EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA

In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data manipulations, referred to as preprocessing, can influence the quality of the ultimate measurements. In the last few years, the high-throughput measurement of gene expression is the most popular application of microarray technology. For this application, various groups have demonstrated that the use of modern statistical methodology can substantially improve accuracy and precision of gene expression measurements, relative to ad-hoc procedures introduced by designers and manufacturers of the technology. Currently, other applications of microarrays are becoming more and more popular. In this paper we describe a preprocessing methodology for a technology designed for the identification of DNA sequence variants in specific genes or regions of the human genome that are associated with phenotypes of interest such as disease. In particular we describe methodology useful for preprocessing Affymetrix SNP chips and obtaining genotype calls with the preprocessed data. We demonstrate how our procedure improves existing approaches using data from three relatively large studies including one in which large number independent calls are available. Software implementing these ideas are avialble from the Bioconductor oligo package.

Irradiation of intracerebral 9L gliosarcoma by a single array of microplanar x-ray beams from a synchrotron: balance between curing and sparing

The purpose of this work was the understanding of microbeam radiation therapy at the ESRF in order to find the best compromise between curing of tumors and sparing of normal tissues, to obtain a better understanding of survival curves and to report its efficiency. This method uses synchrotron-generated x-ray microbeams. Rats were implanted with 9L gliosarcomas and the tumors were diagnosed by MRI. They were irradiated 14 days after implantation by arrays of 25 microm wide microbeams in unidirectional mode, with a skin entrance dose of 625 Gy. The effect of using 200 or 100 microm center-to-center spacing between the microbeams was compared. The median survival time (post-implantation) was 40 and 67 days at 200 and 100 microm spacing, respectively. However, 72% of rats irradiated at 100 microm spacing showed abnormal clinical signs and weight patterns, whereas only 12% of rats were affected at 200 microm spacing. In parallel, histological lesions of the normal brain were found in the 100 microm series only. Although the increase in lifespan was equal to 273% and 102% for the 100 and 200 microm series, respectively, the 200 microm spacing protocol provides a better sparing of healthy tissue and may prove useful in combination with other radiation modalities or additional drugs.

Active surgical positioning device for a cochlear implant electrode array

Cochlear implants have been of great benefit in restoring auditory function to individuals with profound bilateral sensorineural deafness. The implants are used to directly stimulate auditory nerves and send a signal to the brain that is then interpreted as sound. This project focuses on the development of a surgical positioning tool to accurately and effectively place an array of stimulating electrodes deep within the cochlea. This will lead to improved efficiency and performance of the stimulating electrodes, reduced surgical trauma to the cochlea, and as a result, improved overall performance to the implant recipient. The positioning tool reported here consists of multiple fluidic chambers providing localized curvature control along the length of the attached silicon electrode array. The chambers consist of 200μm inner diameter PET (polyethylene therephthalate) tubes with 4μm wall thickness. The chambers are molded in a tapered helical configuration to correspond to the cochlear shape upon relaxation of the actuators. This ensures that the optimal electrode placement within the cochlea is retained after the positioning tool becomes dormant (for chronic implants). Actuation is achieved by injecting fluid into the PET chambers and regulating the fluidic pressure. The chambers are arranged in a stacked, overlapping design to provide fluid connectivity with the non-implantable pressure controller and allow for local curvature control of the device. The stacked tube configuration allows for localized curvature control of various areas along the length of the electrode and additional stiffening and actuating power towards the base. Curvature is affected along the entire length of a chamber and the result is cumulative in sections of multiple chambers. The actuating chambers are bonded to the back of a silicon electrode array.

Advanced mechanics of materials with microstructure

The study of advanced materials aimed at improving human life has been performed since time immemorial. Such studies have created everlasting and greatly revered monuments and have helped revolutionize transportation by ushering the age of lighter–than–air flying machines. Hence a study of the mechanical behavior of advanced materials can pave way for their use for mankind’s benefit. In this school of thought, the aim of this dissertation is to broadly perform two investigations. First, an efficient modeling approach is established to predict the elastic response of cellular materials with distributions of cell geometries. Cellular materials find important applications in structural engineering. The approach does not require complex and time-consuming computational techniques usually associated with modeling such materials. Unlike most current analytical techniques, the modeling approach directly accounts for the cellular material microstructure. The approach combines micropolar elasticity theory and elastic mixture theory to predict the elastic response of cellular materials. The modeling approach is applied to the two dimensional balsa wood material. Predicted properties are in good agreement with experimentally determined properties, which emphasizes the model’s potential to predict the elastic response of other cellular solids, such as open cell and closed cell foams. The second topic concerns intraneural ganglion cysts which are a set of medical conditions that result in denervation of the muscles innervated by the cystic nerve leading to pain and loss of function. Current treatment approaches only temporarily alleviate pain and denervation which, however, does not prevent cyst recurrence. Hence, a mechanistic understanding of the pathogenesis of intraneural ganglion cysts can help clinicians understand them better and therefore devise more effective treatment options. In this study, an analysis methodology using finite element analysis is established to investigate the pathogenesis of intraneural ganglion cysts. Using this methodology, the propagation of these cysts is analyzed in their most common site of occurrence in the human body i.e. the common peroneal nerve. Results obtained using finite element analysis show good correlation with clinical imaging patterns thereby validating the promise of the method to study cyst pathogenesis.

High-resolution morphological and biochemical imaging of articular cartilage of the ankle joint at 3.0 T using a new dedicated phased array coil: in vivo reproducibility study

OBJECTIVE: The objective of this study was to evaluate the feasibility and reproducibility of high-resolution magnetic resonance imaging (MRI) and quantitative T2 mapping of the talocrural cartilage within a clinically applicable scan time using a new dedicated ankle coil and high-field MRI. MATERIALS AND METHODS: Ten healthy volunteers (mean age 32.4 years) underwent MRI of the ankle. As morphological sequences, proton density fat-suppressed turbo spin echo (PD-FS-TSE), as a reference, was compared with 3D true fast imaging with steady-state precession (TrueFISP). Furthermore, biochemical quantitative T2 imaging was prepared using a multi-echo spin-echo T2 approach. Data analysis was performed three times each by three different observers on sagittal slices, planned on the isotropic 3D-TrueFISP; as a morphological parameter, cartilage thickness was assessed and for T2 relaxation times, region-of-interest (ROI) evaluation was done. Reproducibility was determined as a coefficient of variation (CV) for each volunteer; averaged as root mean square (RMSA) given as a percentage; statistical evaluation was done using analysis of variance. RESULTS: Cartilage thickness of the talocrural joint showed significantly higher values for the 3D-TrueFISP (ranging from 1.07 to 1.14 mm) compared with the PD-FS-TSE (ranging from 0.74 to 0.99 mm); however, both morphological sequences showed comparable good results with RMSA of 7.1 to 8.5%. Regarding quantitative T2 mapping, measurements showed T2 relaxation times of about 54 ms with an excellent reproducibility (RMSA) ranging from 3.2 to 4.7%. CONCLUSION: In our study the assessment of cartilage thickness and T2 relaxation times could be performed with high reproducibility in a clinically realizable scan time, demonstrating new possibilities for further investigations into patient groups.

Effect of microstructure and alloying elements on the resistance of fastener grade steels to hydrogen assisted cracking

Fastener grade steels with varying alloy contents and heat treatments were employed to measure changes in resistance to hydrogen assisted cracking. The testing procedure compared notched tension specimens fractured in air to threshold stress values obtained during hydrogen charging, utilizing a rising step load procedure. Bainitic structures improved resistance by 10-20% compared to tempered martensite structures. Dual phase steels with a tempered martensite matrix and 20% ferrite were more susceptible and notch sensitive. High strength, fully pearlitic structures showed an improvement in resistance. Carbon content, per se, had no effect on the resistance of steel to hydrogen assisted cracking. Chromium caused a deleterious effect but all other alloying elements studied did not cause much change in hydrogen assisted cracking susceptibility.

Experimental and theoretical study of microstructure effect on piezoelectric property of one dimensional ZnO nanostructures

Emerging nanogenerators have attracted the attention of the research community, focusing on energy generation using piezoelectric nanomaterials. Nanogenerators can be utilized for powering NEMS/MEMS devices. Understanding the piezoelectric properties of ZnO one-dimensional materials such as ZnO nanobelts (NBs) and Nanowires (NWs) can have a significant impact on the design of new devices. The goal of this dissertation is to study the piezoelectric properties of one-dimensional ZnO nanostructures both experimentally and theoretically. First, the experimental procedure for producing the ZnO nanostructures is discussed. The produced ZnO nanostructures were characterized using an in-situ atomic force microscope and a piezoelectric force microscope. It is shown that the electrical conductivity of ZnO NBs is a function of applied mechanical force and its crystalline structure. This phenomenon was described in the context of formation of an electric field due to the piezoelectric property of ZnO NBs. In the PFM studies, it was shown that the piezoelectric response of the ZnO NBs depends on their production method and presence of defects in the NB. Second, a model was proposed for making nanocomposite electrical generators based on ZnO nanowires. The proposed model has advantages over the original configuration of nanogenerators which uses an AFM tip for bending the ZnO NWs. Higher stability of the electric source, capability for producing larger electric fields, and lower production costs are advantages of this configuration. Finally, piezoelectric properties of ZnO NBs were simulated using the molecular dynamics (MD) technique. The size-scale effect on piezoelectric properties of ZnO NBs was captured, and it is shown that the piezoelectric coefficient of ZnO NBs decreases by increasing their lateral dimensions. This phenomenon is attributed to the surface charge redistribution and compression of unit cells that are placed on the outer shell of ZnO NBs.

COMPUTATIONAL STUDY OF MICROSTRUCTURE-PROPERTYMECHANISM RELATIONS IN FERROIC COMPOSITES

Ferroic materials, as notable members of smart materials, have been widely used in applications that perform sensing, actuation and control. The macroscopic property change of ferroic materials may become remarkably large during ferroic phase transition, leading to the fact that the macroscopic properties can be tuned by carefully applying a suitable external field (electric, magnetic, stress). To obtain an enhancement in physical and/or mechanical properties, different kinds of ferroic composites have been fabricated. The properties of a ferroic composite are determined not only by the properties and relative amounts of the constituent phases, but also by the microstructure of individual phase such as the phase connectivity, phase size, shape and spatial arrangement. This dissertation mainly focuses on the computational study of microstructure – property – mechanism relations in two representative ferroic composites, i.e., two-phase particulate magnetoelectric (ME) composite and polymer matrix ferroelectric composite. The former is a great example of ferroic composite exhibiting a new property and functionality that neither of the constituent phases possesses individually. The latter well represents the kind of ferroic composites having property combinations that are better than the existing materials. Phase field modeling was employed as the computing tool, and the required models for ferroic composites were developed based on existing models for monolithic materials. Extensive computational simulations were performed to investigate the microstructure-property relations and the underlying mechanism in ferroic composites. In particulate, it is found that for ME composite 0-3 connectivity (isolated magnetostrictive phase) is necessary to exhibit ME effect, and small but finite electrical conductivity of isolated magnetic phase can beneficially enhance ME effect. It is revealed that longitudinal and transverse ME coefficients of isotropic 0-3 particulate composites can be effectively tailored by controlling magnetic domain structures without resort to anisotropic two-phase microstructures. Simulations also show that the macroscopic properties of the ferroelectricpolymer composites critically depend on the ferroelectric phase connectivity while are not sensitive to the sizes and internal grain structures of the ceramic particles. Texturing is found critical to exploit the paraelectric«ferroelectric phase transition and nonlinear polarization behavior in paraelectric polycrystal and its polymer matrix composite. Additionally, a Diffuse Interface Field model was developed to simulate packing and motion in liquid phase which is promising for studying the fabrication of particulatepolymer composites.

Fabrication of a Large, Ordered, Three-Dimensional Nanocup Array

Metallic nanocups provide a unique method for redirecting scattered light by creating magnetic plasmon responses at optical frequencies. Despite considerable development of nanocup fabrication processes, simultaneously achieving accurate control over the placement, orientation, and geometry of nanocups has remained a significant challenge. Here we present a technique for fabricating large, periodically ordered arrays of uniformly oriented three-dimensional gold nanocups for manipulating light at subwavelength scales. Nanoimprint lithography, soft lithography, and shadow evaporation were used to fabricate nanocups onto the tips of polydimethylsiloxane nanopillars with precise control over the shapes and optical properties of asymmetric nanocups.