Matching Items (87)
Description
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
The object of this study is to charac terize the effect of focused ultrasound stimulation (FUS) on the rat ce rvix which has been observed to speed its ripening during pregnancy. Ce rvical ripening is required for successful fetal delivery. Timed-pregnant Sprague-Dawley rats (n=36) were used. On day 14 of gestation, the FUS system was placed on the body surface of the rat over the cervix and ultrasound energy was applied to cervix for variable times up to 1 hour in the control group, the FUS system was placed on rats but no energy was applied. Daily measurement of cervix light-induced florescence (LIF, photon counts of collagen x-bridge fluorescence) were made on days 16 of gestation and daily until spont-aneous delivery (day22) to estimate changes in cervical ripening. We found that pulses of 680 KHz ultrasound at 25 Hertz, 1 millisecond pulse duration at 1W/cm^2 applied for as little as 30 minutes would immediately afterwards show the cervix to hav e ripened to the degree seen just before delivery on day 22. Delivery times, fetal weights and viability were unaffected in the FUS-treated animals.
ContributorsLuo, Daishen (Author) / Towe, Bruce C (Thesis advisor) / Wang, Xiao (Committee member) / Caplan, Michael (Committee member) / Arizona State University (Publisher)
Created2012
Description
Communication networks, both wired and wireless, are expected to have a certain level of fault-tolerance capability.These networks are also expected to ensure a graceful degradation in performance when some of the network components fail. Traditional studies on fault tolerance in communication networks, for the most part, make no assumptions regarding the location of node/link faults, i.e., the faulty nodes and links may be close to each other or far from each other. However, in many real life scenarios, there exists a strong spatial correlation among the faulty nodes and links. Such failures are often encountered in disaster situations, e.g., natural calamities or enemy attacks. In presence of such region-based faults, many of traditional network analysis and fault-tolerant metrics, that are valid under non-spatially correlated faults, are no longer applicable. To this effect, the main thrust of this research is design and analysis of robust networks in presence of such region-based faults. One important finding of this research is that if some prior knowledge is available on the maximum size of the region that might be affected due to a region-based fault, this piece of knowledge can be effectively utilized for resource efficient design of networks. It has been shown in this dissertation that in some scenarios, effective utilization of this knowledge may result in substantial saving is transmission power in wireless networks. In this dissertation, the impact of region-based faults on the connectivity of wireless networks has been studied and a new metric, region-based connectivity, is proposed to measure the fault-tolerance capability of a network. In addition, novel metrics, such as the region-based component decomposition number(RBCDN) and region-based largest component size(RBLCS) have been proposed to capture the network state, when a region-based fault disconnects the network. Finally, this dissertation presents efficient resource allocation techniques that ensure tolerance against region-based faults, in distributed file storage networks and data center networks.
ContributorsBanerjee, Sujogya (Author) / Sen, Arunabha (Thesis advisor) / Xue, Guoliang (Committee member) / Richa, Andrea (Committee member) / Hurlbert, Glenn (Committee member) / Arizona State University (Publisher)
Created2013
Description
Sensitivity is a fundamental challenge for in vivo molecular magnetic resonance imaging (MRI). Here, I improve the sensitivity of metal nanoparticle contrast agents by strategically incorporating pure and doped metal oxides in the nanoparticle core, forming a soluble, monodisperse, contrast agent with adjustable T2 or T1 relaxivity (r2 or r1). I first developed a simplified technique to incorporate iron oxides in apoferritin to form "magnetoferritin" for nM-level detection with T2- and T2* weighting. I then explored whether the crystal could be chemically modified to form a particle with high r1. I first adsorbed Mn2+ ions to metal binding sites in the apoferritin pores. The strategic placement of metal ions near sites of water exchange and within the crystal oxide enhance r1, suggesting a mechanism for increasing relaxivity in porous nanoparticle agents. However, the Mn2+ addition was only possible when the particle was simultaneously filled with an iron oxide, resulting in a particle with a high r1 but also a high r2 and making them undetectable with conventional T1-weighting techniques. To solve this problem and decrease the particle r2 for more sensitive detection, I chemically doped the nanoparticles with tungsten to form a disordered W-Fe oxide composite in the apoferritin core. This configuration formed a particle with a r1 of 4,870mM-1s-1 and r2 of 9,076mM-1s-1. These relaxivities allowed the detection of concentrations ranging from 20nM - 400nM in vivo, both passively injected and targeted to the kidney glomerulus. I further developed an MRI acquisition technique to distinguish particles based on r2/r1, and show that three nanoparticles of similar size can be distinguished in vitro and in vivo with MRI. This work forms the basis for a new, highly flexible inorganic approach to design nanoparticle contrast agents for molecular MRI.
ContributorsClavijo Jordan, Maria Veronica (Author) / Bennett, Kevin M (Thesis advisor) / Kodibagkar, Vikram (Committee member) / Sherry, A Dean (Committee member) / Wang, Xiao (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2012
Description
Contention based IEEE 802.11MAC uses the binary exponential backoff algorithm (BEB) for the contention resolution. The protocol suffers poor performance in the heavily loaded networks and MANETs, high collision rate and packet drops, probabilistic delay guarantees, and unfairness. Many backoff strategies were proposed to improve the performance of IEEE 802.11 but all ignore the network topology and demand. Persistence is defined as the fraction of time a node is allowed to transmit, when this allowance should take into account topology and load, it is topology and load aware persistence (TLA). We develop a relation between contention window size and the TLA-persistence. We implement a new backoff strategy where the TLA-persistence is defined as the lexicographic max-min channel allocation. We use a centralized algorithm to calculate each node's TLApersistence and then convert it into a contention window size. The new backoff strategy is evaluated in simulation, comparing with that of the IEEE 802.11 using BEB. In most of the static scenarios like exposed terminal, flow in the middle, star topology, and heavy loaded multi-hop networks and in MANETs, through the simulation study, we show that the new backoff strategy achieves higher overall average throughput as compared to that of the IEEE 802.11 using BEB.
ContributorsBhyravajosyula, Sai Vishnu Kiran (Author) / Syrotiuk, Violet R. (Thesis advisor) / Sen, Arunabha (Committee member) / Richa, Andrea (Committee member) / Arizona State University (Publisher)
Created2013
Description
As networks are playing an increasingly prominent role in different aspects of our lives, there is a growing awareness that improving their performance is of significant importance. In order to enhance performance of networks, it is essential that scarce networking resources be allocated smartly to match the continuously changing network environment. This dissertation focuses on two different kinds of networks - communication and social, and studies resource allocation problems in these networks. The study on communication networks is further divided into different networking technologies - wired and wireless, optical and mobile, airborne and terrestrial. Since nodes in an airborne network (AN) are heterogeneous and mobile, the design of a reliable and robust AN is highly complex. The dissertation studies connectivity and fault-tolerance issues in ANs and proposes algorithms to compute the critical transmission range in fault free, faulty and delay tolerant scenarios. Just as in the case of ANs, power optimization and fault tolerance are important issues in wireless sensor networks (WSN). In a WSN, a tree structure is often used to deliver sensor data to a sink node. In a tree, failure of a node may disconnect the tree. The dissertation investigates the problem of enhancing the fault tolerance capability of data gathering trees in WSN. The advent of OFDM technology provides an opportunity for efficient resource utilization in optical networks and also introduces a set of novel problems, such as routing and spectrum allocation (RSA) problem. This dissertation proves that RSA problem is NP-complete even when the network topology is a chain, and proposes approximation algorithms. In the domain of social networks, the focus of this dissertation is study of influence propagation in presence of active adversaries. In a social network multiple vendors may attempt to influence the nodes in a competitive fashion. This dissertation investigates the scenario where the first vendor has already chosen a set of nodes and the second vendor, with the knowledge of the choice of the first, attempts to identify a smallest set of nodes so that after the influence propagation, the second vendor's market share is larger than the first.
ContributorsShirazipourazad, Shahrzad (Author) / Sen, Arunabha (Committee member) / Xue, Guoliang (Committee member) / Richa, Andrea (Committee member) / Saripalli, Srikanth (Committee member) / Arizona State University (Publisher)
Created2014
Description
Resource allocation is one of the most challenging issues policy decision makers must address. The objective of this thesis is to explore the resource allocation from an economical perspective, i.e., how to purchase resources in order to satisfy customers' requests. In this thesis, we attend to answer the question: when and how to buy resources to fulfill customers' demands with minimum costs?
The first topic studied in this thesis is resource allocation in cloud networks. Cloud computing heralded an era where resources (such as computation and storage) can be scaled up and down elastically and on demand. This flexibility is attractive for its cost effectiveness: the cloud resource price depends on the actual utilization over time. This thesis studies two critical problems in cloud networks, focusing on the economical aspects of the resource allocation in the cloud/virtual networks, and proposes six algorithms to address the resource allocation problems for different discount models. The first problem attends a scenario where the virtual network provider offers different contracts to the service provider. Four algorithms for resource contract migration are proposed under two pricing models: Pay-as-You-Come and Pay-as-You-Go. The second problem explores a scenario where a cloud provider offers k contracts each with a duration and a rate respectively and a customer buys these contracts in order to satisfy its resource demand. This work shows that this problem can be seen as a 2-dimensional generalization of the classic online parking permit problem, and present a k-competitive online algorithm and an optimal online algorithm.
The second topic studied in this thesis is to explore how resource allocation and purchasing strategies work in our daily life. For example, is it worth buying a Yoga pass which costs USD 100 for ten entries, although it will expire at the end of this year? Decisions like these are part of our daily life, yet, not much is known today about good online strategies to buy discount vouchers with expiration dates. This work hence introduces a Discount Voucher Purchase Problem (DVPP). It aims to optimize the strategies for buying discount vouchers, i.e., coupons, vouchers, groupons which are valid only during a certain time period. The DVPP comes in three flavors: (1) Once Expire Lose Everything (OELE): Vouchers lose their entire value after expiration. (2) Once Expire Lose Discount (OELD): Vouchers lose their discount value after expiration. (3) Limited Purchasing Window (LPW): Vouchers have the property of OELE and can only be bought during a certain time window.
This work explores online algorithms with a provable competitive ratio against a clairvoyant offline algorithm, even in the worst case. In particular, this work makes the following contributions: we present a 4-competitive algorithm for OELE, an 8-competitive algorithm for OELD, and a lower bound for LPW. We also present an optimal offline algorithm for OELE and LPW, and show it is a 2-approximation solution for OELD.
The first topic studied in this thesis is resource allocation in cloud networks. Cloud computing heralded an era where resources (such as computation and storage) can be scaled up and down elastically and on demand. This flexibility is attractive for its cost effectiveness: the cloud resource price depends on the actual utilization over time. This thesis studies two critical problems in cloud networks, focusing on the economical aspects of the resource allocation in the cloud/virtual networks, and proposes six algorithms to address the resource allocation problems for different discount models. The first problem attends a scenario where the virtual network provider offers different contracts to the service provider. Four algorithms for resource contract migration are proposed under two pricing models: Pay-as-You-Come and Pay-as-You-Go. The second problem explores a scenario where a cloud provider offers k contracts each with a duration and a rate respectively and a customer buys these contracts in order to satisfy its resource demand. This work shows that this problem can be seen as a 2-dimensional generalization of the classic online parking permit problem, and present a k-competitive online algorithm and an optimal online algorithm.
The second topic studied in this thesis is to explore how resource allocation and purchasing strategies work in our daily life. For example, is it worth buying a Yoga pass which costs USD 100 for ten entries, although it will expire at the end of this year? Decisions like these are part of our daily life, yet, not much is known today about good online strategies to buy discount vouchers with expiration dates. This work hence introduces a Discount Voucher Purchase Problem (DVPP). It aims to optimize the strategies for buying discount vouchers, i.e., coupons, vouchers, groupons which are valid only during a certain time period. The DVPP comes in three flavors: (1) Once Expire Lose Everything (OELE): Vouchers lose their entire value after expiration. (2) Once Expire Lose Discount (OELD): Vouchers lose their discount value after expiration. (3) Limited Purchasing Window (LPW): Vouchers have the property of OELE and can only be bought during a certain time window.
This work explores online algorithms with a provable competitive ratio against a clairvoyant offline algorithm, even in the worst case. In particular, this work makes the following contributions: we present a 4-competitive algorithm for OELE, an 8-competitive algorithm for OELD, and a lower bound for LPW. We also present an optimal offline algorithm for OELE and LPW, and show it is a 2-approximation solution for OELD.
ContributorsHu, Xinhui (Author) / Richa, Andrea (Thesis advisor) / Schmid, Stefan (Committee member) / Sen, Arunabha (Committee member) / Xue, Guoliang (Committee member) / Arizona State University (Publisher)
Created2015
Description
Single cell phenotypic heterogeneity studies reveal more information about the pathogenesis process than conventional bulk methods. Furthermore, investigation of the individual cellular response mechanism during rapid environmental changes can only be achieved at single cell level. By enabling the study of cellular morphology, a single cell three-dimensional (3D) imaging system can be used to diagnose fatal diseases, such as cancer, at an early stage. One proven method, CellCT, accomplishes 3D imaging by rotating a single cell around a fixed axis. However, some existing cell rotating mechanisms require either intricate microfabrication, and some fail to provide a suitable environment for living cells. This thesis develops a microvorterx chamber that allows living cells to be rotated by hydrodynamic alone while facilitating imaging access. In this thesis work, 1) the new chamber design was developed through numerical simulation. Simulations revealed that in order to form a microvortex in the side chamber, the ratio of the chamber opening to the channel width must be smaller than one. After comparing different chamber designs, the trapezoidal side chamber was selected because it demonstrated controllable circulation and met the imaging requirements. Microvortex properties were not sensitive to the chambers with interface angles ranging from 0.32 to 0.64. A similar trend was observed when chamber heights were larger than chamber opening. 2) Micro-particle image velocimetry was used to characterize microvortices and validate simulation results. Agreement between experimentation and simulation confirmed that numerical simulation was an effective method for chamber design. 3) Finally, cell rotation experiments were performed in the trapezoidal side chamber. The experimental results demonstrated cell rotational rates ranging from 12 to 29 rpm for regular cells. With a volumetric flow rate of 0.5 µL/s, an irregular cell rotated at a mean rate of 97 ± 3 rpm. Rotational rates can be changed by altering inlet flow rates.
ContributorsZhang, Wenjie (Author) / Frakes, David (Thesis advisor) / Meldrum, Deirdre (Thesis advisor) / Chao, Shih-hui (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation studies routing in small-world networks such as grids plus long-range edges and real networks. Kleinberg showed that geography-based greedy routing in a grid-based network takes an expected number of steps polylogarithmic in the network size, thus justifying empirical efficiency observed beginning with Milgram. A counterpart for the grid-based model is provided; it creates all edges deterministically and shows an asymptotically matching upper bound on the route length. The main goal is to improve greedy routing through a decentralized machine learning process. Two considered methods are based on weighted majority and an algorithm of de Farias and Megiddo, both learning from feedback using ensembles of experts. Tests are run on both artificial and real networks, with decentralized spectral graph embedding supplying geometric information for real networks where it is not intrinsically available. An important measure analyzed in this work is overpayment, the difference between the cost of the method and that of the shortest path. Adaptive routing overtakes greedy after about a hundred or fewer searches per node, consistently across different network sizes and types. Learning stabilizes, typically at overpayment of a third to a half of that by greedy. The problem is made more difficult by eliminating the knowledge of neighbors' locations or by introducing uncooperative nodes. Even under these conditions, the learned routes are usually better than the greedy routes. The second part of the dissertation is related to the community structure of unannotated networks. A modularity-based algorithm of Newman is extended to work with overlapping communities (including considerably overlapping communities), where each node locally makes decisions to which potential communities it belongs. To measure quality of a cover of overlapping communities, a notion of a node contribution to modularity is introduced, and subsequently the notion of modularity is extended from partitions to covers. The final part considers a problem of network anonymization, mostly by the means of edge deletion. The point of interest is utility preservation. It is shown that a concentration on the preservation of routing abilities might damage the preservation of community structure, and vice versa.
ContributorsBakun, Oleg (Author) / Konjevod, Goran (Thesis advisor) / Richa, Andrea (Thesis advisor) / Syrotiuk, Violet R. (Committee member) / Czygrinow, Andrzej (Committee member) / Arizona State University (Publisher)
Created2011
Description
The Dual Marching Tetrahedra algorithm is a generalization of the Dual Marching Cubes algorithm, used to build a boundary surface around points which have been assigned a particular scalar density value, such as the data produced by and Magnetic Resonance Imaging or Computed Tomography scanner. This boundary acts as a skin between points which are determined to be "inside" and "outside" of an object. However, the DMT is vague in regards to exactly where each vertex of the boundary should be placed, which will not necessarily produce smooth results. Mesh smoothing algorithms which ignore the DMT data structures may distort the output mesh so that it could incorrectly include or exclude density points. Thus, an algorithm is presented here which is designed to smooth the output mesh, while obeying the underlying data structures of the DMT algorithm.
ContributorsJohnson, Sean (Author) / Farin, Gerald (Thesis advisor) / Richa, Andrea (Committee member) / Nallure Balasubramanian, Vineeth (Committee member) / Arizona State University (Publisher)
Created2011