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Title: SURVIVAL AND GROWTH OF LISTERIA MONOCYTOGENES IN CHOPPED GREEN AND RED BELL PEPPERS USING PREDICTIVE MODELING
Creator: Zhang, L1jie
Date: 2015, 2015-07
Description: Listeria monocytogenes (L. monocytogenes) is a Gram-positive pathogenic organism and the causative agent of human and animal listeriosis....
Show moreListeria monocytogenes (L. monocytogenes) is a Gram-positive pathogenic organism and the causative agent of human and animal listeriosis. Listeriosis is a gastrointestinal or invasive systemic illness resulting from consumption of contaminated food products, mainly cheese, deli meats, and fresh produce, by L. monocytogenes. In recent years, several foodborne outbreaks have been reported that were associated with fresh produce, such as cantaloupe, celery and sprouts. Temperature is considered a major factor that affects L. monocytogenes growth during storage. The proliferation of L. monocytogenes varies on different produce items based on storage temperature. In this study, the persistence and population dynamics of three L. monocytogenes strains, LS806 (cheese isolate), LS810 (cantaloupe isolate) and LS808 (celery isolate) were evaluated by incubating inoculated fresh-cut green bell pepper and red bell pepper at various temperatures (5oC, 10oC, and 25oC) for 14 days. To assess the risk of L. monocytogenes in these fresh-cut vegetable items, a primary predictive model was fitted for L. monocytogenes growth data using DMFit. Green bell pepper had significantly (P<0.05) higher pH and aw, and higher amounts of yeast and mold and Enterobacteriaceae than did red bell pepper. In green bell pepper, all three strains showed no significant difference (P>0.05) in growth rate when incubated at the same temperature. In red bell peppers, LS808 had the highest (P<0.05) growth rate at both 5°C and 25°C out of the three strains. All of the three strains grew significantly faster (P<0.01) at 25°C than either 5°C or 10°C in both green and red bell peppers. All three strains obtained less than 1 log10 growth increase after incubating at 25°C for 6 hours on pre-chilled produce. Some strains (LS806 and LS810) significantly increased (P<0.01) during two 5-hour 25°C incubations, but did not reach 1 log10 growth increase. The results indicate that L. monocytogenes not only persists, but also grows in chopped green and red bell peppers at 5, 10, and 25°C, and strains grew faster at the higher temperature (25°C). Data obtained could be further evaluated for determining whether Time/temperature control for safety (TCS) designation should be applied to chopped green and red bell peppers.
M.S. in Food Safety and Technology, July 2015
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Title: STUDY OF SALMONELLA SURVIVAL ON THE SURFACE OF FRUITS
Creator: Sui, Ke
Date: 2017, 2017-05
Description: Salmonella enterica has been frequently linked to the major foodborne disease outbreaks. The molecular mechanisms underlying this pathogen...
Show moreSalmonella enterica has been frequently linked to the major foodborne disease outbreaks. The molecular mechanisms underlying this pathogen survival on the fresh fruit surface remain largely unexplored. In this study, the environmental factors that affect the survival of Salmonella strains on the surface of selected fruits were studied. Grape tomatoes (or cantaloupe peels) were inoculated in three separate trials with 1 mL Salmonella enterica serotypes Enteritidis or Typhimurium (approximately 1010-11 CFU/mL). Storage of grape tomatoes at 4 ℃ resulted in significant decrease in populations of S. Enteritidis; this trend was observed at both of the tested relative humidity with the D-value as 7.25±1.05 d and 7.28±2.34 d, respectively. At different temperatures, relative humidity only had marginal effects on the bacterial survival on the surface of grape tomato and cantaloupe. In addition, S. Typhimurium apparently survived better than S. Enteritidis on the surface of grape tomato. Furthermore, a transposonmutagenesis library with random transposon insertion mutants of S. Enteritidis and high-throughput sequencing analysis showed that the expression of genes rcsB and nlpD were hypothesized to be associated with the survival of S. Enteritidis on grape tomatoes. Inframe deletions of the two genes in S. Enteritidis were constructed by lambda red recombinase system and respective complementation mutants were also obtained for identification of the contribution of the two genes to the bacterial survival on the surface of grape tomato. Thus, this study provided microbiological and molecular microbiological basis to probe the roles of putative genes in Salmonella enterica survival on the surface of fresh fruits.
M.S. in Food Safety and Technology, May 2017
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Title: DESIGN OF A SECURE WIRELESS HEALTH DATA MANAGEMENT SYSTEM FOR PERSONAL BODY SENSOR NETWORKS
Creator: Wu, Pingping
Date: 2016, 2016-07
Description: In this research, we have explored and verified the data security and real-time performance of a Secure Wireless Health Data Management (SWHDM...
Show moreIn this research, we have explored and verified the data security and real-time performance of a Secure Wireless Health Data Management (SWHDM) system applied to personal body sensor networks. Security must be considered critical for any healthrelated information system. The SWHDM examined for this study consists of multiple wireless health-related sensors, one central data coordinator called the Wireless Intelligent Personal Communication Node (W-iPCN), a custom application designed for an Android smartphone, and a remotely located central medical server. There are two major communication channels involved in wireless data transmission. We extensively studied the body sensor data for wireless data transmission. We also focused on applying cryptographic algorithms in order to provide data confidentiality, integrity and authentication. This security assessment aims to observe the performance of data encryption and decryption, and feasibility to remotely monitor patients' health in realtime. The test result based on ECG examples is favorable towards the real-time processing requirements of the system.
M.S. in Electrical Engineering, July 2016
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Title: SPECTRUM SHARING USING CYCLOSTATIONARY SIGNATURES FOR PUBLIC SAFETY PROVISION
Creator: Iyer, Swapna
Date: 2011-11-21, 2011-12
Description: With the growth in wireless technology, and the ever increasing use of the available spectrum by radio systems, Spectrum Access and Sharing is...
Show moreWith the growth in wireless technology, and the ever increasing use of the available spectrum by radio systems, Spectrum Access and Sharing is highly desired in order to completely utilize the available band of frequencies and thus improve the overall Spectrum E ciency. Cognitive Radio can be used as a technology to improve the spectrum utilization in case of Public Safety Systems. With FCC reserving a 10 MHz band of dedicated spectrum allocated in the 700 MHz band for Broadband Communications, the need to use this band e ciently is necessary. In this thesis, we propose a method by which the available spectrum can be shared among multiple cognitive users in the presence of a high priority cognitive user. We use a Cyclostationary Signature to improve the detection method by other cognitive users. By using this signature we can achieve faster and reliable detection which in turn will improve the Spectrum Utilization.
M.S. in Electrical Engineering, December 2011
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Title: ENABLING TOOLS FOR SINGLE CELL ANALYSIS
Creator: Li, Zhaoxia
Date: 2011-07, 2011-07
Description: Cells are basic functional units of life. A cell function is mediated by proteins and genes, whose distribution and expression level depends...
Show moreCells are basic functional units of life. A cell function is mediated by proteins and genes, whose distribution and expression level depends remarkably on the microenvironment. In the native environment, individual cells behave differently but communicate with surrounding cells. It is imperative to investigate proteins and genes at the single cell level in their native environment. The current representative single cell analysis methods, fluorescent techniques, are the most direct tools to study a single cell. The commonly used methods to measure protein and gene expression levels in single cells are on the basis of fluorescence labeling, such as fluorescence-activated cell sorting and live cell microscopy. They become more powerful when combine with the use of microfluidic devices. The disadvantages of these methods are, (1) their limited sensitivity doesn’t allow the detection of low-abundance proteins and genes; (2) they are unable to detect the cell-to-cell difference within a population; (3) the cell-sorting based method is lack of spatial resolution since the isolation of cells from the natural environment is required for analysis. To tackle these challenges, we established atomic force microscopy based approaches for in-situ gene and protein analysis on a target single live cell. The methods provide the spatial and quantitative information of cells in their native culture environment. They are effective and sensitive to detect low-abundant proteins and genes. In this thesis work, we developed a novel immunofluorescence assisted affinity mapping (IF-AM) method, in which immunofluorescence provides the guidance to locate a desired type of cell in a cell community for performing affinity mapping to quantify the local protein density at a high spatial resolution. Due to the ability of directly assessing proteins of individual cells, the IF-AM method is shown to be a sensitive tool for xiii resolving subtle differences in the local expression of membrane proteins even at low abundance. In the following work, we improved the accuracy of protein quantification by adapting the separation work based calculation rather than the previously used maximum adhesion force based calculation, and established a practical model to analyze the data systematically. We applied the methods to investigate the membrane proteins TRA-1-81 and E-cadherin on human embryonic stem cells. The heterogeneous distribution of TRA- 1-81 and the homogeneous distribution of E-cadherin as well as the quantitative measurement of the protein local abundance provided comprehensive information in understanding the strategy of hES cells to maintain the stemness during cell proliferation and to initiate the differentiation. An mRNA retrieval method was also developed to perform the gene expression analysis on a single cell of a desired type in a cell community. This was achieved by using a functionalized AFM tip as a bait to bind and retrieve mRNA from a desired single cell, followed by sensitive Quantitative Polymerase Chain Reaction (Q-PCR) analysis. The extraction of mRNA from live cells was performed with non/negligible damage to the cells. The established method here enabled the gene expression analysis of individual live cells at the original sites without disrupting the cell context. Thus the gene expression of a target cell and its surrounding cells can be analyzed in parallel, deriving concrete data for understanding the behavior of one cell in concert with that of the surrounding cells in the same or different cell population. The method was successfully applied in the study of side population cells in ovarian cancer cells. The methods developed in this thesis are versatile, and can be broadly applied to the study of different membrane proteins and genes of various cell types.
Ph.D. in Chemistry, July 2011
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Title: 3D RECONSTRUCTION FROM MULTIPLE IMAGES USING SINGLE MOVING CAMERA
Creator: Zhou, Zhen
Date: 2015, 2015-05
Description: A new technique to reconstruct an object or environment in 3D using a single moving camera was developed. The technique requires only one...
Show moreA new technique to reconstruct an object or environment in 3D using a single moving camera was developed. The technique requires only one camera moving through the environment. Once a set of images or a video is captured, a point cloud and the camera path of the environment or the object can be generated. The camera has to be calibrated in advance. The procedure of 3D reconstruction consists of the SIFT feature matching algorithm, the Epipolar geometry reconstruction, fundamental matrix algebra, points cloud triangulation, and the estimation of the camera motion. The algorithm explored in this thesis is only based on visual information captured by a single moving RGB-camera.
M.S. in Electrical Engineering, May 2015
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Title: WIRELESS SCHEDULING IN MULTI-CHANNEL MULTI-RADIO MULTIHOP WIRELESS NETWORKS
Creator: Wang, Zhu
Date: 2014, 2014-07
Description: Maximum multi ow (MMF) and maximum concurrent multi ow (MCMF) in multi-channel multi-radio (MC-MR) wireless networks have been well-studied in...
Show moreMaximum multi ow (MMF) and maximum concurrent multi ow (MCMF) in multi-channel multi-radio (MC-MR) wireless networks have been well-studied in the literature. They are NP-hard even in single-channel single-radio (SC-SR) wireless networks when all nodes have uniform (and xed) interference radii and the positions of all nodes are available. This disertation studies maximum multi ow (MMF) and maximum concur- rent multi ow (MCMF) in muliti-channel multi-radio multihop wireless networks under the protocol interference model in the bidirectional mode or the unidirectional mode. We introduce a ne-grained network representation of multi-channel multi- radio multihop wireless networks and present some essential topological properties of its associated con ict graph. It was proved that if the number of channels is bounded by a constant (which is typical in practical networks), both MMF and MCMF admit a polynomial-time ap- proximation scheme under the protocol interference model in the bidirectional mode or the unidirectional mode with some additional mild conditions. However, the run- ning time of these algorithms grows quickly with the number of radios per node (at least in the sixth order) and the number of channels (at least in the cubic order). Such poor scalability stems intrinsically from the exploding size of the ne-grained network representation upon which those algorithms are built. In Chapter 2 of this dissertation, we introduce a new structure, termed as concise con ict graph, on the node-level links directly. Such structure succinctly captures the essential advantage of multiple radios and multiple channels. By exploring and exploiting the rich structural properties of the concise con ict graphs, we are able to develop fast and scalable link scheduling algorithms for either minimizing the communication latency or maximizing the (concurrent) multi ow. These algorithms have running time growing linearly in both the number of radios per node and the number of channels, while not sacri cing the approximation bounds. While the algorithms we develop in Chapter 2 admit a polynomial-time ap- proximation scheme (PTAS) when the number of channels is bounded by a constant, such PTAS is quite infeasible practically. Other than the PTAS, all other known approximation algorithms, in both SC-SR wireless networks and MC-MR wireless networks, resorted to solve a polynomial-sized linear program (LP) exactly. The s- calability of their running time is fundamentally limited by the general-purposed LP solvers. In Chapter 3 of this dissertation, we rst introduce the concept of interference costs and prices of a path and explore their relations with the maximum (concurrent) multi ow. Then we develop purely combinatorial approximation algorithms which compute a sequence of least interference-cost routing paths along which the ows are routed. These algorithms are faster and simpler, and achieve nearly the same approximation bounds known in the literature. This dissertation also explores the stability analysis of two link scheduling in MC-MR wireless networks under the protocol interference model in the bidirectional mode or the unidirectional mode. Longest-queue- rst (LQF) link scheduling is a greedy link scheduling in multihop wireless networks. Its stability performance in single-channel single-radio (SC-SR) wireless networks has been well studied recently. However, its stability performance in multi-channel multi-radio (MC-MR) wireless networks is largely under-explored. We present a stability subregion with closed form of the LQF scheduling in MC-MR wireless networks, which is within a constant factor of the network stability region. We also obtain constant lower bounds on the efficiency ratio of the LQF scheduling in MC-MR wireless networks under the protocol interference model in the bidirectional mode or unidirectional mode. Static greedy link schedulings have much simpler implementation than dy- namic greedy link schedulings such as Longest-queue-frst (LQF) link scheduling. However, its stability performance in multi-channel multi-radio (MC-MR) wireless networks is largely under-explored. In this dissertation, we present a stability subre- gion with closed form of a static greedy link scheduling in MC-MR wireless networks under the protocol interference model in the bidirectional mode. By adopting some special static link orderings, the stability subregion is within a constant factor of the stable capacity region of the network. We also obtain constant lower bounds on the throughput efficiency ratios of the static greedy link schedulings in some special static link orderings.
Ph.D. in Computer Science, July 2014
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Title: ELECTROSPUN COLLAGEN/SILK TISSUE ENGINEERING SCAFFOLDS: FIBER FABRICATION, POST-TREATMENT OPTIMIZATION, AND APPLICATION IN NEURAL DIFFERENTIATION OF STEM CELLS
Creator: Zhu, Bofan
Date: 2017, 2017-05
Description: Biocompatible scaffolds mimicking the locally aligned fibrous structure of native extracellular matrix (ECM) are in high demand in tissue...
Show moreBiocompatible scaffolds mimicking the locally aligned fibrous structure of native extracellular matrix (ECM) are in high demand in tissue engineering. In this thesis research, unidirectionally aligned fibers were generated via a home-built electrospinning system. Collagen type I, as a major ECM component, was chosen in this study due to its support of cell proliferation and promotion of neuroectodermal commitment in stem cell differentiation. Synthetic dragline silk proteins, as biopolymers with remarkable tensile strength and superior elasticity, were also used as a model material. Good alignment, controllable fiber size and morphology, as well as a desirable deposition density of fibers were achieved via the optimization of solution and electrospinning parameters. The incorporation of silk proteins into collagen was found to significantly enhance mechanical properties and stability of electrospun fibers. Glutaraldehyde (GA) vapor post-treatment was demonstrated as a simple and effective way to tune the properties of collagen/silk fibers without changing their chemical composition. With 6-12 hours GA treatment, electrospun collagen/silk fibers were not only biocompatible, but could also effectively induce the polarization and neural commitment of stem cells, which were optimized on collagen rich fibers due to the unique combination of biochemical and biophysical cues imposed to cells. Taken together, electrospun collagen rich composite fibers are mechanically strong, stable and provide excellent cell adhesion. The unidirectionally aligned fibers can accelerate neural differentiation of stem cells, representing a promising therapy for neural tissue degenerative diseases and nerve injuries.
Ph.D. in Chemistry, May 2017
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Title: P21 IS A BIOMARKER OF CELL FATE AFTER UV IRRADIATION
Creator: Lu, Ziyan
Date: 2011-04-19, 2011-05
Description: UV irradiation can cause DNA damage, which leads to either cell cycle arrest or apoptosis. As a major transcriptional target of p53 protein in...
Show moreUV irradiation can cause DNA damage, which leads to either cell cycle arrest or apoptosis. As a major transcriptional target of p53 protein in response to DNA damage, p21 protein plays critical roles in both cell cycle arrest and apoptosis. However, the specific range of UV doses and functions of p21 protein leading to the determination of cell fate in human androgen-independent prostate cancer cells has not been completely elucidated. Here, we show that low doses of UV irradiation (< 40 J/m2) induced cell cycle arrest with up-regulation of p21 protein. However, high doses of UV irradiation (> 60 J/m2) can induce apoptotic cell death as indicated by caspase-3 activation, which is also consistent with apoptotic morphological changes. Interestingly, p21 protein is degraded at early time course of high-dose UV irradiation-induced apoptosis, pretreatment of proteasome inhibitor MG132 which can block p21 degradation but partially inhibits apoptotic cell death. Consistently, similar results were obtained in both 104-R1 cells and 104-IS cells. Taken together, the results suggest that there is a narrow window of UV doses range that serves as a “switch” point, in which cells make a decision: either cell cycle arrest or cell death. p21 protein serves as a good indicator for both cell cycle arrest and apoptotic cell death post-UV irradiation in human androgen-independent prostate cancer cells. Therefore, p21 may be a potential therapeutic target in prostate cancer.
M.S. in Biology, May 2011
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Title: STUDY OF VITREOSCILLA HEMOGLOBIN VARIANTS PRODUCED BY RANDOM MUTAGENESIS
Creator: Lin, Xiaodan
Date: 2015, 2015-05
Description: This study is focused on comparing the wild type and mutated versions of the Vitreoscilla hemoglobin gene (vgb). The purpose of this focus is...
Show moreThis study is focused on comparing the wild type and mutated versions of the Vitreoscilla hemoglobin gene (vgb). The purpose of this focus is to find out whether any of the vgb mutations provides an advantage regarding cell growth rate, as well as on the expression level of Vitreoscilla hemoglobin protein (VHb). A negative control Escherichia coli DH5α (E. coli DH5α) bearing no pUC plasmid, as well as seven E. coli DH5α strains bearing different pUC-based plasmids were tested in the experiments. Among these were one vector-only negative control (pUC18), one wild type positive control (pUC8:16, which carries wild type vgb) and five different types of pUC-bearing vgb mutants (pUC-vgb M1, M2, M3, M4 and pUC18-vgb M3). In order to compare cell growth rate among these strains, the growth rate assay was carried out under three different conditions: (1) Luria-Bertani (LB) medium, aerobic conditions; (2) Terrific Broth (TB) medium, low oxygen conditions; and (3) TB medium, microaerobic conditions. In addition, the carbon monoxide (CO) difference spectra assay was conducted to measure functioning VHb protein expression levels for the strains grown under aerobic conditions. In contrast to the results obtained by our Australian collaborators, our growth rate assay and CO difference spectra assay showed no growth advantage or higher expression level of functioning VHb protein due to any of the vgb mutations. For the further study of the vgb mutants, four different recombinant plasmids were constructed by cloning three types of mutated vgb (vgb M1, M3 and M4) as well as wild type vgb into the prokaryotic expression vector pUC8 with ampicillin (Amp) resistance. After being transformed into competent E. coli DH5α cell, these resulting xii strains, as well as the plasmid-free negative control (E. coli DH5α) and vector-only negative control (E. coli DH5α bearing plasmid pUC8) were tested by the CO difference spectra assay. Except strain E. coli DH5α [pUC8-vgb M3], which showed a slight increase in the VHb expression level, the strain bearing other mutated vgbs did not demonstrate any elevation in VHb protein expression level, compared to the positive control containing wild type vgb.
M.S. in Biology, May 2015
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Title: IMAGE PROCESSING ALGORITHMS FOR PROSTATE CANCER LOCALIZATION WITH MULTISPECTRAL MAGNETIC RESONANCE IMAGING
Creator: Xin, Liu
Date: 2011-11, 2011-12
Description: In this thesis, we develop a series of image processing algorithms to localize prostate cancer with multispectral magnetic resonance (MR)...
Show moreIn this thesis, we develop a series of image processing algorithms to localize prostate cancer with multispectral magnetic resonance (MR) images to guide biopsy, surgery and minimally invasive therapy. Besides, we develop a new method to for evaluation of image classification algorithms considering correlation between neighboring pixels. Prostate cancer is one of the most prevalent cancer types and one of the leading causes of cancer death among men in the United States. High-resolution MRI has shown higher accuracy than trans-rectal ultrasound (TRUS) to ascertain the presence of prostate cancer. In this work, three different types of MR techniques are employed to provide both morphological and functional information about the benign and malignant tissues of the prostate. These are T2-weighted (T2w) MRI, diffusionweighted imaging MRI (DWI) and dynamic contrasted enhanced MRI (DCE MRI). In the first chapter of this thesis, we briefly describe the fundamentals of different MR techniques, and the multispectral MR dataset used in our experiment. Then, we focus on two tasks of the prostate cancer localization problem: prostate gland extraction and prostate tumor localization. For each topic, we review the previous studies available in the literature, and present our methods with their advantages. Finally, the new image evaluation method considering correlation between pixels is presented. Our prostate segmentation method is fully unsupervised and extracts the prostate gland from DWI MRI in 3D by fusing the active contour model and shape prior information. For tumor localization, we develop an unsupervised approach which is based on fuzzy Markov random field (fuzzy MRF) model, a new scheme based on relative intensity values which can be combined with supervised segmentation classifiers to mimic the cancer localization procedures performed by human readers and a new feature named location map which incorporates the spatial inforx mation of the tumors to remove the need for manual peripheral zone extraction. The proposed image evaluation algorithm is based on receiver operating characteristics (ROC) analysis and it considers the correlation between neighboring pixels. This method could replace the conventional ROC analysis and offers a more accurate evaluation of the test image. Our algorithms are tested on 20 patients’ multispectral MR images, and the qualitative as well as quantitative experimental results demonstrate the efficacy of our segmentation methods and show that the proposed segmentation methods outperform the currently available used approaches. The evaluation method has been tested on computer simulated images and shows very promising results. The summary and future work is also described at the end of the thesis.
Ph.D. in Electrical Engineering, December 2011
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Title: LINEAR AND NONLINEAR BEHAVIOR OF TRANSIENT LIFT RESPONSE TO PULSE-ACTUATION
Creator: An, Xuanhong
Date: 2014, 2014-07
Description: The transient lift coe cient for a NACA0009 airfoil with pulsed jet actuation type of active ow control at stall conditions is investigated....
Show moreThe transient lift coe cient for a NACA0009 airfoil with pulsed jet actuation type of active ow control at stall conditions is investigated. The experimental mea- surements show the lift coe cient dependence to a single-pulse with di erent pulse widths and amplitudes. Based on the single-pulse with optimal parameters, multi- pulse and continuous pulse actuation cases are studied, which indicate that the pulse interval is the major factor of the active ow control system capability. Linear and nonlinear model are used to predict the lift coe cient variation for di erent input signals to the actuators. A combined nonlinear model is introduced to predict lift coe cient change due to arbitrary unsteady pitching motion with active ow control.
M.S. in Mechanical and Aerospace Engineering, July 2014
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Title: INTEGRATION OF TANGENTIAL FLOW FILTRATION AND IMMUNOMAGNETIC SEPARATION FOR RAPID DETECTION OF ESCHERICHIA COLI 0157:H7 IN PRODUCE WASH WATER
Creator: Ren, Yan
Date: 2011-12-12, 2011-12
Description: Escherichia coli O157:H7 is one of the most commonly reported pathogens associated with microbial contamination of leafy greens. Since washing...
Show moreEscherichia coli O157:H7 is one of the most commonly reported pathogens associated with microbial contamination of leafy greens. Since washing is a major postharvest processing step, microbial testing of spent wash water has been suggested as a good marker to determine the contamination status of the products. In this study, the efficiency of four commercial rapid methods (BAX®, IQ-Check, Reveal® and mini-VIDAS®) for detection of E.coli O157:H7 in lettuce wash water was evaluated in comparison with the FDA BAM method. The improvement of the detection sensitivity of these tests by immunomagnetic separation (IMS) technology and sample pre-concentration by Tangential Flow Filtration (TFF) was determined. Twenty-five ml of lab prepared lettuce wash water samples were spiked with 0, 1, 10, 100 CFU of E.coli O157:H7, and subjected to enrichment protocols recommended by each of the methods. The presence of E.coli O157:H7 in the enriched samples were then assayed by the test kits, either directly or after IMS (IMS-Pathatrix ™ or IMS-Dynabeads™) treatments. All four test kits and BAM were able to detect E.coli O157:H7 at levels as low as 1 CFU/25ml of wash water. IMS treatments did not lead to further improvement in detection sensitivity. Experiments were also performed to determine the feasibility of incorporating IMS and sample pre-concentration to achieve culture-free detection. Fifty ml of wash water samples were inoculated with E.coli O157:H7 at levels of 0 to 107 CFU and analyzed by the test kits either directly or after IMS-Pathatrix™ treatment. Additionally, 10 L of wash water either prepared in the lab or collected from a commercial fresh-cut processing facility were inoculated with 0 – 106 CFU of the pathogen and subjected to TFF concentration prior to IMS or test kit analyses. IQ-Check showed the highest sensitivity with a detection limit as low as 103 CFU/50ml, and, with IMS, achieved a sensitivity of 100 CFU/50ml. Combining TFF concentration and IMS, 10 L of lab prepared wash water can be tested with IQ-Check and achieve a detection limit of approx. 100 CFU/10 L within 6 hours. For 10L of industry spent wash water, IQ-check also showed the highest sensitivity but the results lacked consistency and required additional evaluations.
M.S. in Food Safety and Technology, December 2011
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Title: INCORPORATING INVARIANCE INTO SUPPORT VECTOR MACHINE FOR DETECTION OF MICROCALCIFICATIONS
Creator: Yang, Yan
Date: 2011-11-16, 2011-12
Description: In this thesis, we explore methods for incorporating invariance into a support vector machine (SVM) classifier in detection of clustered...
Show moreIn this thesis, we explore methods for incorporating invariance into a support vector machine (SVM) classifier in detection of clustered microcalcifications (MC) in mammogram images. Unlike standard SVM, both virtual SVM and tangent vector SVM can include prior information into a trained model. We formulate MC detection as a two-class classification problem and apply these three types of SVM classifiers to this problem. The issue of dimensional reduction is considered in the tangent vector SVM, which has influence on the computational cost and complexity of the algorithm. We test and compare their performance on a set of 200 clinical mammogram images which contain a total of 5,115 MCs. In the experiments these classifiers are optimized with a training procedure for model selection. We evaluate the detection performance using both receiver operating characteristic (ROC) curves and free-response operating characteristic (FROC) curves. The results show that both virtual SVM and tangent vector SVM can outperform the standard SVM. The use of dimensional reduction in tangent vector SVM can effectively reduce the computational cost.
M.S. in Electrical Engineering, December 2011
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Title: APPLICATION-AWARE OPTIMIZATIONS FOR BIG DATA ACCESS
Creator: Yin, Yanlong
Date: 2014, 2014-07
Description: Many High-Performance Computing (HPC) applications spend a significant portion of their execution time in accessing data from les and they are...
Show moreMany High-Performance Computing (HPC) applications spend a significant portion of their execution time in accessing data from les and they are becoming increasingly data-intensive. For them, I/O performance is a significant bottleneck leading to wastage of CPU cycles and the corresponding wasted energy consumption. Various optimization techniques exist to improve data access performance. However, the existing general-purpose optimization techniques are not able to satisfy diverse applications' demands. On the other hand, the application-specific optimization pro- cess is usually a difficult task due to the complexity involved in understanding the parallel I/O system and the applications' I/O behaviors. To address these challenges, this thesis proposes an application-aware data access optimization framework and claims that it is feasible and useful to utilize applications' characteristics to improve the performance and efficiency of the parallel I/O system. Under this framework, an optimization may consist of several basic but challenging steps, including capturing the application's characteristics, identifying the causality of I/O performance degra- dation, and delivering optimization solutions. To make these steps easier, we design and implement the IOSIG toolkit as an essential system support for the default par- allel I/O system. The toolkit is able to pro le the applications' I/O behaviors and then generate comprehensive characteristics through trace analysis. With the help of IOSIG, we design several optimization techniques on data layout optimization, data reorganization, and I/O scheduling. The proposed framework has significant poten- tial to boost application-aware I/O optimization. The results prove that the proposed optimization techniques can significantly improve the data access performance.
Ph.D. in Computer Science, July 2014
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Title: THERMAL RESISTANCE OF SALMONELLA ENTERICA AND ESCHERICHIA COLI 0157:H7 IN PEANUT BUTTER
Creator: He, Yingshu
Date: 2014, 2014-05
Description: Salmonella enterica is a frequent food contaminant and the leading cause of foodborne bacterial illnesses in the United States. Our study...
Show moreSalmonella enterica is a frequent food contaminant and the leading cause of foodborne bacterial illnesses in the United States. Our study demonstrated that a 5-strain S. enterica cocktail displayed increased heat resistance in peanut butter of low water activity (aw). Significant differences (P < 0.05) were found between the survival rates of Salmonella enterica and Escherichia coli O157:H7 in peanut butter with different formulations and water activity. High carbohydrate content in peanut butter and low incubation temperature resulted in higher levels of bacterial survival during storage but lower levels of bacterial resistance to heat treatment. Furthermore, we also compared the relative heat resistance of three individual strains of S. enterica representing serotypes Typhimurium, Enteritidis and Tennessee and the 3-strain cocktail treated at both 90oC and 126oC in two different peanut butter formulations with varied fat and carbohydrate contents and adjusted water activities (aw from 0.2 to 0.8). When treated at 90oC, increased water activity in peanut butter significantly (P < 0.05) reduced the heat resistance of desiccation-stressed S. enterica cells. Differences in heat resistance were also detected among the three S. enterica serotypes and between the two peanut butter formulations. When treated at 126oC, the differences in bacterial heat resistance among serotypes and adjusted water activities were less notable (P > 0.05). Based on the Weibull model, an average of 52 to 132 min was required to achieve a 5-log reduction of the 3-strain cocktail at 90oC in peanut butter with an aw of 0.2. When aw was increased to 0.6, to achieve the same 5-log reduction required only 23-27 min. At aw of 0.8, S. enterica could be completely killed in less than 10 min in peanut butter with a fat content of 48.49%. Using scanning electron microscopy, we observed minor morphological changes xiii of S. enterica cells during desiccation and rehydration processes in peanut oil, which was used as a surrogate for peanut putter. Results from this study collectively suggest that water activity plays a critical role in determining S. enterica heat resistance in peanut butter. The variability that exists among the heat resistance of different S. enterica serotypes in different peanut butter formulations should also be taken into consideration for developing and validating effective intervention and mitigation strategies in peanut butter production.
PH.D in Biology, May 2014
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Title: EFFECTS OF THERMAL TREATMENTS ON ELISA DETECTION OF MILK PROTEINS
Creator: Lu, Yingshuang
Date: 2011-07-27, 2011-07
Description: Cow’s milk allergy is one of the most prevalent food allergies in the United States. Commercial ELISA test kits, based on antigen-antibody...
Show moreCow’s milk allergy is one of the most prevalent food allergies in the United States. Commercial ELISA test kits, based on antigen-antibody reactions, are increasingly used by food manufacturers to detect the presence of allergen residues. Milk is a common ingredient used in a variety of foods that are subjected to different degrees of cooking. How thermal processing may affect the quantitative analysis of milk allergens by ELISA test kits needs to be determined. This study first examined the performance of four total protein assays (Pierce 660nm, Modified Lowry, Coomassie, BCA) for quantification of protein residues in thermally processed milk. BCA and Lowry assays were affected by lactose and its Maillard reaction byproducts resulting in the overestimation of protein concentrations in the samples. Pierce 660 nm assay was not affected and therefore was picked as the method for total protein analysis when evaluating commercial ELISA kits. Performances of four ELISA test kits (Veratox for Total Milk Allergen, BioKits BLG Assay Kits, ELISA SYSTEMS Casein and Beta-Lactoglobulin Residue assays) in comparison with the Pierce 660 nm assay for detection of thermally treated milk samples was also evaluated. NIST non-fat milk powder standard reference material 1549 and Backpacker’s Pantry Powdered Whole Milk were either heated in water at 60◦C, 63◦C, boiled, or autoclaved for 10 or 30 min, dry-heated in a mini-oven at 100 - 232◦C for 10 min, or fried in corn oil at 150◦C or 180◦C for 3 min in a deep fryer. Milk proteins in the oil samples were analyzed either directly or after extraction with phosphate-buffered saline with 0.05% Tween (PBST) followed by partitioning in hexane to remove residual oil. The results show that all four ELISA test kits were able to accurately quantify the amount of milk proteins in uncooked oils. Inclusion of the PBST/hexane extraction step prior to test kit analyses did not improve the detection. Elevated heat resulted in a lower level of proteins extracted. While the amount of protein residues determined by Veratox and ELISA SYSTEMS Casein kits were similar to those obtained by the Pierce assay, the BioKits BLG kits registered the highest amount of proteins in samples. On the other hand, ELISA SYSTEMS Beta-Lactoglobulin assay registered the lowest level of proteins in these samples. These results suggest that heat treatment could affect the solubility and possibly the antigenic properties of proteins. Depending on the test kits used, these changes could result in over- or underestimation of protein residues in thermally treated foods.
M.S. in Food Safety and Technology, July 2011
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Title: LICENSE PLATE RECOGNITION SYSTEM USING K NEAREST NEIGHBOR ALGORITHM
Creator: Xia, Yong
Date: 2012-12-03, 2012-12
Description: License Plate Recognition (LPR) is an image-processing technology, also known as Automatic Number Plate Recognition (ANPR). This technology is...
Show moreLicense Plate Recognition (LPR) is an image-processing technology, also known as Automatic Number Plate Recognition (ANPR). This technology is very popular in fighting crime, locating stolen car, identifying parking-ticket and so on. In LPR system, the image is taken of the front or rear of the car and its quality needs to be enhanced for further process. With this enhanced image, first license plate region is located and extracted. Then character segmentation is performed on extracted license plate image. In this thesis, we use K Nearest Neighbor (KNN) algorithm to recognize these segmented characters. Keywords: LPR, Plate location, character segmentation, Image Processing, KNN
M.S.in Electrical Engineering, December 2012
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Title: FUNCTIONAL ANALYSIS OF POTENTIAL PHOSPHORYLATION SITES IN BAXΔ2 UNIQUE OLIGOPEPTIDE
Creator: Tsai, Yu-tseng
Date: 2014, 2014-07
Description: The tumor suppressor gene, Bax, plays a critical role in tumor progression through regulating cell apoptosis. Mutations on the BAX gene often...
Show moreThe tumor suppressor gene, Bax, plays a critical role in tumor progression through regulating cell apoptosis. Mutations on the BAX gene often result in silencing its expression and the loss of pro-death ability. However, there is a unique Bax isoform, BaxΔ2, recently discovered in these Bax mutated cancer cells. BaxΔ2 isoform shows higher pro-apoptotic activity than Baxα. Unlike the parental Baxα, BaxΔ2 does not target mitochondria and forms aggregates in cytosol. There is a unique 10-amino-acid peptide in the N-terminus of BaxΔ2 protein possible function as a special signal. Two serines in this region are predicted as potential phosphorylation sites for regulation of the protein activity. To test this hypothesis, we mutated both serines (SS) into non-phosphorylatable alanines (AA) by site-directed mutagenesis approach. Both BaxΔ2 wild type (BaxΔ2-SS) and mutants (BaxΔ2-AA) were tagged with GFP, which allows us to monitor the protein expression and cellular localization in live cells. Here, we found that the distribution patterns of BaxΔ2-AA and BaxΔ2-SS were similar and appeared as aggregates in cytosol. BaxΔ2-AA mutant also possessed the similar pro-apoptotic activity with BaxΔ2-SS wild type. These results suggested that the two serines in BaxΔ2 unique oligopeptide might not play a critical role in BaxΔ2 localization and pro-death activity under the current ectopic expression conditions. Further study is needed to have better understanding of phosphorylation in contribution to unique behavior of BaxΔ2.
M.S. in Biology, July 2014
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Title: REAL-TIME FACEDETECTION ANDRECOGNITION SYSTEM INCOMPLEX BACKGROUNDS
Creator: Zhang, Xin
Date: 2015, 2015-07
Description: This report provides a fast and reliable system for real-time face detection and recognition in complex backgrounds. Most current face...
Show moreThis report provides a fast and reliable system for real-time face detection and recognition in complex backgrounds. Most current face recognition systems identify faces under constrained conditions, such as constant lighting condition, the same background. In the real world, people need to be recognized in complex backgrounds under different conditions, such as tilted head poses, various facial expressions, dark or strong lighting conditions. Meanwhile, because of large amounts of real-time applications for face recognition, such as intelligent robot, unmanned vehicle, security monitor, the fast face recognition rate needs to be satisfied for the real-time requirement. In this project, a fast and reliable system is designed to real-time detect and recognize faces under various conditions. Frames are obtained directly from VGA camera. Image preprocessing and face detection, collection, recognition are sequentially implemented on the frames. Local binary patterns and Haar features are used for face detection and eye detection. Local binary pattern encodes every pixel of the image for texture extraction, which is several times faster than Haar feature detection. Adaptive boosting algorithm is used for selecting the best weak classifiers and cascading method divides the extracted best classifiers into several stages to enhance detection rate. Affine transformation is implemented to unify the size of detected facial images and align two eyes to the desired position for improving recognition accuracy. 3􀁵3 Gaussian filter is designed to remove noises of the pre-processed facial images. Principal component analysis (PCA) is used for face recognition, which is fast to identify high-dimensional faces with few principal components.
M.S. in Electrical Engineering, July 2015
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