Many pathogenic microorganisms are believed to stochastically switch into low metabolic states that display resistance to supra-lethal levels of antibiotics. These so-called “persister” cells have been associated with recurrent infections and the development of antibiotic resistance. Whilst a compound that eliminates Staphylococcus aureus persister cells has been described, it is not active against Gram-negative bacteria. The aim of my PhD project was to develop a high-throughput assay for compounds that eradicate persister cells in the -proteobacterium Burkholderia thailandensis. Further to this, I aimed to develop “hit” compounds from screening into lead series through investigation of structure activity relationships and, use a chemical genetics approach to elucidate potential mechanisms of action. I developed a phenotypic assay to identify compounds that eradicate persister cells. The assay was based on the reduction of the resazurin based dye PrestoBlue. Optimization of the assay gave a Z’ prime of 0.41 when screened in high throughput at the DDU. Screening of the library of 61,250 compounds identified 2,127 compounds that gave a statistically significant reduction in persister cell numbers. Follow-up assays highlighted 29 compounds with a pIC50 greater than five. Detailed investigation allowed me to down select to six “best in class” compounds, which included the licensed drug chloroxine. A time dependent killing assay showed that chloroxine reduced levels of persister cells by three orders of magnitude over 72 hours (P = 0.01). Hit expansion around chloroxine using commercially available compounds did not identify any more potent compounds, but did highlight key features of the molecule for activity. Assay protocols were provided to collaborators at DSTL who were able to iv show that chloroxine is also active against persister cells formed by the tropical pathogen and Tier 1 biological agent Burkholderia pseudomallei. Investigations into the mechanism of action of chloroxine used Next Generation Sequencing of an over expression library, identifying two putative genes involved in inhibition of persister cells by chloroxine. My findings demonstrate a phenotypic assay against persister cells in Gram-negative bacteria, which has the power to identify potent anti-persister agents to assist in chemotherapy. Structural activity relationship and mechanism of action investigations have indicated lead series and genetic starting points for future development of this research. My PhD project has concluded with sufficient data for continuation of research following a number of leads and is at an ideal stage for instigation of a medicinal chemistry program for development of chloroxine as a clinical option for treatment of persistent melioidosis.

Made available in DSpace on 2014-06-12T15:57:37Z (GMT). No. of bitstreams: 2 arquivo3214_1.pdf: 3789743 bytes, checksum: 5121a8308f93d20405e932f1e9bab193 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2010 / Universidade Federal do Amazonas / Um breve exame do atual tráfego Internet mostra uma mistura de serviços conhecidos e desconhecidos, novas e antigas aplicações, tráfego legítimo e ilegítimo, dados solicitados e não solicitados, tráfego altamente relevante ou simplesmente indesejado. Entre esses, o tráfego Internet não desejado tem se tornado cada vez mais prejudicial para o desempenho e a disponibilidade de serviços, tornando escasso os recursos das redes. Tipicamente, este tipo de tráfego é representado por spam, phishing, ataques de negação de serviço (DoS e DDoS), vírus e worms, má configuração de recursos e serviços, entre outras fontes. Apesar dos diferentes esforços, isolados e/ou coordenados, o tráfego Internet não desejado continua a crescer. Primeiramente, porque representa uma vasta gama de aplicações de usuários, dados e informações com diferentes objetivos. Segundo, devido a ineficácia das atuais soluções em identificar e reduzir este tipo de tráfego. Por último, uma definição clara do que é não desejado tráfego precisa ser feita. A fim de solucionar estes problemas e motivado pelo nível atingido pelo tráfego não desejado, esta tese apresenta: 1. Um estudo sobre o universo do tráfego Internet não desejado, apresentado definições, discussões sobre contexto e classificação e uma série de existentes e potencias soluções. 2. Uma metodologia para identificar tráfego não desejado baseada em orquestração. OADS (Orchestration Anomaly Detection System) é uma plataforma única para a identificação de tráfego não desejado que permite um gerenciamento cooperativa e integrado de métodos, ferramentas e soluções voltadas a identificação de tráfego não desejado. 3. O projeto e implementação de soluções modulares integráveis a metodologia proposta. A primeira delas é um sistema de suporte a recuperação de informações na Web (WIRSS), chamado OADS Miner ou simplesmente ARAPONGA, cuja função é reunir informações de segurança sobre vulnerabilidades, ataques, intrusões e anomalias de tráfego disponíveis na Web, indexá-las eficientemente e fornecer uma máquina de busca focada neste tipo de informação. A segunda, chamada Alert Pre- Processor, é um esquema que utilize uma técnica de cluster para receber múltiplas fontes de alertas, agregá-los e extrair aqueles mais relevantes, permitindo correlações e possivelmente a percepção das estratégias usadas em ataques. A terceira e última é um mecanismo de correlação e fusão de alertas, FER Analyzer, que utilize a técnica de descoberta de episódios frequentes (FED) para encontrar sequências de alertas usadas para confirmar ataques e possivelmente predizer futuros eventos. De modo a avaliar a proposta e suas implementações, uma série de experimentos foram conduzidos com o objetivo de comprovar a eficácia e precisão das soluções

This Master's Thesis describes the design and development of an architecture for automated network node discovery and topology analysis, implemented as an extension to the network management and provisioning system NETadmin. The architecture includes functionality for flexible network model assessment, using a method for versatile comparison between off-line database models and real-world models. These models are populated by current node data collected by network sensors. The presented architecture supports (1) efficient creation and synchronization of network topology information (2) accurate recognition of new, replaced and upgraded nodes, including rogue nodes that may exhibit malicious behavior, and (3) provides an extension of an existing vendor-neutral enterprise network management and provisioning system. An evaluation of the implementation shows evidence of accurate discovery and classification of unmatched hosts in a live customer production network with over 400 nodes, and presents data on performance and scalability levels. The work was carried out at Netadmin System i Sverige AB, in Linköping, Sweden.

I denna uppsats undersöks creature design samt narrativ teori kring skräckfilmer för att ta reda på hur man kan skapa filmmonster vars utseende kan berätta och föra fram en fängslande historia. Ett väldesignat monster lever kvar i publikens minnen, och skapar ikoner för sin tidsperiod eller sin genre. Uppsatsen använder sig av en semiotisk metod för att analysera monstren i filmerna Alien, The Thing och Rovdjuret. För att designa monster till science fiction kan man kombinera zoologi, anatomiska studier samt mänsklig psykologi och fobier för att skapa ett visuellt fascinerande monster som skrämmer publiken och lever kvar i det allmänna medvetandet.

M.Ed. (Tertiary Didactics) / Please refer to full text to view abstract

Rapid development of antimicrobial resistance (AMR) among bacteria, combined with diminished new antibiotic discovery rates, is an increasing threat to human health. Bacterially derived antimicrobial peptides (AMP) hold excellent potential as potent novel therapeutics. This study embraces traditional natural AMP discovery methods and the newer in silico genome mining tool BAGEL 3 to facilitate identification of novel antimicrobial agents. The traditional screening efforts led to the discovery of two promising antimicrobial producer strains; Bacillus pumilus J1 producing two AMPs, peptides NI03 and NI04, and Klebsiella pneumoniae A7, which produced peptide NI05. In silico mining of the B. pumilus J1 and K. pneumoniae A7 genomes and those from under exploited anaerobic bacteria using BAGEL 3 yielded 18 putative bacteriocin structures that were associated with multiple known and relevant bacteriocin accessory genes and/or carried significant homologies to known bacteriocins. Peptide NI04 proved to be active against Gram positive species only, including meticillin resistant Staphylococcus aureus and vancomycin resistant enterococci and peptide NI03, in addition to these pathogens, showed activity against E. coli. Peptide NI05 was active against Gram-negative pathogens including extended spectrum β-lactamase producing E. coli. All isolated peptides were observed to be proteinaceous in nature and highly heat stable. Peptides were purified or partially purified using solid phase extraction followed by RP-HPLC. The mass of the peptides was determined using ESI or MALDI-TOF mass spectrometry. Tandem MS fragmentation of peptide NI04 generated several sequence tags. Draft genome sequences of the B. pumilus J1 and K. pneumoniae A7 producer strains were obtained using the Illumina MiSeq platform. This allowed identification of the genes encoding peptide NI04, which was confirmed to be novel and was named pumicin NI04. Further characterisation of pumicin NI04 demonstrated it was non-toxic to keratinocytes, Vero cells and non-haemolytic up to at least 18x the minimum inhibitory concentration. The discovery revealed that pumicin NI04 belongs to the WXG-100 peptide superfamily, having homology with the mycobacterial and staphylococcal virulence factor EsxA. This represents the first report of antimicrobial activity in a WXG-100 peptide and has intriguing evolutionary implications. Although it was not possible to fully characterise peptides NI03 and NI05, when BAGEL 3 was used to mine the B. pumilus J1 genome, a promising putative bacteriocin candidate was identified that was homologous to Enterocin AS-45, which also confers anti Gram-negative activity and may be related to the activity observed for NI03, however more evidence is required. Investigations of the K. pneumoniae A7 bacteriocin on the other hand helped establish that the K. pneumoniae microcin E492 pathway was present and highly conserved in strain A7, and is likely to be responsible for the activity observed indicating that NI05 was not a novel peptide.

Foreign exchange market is the most active market in today’s global financial domains. While the consensus on several aspects of this market is fairly established, the informational efficiency in this market is still unsettled, particularly during unexpected interruptions and unusual or unstable periods. The financial crisis of 2008 is the most recent example of such a period. This dissertation focuses on the efficiency of the foreign exchange market during a unique, turbulent period using the six most actively traded currencies: the Australian dollar, Canadian dollar, Swiss franc, Euro, British pound, and Japanese yen. Considering nine months before the peak of the financial crisis to nine months thereafter, the entire sample is divided into three sub-samples: full-, non-crisis-, and crisis-periods. Both daily and minute-by-minute data are used. A variety of instruments are analyzed, including spot, forward, and exchange traded funds on the currencies. The methodologies that are employed range from standard econometric tests of efficiency to estimation of vector error correction models to identify price discovery, or leadership positions, in each of the currency markets. The findings indicate behavioral similarities and differences. The patterns of the volatility of the currencies are mixed: two-humped for the AUD, CAD, and EUR; W-shaped for the CHF; three-humped for the GBP, and flat U-shaped for the JPY. The daily results from several methodologies provide mixed evidence on market efficiency. Over the entire sample period, the estimated forward premium coefficients from the GARCH (1, 1) model are not significant for all currencies, while the null hypotheses of zero and one cointegrating vectors cannot be rejected for all currencies, except for the AUD. These findings are consistent with some of the previous studies, concluding that the efficiency tests in the foreign exchange market would depend on the methodology and the time period of the study. The high frequency data results show different degrees of price discovery between pair-wise instruments. Specifically, the spot exchange market shows a greater contribution to price discovery than the corresponding exchange traded funds. A possible explanation is the current size of the market and its increased transparency through the use of electronic trading.

The past few years have witnessed a significant evolution in mobile computing and communications, in which new trends and applications have the traditional role of computer networks into that of distributed service providers. In this thesis we explore an alternative way to form wireless ad-hoc networks whose topologies can be customized as required by the users’ software applications. In particular, we investigate the applicability of mobile codes to networks created by devices equipped with Bluetooth technology. Computer simulations results suggest that our proposed approach can achieve this task effectively, while matching the level of efficiency seen in other salient proposals in this area. This thesis also addresses the issue of service discovery in mobile ad-hoc networks. We propose the use of a directory whose network location varies in an attempt to reduce traffic overhead driven by users’ hosts looking for service information. We refer to this scheme as the Service Directory Placement Algorithm, or SDPA. We formulate the directory relocation problem as a Markov Decision Process that is solved by using Q-learning. Performance evaluations through computer simulations reveal bandwidth overhead reductions that range between 40% and 48% when compared with a basic broadcast flooding approach for networks comprising hosts moving at pedestrian speeds. We then extend our proposed approach and introduce a multi-directory service discovery system called the Service Directory Placement Protocol, or SDPP. Our findings reveal bandwidth overhead reductions typically ranging from 15% to 75% in networks comprising slow-moving hosts with restricted memory availability. In the fourth and final part of this work, we present the design foundations and architecture of a middleware system that called WISEMAN – WIreless Sensors Employing Mobile Agents. We employ WISEMAN for dispatching and processing mobile programs in Wireless Sensor Networks (WSNs). Our proposed system enables the dynamic creation of semantic relationships between network nodes that cooperate to provide an aggregate service. We present discussions on the advantages of our proposed approach, and in particular, how WISEMAN facilitates the realization of service-oriented tasks in WSNs. / Applied Science, Faculty of / Electrical and Computer Engineering, Department of / Graduate

The success of the internet over last few decades has mainly depended on various infrastructure technologies to run distributed applications. Due to diversification and multi-provider nature of the internet, radical architectural improvements which require mutual agreement between infrastructure providers have become highly impractical. This escalating resistance towards the further growth has created a rising demand for new approaches to address this challenge. Network virtualization is regarded as a prominent solution to surmount these limitations. It decouples the conventional Internet service provider’s role into infrastructure provider (InP) and service provider (SP) and introduce a third player known as virtual network Provider (VNP) which creates virtual networks (VNs). Resource discovery aims to assist the VNP in selecting the best InP that has the best matching resources for a particular VN request. In the current literature, resource discovery focuses mainly on static attributes of network resources highlighting the fact that utilization on dynamic attributes imposes significant overhead on the network itself. In this thesis we propose a resource discovery approach that is capable of utilizing the dynamic resource attributes to enhance the resource discovery and increase the overall efficiency of VN creation. We realize that recourse discovery techniques should be fast and cost efficient, enough to not to impose any significant load. Hence our proposed scheme calculates aggregation values of the dynamic attributes of the substrate resources. By comparing aggregation values to VN requirements, a set of potential InPs is selected. The potential InPs satisfy basic VN embedding requirements. Moreover, we propose further enhancements to the dynamic attribute monitoring process using a vector based aggregation approach.

Intelligent Transport System (ITS) has become a hot research topic over the past decades. ITS is a system that applies the following technologies to the whole transportation management system efficiently, including information technique, wireless communication, sensor networks, control technique, and computer engineering. ITS provides an accurate, real time and synthetically efficient transportation management system. Obviously, Vehicular Ad Hoc NETworks (VANETs) attract growing attention from both the research community and industry all over the world. This is because a large amount of applications are enabled by VANETs, such as safety related applications, traffic management, commercial applications and general applications. When connecting to the internet or communicating with different networks in order to access a variety of services using VANETs, drivers and passengers in different cars need to be able to exchange messages with gateways from their vehicles. A secure gateway discovery process is therefore critical, because vehicles should not be subject to security attacks while they are communicating; however, currently there is no existing protocol focusing on secure gateway discovery. In this thesis, we first analyze and compare current existing secure service discovery protocols and then we propose a Secure Gateway Localization and Communication System for Vehicular Ad Hoc Networks (SEGAL), which concentrates on the security issue in gateway discovery. We focus on the authentication aspect by proposing secure cluster based VANETs, that can ensure the gateway discovery messages exchanged through secure clusters. We present the principle and specific process of our SEGAL protocol and analyze its performance to guarantee its outstanding practical applicability.