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Title: PROBING THE PAN-GENOME OF LISTERIA MONOCYTOGENES
Creator: Deng, Xiangyu
Date: 2011-04-26, 2011-05
Description: Bacterial pathogens often show significant intra-species variations in ecological fitness, host preference and pathogenic potential to cause...
Show moreBacterial pathogens often show significant intra-species variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors. The genomes of 26 L. monocytogenes strains representing the three lineages are compared based on both in silico comparative genomic analysis and high-density, pan-genomic DNA microarray hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make L. monocytogenes lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among L. monocytogenes strains. The pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomic reconstruction. Application of our method to the pan-genome of L. monocytogenes sheds new insights into the intra-species genomic diversification, niche expansion and evolution of this important foodborne pathogen.
Ph.D. in Biology, May 2011
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Title: IMPROVED SPATIAL-TEMPORAL RECONSTRUCTION FOR CARDIAC AND RESPIRATORY GATED SPECT
Creator: Qi, Wenyuan
Date: 2014, 2014-12
Description: Myocardial perfusion single photon emission computed tomography (SPECT) is an important imaging technique for evaluating coronary artery...
Show moreMyocardial perfusion single photon emission computed tomography (SPECT) is an important imaging technique for evaluating coronary artery disease. It can provide information of both myocardial perfusion and ventricular function. However, SPECT images su er from both cardiac and respiratory motion blur. In order to reduce the motion degrading, cardiac and respiratory gated SPECT imaging is used. In gated SPECT imaging, due to the lowered counts, the gated images will be more noisy than the ungated ones. Spatiotemporal (4D) processing is often used to reduce the noise level in gated images. In this thesis, we aim to investigate spatial and temporal processing techniques for improving the quality in cardiac and respiratory gated SPECT imaging. First, we will investigate a piecewise spatial smoothing prior based on totalvariation (TV) in 4D cardiac SPECT image reconstruction. In previous studies, it was found that spatial smoothing could adversely a ect the accuracy of 4D reconstruction in cardiac gated SPECT when temporal smoothing was applied, even though it could suppress the noise level. Our goal is to explore whether a piecewise spatial smoothing prior will improve the image accuracy while reducing the noise. Toward this goal, we will compare TV based piecewise spatial smoothing with quadratic spatial smoothing with simulated imaging, in which we will evaluate the lesion detectability. Clinical data will also be used to compare the results as a preliminary test. Motion-compensated temporal smoothing is known to play a key role in 4D cardiac gated SPECT reconstruction. Next, we will investigate whether better motion estimation could further improve the accuracy of reconstructed images. We will consider two di erent motion estimation models and the known motion in simulated experiments. The motion estimation methods are the classic optical ow estimation (OFE) and a periodic motion estimation method. We will evaluate the reconstruction from di erent motion models using several numerical quanti cation metrics. Furthermore, we will demonstrate reconstruction with the two motion estimation models using clinical acquisitions. Respiratory motion is known to cause motion blur in SPECT image reconstruction, and respiratory gated SPECT imaging can be e ective to combat its e ect. We will develop reconstruction techniques in respiratory gated SPECT. We will consider two reconstruction schemes for respiratory gated SPECT. The rst scheme is a post motion compensated reconstruction, in which images at di erent respiratory phases are reconstructed seperately, and afterwards are averaged over all the respiratory gates by motion compensation. The second scheme is a model based motion compensated reconstruction approach, in which one reference gate is used to describe the acquisition data of all the respiratory gates. Due to irregular respiratory motion, the data acquisition in each respiratory gate is not uniformly distributed among the acquisition angles, which would lead to limited-angle artifacts. To correct such artifacts, we propose an angle compensation method in the reconstruction. In order to deal with both cardiac and respiratory motion, we will investigate a 4D reconstruction approach for dual cardiac-respiratory gated SPECT reconstruction. This approach can accommodate the acquired data simultaneously from di erent cardiac and respiratory gates. It can exploit the correlation in the signal component among both the cardiac and respiratory phases. Both simulated experiments and clinical reconstruction will be used for evaluating this reconstruction approach. Due to the radiation risk of myocardial perfusion imaging (MPI) scans, there is an urgent need to lower the radiation dose used in SPECT. However, lower radiation dose will lead to more noisy reconstruction, which is even more serious in gated SPECT. We would explore the potential of using 4D reconstruction for lowering the dose in dual cardiac-respiratory gated SPECT.
Ph.D. in Electrical and Computer Engineering, December 2014
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Title: COMPRESSIVE SENSING AND RECONSTRUCTION : THEORY AND APPLICATIONS
Creator: Krishnamurthy, Ritvik Nadig
Date: 2014, 2014-07
Description: Conventional approach in acquisition and reconstruction of images from frequency domain strictly follow the Nyquist sampling theorem. The...
Show moreConventional approach in acquisition and reconstruction of images from frequency domain strictly follow the Nyquist sampling theorem. The principle states that the sampling frequency required for complete reconstruction of a signal is at least twice the maximum frequency of the original signal. This dissertation studies an emerging theory called Compressive Sensing or Compressive Sampling which goes against the conventional wisdom. Theoretically, it is possible to reconstruct images or signals accurately from a number of samples which is far smaller than the Nyquist samples. Compressive Sensing has proven to have farther implications than merely reducing sampling frequency of the signal. Possibility of new data acquisition methods from analog domain to digital form using fewer sensors, image acquisition using much smaller sensors array, to name a few. This novel theory combines sampling and compression methods thereby reducing the data acquisition resources, such as number of sensors, storage memory for collected samples and maximum operating frequency. This dissertation presents some insights into reconstruction of grey scale images and audio signals using OMP and CoSaMP algorithms. It also delves into some of the key mathematical insights underlying this new theory and explains some of the interactions between Compressive Sensing and related elds such as statistics, coding theory and theoretical computer science. viii
M.S. in Computer Engineering, July 2014
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Title: SYSTEM SUPPORT FOR RESILIENCE IN LARGE-SCALE PARALLEL SYSTEMS: FROM CHECKPOINTING TO MAPREDUCE
Creator: Jin, Hui
Date: 2012-05-31, 2012-05
Description: High-Performance Computing (HPC) has passed the Petascale mark and is moving forward to Exascale. As the system ensemble size continues to...
Show moreHigh-Performance Computing (HPC) has passed the Petascale mark and is moving forward to Exascale. As the system ensemble size continues to grow, the occurrence of failures is the norm rather than the exception during the execution of parallel applications. Resilience is widely recognized as one of the key obstacles towards Exascale computing. Checkpointing is currently the de-facto fault tolerant mechanism for parallel applications. However, parallel checkpointing at scale usually generates bursts of concurrent I/O requests, imposes considerable overhead to I/O subsystems, and limits the scalability of parallel applications. Despite the doubt in the feasibility of checkpointing continues to increase, there is still no promising alternative on the horizon yet to replace checkpointing. MapReduce is a new programming model for massive data processing. It has demonstrated a compelling potential in reshaping the landscape of HPC from various perspectives. The resilience of MapReduce applications and its potential in benefiting HPC fault tolerance are active research topics that require extensive investigation. This thesis work targets at building a systematic framework to support resilience in large-scale parallel systems. We address the identified checkpointing performance issue through a three-fold approach: reduce the I/O overhead, exploit storage alternatives, and determine the optimistic checkpointing frequency. This three-fold approach is achieved with three different mechanisms, namely system coordination and scheduling, the utilization of MapReduce framework, and stochastic modeling. To deal with the increasing concerns about MapReduce resilience, we also strive to improve the reliability of MapReduce applications, and investigate the tradeoffs in the programming model selection (e.g., MPI v.s. MapReduce) from the perspective of resilience. This thesis provides a thorough study and a practical solution for solving the outstanding resilience problem of large-scale MPI-based HPC applications and beyond. It makes a noticeable contribution to the state-of-the-art and opens a new research direction for many to follow.
Ph.D. in Computer Science, May 2012
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Title: SEARCHING ENCRYPTED CLOUD DATA
Creator: Urs, Karthik Mahendra Raje
Date: 2011-05-04, 2011-05
Description: The major setback of the cloud is its inability to induce strong trust in its users. For us, the users of the cloud, to be sure of the...
Show moreThe major setback of the cloud is its inability to induce strong trust in its users. For us, the users of the cloud, to be sure of the security of the data from other users, we have to trust cloud. In most of the cases, say if the data were to be hosted on Microsoft’s servers, we can trust Microsoft in its policies to prevent unauthorized access to it from other users (via hacking). But, the issue that is haunting the cloud is this - ”How can we be sure that our data is safe from Cloud service providers themselves?” The most intuitive solution for the cloud service provider to gain trust is to insist we encrypt our data. That is an irrefutable act of honesty from the cloud. But this has some obvious setbacks, few of which would negate the very advantages of cloud. One such issue that dictates the scope of this thesis is this - Typical cryptographic algorithms are not amenable to search. Now, if we were to implement a search engine on cloud (which has the data encrypted), the native search techniques have to be extended on to the cryptographic domain so that the cloud can perform the tasks of a search engine. This thesis explores the solutions to the above mentioned problem of searching over encrypted data, specifically using a secure pre-processed index approach. Though significant ideas have been proposed in the area, there is no concrete implementation to analyze if it can be used in the industrial setting. The main goal of the thesis is to implement a system which supports a variety of searching techniques. We make use of Amazon EC2 and test out the designed systems to evaluate how feasible they are for immediate consumption by the industry.
M.S. in Computer Engineering, May 2011
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Title: MICROCALCIFICATION DETECTION WITH DEEP BELIEF NETWORK
Creator: Liu, Lu
Date: 2012-04-24, 2012-05
Description: In this thesis, deep belief net (DBN) is applied for detection of microcalcification (MC) clusters in digital mammograms. DBN is a relatively...
Show moreIn this thesis, deep belief net (DBN) is applied for detection of microcalcification (MC) clusters in digital mammograms. DBN is a relatively new type of neural network in machine learning which can learn complex structures from data by using a deep architecture. Based on a database of 200 clinical mammograms, a 3-level unsupervised network followed by a supervised back-propagation fine-tuning classifier is trained and tested. For each location in the image, the classifier is applied to decide whether there is an MC, and subsequently all the detected MCs are grouped into clusters. Free-response receiver operating characteristic (FROC) curves are used to evaluate the performance. The performance of DBN is compared to a well-known support vector machine (SVM) detector. Experimental results show that DBN can outperform SVM. In particular, DBN can achieve a detection rate of 83% at the cost of only one false positive cluster per image. These promising results show that DBN can be adopted in the study of object detection in medical image.
M.S. in Electrical Engineering, May 2012
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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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