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Title: AN ITERATIVE APPROACH TO COMBINED IMAGE REGISTRATION AND SEGMENTATION WITH APPLICATIONS TO PROSTATE CANCER IMAGING
Creator: Bukowy, John
Date: 2012-04-19, 2012-05
Description: Machine learning techniques have shown to be a viable means of analyzing medical images for tumor segmentation. Implementation of classi ers...
Show moreMachine learning techniques have shown to be a viable means of analyzing medical images for tumor segmentation. Implementation of classi ers used for tu- mor segmentation requires training data constructed from known data sets. In most applications, obtaining the training dataset requires image registration. This thesis proposes a new combined image registration-segmentation framework to be applied to prostate tumor segmentation in MR images in the future. In order to construct training sets, known pathology from histological slides must be transferred to the MR images. Both manual and automated registration techniques have been previ- ously developed to accomplish this information transfer. Automated methods provide a reproducible, measurable result; however there is still room for improvement. The focus of this thesis is on improvement of the accuracy of the training data set through an iterative approach combining automated registration and segmenta- tion. The performance of the automated method of registration improves with an increase in the number of landmarks for matching. These extra landmarks used for registration are obtained from tumor segmentation; hence the name iterative segmentation-registration. This improvement leads to more accurate data transfer between histology and MR images and hence more accurate training data. Through numerical simulations, we show that by increasing the number of landmarks, using not only anatomical features but obtained segmentation results, the quality of the train- ing data can be improved. The proposed method results in a measurable increase in registration performance which leads to improved training data and consequently improved tumor segmentation performance.
M.S. in Electrical Engineering, May 2012
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Title: SEISMIC COLLAPSE EVALUATION OF NON-DUCTILE CONCENTRICALLY BRACED FRAMES
Creator: Wen, Rou
Date: 2012-11-21, 2012-12
Description: More attentions have been paid on the Non-Ductile Concentrically Braced Frames (ND-CBFs) in low and moderate seismicity regions recently due...
Show moreMore attentions have been paid on the Non-Ductile Concentrically Braced Frames (ND-CBFs) in low and moderate seismicity regions recently due to their low ductility detailing requirements for design and construction. In this work, seismic collapse performances of two ND-CBFs are studied. One 3-story and one 9-story ND-CBF using small response modification coefficients (R=3) are designed firstly. Nonlinear finite element technologies are used to study the behaviors of local components. Practical analytical models for brace/gusset-plate assemblies and steel gravity frames are developed based on finite element simulations and engineering judgment. Three 2D structural models having increased local modeling complexity are developed for each braced frame. Nonlinear static pushover analyses on 3-story frames are conducted to get basic understandings of the damage evolution patterns and the interactions between main brittle braced frames and the steel gravity frames. Nonlinear dynamic analyses references the concepts of Incremental Dynamic Analysis are followed to investigate the seismic collapse responses of studied frames. The seismic assessments referenced the evaluation methods in FEMA P695 for ductile seismic load resisting frames through incremental dynamic analysis are carried out. Studied results show that Non-Ductile Concentrically Braced Frames would have little chance to prevent building collapse under severe ground motions. However, it seems that such buildings at least with low-to-moderate heights would have high probability of collapse prevention for up to moderate ground motions with conventional gravity framing systems used in modern steel buildings.
PH.D in Civil Engineering, December 2012
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Title: CHILD AND PARENT PSYCHOPATHOLOGY: COMBINATIONS RELATED TO THERAPY ATTENDANCE AND PROGRESS
Creator: Giannone, Carolyn D.
Date: 2012-04-30, 2012-05
Description: Disruptive behavior disorders (DBDs) are among the most common and challenging diagnoses in children. It is well documented that family...
Show moreDisruptive behavior disorders (DBDs) are among the most common and challenging diagnoses in children. It is well documented that family therapy services can provide effective treatment for DBDs, but therapy dropout rates are high. This leaves many children untreated, particularly in urban settings. Literature supports relationships between several variables and premature termination of therapy services, including child gender, child psychopathology, parent psychopathology, and perceived barriers to treatment participation. The current study aimed explore if combinations of parent and child psychopathology and their relationship related to therapy completion. Multiple imputation was utilized due to the presence of several missing data points. Results indicated that combinations did not significantly predict therapy completion. Implications of the research, limitations, and suggestions for future research are discussed.
Ph.D. in Clinical Psychology, May 2012
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Title: ASSESSMENT OF STRUCTURAL MATERIALS BY HIGH TEMPERATURE INSTRUMENTED INDENTATION
Creator: Gan, Bin
Date: 2012-12-03, 2012-12
Description: This is an ideal place for me to express my gratefulness to my Ph.D. advisor, Prof. Sammy Tin, who has offered me the financial support and...
Show moreThis is an ideal place for me to express my gratefulness to my Ph.D. advisor, Prof. Sammy Tin, who has offered me the financial support and tremendous freedom in doing research. From working with me through publications and thesis, mentoring me what constitutes a professional and high quality work, nurturing my patience, to giving me advice on how to deliver an insightful presentation, Prof. Tin puts his effort in helping me on every small step that I need to make, as I gradually become more experienced in research and start to make a few achievement along the way. I am deeply indebted to Prof. Tin’s vision, guidance and sustained support. I would like to thank Prof. Philip Nash, Prof. Sheldon Mostovoy and Prof. Sudhakar Nair for being the committee member of my thesis defense, and offering me so many invaluable suggestions. The indispensable help from Russ Janota, the faculty and staff in the MMAE department is acknowledged. The enjoyable interaction with Mengtao, Qizheng, Matt, and other TPTC friends helps me in various aspects. I would like to thank Dr. Hideyuki Murakami and Dr. Takahito Ohmura for hosting me in NIMS. The experience had broadened my horizon and tremendously enhanced my capabilities to conduct independent research. In addition, the research collaboration with Prof. Julia R. Greer and Dr. Robert Maass on freestanding Ni3Al nanoparticles is also fully acknowledged. Furthermore, I am grateful to Prof. Qiang Feng and Prof. Roman Nowak. Their constant support, encouragement, mentoring and nurturing have a profound influence on me. This thesis is dedicated to my beloved parents, Jinlong Gan and Yuxiang Lai, who have built the fortitude into my mind. I also thank my sisters, Liping Gan and Lihong Gan, for their sustained support. Their love and understanding enable me to have a peaceful mind that makes this study possible. I also feel grateful to the deep love and endless patience from Xiaomo Li and the support from her parents.
PH.D in Materials Science and Engineering, December 2012
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Title: BLOCK COPOLYMER BASED MICELLE FOR EFFICIENT IMMUNOSENSING
Creator: Li, Ying
Date: 2012-11-26, 2012-12
Description: This thesis demonstrates the formation of micelles from a block copolymer and the application in establishing the micelle based immunosensing...
Show moreThis thesis demonstrates the formation of micelles from a block copolymer and the application in establishing the micelle based immunosensing system. The utilization of polymeric micelle as probe container and antibody carrier increases the probe to antibody ratio, which is expected to leads to better detection efficiency. The substrate used in the immunosensing is a porous 0.45 μm PVDF membrane which allows the stable immobilization of proteins. Tetraphenylporphyrin, a hydrophobic fluorescent dye, was chosen as the probe encapsulated in micelles. The block copolymer is a self synthesized α-carboxyl-ω-hydroxyl terminated Poly(ethylene oxide)-Polycaprolactone with carboxyl group on the hydrophilic end, permitting the conjugation of antibody to the micelle surface. We choose mouse IgG and its antibody anti-IgG as the pair of protein conjugates to demonstrate the immunoassay. So far, the detection limit of mouse IgG is 1.5 μg/ml (10-8 M) in this immunosensing system, which is expected to improve by modifying the system.
M.S. in Chemistry, December 2012
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Title: TOWARDS THE OPTIMAL CONFIGURATION OF USING SSDS UNDER HYBRID PARALLEL I/O AND STORAGE SYSTEMS
Creator: Feng, Bo
Date: 2014, 2014-05
Description: The performance gap between computing devices and storage devices is con- tinuously getting larger during the past a few decades. This issue...
Show moreThe performance gap between computing devices and storage devices is con- tinuously getting larger during the past a few decades. This issue incurs many I/O problems even in the eld of supercomputing. On one hand, the computing facilities grow very fast as well as the supercomputers are getting more powerful. In addition, the traditional storage devices, such as hard disk drives (HDD) fail to catch up the paces of this growth. On the other hand, applications, from both industries and sciences, are becoming data-intensive, meaning that I/O is highly demanded. Newly emerging non-volatile memory (NVM), such as ash-based solid state drives (SSD), becomes popular in both consuming and enterprise markets. Datacen- ters and supercomputing centers already glimpse this transition and are getting to deploy SSDs in their I/O systems but SSDs still have monetary problems compared to HDDs. Substantial work has been done using SSDs to accelerate I/O and storage systems. However, to the best of our knowledge, there remain some fundamental questions to be addressed, such as what type of storage con guration is suitable to HDD-SSD heterogeneity. Therefore, in this study, we built a high performance hybrid parallel I/O and storage simulator to simulate these con gurations. We also imple- mented an algorithm to approach an optimal con guration using SSDs under parallel I/O and storage systems. This methodology consists of tracing users' applications, analyzing users' requirements including hardware properties, and generating the con- guration suggestions. The experiments show its delity with the minimal error rate is 2% and practical scalability up to 256 processes. The result of this study can help system designers to either optimize current system or predict larger scale design of parallel systems in the future.
M.S. in Computer Science, May 2014
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Title: DYSFUNCTION OF BONE-MARROW-DERIVED MACROPHAGES IN GDX KNOCKOUT MICE
Creator: Bonomo, Raiza Rafael
Date: 2016, 2016-05
Description: Macrophages are cells of the immune system responsible for clearing up the organism, removing damaged and dead cells, pathogens and other...
Show moreMacrophages are cells of the immune system responsible for clearing up the organism, removing damaged and dead cells, pathogens and other foreign substances. They remove and destroy these compounds by a process called phagocytosis, in which the macrophages recognize what is to be destroyed, engulf it and digest it in the lysosome. The phagocytosis mechanism requires special cytoskeleton configurations formed by actin branches that allow the engulfment of substances into the cells. The cytoskeleton structures formed by actin branching are also known to be necessary during the macrophage migration towards its target. Our group has shown that the small cytosolic GdX protein has an important role in the actin filament branching. Therefore, the aim of this study is to analyze the migration ability and the phagocytosis potential of wild-type (WT) and GdX knockout macrophages (KO). Bone marrow cells from mice were isolated and cultured in presence of Macrophage Colony-Stimulating Factor (MCSF) to induce cell differentiation into macrophages. The bone marrow derived macrophages were then subjected to phagocytosis and migration assays. The results from the phagocytosis assay indicated no significant difference in the percentage of cells capable of internalizing the beads or in the amount of engulfed beads between WT and KO macrophages. However, the results from the migration assay suggested a decrease in the migration ability in GdX KO cells when compared to WT macrophages. Therefore,our results imply that the lack of GdX may cause macrophage dysfunction.
M.S. in Cellular and Molecular Biology, May 2016
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Title: RECONFIGURABLE ULTRASONIC SIGNAL PROCESSING SYSTEM SOLUTION BASED ON ZYNQ PLATFORM
Creator: Wang, Boyang
Date: 2015, 2015-05
Description: Ultrasonic systems are widely used in industrial and medical diagnostics ap- plications. However, an ultrasonic system has very strict...
Show moreUltrasonic systems are widely used in industrial and medical diagnostics ap- plications. However, an ultrasonic system has very strict requirements on signal capturing and processing speed because of the high frequency of the target signal. The objective of this thesis was to design an ultrasonic system including signal capturing and processing on Zynq System-On-Chip (SoC). Zynq SoC is a new technology from Xilinx which integrates both dual core ARM processors and FPGA on the same chip. This not only allows for hardware and software co-design, but also enables the I/O extensions on Zynq from FPGA. An Analog Front End (AFE) is used to gener- ate, transmit, receive, and amplify the ultrasonic signal. The AFE is controlled by a Zynq processor via Serial Peripheral Interface (SPI) and several separate control lines from General Purpose I/O(GPIO). A high speed Analog to Digital Converter (ADC) is used in the system to capture the high speed ultrasonic echo received by AFE. The ADC which is controlled through SPI, communicates with the Zynq processor by Direct Memory Access (DMA). Besides hardware platform con guration, Discrete Wavelet Transform (DWT) based compression algorithm was implemented and optimized using different methods in order to find out the best solution for realizing on the Zynq SoC. Initially, MATLAB was used to explore and verify the algorithm. Then the algorithm was implemented in hardware using VHDL language, and in soft-ware using C++. Furthermore, the compression algorithm was implemented in Open Computer Language (OpenCL) using hardware and software co-design method.
M.S. in Electrical Engineering, May 2015
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Title: CHEMICAL INACTIVATION OF RICIN ON FOOD CONTACT SURFACES
Creator: Aluri, Bharat
Date: 2011-08, 2011-07
Description: Ricin is a glycoprotein which can be easily extracted from the seeds of the castor bean plant. Ricin has potential for being used as a...
Show moreRicin is a glycoprotein which can be easily extracted from the seeds of the castor bean plant. Ricin has potential for being used as a biological weapon since it is highly toxic, relatively easy to isolate and purify and can be disseminated as a food contaminant. Thus in the case deliberate contamination event with ricin in a food processing facility, remediation of the food-contact surfaces must be done safely and effectively. The objectives of this project were to 1) identify cleaning/sanitizing treatments that result in inactivation of ricin on food contact surfaces in the absence and presence of different classes of food matrices (high fat and high starch), and 2) evaluate glucose oxidase as a surrogate for ricin in chemical inactivation studies. Ricin dissolved in PBS or mixed with a slurry of peanut butter or pancake mix was treated with different classes of detergents (phosphoric acid-based, chlorinated alkaline-based) and a sanitizer (peroxy acid-based) used to clean and sanitize food-contact surfaces. A commercially available ELISA kit was used to detect ricin after chemical treatments. Of the cleaning solutions evaluated, the phosphoric acid-based detergent was the least effective at reducing ricin detection after exposure to the cleaning chemical. In contrast, chlorinated alkaline detergent was the most effective cleaning solution for chemically inactivating ricin. The half-lives for inactivation of ricin on coupons (without food matrices) exposed to 0.5, 2 and 5% chlorinated alkaline detergent were 2.38 ± 0.25, 0.48 ± 0.05 and <0.1 min, respectively, and half-live values for inactivation of ricin in solution were 3.05 ± 0.33, 0.36 ± 0.04 and <0.1 min, respectively. The half-lives for inactivation of ricin on coupons (without food matrices) treated with 0.1, 0.5 and 1% peroxyacid-based sanitizer were 4.28 ± 0.44, 0.45 ix ± 0.05 and 0.13 ± 0.01 min, respectively, and half-live values for inactivation of ricin in solution were 6.09 ± 0.70, 0.34 ± 0.03 and 0.12 ± 0.01 min, respectively. Although no significant difference was found for ricin stability in solution vs. on coupons, in the presence of food matrices, ricin on coupons was significantly more stable than ricin in the absence of food residue. Overall, the results from this study indicated that significantly (p<0.05) higher cleaning solution concentrations were needed to inactivate the toxin in the presence of food matrices. Initial studies aimed at the evaluation of glucose oxidase as a surrogate for ricin in chemical inactivation studies indicated that the enzyme demonstrates similar susceptibility to inactivation in the presence of chemical sanitizers (sodium hypochlorite, peroxy acetic acid) as ricin. More work is needed to validate the results found in this lab-scale study with experiments conducted in a pilot-scale operation and to determine if loss of ricin activity after chemical inactivation studies also corresponds to loss in biological activity of toxin.
M.S. in Food Safety and Technology, July 2011
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Title: CHANGES OF ZEBRAFISH BEHAVIORAL RESPONSES TO ODORANTS BY OLFACTORY IMPRINTING AND LEARNING
Creator: Deng, Xin
Date: 2014, 2014-12
Description: This study reports the improved behavioral responses to odorants due to olfactory imprinting and learning. Learning is a process thereby an...
Show moreThis study reports the improved behavioral responses to odorants due to olfactory imprinting and learning. Learning is a process thereby an individual obtains the information from the environment and the retained information facilitates the subsequent reactions to the same or related information. Olfactory imprinting is a special form of learning in that it occurs in a specific stage of life such as development, and the learned information has a life long influence on animal behavior or physiology when animals encounter the same stimuli later in their life. Olfactory imprinting is an important physical process for many species. Studies in our laboratory have shown that zebrafish can be imprinted by amino acids and bile acids. Here, I studied the influence of olfactory imprinting and learning on olfactory detection sensitivity of zebrafish using behavioral tests. The experimental zebrafish included the following groups: the BA group, imprinted by two bile acids, deoxycholic acid and taurocholic acid (TCA); the AA group, imprinted by two amino acids, L-arginine and L-cysteine, and the control group without odorant stimuli. Odorant exposure for imprinting was completed on 40 days post-fertilization and behavioral tests were conducted in adult fish of one year old. TCA and lithocholic acid (LCA) were used in the adult fish behavioral tests. My results showed that zebrafish from the BA group had significant lower detection thresholds to both TCA and LCA compared with the corresponding detection thresholds in the control group of zebrafish. In contrast, the AA group of fish did not show lower detection threshold to TCA compared with the control fish. The results indicated that imprinting can increase the sensitivity of BA fish to bile acids, while imprinting of amino acids did not improve the sensitivity of the AA fish to bile acids. Learning tests were conducted in my study because the data indicated that learning might also be responsible for the lowered detection thresholds in the BA and control groups due to repeated exposure to TCA in behavioral tests. Age matched naive zebrafish were used in behavioral tests from low concentration to high concentration of TCA. Then the behavioral tests were conducted in the opposite direction, from high to low concentrations.The detection threshold obtained in the former experiments was one log unit higher than that from the later experiments. Thus, it appears that learning can also increase the sensitivity of zebrafish to bile acids. Taken together, my data indicate that the improved sensitivity to TCA in the BA group might result from a combination of both olfactory imprinting and learning.
M.S. in Biology, December 2014
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Title: Efforts to Obtain Desulfurization Competent Cultures from Environmental Samples with Increased Desulfurization Activity
Creator: Davaadelger, Batzaya
Date: 2011-04-18, 2011-05
Description: In this study, environmental samples were collected from different places to obtain various desulfurization competent cultures with increased...
Show moreIn this study, environmental samples were collected from different places to obtain various desulfurization competent cultures with increased desulfurization activity. In order to obtain the cultures the soil samples were inoculated in enriched medium and minimal medium containing DBT as the sole source of sulfur. The cultures grown in minimal medium with DBT were transferred multiple times with increasing temperatures, where as the cultures grown in enriched media were grown only one cycle at 37 degrees. After a certain growth period the cells were isolated and DNA was extracted. Efforts to amplify dsz genes from the obtained cultures with universal dszABC primers were mostly unsuccessful. DNA from bacterial strains isolated from the environmental samples were amplified with universal primers and amplicons were cloned. Samples #2, #6, #17, #21, #32 were amplified successfully but sequencing analyses showed little homology with dszABC genes. DNA from samples #32*, 32*Y and 32*W was isolated with Power Soil kit and PCR analysis showed a 3 kb amplicon. Sequencing analyses, however, showed less homology with dszABC and revealed homology instead with proteins such as those involved in Fe/S biogenesis and thiol:disulphide interchange. In addition, alternate universal primers were designed and PCR analyses were made with R .erythropolis IGTS8 and sample #32*. Alternate primer combination #3 (A1 and C1) and combination #8 (B1 and C2) amplified expected bands with IGTS8 DNA. Combination #8 amplified a 1 kb band from sample #32* DNA. Cultures #32*, #32*Y and #32*W were selected due to their ability to grow in minimal medium with DBT as high as 55 ˚C for multiple transfers. These isolated cultures from a soil sample from the Chicago area are able to catabolize dibenzothiophene (DBT) to 2-hydroxybiphenyl (2-HBP), which was detected by the Gibbs assay.
M.S. in Biology, May 2011
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Title: THE TRANSCRIPTIONAL RESPONSE OF ARTIFICIALLY-INOCULATED LISTERIA MONOCYTOGENES DURING THE MANUFACTURE OF UNPASTEURIZED GOUDA CHEESE
Creator: Carstens, Christina K.
Date: 2017, 2017-05
Description: Listeriosis outbreaks indicate that L. monocytogenes contamination is an issue for various food types, such as unpasteurized (raw) cheese....
Show moreListeriosis outbreaks indicate that L. monocytogenes contamination is an issue for various food types, such as unpasteurized (raw) cheese. Current regulation prevents the interstate sale and distribution of raw cheese and mandates a ≥60 day aging period at ≥2˚C to ensure product safety; yet studies demonstrate that pathogens can persist during aging. Environmental stress can alter the transcriptomic profiles of pathogens; however, these surveys are rarely conducted in food matrices. This study aimed to assess the transcriptomic profiles of L. monocytogenes strain F2365 during environmental stressors inherent throughout cheesemaking. First, quantitative polymerase chain reaction (qPCR) was used to monitor transcription levels of nine L. monocytogenes genes involved in virulence, stress response, energy transport, and metabolism during osmotic stress (11% NaCl) and varying temperature/time (5˚C 24 h, 25˚C 24 h, 38˚C 30 min) conditions in Brain Heart Infusion (BHI) broth, raw milk, and pasteurized milk. Generally, the genes prfA, lmo1381, lmo0963, and lmo1875 were down-regulated, whereas the genes lmo1864, lmo0914, lmo0348, lmo1428, and lmo1264 were up-regulated. Virulence gene, prfA, was most down-regulated when L. monocytogenes was grown in raw milk with salt at 25˚C (4774.72±838.14 fold; relative to 24 h growth at 37˚C). The stress response gene lmo0914, encoding σB, was most up-regulated when L. monocytogenes was grown in BHI at 25˚C with salt (14.61±7.72 fold). Additionally, transcription levels of the nine genes were assessed at points during the laboratory-scale manufacture of Gouda cheese made with raw milk artificially-inoculated with L. monocytogenes via qPCR. Similar differential regulation for both prfA and lmo0914 in L. monocytogenes was observed during cheesemaking. The gene lmo1864, encoding a putative pore-forming hemolysin, was up-regulated throughout the cheesemaking process, but was most up-regulated after stirring the curd (449.81±432.53 fold). Ultimately, these results indicate that the lmo1864 gene may play a role in L. monocytogenes survival during cheesemaking. Methods developed in this study can be used to assess the risk of L. monocytogenes, not only during cheesemaking, but during the ≥60-day aging process. Overall, these results contribute to the understanding of L. monocytogenes survival mechanisms during the cheesemaking process.
M.S. in Food Safety and Technology, May 2017
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Title: LISTERIA MONOCYTOGENES SURVIVAL AND GROWTH IN FLAVORED MILKSHAKES MADE FROM NATURALLY-AND ARTIFICIALLY-CONTAMINATED ICE CREAM
Creator: Bathija, Vriddi Mahesh
Date: 2016, 2016-12
Description: Listeria monocytogenes is the causative agent of the disease listeriosis and was implicated in a multistate foodborne outbreak associated with...
Show moreListeria monocytogenes is the causative agent of the disease listeriosis and was implicated in a multistate foodborne outbreak associated with ice cream spread over four years from 2010 to 2014 in Kansas, Oklahoma, Texas and Arizona. Ten illnesses were reported during the course of this outbreak, resulting in 100% hospitalization and a mortality rate of 33%; the individuals who died in the outbreak had consumed milkshakes made with the contaminated ice cream. The ice cream was found to be contaminated uniformly at 10 MPN/g. This study assessed the growth kinetics of L. monocytogenes in milkshakes made with naturally- and artificially-contaminated ice cream, and with or without flavoring agents. Artificial-contamination of ice cream samples included inoculation with a cocktail of rifampicin-resistant L. monocytogenes into the middle of the product using a wide-orifice pipet tip. Milkshake were prepared with or without strawberry, chocolate, or mint flavoring, using the recipe associated with the healthcare facility where the illnesses occurred. Milkshakes were stored in sterile plastic cups at 10ºC and an asymmetric (3 tubes of 100ml, 5 tubes of 10 ml, 8 tubes of 1ml and 8 tubes of 0.1ml sampling scheme) most probable number (MPN) enumeration was conducted after 0, 12, 24, 48, 72, 96 and 144 h. The Baranyi model was used to model L. monocytogenes growth rates, maximum populations, and lag phases. Compared to milkshakes made with no flavoring agents, the milkshakes with flavoring resulted in decreased growth rates for L. monocytogenes for both contamination states; the lowest growth rate of the pathogen was observed in strawberry flavored milkshakes made from artificially-contaminated ice cream (0.029 log CFU/ml per hour). Chocolate and mint flavorings resulted in significantly (P < 0.05) longer lag phases for both natural (68.2 and 83.0 h) and artificial-contamination (47.7 and 54.2 h, respectively). The highest maximum population (5.79 log CFU/ml) was achieved by L. monocytogenes in naturallycontaminated milkshakes without any flavoring agent. Since challenge studies often depend on the artificial contamination of a food product, this study evaluated the differences between artificial and natural contamination of L. monocytogenes in milkshakes. The data obtained can be used for risk assessment purposes.
M.S. in Food Safety and Technology, December 2016
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Title: STUDY OF THE FUNCTION AND TARGET GENES OF THE MIR-17-92 CLUSTER IN MLL-ASSOCIATED LEUKEMIA
Creator: Wiley, Anissa
Date: 2011-04-19, 2011-05
Description: MicroRNAs (miRs) have recently been found to be important regulatory agents in cancers. More specifically, the miR-17-92 cluster, which is...
Show moreMicroRNAs (miRs) have recently been found to be important regulatory agents in cancers. More specifically, the miR-17-92 cluster, which is overexpressed in acute leukemias with fusions of the mixed lineage leukemia (MLL) gene, such as MLL-AF9 and MLL-ELL, has been shown to affect regulation of normal genes in human acute leukemias. Studies show that the miR-17-92 cluster targets genes in acute leukemias that play roles in cell differentiation and proliferation. To study this, a luciferase reporter assay was performed showing that miR-17-92 targets transforming growth factor beta induced (TGF!I) and suppressor of zeste 12 (SUZ12). Studies have shown TGF!I to be downregulated in MLL fusion acute leukemias and SUZ12 to have an inverse correlation of expression with miR-17-92. Both genes are important in the regulation of cell differentiation and proliferation. Furthermore, previous studies have shown that the miR- 17-92 cluster partially blocks cell differentiation and induces cell proliferation, and when combined with MLL fusions, these effects are amplified. To further validate the results of these studies, a colony forming assay was performed confirming that a knock-in version of the miR-17-92 cluster promotes formation of colonies of non-differentiating cells, especially in the presence of MLL-AF9 and MLL-ELL. These studies implicate the miR- 17-92 cluster as an important regulator in acute leukemias with MLL fusions given its effect on cell differentiation and proliferation.
M.S. in Biology, May 2011
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Title: PHOTOCONDUCTIVE SWITCH IMPLEMENTED WITH GALLIUM ARSENIDE ON SILICON NITRIDE FOR COPLANAR WAVEGUIDE BASED TERAHERTZ SPECTROMETER
Creator: Fu, Xiaohuan
Date: 2015, 2015-12
Description: Over the years, pulsed terahertz (THz) time domain spectroscopy has attracted a lot of interest since it can not only measure the intensity of...
Show moreOver the years, pulsed terahertz (THz) time domain spectroscopy has attracted a lot of interest since it can not only measure the intensity of the transient electric eld but also determine the amplitude and phase of the spectral components that make up the pulse. This provides a convenient method to obtain the molecular network information of chemical or biological samples. Signi cant e orts have been directed towards free space spectroscopy in which THz pulses travel in free space between photoconductive transceivers. Due to di raction limit, the resolution is insu cient for many applications and it results in extreme power requirements or low power densities of the probe pulse. To overcome this issue, we propose a planar THz spectrometer which uses the same photoconductive excitation and detection mechanism as free space spectroscopy, but the excited THz pulses are directly coupled into lithographically de ned coplanar transmission lines. To reduce the power loss in the substrate, a thin lm with lower permittivity is employed to replace the conventional silicon substrate at the location where the coplanar waveguide is fabricated. To obtain high sensitivity, sample can be directly placed on the coplanar waveguide for tight coupling of the eld. Conceptual design and EM simulations have been completed and a variety of experimental studies have been carried out at Argonne National Laboratory to understand the fundamentals of coplanar waveguide. The fabrication of the coplanar waveguide prototype have been conducted at Northern Illinois University. The challenge of building a photoconductive switch with LTG-GaAs on Si3N4 was encountered and an innovative wafer bonding technique was discovered. Several wafer treatments prior to and after wafer bonding have been demonstrated to improve the bonding strength and reduce the defects. A standard pump-probe optics setup has been built at DePaul University and the photoconductive switch have been tested with femtosecond laser. The results con rmed that the photoconductive switches are functioning as design and the device system is ready for THz spectroscopy application. The historical overview of THz spectroscopy research and fundamentals of coplanar waveguide and photoconductive switches are presented in Chapter 1-3, followed by EM simulation, conceptual design in Chapter 4. The details of microfabrication process and the testing results are discussed in Chapter 5 and 6. The project is summarized in Chapter 7.
Ph.D. in Electrical Engineering, December 2015
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Title: RECONFIGURABLE SYSTEM-ON.CHIP SOLUTION FOR ULTRASONIC IMAGING APPLICATIONS
Creator: Gal, Paul
Date: 2015, 2015-12
Description: Ultrasonic system have evolved from a basic single transducer system to full arrays capable of 3-dimensional scans. These advanced systems are...
Show moreUltrasonic system have evolved from a basic single transducer system to full arrays capable of 3-dimensional scans. These advanced systems are design for specific applications and target materials. These systems need to be able to process the vast amount of data that is generated while maintaining portability a flexible and reconfigurable system. Specific hardware accelerators are built to perform ultrasonic signal processing quickly and efficiently. This system allows for a variety of parameters like signal lengths and processing characteristics to be reconfigurable to allow for flexibility for different applications. A system is developed to provide an effective storage and data transfer system which will allows researchers to quickly gather data. Specific compression and reconstruction algorithms are implemented as accelerators to increase the systems overall performance. For data transfer a simple Real Time Operating System and Ethernet connective is developed. This is all implemented on the ZEDBoard Zynq SoC for maximum flexibility and performance.Ultrasonic system have evolved from a basic single transducer system to full arrays capable of 3-dimensional scans. These advanced systems are design for specific applications and target materials. These systems need to be able to process the vast amount of data that is generated while maintaining portability a flexible and reconfigurable system. Specific hardware accelerators are built to perform ultrasonic signal processing quickly and efficiently. This system allows for a variety of parameters like signal lengths and processing characteristics to be reconfigurable to allow for flexibility for different applications. A system is developed to provide an effective storage and data transfer system which will allows researchers to quickly gather data. Specific compression and reconstruction algorithms are implemented as accelerators to increase the systems overall performance. For data transfer a simple Real Time Operating System and Ethernet connective is developed. This is all implemented on the ZEDBoard Zynq SoC for maximum flexibility and performance.Ultrasonic system have evolved from a basic single transducer system to full arrays capable of 3-dimensional scans. These advanced systems are design for specific applications and target materials. These systems need to be able to process the vast amount of data that is generated while maintaining portability a flexible and reconfigurable system. Specific hardware accelerators are built to perform ultrasonic signal processing quickly and efficiently. This system allows for a variety of parameters like signal lengths and processing characteristics to be reconfigurable to allow for flexibility for different applications. A system is developed to provide an effective storage and data transfer system which will allows researchers to quickly gather data. Specific compression and reconstruction algorithms are implemented as accelerators to increase the systems overall performance. For data transfer a simple Real Time Operating System and Ethernet connective is developed. This is all implemented on the ZEDBoard Zynq SoC for maximum flexibility and performance.
M.S. in Electrical Engineering, December 2015
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Title: HARDWARE/SOFTWARE CO-DESIGN PARTITIONING ALGORITHM FOR MACHINE VISION APPLICATIONS
Creator: Gonnot, Thomas
Date: 2017, 2017-05
Description: Advancements in FPGA technologies now allows the implementation of machine vision using hardware component rather than processors for...
Show moreAdvancements in FPGA technologies now allows the implementation of machine vision using hardware component rather than processors for increased efficiency. The combination of hardware and software implementations, however, can provide even more efficient results by combining the advantages of both technologies. This leads to the problem of partitioning the machine vision algorithms between hardware and software. The hardware/software partition problem is NP-hard, which means that a solution to the problem can be checked in polynomial time, but the time to find the solution is not predictable. Automated methods based on a genetic algorithm or discrete particle swarm optimization algorithm allow a designer to implement computer vision algorithms without concerns for the hardware/software partitioning. Their reliance on randomness to explore different partitioning selections, however, means that the optimum result might not be reached and that the processing time cannot be predicted. This dissertation introduces a model for image processing and computer vision algorithms in a set of elementary blocks, each of which is assigned one or more configuration. This configuration can be either hardware or software and is linked to the corresponding resource utilization and performance. A procedure is also introduced to allocate the different blocks to either hardware or software, and a cost function is defined to evaluate the relevance of the generated design. The implementation of the model and procedure allows for the partitioning of any image processing in polynomial time by checking various implementations and selecting the optimum solution. This thesis includes two test cases used to test the efficiency of the method. The shift-invariant features transform is used to demonstrate the viability of the partitioning results on an algorithm containing multiple image convolution operations in parallel. The neural network, on the other hand, is used to demonstrate the performances of the procedure when machine vision algorithm contains many blocks. Finally, this dissertation present a set of machine vision applications, such as object tracking, object recognition, optical character recognition, facial recognition, and visually impaired assistance. The proposed model and procedure could be included in the design flow of hardware/software co-design tools and provide a library of image processing blocks ready to be implemented. This would allow image processing and computer vision designers would be able to implement any algorithm efficiently in hardware/software co-design without the need to know how to partition it.
Ph.D. in Electrical Engineering, May 2017
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Title: POWER GRID VERIFICATION ON CLOUD
Creator: Gupte, Naval
Date: 2016, 2016-05
Description: Reliability and performance of modern ICs is becoming increasingly susceptible to supply voltage variations. Increased demand for low voltage...
Show moreReliability and performance of modern ICs is becoming increasingly susceptible to supply voltage variations. Increased demand for low voltage integrated circuits has made power grid analysis extremely critical and indispensable in modern design flows. Efficient validation of on-chip power distribution network is computationally demanding because of increasing grid sizes. Power grid simulation is critical for analysis and verification of power supply noises for robust and reliable IC designs. Computational demands to simulate power grids for ICs with increasing complexity is never-ending. Cloud computing platforms can be leveraged to mitigate costs associated with making these resources available. However, since simulation data usually contains sensitive design information, simulating on third-party platforms lead to major security concerns. In this study, we propose a framework for secure power grid simulation on Cloud. A transformation algorithm to hide current excitations is presented, while still allowing a majority of computations to be completed on Cloud. We employ multiple compression strategies to significantly reduce communication and storage overheads. Experiments show that our framework can achieve similar turn-around time as an insecure simulator on Cloud, while securing current excitations and output voltage vectors with reasonable communication and computational overheads. Vectorless technique to grid verification estimates worst-case voltage noises without detailed enumeration of load current excitations. We study voltage noise assessment in RLC models of VDD and GND networks in integrated power grids. Abstract grid model is utilized to abbreviate runtime, while transient constraints capture transitory circuit behaviour. Heuristics are employed to extract constraints that restrict power consumption profiles to realistic scenarios. Multiple linear programming problems are formulated to evaluate bounds on voltage overshoots and undershoots. We propose ways to mitigate storage and computational requirements on processing resources, enabling users to deploy computations on economical Cloud Computing platforms. Recommended solution is parallelizable, thereby reducing the overall verification time. Data compression is applied to fully exploit the compute capabilities of contemporary processors for higher throughputs. Experimental results suggest that the proposed technique is practical and scalable for industrial grids.
Ph.D. in Electrical Engineering, May 2016
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Title: POLARIZATION COUPLING IN SEMICONDUCTOR NANO-DIMERS IN THE TERAHERTZ RANGE
Creator: Hu, Zhijing
Date: 2017, 2017-05
Description: Surface plasmon resonance (SPR) occurs at the interface of a semiconductor and a dielectric when certain conditions are satisfied. SPR is...
Show moreSurface plasmon resonance (SPR) occurs at the interface of a semiconductor and a dielectric when certain conditions are satisfied. SPR is impetus to new sensor and device development in the optical range, with nanoparticles of noble metals taking up major roles. Typical conduction band electron concentrations in semiconductors lead to resonance frequencies in the terahertz and infrared bands. While the response strength is weaker than those exhibited by metals, it can be made up for by the formation of aggregates. The added degree of freedom by doping or carrier injection further enhances the versatility of semiconductor nanoclusters. To obtain a first principle solution to the coupled set of equations for charge carrier transport and electrodynamics in a conductive cluster is a formidable task with a high computational cost. Employing a finite-element based tool, the COMSOL Multiphysics Simulation Software, the interaction inside and outside some elementary semiconductor structures such as slab and sphere have been solved, which revealed the screening of the internal field while displaying dispersion and absorptions effects. The study of semiconductor dimer also showed a significant field enhancement and frequency shift. Under strong applied field, asymmetric polarization within the particles is revealed. The accompanying nonlinear polarization response can be employed to develop new devices. These model structures can serve to provide insight to the analysis and synthesis more complex structures.
Ph.D. in Electrical Engineering, May 2017
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Title: INDEX CODING VIA RANK MINIMIZATION
Creator: Huang, Xiao
Date: 2015, 2015-07
Description: Index codes reduce the number of bits broadcast by a wireless transmitter to a number of receivers with different demands and with side...
Show moreIndex codes reduce the number of bits broadcast by a wireless transmitter to a number of receivers with different demands and with side information. It is known that the problem of finding optimal linear index codes is NP-hard (a worst-case result). Many heuristic solutions based on graph coloring have been proposed. However, graph coloring is also a NP-hard problem, and it only gives an upper bound of the index coding. Motivated by a connection between index coding and rank minimization, this thesis investigates the performance of different heuristics based on rank minimization and matrix completion methods, such as alternating projections and alternating minimization, for constructing linear index codes over the reals. The underlying matrices representing an index coding problem have a special structure that makes celebrated methods, such as nuclear norm minimization, perform badly. The performance of different methods, such as alternating projections, directional alternating projections and alternating minimization are presented, through extensive simulation results on random instances of the index coding problem. This thesis makes the following contributions: 1) The proposed alternating projections method gives the best performance compared to other graph based algorithms in the literature. 2) This proposed method leads to up to 13% savings on average communication cost compared to the well know greedy graph coloring algorithm. 3) The thesis describes how the proposed methods can be used to construct linear network codes for non-multicast networks. Our computer code is available online.
M.S. in Electrical Engineering, July 2015
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