This thesis presents a protocol for intervehicle communication for use in Vehicular Ad Hoc Networks (VANET). VANET is a natural extension of mobile ad hoc networks (MANET) in which the restrictions related to power and mobility are relaxed. The routing protocols used for MANETs are generally dependent on the state of the network. With changes in the network topology, routing messages are generated so that the states of the routers in the network are updated. In the case of VANETs, in which the level of node mobility is high, message-routing overhead has serious implications for the scalability and throughput of the routing protocol. This thesis introduces criteria that are recommended for use when protocols are designed for VANET applications and presents the Selected Node Geographic Forwarding (SNGF) protocol. The SNGF protocol implements controlled flooding in an efficient manner in order to reduce unnecessary communication overhead. The protocol has a destination discovery mechanism that allows it to initiate correspondence between nodes without reliance on static location services. The protocol avoids formation of clusters by using the concept of selective forwarding, thus providing the advantages of cluster based approaches without actually forming one itself. It effectively deals with blind flooding by introducing a comprehensive retransmission time delay in the nodes. This retransmission delay favors the nodes in the direction of the destination and prevents other nodes from retransmitting the same message. The SNGF protocol does not use routing tables, which require frequent updates in mobile networks, instead it relies on directing the messages to geographic locations which are forwarded by any available intermediary nodes. The protocol also provides techniques for handling network fragmentation which can be a frequent problem in vehicular networks. It is capable of delayed message transmission and multiple route discovery in the case of the non-availability of the shortest path to the destination. To evaluate the performance of the SNGF protocol, an extensive study of mobile networks was conducted using the NS2 simulator. The simulation results demonstrate the reachability of the protocol, its scalability advantages and its total independence from location services. The SNGF protocol allows each participating node to operate independently of other nodes in the network. Nodes in the network are able to communicate with other nodes without ever becoming dependent on intermediary nodes. This feature opens new possibility for individual node based application development in ad hoc networks. The traffic profiling is described as it would be observed by an independent node participating in VANET using the SNGF protocol. The node communicates with other nodes and collects relevant data through the discourse capability of SNGF. The data collected by the node is viewed as a snapshot in time of the traffic conditions down the road based upon which future traffic condition is predicted. Traffic profiling is investigated for different levels of VANET deployment. The simulation results show that the proposed method of traffic profiling in a VANET environment using the SNGF protocol is viable for even lower levels of deployment.

Racial profiling, in the context of the current study, concerns the association of racial and/or ethnic status with criminality and manifests in the traffic stop. The body of knowledge now available on racial profiling has documented well the incidence of numerical disparity of traffic stops between racial groups, with motorists of color subject to intrusion by the state at greater rates than White motorists (Withrow 2005). Criminologists then turned to ‘perception’-based research to examine what makes an individual ‘perceive’ he has been racially profiled. I argue that the second wave of research is dominated by a narrow survey approach, concentrates on the microlevel police-citizen encounter, and lacks a theoretical grounding, particularly in race theory. The ‘perception’ orientation, I argue, discursively diminishes the experiences of communities of color in their experiences with the state. The current study re-examines the two main components of the ‘perception’ based research -- personal and vicarious experience with the police – to extend our understanding of the meanings behind personal and vicarious encounters with law enforcement. The current qualitative study, based on more than two dozen in-depth interviews, informs our understanding of racial profiling on a number of levels. Citizenship emerges as a dominant narrative from my respondents, thus extending the effects of the racialized traffic stop effects beyond the particularistic police-minority relationship and into larger legal and political realms not anticipated in the current literature. I find that the ‘shadow citizenship’ identity imposed by the state through racializing and criminalizing processes like racial profiling is regularly rejected by people of color through various forms of resistance to racial oppression. A third important finding concerns the complication of ‘vicarious experiences.’ My respondents indicate that they do not summarily adopt views about the police but contextualize their own experiences within understandings of collective memory. Finally, because I engage racial profiling through the theoretical perspectives of Collins, DuBois, Feagin, and Foucault, among others, and frame my overall research approach using critical race theory, the salience of race in racial profiling processes is undeniably evident, contrary to the racial vacuum dominating the current literature.

There seems to be more security events happening on the network nowadays, so the administrators have to be able to find the malicious activities in progress as soon as possible in order to launch effective and efficient countermeasures. The Network administrators need to monitor the networks through collecting real time traffic measurement data on their networks, but they might find that the data gathered seems to be too little or too much detail. SNMP-based tools traditionally adopted most often give too little. However, packet sniffing tools investigate too much, so that the performance is sacrificed, especially on a large network with heavy traffic. Flows are defined as a series of packets traveling between the two communicating end hosts. Flow profiling functionality is built into most networking devices today, which efficiently provide the information required to record network and application resource utilization. Flow strikes a balance between detail and summary. NetFlow is the de facto standard in flow profiling. We introduce¡A describe¡Aand investigate its features, advantages, and strengths. Many useful flow-related tools are freely available on the Internet. A mechanism is proposed to make use of the flow logs to monitor the network effectively and efficiently. Through verification, it is believed that using flow logs can benefit the network administrator so much. The administrators can use them for timely monitoring, DoS and worm propagation detection, forensics et al.

Bladder cancer is a common malignancy affecting the genitourinary system. Although a large number of studies have been carried out on these areas for a long time, little is know about the molecular events which may involve in tumorigenesis. Until now, no profound immunohistological or molecular markers have been identified to define clinically relevant subsets of bladder cancer. The purpose of this thesis is to identify a novel bladder cancer carcinogenesis related genes. Chapter 1 attempts to illustrate the background, molecular markers, chromosomal abnormalities and genetic instability related to bladder cancer. In Chapter 2, various bioinformatics methodologies were used to annotate and identify candidate genes. Twenty-one genes were identified 1.5-fold up- or down-regulated in mRNA expression from RT4, TSGH8301 and J82, three different stages of bladder cancer cell lines by microarray chips (Dr. Liu, personal communications). Another eight candidate tumor suppressor genes were preliminarily identified from suppression subtractive hybridization (SSH) cDNA library of RT4 cell line based on an isoflavones-treated minus non-treated and further subjected to quantitative RT-PCR analyses to confirm the mRNA expression level in different stages of bladder cancer cell lines. Chapter 3 studies on the ANXA10 gene with special emphasis on its cloning, protein expression, subcellular localization and the preparation of polyclonal antibody. The result suggests that ANXA10 is a cytoplasmic protein in N18 cells. Chapter 4 analyzes the CDK2AP1 gene in mRNA and protein level at different bladder cancer cell lines and various specimens. In our preliminary observations, there are lost of CDK2AP1 expressions at invasive TCCs specimens when compared to noninvasive TCCs specimens. The mechanism of the tumor-associated loss of the CDK2AP1 expression is currently not clear. In Chapter 5, bladder cancer cell lines TSGH8301, UB37, TCCSUP and J82 in SCID mice xenograft model were established for further in vivo studies.

In this thesis, a content recommendation system has been developed. The system makes recommendations based on the preferences of the users on some aspects of the content and also preferences of similar users. The preferences of a user are extracted from the choices of that user made in the past. Similarities between users are defined by the similarities of their preferences. Such a system requires both qualified content and user information. The proposed system uses semantic user and content profiles to more effectively define the relationships between the two and make better inferences. An ontology is defined using the existing domain ontologies and the semi-structured data on the web. The system is implemented mainly for the movie domain in which well-defined ontologies and user information are easier to access.

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A study was undertaken to improve the signal quality and the resolution of the velocity profile for deep downhole seismic testing. Deep downhole testing is defined in this research as measurements below 225 m (750 ft). The study demonstrated that current testing procedures can be improved to result in higher signal quality by customizing the excitation frequency of the vibrator to local site conditions of the vibrator-earth system. The earth condition beneath the base plate can be an important factor in the signal quality subject to variations with time when tests are repetitive. This work proposes a convenient method to measure the site localized natural frequency and damping ratio, and recommends using different excitation frequencies for P- and S-wave generation. Properly increasing the excitation duration of the source signal also contributes to the quality of the receiver signal. The source signature of sinusoidal vibratory source is identified. Conventional travel time analysis using vibratory source generally focuses on chirp sweeps. After testing with impulsive sources and chirp sweeps and comparing the results with the durational sinusoidal source, the sinusoidal source was then chosen. This work develops an approach to identifying the source signature of the sinusoidal source and concludes that the normalized source signature is relevant only to four parameters: the fixed-sine excitation frequency, the duration of excitation, the damping ratio of the vibrator-earth system, and the damped natural frequency of the vibrator-earth system. Two of the parameters are designated input to the vibrator and the other two parameters are measured in the field test using the proposed method in this work. A new wavelet-response technique based on deconvolution and consideration of velocity dispersion is explored in travel-time analyses. The wavelet-response technique is also used for development of a new approach to correcting disorientation of receiver tool. The improved downhole procedures and analyses are then used in the analysis of deep downhole test data obtained at Hanford, WA. Downhole testing was performed to a depth of about 420 m (1400 ft) at Hanford site. Improvements in resolving the wave velocity profiles to depths below 300 m (1000) ft are clearly shown. / text

Inorganic phosphate \((P_i)\) is an essential nutrient whose intracellular levels are maintained by the PHO pathway in Saccharomyces cerevisiae. \(P_i\) limitation triggers upregulation of the PHO genes whose gene products primarily function to counterbalance the \(P_i\) deficiency. Despite a growing catalogue of genes that are involved in signaling of the PHO pathway, little is known about how cells actually sense \(P_i\) limitation. To better characterize the \(P_i\) sensing mechanism, I exploited two comprehensive and orthogonal approaches: 1) genome-wide genetic screening to identify novel genes involved in signaling \(P_i\) limitation through the PHO pathway and characterization of genetic interactions among these genes and 2) liquid chromatography /mass spectrometry (LC/MS)-based metabolic profiling to characterize the metabolomic response to changes in \(P_i\) availability. In genome-wide screening, I found that the aah1 mutant constitutively activated the PHO pathway and showed that AAH1 is involved in regulating PHO pathway activity. Moreover, I identified several novel genetic interactions of genes involved in inositol polyphosphate metabolism with those involved in purine metabolism and mitochondrial fatty acid biosynthesis.Through metabolomic profiling, I showed that all adenine nucleotides were downregulated in the constitutively induced ado1, adk1, and aah1 mutants in high \(P_i\) as well as in the wild type strain in low \(P_i\). These observations led to the hypothesis that downregulation of adenine nucleotides triggers activation of the PHO pathway. However, I find that decreases in adenine nucleotides appear to be the consequence of downregulation of glycolysis and of the pentose phosphate pathway rather than an activation signal for the PHO pathway.Among all the detected metabolites, S-adenosyl-L-homocysteine (SAH) responded the most quickly and significantly to changes in \(P_i\) concentration. It was known that SAH is an inhibitor of de novo synthesis of phosphatidylcholine (PC). I showed that overall PC levels were downregulated in low \(P_i\), suggesting that phospholipid metabolism is downregulated in low \(P_i\) conditions. Furthermore, I observed that exogenous SAH induces activation of the PHO pathway in high \(P_i\) implying a possible role of SAH as an initiating activation signal of the PHO pathway. / Chemistry and Chemical Biology

Much research has been conducted on the police-minority relationship, primarily from the view of the civilian. As central actors, the police view is noticeably absent from the research. I employed in-depth interviews and open-ended survey questions of patrol officers and sergeants in the Novad Texas Police Department about their views on the police-minority relationship and racial profiling. Through content analysis of the data, I examined two common themes that emerged from the discourse. The first was how "the past" was used to frame contemporary police-minority relations. The dominant narrative was that the historical police-minority relationship was something minorities should "get over" as those practices no longer applied to the current relationship. Counter views to this narrative acknowledged both past and present practices as influential. The second theme that emerged during the discussion of racial profiling was the primacy of socio-spatial control, encapsulated in one officer's comment about a "white boy in a no white boy zone." For many of the officers, control of predominantly minority and predominantly white neighborhoods meant that individuals who "did not fit" those respective spaces were subject to increased law enforcement attention. The frequency of the "white boy in a no white boy zone" scenario specifically, and not the reverse scenario that currently charges the debate surrounding racial profiling, suggests that the officers were more comfortable discussing the sensitive issue of racial profiling in this manner. Three additional areas were examined. The "out of place" doctrine evident in the officers' discussions of racial profiling creates a dilemma for the police officer because the doctrine may be considered both an effective police practice given current community policing initiatives and one that enforces the racial order in the United States. Secondly, statistical discrimination theory was employed by some of the officers to rationalize the targeting of minorities and minority space. Finally, some of the officers discussed the conflux of race/ethnicity with class, and viewed "profiling" of particular groups as based in socioeconomic status.

The development of new and effective drugs is strongly affected by the need to identify drug targets and to reduce side effects. Unfortunately, resolving these issues depends partially on a broad and thorough understanding of the biological function of many proteins, and the experimental determination of protein function is expensive and time consuming. In response to this problem, algorithms for computational function prediction have been designed to expand experimental impact by finding proteins with predictably similar function, mapping experimental knowledge onto very similar, unstudied proteins. This thesis seeks to develop one method that can identify useful geometric and chemical similarities between well studied and unstudied proteins. Our approach is to identify matches of geometric and chemical similarity between motifs , representing known functional sites, and substructures of functionally uncharacterized proteins ( targets ). It is commonly hypothesized that the existence of a match could imply that the target contains an active site similar to the motif. We have designed the MASH ( M atch A ugmentation with S tatistical H ypothesis Testing) pipeline, a software tool for computing matches. MASH is the first method to match point-based motifs, developed in earlier work, that represent functional sites as points in space with ranked priorities and alternative chemical labels. MASH is also first to match cavity-aware motifs, a novel contribution of this work, that extend point-based motifs with volumetric information describing active clefts critical to protein function. Controlled experiments demonstrate that matches for both types of motifs can identify cognate active sites. However, motifs can also identify matches to functionally unrelated proteins. For this reason, we developed M otif Profiling (MP), the first method for motif refinement that reduces geometric similarity to functionally unre lated proteins. MP is implemented in two forms: Geometric Sieving (GS) refines point-based motifs and Cavity Scaling (CS) refines cavity-aware motifs. Controlled experimentation demonstrates that GS and CS identify motif refinements that have more matches to functionally related proteins and less matches to functionally unrelated proteins. This thesis demonstrates the importance of computational tools for matching and refining motifs, emphasizing the applicability of large-scale geometric and statistical analysis for functional annotation. / National Science Foundation, National Library of Medicine, AMD, Cray