probes under different profiles of NO generation. This platform can be used to improve the efficacy of NO release materials in mitigating the host response.

CHARACTERIZATION OF ELECTRODEPOSITED POLYANILINE BIOSENSOR PLATFORM FOR ESCHERICHIA COLI O157:H7 DETECTION

Amperometric electrodeposition has been used to obtain uniform, conductive, and repeatable polyaniline (PANi) thin films for use in nano scaled biochemical sensors. This report describes the characterization of these films. Techniques such as ellipsometry were used to test repeatability of the deposition and the uniformity of the deposited thin films. Raman spectroscopy was utilized to confirm the composition of the deposited PANi thin films. Fluorescence microscopy was used to determine the immobilization of antibodies to the PANi thin films using biotin-avidin interactions, as well as the density of active binding sites. Ellipsometry results demonstrated that biomolecules could be immobilized on PANi films as thin as 9nm. Evidence from the Raman spectroscopy demonstrated the conductive nature of the PANi films. The fluorescence microscopy demonstrated that antibodies could be immobilized on PANi films, although the experiment also demonstrated a low density of binding sites. The characterization demonstrates the utility of the PANi thin films as a conductive interface between the inorganic sensor platform and biochemical molecules.

Geochemistry and Stable Isotopes of Surface Water and Groundwater in the Continental Pit in Butte, Montana, USA

The Continental porphyry Cu‐Mo mine, located 2 km east of the famous Berkeley Pit lake of Butte, Montana, contains two small lakes that vary in size depending on mining activity. In contrast to the acidic Berkeley Pit lake, the Continental Pit waters have near-neutral pH and relatively low metal concentrations. The main reason is geological: whereas the Berkeley Pit mined highly‐altered granite rich in pyrite with no neutralizing potential, the Continental Pit is mining weakly‐altered granite with lower pyrite concentrations and up to 1‐2% hydrothermal calcite. The purpose of this study was to gather and interpret information that bears on the chemistry of surface water and groundwater in the active Continental Pit. Pre‐existing chemistry data from sampling of the Continental Pit were compiled from the Montana Bureau of Mines and Geology and Montana Department of Environmental Quality records. In addition, in March of 2013, new water samples were collected from the mine’s main dewatering well, the Sarsfield well, and a nearby acidic seep (Pavilion Seep) and analyzed for trace metals and several stable isotopes, including dD and d18O of water, d13C of dissolved inorganic carbon, and d34S of dissolved sulfate. In December 2013, several soil samples were collected from the shore of the frozen pit lake and surrounding area. The soil samples were analyzed using X‐ray diffraction to determine mineral content. Based on Visual Minteq modeling, water in the Continental Pit lake is near equilibrium with a number of carbonate, sulfate, and molybdate minerals, including calcite, dolomite, rhodochrosite (MnCO3), brochantite (CuSO4·3Cu(OH)2), malachite (Cu2CO3(OH)2), hydrozincite (Zn5(CO3)2(OH)6), gypsum, and powellite (CaMoO4). The fact that these minerals are close to equilibrium suggests that they are present on the weathered mine walls and/or in the sediment of the surface water ponds. X‐Ray Diffraction (XRD) analysis of the pond “beach” sample failed to show any discrete metal‐bearing phases. One of the soil samples collected higher in the mine, near an area of active weathering of chalcocite‐rich ore, contained over 50% chalcanthite (CuSO4·5H2O). This water‐soluble copper salt is easily dissolved in water, and is probably a major source of copper to the pond and underlying groundwater system. However, concentrations of copper in the latter are probably controlled by other, less‐soluble minerals, such as brochantite or malachite. Although the acidity of the Pavilion Seep is high (~ 11 meq/L), the flow is much less than the Sarsfield Well at the current time. Thus, the pH, major and minor element chemistry in the Continental Pit lakes are buffered by calcite and other carbonate minerals. For the Continental Pit waters to become acidic, the influx of acidic seepage (e.g., Pavilion Seep) would need to increase substantially over its present volume.