No description available.

WWOX is a tumor suppressor and the down-regulation of WWOX has been demonstrated in prostate, lung, breast, gastric cancers. However, the role of WWOX in renal cell carcinoma (RCC) remains unknown. It has been demonstrated that WWOX addressed in mitochondria, golgi apparatus, rough ER, lysosome, plasma membrane and nuclear. The Subcellular localization of WWOX has been controversial. There are two parts in this study: (I) The expression of WWOX in RCC and the probability of WWOX to be a diagnostic and a prognostic marker. (II) The regulation of WWOX by phosphorylation. For the study of WWOX expression in RCC, we prepared polyclonal WWOX antibody and characterized the specificity of the antibody. We applied this specific antibody to 33 NT paring RCC tissue specimen for immunoblotting study and 138 cases of paraffin-embedded specimens for IHC, respectively. Our results demonstrated that hWOX1 was specifically down-regulated in clear cell type RCC (p=0.018). The percentage of down-regulation in patient specimen is 60.7 % and 90.7 % in immunoblotting and IHC study, respectively. And in clear cell and clear-granular combined type RCC, down-regulation of WWOX was significantly correlated with the survival rate of patients (p=0.0482). Therefore, WWOX could be used as a diagnostic and a prognostic marker in clear cell type RCC. Besides, we performed bioinformatics to predict the phosphorylation site of WWOX and investigated the effect of phosphorylation on WWOX subcellular localization. Our results demonstrated that hWOX1 was phosphorylated by PKC at Thr49 and Thr102 and the phosphorylation regulated the subcellular localization of WWOX.

Detection of targets in hyperspectral images is a specific case of one-class classification. It is particularly relevant in the area of remote sensing and has received considerable interest in the past few years. The thesis proposes the use of wavelet functions as kernels with Support Vector Data Description for target detection in hyperspectral images. Specifically, it proposes the Adaptive Wavelet Kernel Support Vector Data Description (AWK-SVDD) that learns the optimal wavelet function to be used given the target signature. The performance and computational requirements of AWK-SVDD is compared with that of existing methods and other wavelet functions. An introduction to target detection and target detection in the context of hyperspectral images is given. This thesis also includes an overview of the thesis and lists the contributions of the thesis. A brief mathematical background into one-class classification in reference to target detection is included. Also described are the existing methods and introduces essential concepts relevant to the proposed approach. The use of wavelet functions as kernels with Support Vector Data Description, the conditions for use of wavelet functions and the use of two functions in order to form the kernel are checked and analyzed. The proposed approach, AWKSVDD, is mathematically described. The details of the implementation and the results when applied to the Urban dataset of hyperspectral images with a random target signature are given. The results confirm the better performance of AWK-SVDD compared to conventional kernels, wavelet kernels and the two-function Morlet-Radial Basis Function kernel. The problems faced with convergence during the Support Vector Data Description optimization are discussed. The thesis concludes with the suggestions for future work.

Antibody phage display technology mimics the natural immune system, and has been widely used for rapid isolation of single-domain antibodies (sdAbs) with various binding specificities and affinities in the micromolar to low nanomolar range. SdAbs are the variable regions of immunoglobulins (e.g., VH, VL, VHH) and serve as potential probes with therapeutic value. The small size, high solubility, high expression and stability, and high specificity and affinity for the cognate antigen, make sdAbs ideal in improving drug delivery and the overall therapeutic value of antibodies. The main objective of this thesis was to construct a large VL phage display library (~1010 diversity); analyze it via sequence analysis, and to subtractively pan the library for isolation of Neuropilin-1 (NRP1)-specific VLs. Neuropilin-1 (NRP1), a cell-surface receptor for both vascular endothelial growth factor (VEGF) and class 3 Semaphorins (Sema3A), contributes to neuron cell death through its interaction with Sema3A in stroke patients. Disruption of this NRP1-Sema3A interaction would allow for axonal outgrowth and neuron regeneration in the area of the brain affected by stroke. Construction of the synthetic phage antibody library utilized a single VL framework with selected positions in the complementarity-determining regions (CDRs) targeted for randomization in vitro using synthetic oligonucleotides that introduced sequence degeneracy. Specific VLs were then selected from the repertoire through subtractive panning against a cell line endogenously expressing NRP1 (PC12) as well as a negative cell line that does not express NRP1 (HEK293) with competitive elution carried out using a synthetic Sema3A-derived peptide. Fifteen VL clones were isolated, cloned in E. coli, expressed and purified, and of these, nine were determined to be non-aggregating by size exclusion chromatography. Further studies will determine the potential therapeutic use of these VL sdAbs as agents in recovery from stroke and neuron degeneration.

Until now, few rigorous studies of the precursors in structures exhibiting superluminal group velocities have been performed. One dimensional photonic crystals(1DPC) and active Lorentzian media are among the ones which are able to exhibit superluminal propagation. In the first part of the thesis we have studied the evolution of the precursors in active Lorentzian media and 1DPC. The problem of the propagation of the precursors in active Lorentzian media is addressed, by employing the steepest descent method to provide a detailed description of the propagation of the pulse inside the dispersive medium in the time domain. The problem of the time and frequency evolution of the precursors in 1DPC is studied, using the finite-difference time-domain (FDTD) techniques in conjunction with joint time-frequency analysis (JTFA). Our study clearly shows that the precursor fields associated with superluminal pulse propagation travel at subluminal speeds. It is also shown that FDTD analysis and JTFA can be combined to study the dynamic evolution of the transient and steady state pulse propagation in dispersive media. The second part of the thesis concentrates on the applications of the precursors. An interesting property of the precursors is their lower than exponential attenuation rate inside a lossy dielectric, such as water. This property of the precursors has made them an interesting candidate for applications such as ground penetrating radar and underwater communication. It was recently pointed out that a pulse which is generated inside of water and assumes the shape of the Brillouin precursor would be optimally suited for long range propagation in water (described by the single-pole Debye model). Here, we have considered the optimal pulse propagation problem, accounting for the interaction of the pulse with the air/water interface at oblique incidence. In addition, we argue that pulse excitations which are rough approximation of the Brillouin precursor will eventually evolve into the Brillouin precursor itself shortly after they enter water. Therefore, the excitation of a long-propagating pulse is not sensitive to its shape. Finally, we studied the performance of the optimized pulse in terms of the energy of the scattered field from an object inside water. Based on the simulation results the optimized pulse scattered field has higher energy compared to pulses with the same energy and different temporal distribution. The FDTD technique is employed in all the simulations.

Streptococcus pyogenes (Group A Streptococcus) is a Gram-positive bacterial pathogen that causes significant superficial and invasive diseases. Iron acquisition is an important component of GAS pathogenesis in the human host. The 10 gene sia operon of GAS is involved in the acquisition of iron via heme or heme-binding proteins and encodes an ABC transporter as well as the large multifunctional receptor Shr. Domain analysis of Shr shows that it contains two copies of the DUF1533 (domain of unknown function) in its N-terminal part and two NEAT (NEAr Transporter) domains. NEAT domains are found in variable copy number in surface proteins of Gram-positive pathogens and are implicated in binding to various ligands. A new recombinant Shr protein was cloned and a purification protocol was developed, improving the yield of the full-length protein. A solid phase binding assay was developed and used to demonstrate Shr binding to hemoglobin. Several truncated Shr proteins were expressed and purified: the N-terminal Domain (NTD) up to but not including the first NEAT domain of Shr, the NTD plus the first NEAT domain (NTD-NEAT1) and the second NEAT domain alone (NEAT2). It was determined that Shr’s NTD mediates hemoglobin binding, demonstrating that a new protein pattern in Shr is involved in hemoglobin binding, and implicating the DUF1533 in this process. It was also determined that NTD-N1 and NEAT2 bind heme while NTD does not. Therefore, both NEAT domains may participate in the capture of heme from the host hemoglobin by Shr.

Until now, few rigorous studies of the precursors in structures exhibiting superluminal group velocities have been performed. One dimensional photonic crystals(1DPC) and active Lorentzian media are among the ones which are able to exhibit superluminal propagation. In the first part of the thesis we have studied the evolution of the precursors in active Lorentzian media and 1DPC. The problem of the propagation of the precursors in active Lorentzian media is addressed, by employing the steepest descent method to provide a detailed description of the propagation of the pulse inside the dispersive medium in the time domain. The problem of the time and frequency evolution of the precursors in 1DPC is studied, using the finite-difference time-domain (FDTD) techniques in conjunction with joint time-frequency analysis (JTFA). Our study clearly shows that the precursor fields associated with superluminal pulse propagation travel at subluminal speeds. It is also shown that FDTD analysis and JTFA can be combined to study the dynamic evolution of the transient and steady state pulse propagation in dispersive media. The second part of the thesis concentrates on the applications of the precursors. An interesting property of the precursors is their lower than exponential attenuation rate inside a lossy dielectric, such as water. This property of the precursors has made them an interesting candidate for applications such as ground penetrating radar and underwater communication. It was recently pointed out that a pulse which is generated inside of water and assumes the shape of the Brillouin precursor would be optimally suited for long range propagation in water (described by the single-pole Debye model). Here, we have considered the optimal pulse propagation problem, accounting for the interaction of the pulse with the air/water interface at oblique incidence. In addition, we argue that pulse excitations which are rough approximation of the Brillouin precursor will eventually evolve into the Brillouin precursor itself shortly after they enter water. Therefore, the excitation of a long-propagating pulse is not sensitive to its shape. Finally, we studied the performance of the optimized pulse in terms of the energy of the scattered field from an object inside water. Based on the simulation results the optimized pulse scattered field has higher energy compared to pulses with the same energy and different temporal distribution. The FDTD technique is employed in all the simulations.

Antibody phage display technology mimics the natural immune system, and has been widely used for rapid isolation of single-domain antibodies (sdAbs) with various binding specificities and affinities in the micromolar to low nanomolar range. SdAbs are the variable regions of immunoglobulins (e.g., VH, VL, VHH) and serve as potential probes with therapeutic value. The small size, high solubility, high expression and stability, and high specificity and affinity for the cognate antigen, make sdAbs ideal in improving drug delivery and the overall therapeutic value of antibodies. The main objective of this thesis was to construct a large VL phage display library (~1010 diversity); analyze it via sequence analysis, and to subtractively pan the library for isolation of Neuropilin-1 (NRP1)-specific VLs. Neuropilin-1 (NRP1), a cell-surface receptor for both vascular endothelial growth factor (VEGF) and class 3 Semaphorins (Sema3A), contributes to neuron cell death through its interaction with Sema3A in stroke patients. Disruption of this NRP1-Sema3A interaction would allow for axonal outgrowth and neuron regeneration in the area of the brain affected by stroke. Construction of the synthetic phage antibody library utilized a single VL framework with selected positions in the complementarity-determining regions (CDRs) targeted for randomization in vitro using synthetic oligonucleotides that introduced sequence degeneracy. Specific VLs were then selected from the repertoire through subtractive panning against a cell line endogenously expressing NRP1 (PC12) as well as a negative cell line that does not express NRP1 (HEK293) with competitive elution carried out using a synthetic Sema3A-derived peptide. Fifteen VL clones were isolated, cloned in E. coli, expressed and purified, and of these, nine were determined to be non-aggregating by size exclusion chromatography. Further studies will determine the potential therapeutic use of these VL sdAbs as agents in recovery from stroke and neuron degeneration.

We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem. (author's abstract) / Series: Preprint Series / Department of Applied Statistics and Data Processing

This study was carried out in order to investigate the purpose of Bob Dylan’s creative metaphors. Focus was on whether they were used for artistic effect or to simplify and concretize abstract concepts. Ten songs written in the last five decades were randomly selected and searched for occurrences of creative metaphors. The metaphors found were chronologically listed and discussed in terms of potential source and target domains in order to determine their purpose. The results showed rather clearly that Dylan’s creative metaphors, regardless of whether the domains were abstract or concrete, seemed to complicate rather than simplify the interpretation of a line. There were a few instances where the creative metaphors could be interpreted as being explanatory; however, this was regarded as a secondary effect since it was clear that the primary purpose for Dylan’s creative metaphors was to add an artistic touch. Moreover, this purpose did not seem to have changed in any way during the last five decades.