The Internet has evolved into a medium centered around content: people watch videos on YouTube, share their pictures via Flickr, and use Facebook to keep in touch with their friends. Yet, the only globally deployed service to discover content - i.e., Domain Name System (DNS) - does not discover content at all; it merely translates domain names into locations. The lack of persistent naming, in particular, makes content discovery, instead of domain discovery, challenging. Content Distribution Networks (CDNs), which augment DNSs with location-awareness, also suffer from the same problem of lack of persistent content names. Recently, several infrastructure- level solutions to this problem have emerged, but their fundamental limitation is that they fail to preserve the autonomy of network participants. Specifically, the storage requirements for resolution within each participant may not be proportional to their capacity. Furthermore, these solutions cannot be incrementally deployed. To the best of our knowledge, content discovery services based on peer-to-peer (P2P) networks are the only ones that support persistent content names. These services also come with the built-in advantage of scalability and deployability. However, P2P networks have been deployed in the real-world only recently, and their real-world characteristics are not well understood. It is important to understand these real-world characteristics in order to improve the performance and propose new designs by identifying the weaknesses of existing designs. In this dissertation, we first propose a novel, lightweight technique for capturing P2P traffic. Using our captured data, we characterize several aspects of P2P networks and draw conclusions about their weaknesses. Next, we create a botnet to demonstrate the lethality of the weaknesses of P2P networks. Finally, we address the weaknesses of P2P systems to design a P2P-based content discovery service, which resolves the drawbacks of existing content discovery systems and can operate at Internet-scale. This dissertation includes both previously published/unpublished and co-authored material.

Doctor of Philosophy / Department of Plant Pathology / Anna E. Whitfield / The Bunyaviridae is a family of animal and plant viruses that pose a threat to human, animal, and plant health worldwide. In nature, the dissemination of these viruses is dependent on arthropod vectors (genera Orthobunyavirus, Nairovirus, Phlebovirus, and Tospovirus) or rodent vectors (genus Hantavirus). The genus Tospovirus is the only one within this virus family that is composed of plant-infecting viruses transmitted by thrips. Tomato spotted wilt virus (TSWV), the type species of the Tospovirus genus, is one of the ten most devastating plant viruses known. It is most efficiently transmitted by the western flower thrips, Frankliniella occidentalis Pergande, in a persistant propagative manner. The insect molecules associated with virus infection and transmission by the thrips vector remain unidentified to date. The aim of this work was to identify F. occidentalis larval thrips proteins that are differentially expressed during TSWV infection of the insect vector and those that directly interact with TSWV. To achieve these goals, I used two-dimensional (2-D) gel electrophoresis and mass spectrometry coupled with Mascot searches. I identified 26 protein spots that displayed differential abundances in response to TSWV infection, which contained 37 proteins. Sixty two percent of these proteins were down-regulated by the viral infection demonstrating a complex response. Moreover, 8 and 11 protein spots that directly interacted with purified TSWV virions and a TSWV glycoprotein (GN), respectively, were identified in overlay assays of larval thrips proteins resolved by 2-D gel electrophoresis. A total of five proteins were identified from these spots. These interacting proteins might play roles in attachment and entry, endocytosis/exocytosis, and escape from different tissues for transmission to occur. Injection of double-stranded RNA (dsRNA) into adult female thrips triggered an RNAi response that resulted in 23% reduction of the target gene transcript level. This significant reduction resulted in increased mortality and decreased fertility compared to insects injected with control dsRNA or water and non-injected insects as well. The work presented here provides new insights on the molecular basis of this virus-vector interaction and describes new tools to conduct functional genomic assays to study gene function and design control strategies of F. occidentalis.

In this study the phenomenon of persistent physical symptoms (PPS) has been examined by realist evaluation of research and practice. Nimnuan et al., (2001) have shown that up to 35% of patients in primary care and 66% in specialist out-patient clinics have presented with such ‘medically unexplained’ symptoms. The cost in medical investigation to reach diagnosis for PPS is an estimated 10% of the annual UK National Health Service budget (Bermingham et al., 2010) but poor patient outcomes prevail (Dwamena et al., 2009). Currently, PPS is linked to high comorbidity with anxiety and depression (DH 2011b) and Cognitive Behavioural Therapy (CBT) is advised as the evidence based treatment for PPS (IAPT, 2014). However, a shortfall in clinical skills to address PPS is also demonstrated and engagement could be improved (De Lusignan et al., 2014). Moreover, the pragmatic study of alternative therapy modalities and processes for PPS is recommended (Leichsenring, 2005). To obtain a broader knowledge of process for patients with or without co-morbidity, practice based experience suggests that one such alternative is a brief psychodynamic intervention (STPP) for PPS. A Realist Literature Synthesis (Wong et al. 2013) highlights effective psychotherapeutic STPP interventions in real world circumstances in 5 comparison with CBT interventions for heterogenous PPS. STPP for PPS is found at least as effective as CBT, with improved engagement rates. Additionally, common factors were discovered between ‘third generation’ STPP and CBT for effective PPS interventions and these were developed into a preliminary cross-modality theoretical analytical framework. In the realist contextual evaluation (Pawson and Tilley, 1997) of a psychosexual service delivery, the majority of PPS sufferers were found only moderately co-morbid with anxiety and depression. For complete investigative study, clinical tools are developed providing integrative CBT/STPP principles for engagement with PPS for teaching, training and practice. In conclusion, the findings suggest that the reflexive insider position of the realist Therapist-Evaluator facilitates systematically derived Practice-Based Evidence of PPS process, meeting recommendations of Deary et al., (2007) to explore and define process and outcomes with PPS. The findings contribute to development of a conceptual platform to support health professionals in overcoming physical/mental health barriers to addressing PPS and wider patient access to effective care (NHSE, 2014, 2015).

abstract: A Virtual Private Network (VPN) is the traditional approach for an end-to-end secure connection between two endpoints. Most existing VPN solutions are intended for wired networks with reliable connections. In a mobile environment, network connections are less reliable and devices experience intermittent network disconnections due to either switching from one network to another or experiencing a gap in coverage during roaming. These disruptive events affects traditional VPN performance, resulting in possible termination of applications, data loss, and reduced productivity. Mobile VPNs bridge the gap between what users and applications expect from a wired network and the realities of mobile computing. In this dissertation, MobiVPN, which was built by modifying the widely-used OpenVPN so that the requirements of a mobile VPN were met, was designed and developed. The aim in MobiVPN was for it to be a reliable and efficient VPN for mobile environments. In order to achieve these objectives, MobiVPN introduces the following features: 1) Fast and lightweight VPN session resumption, where MobiVPN is able decrease the time it takes to resume a VPN tunnel after a mobility event by an average of 97.19\% compared to that of OpenVPN. 2) Persistence of TCP sessions of the tunneled applications allowing them to survive VPN tunnel disruptions due to a gap in network coverage no matter how long the coverage gap is. MobiVPN also has mechanisms to suspend and resume TCP flows during and after a network disconnection with a packet buffering option to maintain the TCP sending rate. MobiVPN was able to provide fast resumption of TCP flows after reconnection with improved TCP performance when multiple disconnections occur with an average of 30.08\% increase in throughput in the experiments where buffering was used, and an average of 20.93\% of increased throughput for flows that were not buffered. 3) A fine-grained, flow-based adaptive compression which allows MobiVPN to treat each tunneled flow independently so that compression can be turned on for compressible flows, and turned off for incompressible ones. The experiments showed that the flow-based adaptive compression outperformed OpenVPN's compression options in terms of effective throughput, data reduction, and lesser compression operations. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2017

abstract: Topological methods for data analysis present opportunities for enforcing certain invariances of broad interest in computer vision: including view-point in activity analysis, articulation in shape analysis, and measurement invariance in non-linear dynamical modeling. The increasing success of these methods is attributed to the complementary information that topology provides, as well as availability of tools for computing topological summaries such as persistence diagrams. However, persistence diagrams are multi-sets of points and hence it is not straightforward to fuse them with features used for contemporary machine learning tools like deep-nets. In this paper theoretically well-grounded approaches to develop novel perturbation robust topological representations are presented, with the long-term view of making them amenable to fusion with contemporary learning architectures. The proposed representation lives on a Grassmann manifold and hence can be efficiently used in machine learning pipelines. The proposed representation.The efficacy of the proposed descriptor was explored on three applications: view-invariant activity analysis, 3D shape analysis, and non-linear dynamical modeling. Favorable results in both high-level recognition performance and improved performance in reduction of time-complexity when compared to other baseline methods are obtained. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2017

In this Thesis either advanced oxidation or reductive processes are investigated for the degradation of two pesticides considered persistent in the environment: amicarbazone (AMZ) and chlorpyrifos (CP). In chapter I, different advanced oxidation processes (AOPs) driven by sulfate (SO4o-) and hydroxyl radicals (oOH) were applied to the degradation of AMZ. In the first study, several persulfate (PS) activated reactions were explored for AMZ degradation, namely activation with UVA radiation, Fe(II) and H2O2, as well as the combination of UVA radiation with Fe(II), Fe(III) and Fe(III)-complexes. Here, the influence of different reaction variables, such as solution pH, reactants and pesticide initial concentrations, addition of a second oxidant (H2O2) and the addition of different iron catalysts were also investigated. Control experiments regarding the photolysis of iron species in the absence of PS captured our interest and, with the aim of exploring more deeply this process on AMZ degradation, a second investigation was carried out. In this second study, a Doehlert experimental design was applied to investigate the simultaneous effects of two variables on AMZ degradation: pH and Fe(III):carboxylate ratio, where the carboxylate could be oxalate, citrate or tartrate. A response surface model for the observed degradation rate (kobs) as a function of pH and Fe(III):carboxylate ratio was obtained. The processes explored in both aforementioned studies revealed to be effective for AMZ removal, although nothing is known yet about their effectiveness regarding toxicity removal. Given that, a third study was carried out, where the toxicity of AMZ solutions, before and after submission to the processes studied was evaluated towards five microorganisms: Vibrio fischeri (acute toxicity), Tetrahymena thermophile, Chlorella vulgaris (chronic toxicity), Escherichia coli and Bacilus subtilis (antimicrobial activity). The last investigation detailed in chapter I is related with the application of zero-valent-metals on PS activation, which is a subject that links this chapter with the following one. For that, zero-valent-iron (ZVI) was investigated as a PS activator and the influence of variables that help to assess the environmental applicability of this process. In general, organochlorine pesticides reveal a higher resistance to oxidation than reduction, the latter process preferred when the aim is to degrade that important class of contaminants. Therefore, in chapter II the reductive degradation of CP by means of zero-valent-metals and bimetallic particles was investigated. ZVI has been extensively applied for that purpose. However, besides iron, other zero-valent metals can be potential reactive materials for reductive degradation and hence, in this study, the effectiveness of Zn0 and Cu0 was also explored in comparison to that widely reported for ZVI. Furthermore, two different ways of enhancing metals reactivity were here explored: i) by coating ZVI or Zn0 with a more noble metal (Cu), in order to analyze the copper catalytic effect on the bimetallic system; ii) by different surface pretreatments. / Na presente Tese de Doutorado foram abordados tanto processos oxidativos avançados (POA), como processos redutivos por metais de valência zero, na degradação de dois pesticidas considerados persistentes no meio ambiente: amicarbazona (AMZ) e clorpirifós (CP). No capítulo I são apresentados os estudos realizados com diversos POA, mediados por radicais sulfato (SO4o-) e hidroxila (oOH), aplicados da AMZ. Num primeiro estudo foi explorada a ativação do oxidante persulfato (PS), de diferentes formas, tais como radiação UVA, H2O2 e Fe(II), assim como a combinação de radiação UVA com Fe(II), Fe(III) e complexos de Fe(III). Aqui também foram investigados os efeitos de diversas variáveis reacionais, tais como pH, concentração inicial de reagentes e de pesticida, adição de um segundo oxidante (H2O2) e adição de diferentes espécies de ferro. Os testes realizados, para efeito de controle, referentes à irradiação das espécies de Fe(III) na ausência de PS, despertaram o interesse para um estudo mais aprofundado sobre o efeito da fotólise destas espécies na degradação da AMZ, surgindo assim o segundo trabalho. Neste utilizou-se um projeto experimental de Doehlert, para avaliar o efeito de duas variáveis em simultâneo quanto à degradação da AMZ: pH e proporção Fe(III): ligante, sendo o ligante um dos seguintes carboxilatos: oxalato, citrato ou tartarato. Um modelo de superfície de resposta, que correlaciona a taxa de degradação observada (kobs) em função do pH e proporção Fe(III):ligante foi obtido para cada um dos complexos de Fe(III) estudados. Os processos explorados, tanto no primeiro como no segundo estudo, se mostraram eficazes na remoção da AMZ, porém nada se sabe acerca da remoção da toxicidade. Para tal, foi desenvolvido um terceiro estudo dedicado à avaliação da toxicidade da solução de AMZ, antes e após a aplicação de cada um dos processos anteriormente abordados, contra cinco micro-organismos: Vibrio fischeri (toxicidade aguda); Tetrahymena thermophila, Chlorella vulgaris (toxicidade crônica); Escherichia coli e Bacilus subtilis (atividade antimicrobiana). O último estudo abordado no capitulo I é referente à aplicação de metais de valência zero também nos POA, correlacionado assim o capítulo I e o capítulo II. Como tal, foi feito um estudo de ativação de PS por meio de ferro de valência zero (Fe0), em que se investigou a influência de diversas variáveis por forma a inferir sobre a aplicabilidade prática deste processo. Pesticidas organoclorados apresentam maior resistência à degradação por processos oxidativos do que redutivos, sendo preferível o último na degradação desta importante classe de contaminantes. Como tal, o capítulo II se refere à degradação redutiva, por meio de diferentes metais de valência zero e partículas bimetálicas, do pesticida organoclorado CP. Além do amplamente explorado Fe0, outros metais podem ser aplicados neste processo, pelo que, neste estudo, explorou-se a potencialidade de Zn0 e Cu0 comparativamente ao primeiro. Ainda neste estudo foram investigadas duas formas de aumentar a reatividade dos metais: i) no caso do Fe0 e Zn0, revestindo com um metal mais nobre (Cu), por forma a observar o efeito catalisador do último no sistema bimetálico; ii) realizando um pré-tratamento à superfície dos metais.

An archaeological survey was conducted of the Silver Springs State Park in Ocala, Florida, between August 2014 and December 2015. The project goals were to relocate and assess the previously recorded archaeological sites in the park and attempt to discover new sites. Background research, archaeological fieldwork including surface collection, shovel testing, and informant interview were conducted with this aim. Each site is described and addressed, and most were relocated; twelve new resources were added to the inventory. The Silver Springs and Silver River watershed have been occupied from the Paleo-Indian period at least 13,000 years ago through the twentieth century. Sites from each time period are discussed to detail how use of the landscape developed through time but still remained a persistently occupied place with important, albeit changing roles. Finally, management and research recommendations are provided to assist the state park staff and future archaeologists working in the area.

Persistent organic pollutants such as polychlorinated biphenyls (PCBs), DDT and polybrominated diphenyl ethers (PBDEs) tend to accumulate in biota and are transferred through the aquatic food web, which result in a high accumulation in marine mammals. In recent years various novel flame retardants (nBFRs), which have replaced the banned PBDEs, have also started to occur in the environment. These nBFRs have similar properties as PBDEs, such as long-range transport and accumulation in biota. The purpose with this study was to evaluate a method by using pre-packed silica columns for quantification of PCBs, DDT, PBDEs and nBFRs in seal blubber, in order to facilitate the pre-treatment and decrease the time. To elute the different POPs from the pre-packed silica column; hexane, toluene and dichloromethane were used in different stages. By using this method levels of PCB and DDT were determined. For DDT the concentration was 8.28 ng/g lipid and 8.94 ng/g lipid for the two samples that was analysed, and the analysis of the PCBs showed a higher trend for the higher chlorinated PCBs. As the pre-packed silica columns are a relative new method. Further studies are therefore needed on these columns to further improve the sample clean-up and fractionation of the different POPs in environmental samples.

Abstract Chlamydia pneumoniae is a common human pathogen worldwide, which causes both upper and lower respiratory tract infections. In addition, C. pneumoniae infections have been associated with atherosclerosis and other chronic diseases, and successful treatment and eradication of the organism from tissues would therefore be desirable. The purpose of this study was to assess the effects of C. pneumoniae inoculations on the development of chronic infection and atherosclerotic changes in normocholesterolemic, wild-type mice. We also aimed to elucidate the effects of antibiotic and other treatments on the eradication of chlamydia and on the reduction of the pathologic sequelae induced by these infections. Female C57BL/6J mice were fed either normal chow when assessing the effects of acute infection, or a diet supplemented with 0.2% cholesterol when evaluating the atherosclerotic changes. Primary or repeated inoculations with C. pneumoniae isolate K7 were given to the mice intranasally, and the effects of treatments with telithromycin, levofloxacin and erythromycin antimicrobial agents and with the phenolic compounds quercetin, luteolin and octyl gallate were evaluated. The following methods were used to measure infection and treatment effects and the presence of chlamydia in tissue: chlamydia culture, PCR and RT-PCR methods, histology of lung, heart and aortic tissue, serologic methods and measurements of aortic contractility responses. Repeated C. pneumoniae inoculations induced persistent chlamydial DNA and inflammation in lung tissue and development of mouse Hsp60 autoantibodies. Infection was shown to influence aortic endothelial function, and repeated inoculations significantly increased subendothelial lipid accumulation in the aortic sinus area. A flavonoid, luteolin, was shown to effectively decrease the chlamydial load and inflammatory reactions in lung tissue. All antimicrobial agents eradicated the presence of viable chlamydia effectively; however, PCR positivity persisted in lung tissue despite the treatments. Only immediate treatment after each inoculation was able to decrease aortic sinus lipid accumulation. In conclusion, these data support the role of C. pneumoniae in promoting atherosclerotic development via autoimmune responses and also via direct effects on aortic tissue. Conventional antimicrobial treatments may not effectively eradicate persistent infection, and further studies are warranted to seek for alternative treatment options.

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