African sleeping sickness is a parasitic infection spread by the protozoan parasite Trypanosoma brucei, and drugs used today are toxic and painful. Galactose metabolism is essential for the survival of T. brucei and without a functional UDP galactose 4’ epimerase (GalE) galactose starvation occurs and cell death will follow. In this Master thesis project two assays observing binding of small molecules to TbGalE has been investigated in attempt to establish an assay that in the future could be used for screening for drugs. TbGalE was biotinylated through the Pinpoint Xa vector and expressed in E. coli cells. The protein was successfully immobilized to a Streptavidin chip for Surface Plasmon Resonance experiments and the binding of the substrates UDP-galactose and UDP-glucose was observed. Unfortunately, the assay was not optimal for screening due to low signal response. However, the established protocol for expressing biotinylated proteins that bind to Streptavidin surfaces could be used in further experiments with TbGalE and other drug targets for African sleeping sickness. The fluorescent sugar nucleotide analogue UDPAmNS, which is a known inhibitor for E. coli GalE, was synthesised and purified and then used to establish a displacement assay. IC50 of UDPAmNS against TbGalE was determined and a synergic effect in fluorescence between the protein and the inhibitor was proven. Further, evidence for a reduction in fluorescence by displacing UDPAmNS with UDP was obtained. This reduction in fluorescence was also shown by a predicted cofactor inhibitor. The IC50 against TbGalE for this compound was determined before the displacement assay, which showed that the cofactor inhibitor, at least partly, binds to the active site of TbGalE. The UDPAmNS displacement assay could have the potential of becoming a robust screening assay for TbGalE, in the effort to find a better drug for African sleeping sickness.

With the Internet expansion, real-time transmission over Internet is becoming a new promising application. Successful real-time communication over IP networks requires reasonably reliable, low delay, low loss date transport. Since Internet is a non-synchronous packet switching network, high load and lack of guarantees on data delivery make real-time communication such as Voice and Video over IP a challenging application to become realistic on the Internet. This thesis work is composed of two parts within real-time voice and video communication: network simulation and measurement on the real Internet. In the network simulation, I investigate the requirement for the network"overprovisioning"in order to reach certain quality-of-service. In the experiments on the real Internet, I simulate real-time transmission with UDP packets along two different traffic routes and analyze the quality-of- service I get in each case. The overall contribution of this work is: To create scenarios to understand the concept of overprovisioning and how it affects the quality-of-service. To develop a mechanism to measure the quality-of-service for real-time traffic provided by the current best-effort network.

Controlling systems with multiple robots is quickly becoming the next large hurdle that must be overcome for groups of robots to successfully function as a team. An agent oriented approach for this problem is presented in this thesis. By using an agent oriented method, the robots can act independently yet still work together. To be able to establish communities of robots, a basic agent oriented control system for each robot must first be implemented. This thesis introduces a novel method to create Physical Robot Agents, promoting a separation of cognitive and reactive behaviours into a two layer system. These layers are further abstracted into key subsections that are required for the Physical Robot Agents to function. To test this architecture, experiments are performed with physical robots to determine the feasibility of this approach. <br /><br /> A real-time implementation of a Physical Robot Agent would greatly expand its field of use. The speed of internal communication is analyzed to validate the application of this architecture to real-time tasks. <br /><br /> It is concluded that the Physical Robot Agents are well suited for multiple robot systems and that real-time applications are feasible.

Multimedia applications over the Internet are getting more and more popular. While non-real-time streaming services, such as YouTube and Megavideo, are attracting millions of visiting per day, real-time conferencing applications, of which some instances are Skype and Yahoo Voice Chat, provide an interesting experience of communication. Together, they make the fancy Internet world become more and more amusing. Undoubtedly, multimedia flows will eventually dominate the computer network in the future. As the population of multimedia flows increases gradually on the Internet, quality of their service (QoS) is more of a concern. At the moment, the Internet does not have any guarantee on the quality of multimedia services. To completely surpass this limitation, modifications to the network structure is a must. However, it will take years and billions of dollars in investment to achieve this goal. Meanwhile, it is essential to find alternative ways to improve the quality of multimedia services over the Internet. In the past few years, many endeavors have been carried on to solve the problem. One interesting approach focuses on the development of end-to-end congestion control strategies for UDP multimedia flows. Traditionally, packet losses and delays have been commonly used to develop many known control schemes. Each of them only characterizes some different aspects of network congestion; hence, they are not ideal as feedback signals alone. In this research, the flow accumulation is the signal used in feedback for flow control. It has the advantage of reflecting both packet losses and delays; therefore, it is a better choice. Using network simulations, the accumulations of real-time audio applications are collected to construct adaptive flow controllers. The reason for choosing these applications is that they introduce more control challenges than non-real-time services. One promising flow control strategy was proposed by Bhattacharya and it was based on Model Predictive Control (MPC). The controller was constructed from an ARX predictor. It was demonstrated that this control scheme delivers a good QoS while reducing bandwidth use in the controlled flows by 31 percent to 44 percent. However, the controller sometime shows erratic response and bandwidth usage jumps frequently between lowest and highest values. This is not desirable. For an ideal controller, the controlled bandwidth should vary near its mean. To eliminate the deficiency in the strategy proposed by Bhattacharya, it is proposed to introduce a feed forward term into the MPC formulation, in addition to the feedback terms. Simulations show that the modified MPC strategy maintains the benefits of the Bhattacharya strategy. Furthermore, it increases the probability of bandwidth savings from 58 percent for the case of Bhattacharya model to about 99 percent for this work.

ITC/USA 2014 Conference Proceedings / The Fiftieth Annual International Telemetering Conference and Technical Exhibition / October 20-23, 2014 / Town and Country Resort & Convention Center, San Diego, CA / Yuma Proving Ground (YPG) personnel developed the Video Bus Integrated Telemetry System (VBITS) for air delivery testing at YPG. The system consists of a common rack for mounting both video and telemetry equipment, which makes installation easier and more time efficient. Prior to the one-rack concept, the video, TSPI, and telemetry were all installed as separate entities competing for space, power, and time. Requirements to downlink High-Definition (HD) video from the aircraft prompted research into technological improvements in transmitters, onboard encoders, and recorders. These advances allowed the integration of video, analog sensors, and aircraft bus data into a single telemetry stream. Future advancements will include combining multiple HD video sources in a single downlink.

This paper presents an open system architecture with wireless network centric telemetry and data acquisition over UDP/IP. This networked solution was designed and developed for iron bird and helicopter rotor applications which present a significant challenge for data acquisition and telemetry. Traditionally slip rings were used for data transfer however these result in issues with low bandwidth, electrical noise, installation complexity, and high maintenance costs. This paper describes a networked system using standardized technologies and protocols that was used for data acquisition and recording of parameters such as vibration, strain, and video on DAQ installed on the rotating part. The acquired data was transmitted in real-time via the network-centric wireless telemetry link which was synchronized with a ground-based DAQ used for real time processing of the rotor data.

Communication by wireless technologies has seen a tremendous growth in the last decades. Mobile phone technology and wireless broadband solutions are rapidly replacing the last-hop wireline connectivity for telephones and Internet access.  Research has, however, shown that Internet traffic can experience a performance degradation over wireless compared to wired networks.  The inherent properties of radio communication lead to a higher degree of unreliability, compared to communication by wire or fiber.  This can result in an increased amount of transmission errors, packet loss, delay and delay variations, which in turn affect the performance of the main Internet transport protocols TCP and UDP.  This dissertation examines the cross-layer relationship between wireless transmission and the resulting performance on the transport layer. To this end, experimental evaluations of TCP and UDP over a wireless 4G downlink system proposal are performed.  The experiment results show, in a holistic scenario, that link-level adaptive modulation, channel prediction, fast persistent link retransmissions, and channel scheduling, enables the transport protocols TCP and UDP to perform well and utilize the wireless link efficiently.  Further, a novel approach is proposed where a modified TCP receiver can choose to accept packets that are corrupted by bit errors. Results from network emulation experiments indicate that by accepting and acknowledging even small amounts of corrupted data, a much higher throughput can be maintained compared to standard TCP.

In this thesis we present a suitable way of calibrating and debugging an autonomous underwater vehicle (AUV). The issues that occur when working with an AUV are the inconvenient way of having to constantly recompile the software to change the behavior of the AUV and the lack of feedbacksreceived. If the vehicle does not behave as it should the information needed to be able to trace and fix the problems that occur isin general difficult to retrieve. To tackle this problem a literature study was made on logging libraries, communication protocols as well as AUVs in general. This resulted in identifying a set of existing logging libraries and possible communication protocols. From testing and analyzing these results, Zlog was chosen as the logging library and UDP as the communication protocol. Zlog has then been used in the AUV application to log relevant information on the AUV and UDP allows establishing a connection between the AUV and a desktop program created for Windows to send this logging information to. The desktop program also allows filtering of any incoming logs with the use of a parser. This has been an essential part of the solution to be able to identify specific logging data and help presenting this in a convenient way. To be able to change the format of the log file, the parser has been given a grammar which can be adjusted to adapt to a different log file. Additionally, the desktop application has the ability to send commands to the AUVapplication via the UDP connection to change the behavior of the AUV live.

Jaburetox (Jbtx) é um peptídeo de 10 kDa derivado de uma das isoformas de urease de Canavalia ensiformis. Em um estudo anterior realizado com o triatomíneo vetor da doença de Chagas Triatoma infestans, esse peptídeo foi encontrado interagindo com a proteína UDP-N-acetilglicosamina pirofosforilase (UAP), alterando também sua atividade enzimática no sistema nervoso central, in vivo e in vitro. A UAP já foi encontrada em eucariotos, bactérias e vírus, estando relacionada com as rotas de produção de quitina, N-glicosilação e síntese de glicoinositolfosfolipídeos. Assim, o presente trabalho tem três objetivos: i) investigar o efeito de Jbtx sobre a atividade enzimática e a expressão gênica da UAP do inseto modelo Rhodnius prolixus, ii) clonar e expressar a UAP e iii) estudar a UAP filogeneticamente. Para a primeira parte, foram avaliados, no triatomíneo R. prolixus, a atividade enzimática da UAP e o perfil de expressão dessa enzima e da quitina sintase em insetos controles e alimentados com Jbtx. Para a segunda, o cDNA da enzima de R. prolixus foi clonado em vetor pET-15b e expressado em Escherichia coli Rosetta 2. A purificação da enzima recombinante foi feita por cromatografia de afinidade a níquel. Para a terceira parte, foram buscadas sequências de aminoácidos homólogas às da UAP de R. prolixus no servidor pHmmer e foi construída uma árvore filogenética com o método de Máxima Verossimilhança. Os resultados obtidos indicam que o Jbtx aumenta a atividade enzimática da UAP em glândulas salivares, corpo gorduroso e epiderme, enquanto diminui a expressão da UAP em intestino médio anterior, túbulos de Malpighi, glândulas salivares, corpo gorduroso, epiderme e sistema nervoso central, assim como a expressão da quitina sintase nos mesmos órgãos e no intestino médio posterior. Foi obtida uma UAP recombinante de 56 kDa, compatível com peso molecular previsto in silico. A árvore filogenética construída contém 40 sequências, sendo 38 de insetos e 2 sequências de grupo externo. A árvore segue o padrão de evolução dos insetos e foi identificado um novo organismo com potenciais dois genes codificantes de UAP. Esse trabalho apresenta a primeira evidência de que Jbtx altera a expressão gênica em R. prolixus. O resultado obtido pela análise filogenética indica que a UAP é uma enzima ancestral à diversificação em Insecta. / Jaburetox (Jbtx) is a 10 kDa peptide derived from a urease isoform of Canavalia ensiformis. In a previous work with the triatomine vector of Chagas’ disease Triatoma infestans, this peptide was found interacting with the protein UDP-N-acetylglucosamine pyrophosphorylase (UAP), also increasing the UAP enzymatic activity in the central nervous system in vivo and in vitro. UAP has been described in eukaryotes, bacteria and virus, and is involved in chitin production, N-linked glycosylation and glyco inositol phospholipids synthesis pathway. Thus, the present work has three main aims: i) to understand the effect of Jbtx on this enzyme on the model insect Rhodnius prolixus, ii) to clone and express UAP and iii) to study UAP from a phylogenetic point of view. Firstly, UAP enzymatic activity and its expression profile, as well as the chitin synthase expression, were analysed in the triatomine R. prolixus in saline- or Jbtx-fed insects. Secondly, the cDNA from R. prolixus’ UAP was cloned into the pET-15b vector and expressed in Escherichia coli Rosetta 2. The recombinant enzyme was purified through a nickel affinity chromatography. Thirdly, homolog sequences to R. prolixus’ UAP were searched in pHmmer database and a phylogenetic tree was built using the Maximmum Likelihood method. The results obtained indicate that Jbtx increases UAP enzymatic activity in salivary glands, fat body and epidermis, while decreasing UAP’s expression in the anterior and posterior midgut, Malpighian tubules, salivary glands, fat body, epidermis and central nervous system, as well as the chitin synthase expression in the same organs and the posterior midgut. A 56 kDa recombinant UAP was obtained, in agreement with the in silico estimated size. The phylogenetic tree built has 40 sequences, from which 38 are from insects and 2 are from mammals (external group). The tree follows the insect evolution patterns and a new organism containing two potential UAP coding genes was identified. This work presents the first evidence that Jbtx is able to interfere in the gene expression in R. prolixus. The results obtained through phylogenetic analysis shows that UAP is an enzyme ancestral to the diversification in Insecta.

Jaburetox (Jbtx) é um peptídeo de 10 kDa derivado de uma das isoformas de urease de Canavalia ensiformis. Em um estudo anterior realizado com o triatomíneo vetor da doença de Chagas Triatoma infestans, esse peptídeo foi encontrado interagindo com a proteína UDP-N-acetilglicosamina pirofosforilase (UAP), alterando também sua atividade enzimática no sistema nervoso central, in vivo e in vitro. A UAP já foi encontrada em eucariotos, bactérias e vírus, estando relacionada com as rotas de produção de quitina, N-glicosilação e síntese de glicoinositolfosfolipídeos. Assim, o presente trabalho tem três objetivos: i) investigar o efeito de Jbtx sobre a atividade enzimática e a expressão gênica da UAP do inseto modelo Rhodnius prolixus, ii) clonar e expressar a UAP e iii) estudar a UAP filogeneticamente. Para a primeira parte, foram avaliados, no triatomíneo R. prolixus, a atividade enzimática da UAP e o perfil de expressão dessa enzima e da quitina sintase em insetos controles e alimentados com Jbtx. Para a segunda, o cDNA da enzima de R. prolixus foi clonado em vetor pET-15b e expressado em Escherichia coli Rosetta 2. A purificação da enzima recombinante foi feita por cromatografia de afinidade a níquel. Para a terceira parte, foram buscadas sequências de aminoácidos homólogas às da UAP de R. prolixus no servidor pHmmer e foi construída uma árvore filogenética com o método de Máxima Verossimilhança. Os resultados obtidos indicam que o Jbtx aumenta a atividade enzimática da UAP em glândulas salivares, corpo gorduroso e epiderme, enquanto diminui a expressão da UAP em intestino médio anterior, túbulos de Malpighi, glândulas salivares, corpo gorduroso, epiderme e sistema nervoso central, assim como a expressão da quitina sintase nos mesmos órgãos e no intestino médio posterior. Foi obtida uma UAP recombinante de 56 kDa, compatível com peso molecular previsto in silico. A árvore filogenética construída contém 40 sequências, sendo 38 de insetos e 2 sequências de grupo externo. A árvore segue o padrão de evolução dos insetos e foi identificado um novo organismo com potenciais dois genes codificantes de UAP. Esse trabalho apresenta a primeira evidência de que Jbtx altera a expressão gênica em R. prolixus. O resultado obtido pela análise filogenética indica que a UAP é uma enzima ancestral à diversificação em Insecta. / Jaburetox (Jbtx) is a 10 kDa peptide derived from a urease isoform of Canavalia ensiformis. In a previous work with the triatomine vector of Chagas’ disease Triatoma infestans, this peptide was found interacting with the protein UDP-N-acetylglucosamine pyrophosphorylase (UAP), also increasing the UAP enzymatic activity in the central nervous system in vivo and in vitro. UAP has been described in eukaryotes, bacteria and virus, and is involved in chitin production, N-linked glycosylation and glyco inositol phospholipids synthesis pathway. Thus, the present work has three main aims: i) to understand the effect of Jbtx on this enzyme on the model insect Rhodnius prolixus, ii) to clone and express UAP and iii) to study UAP from a phylogenetic point of view. Firstly, UAP enzymatic activity and its expression profile, as well as the chitin synthase expression, were analysed in the triatomine R. prolixus in saline- or Jbtx-fed insects. Secondly, the cDNA from R. prolixus’ UAP was cloned into the pET-15b vector and expressed in Escherichia coli Rosetta 2. The recombinant enzyme was purified through a nickel affinity chromatography. Thirdly, homolog sequences to R. prolixus’ UAP were searched in pHmmer database and a phylogenetic tree was built using the Maximmum Likelihood method. The results obtained indicate that Jbtx increases UAP enzymatic activity in salivary glands, fat body and epidermis, while decreasing UAP’s expression in the anterior and posterior midgut, Malpighian tubules, salivary glands, fat body, epidermis and central nervous system, as well as the chitin synthase expression in the same organs and the posterior midgut. A 56 kDa recombinant UAP was obtained, in agreement with the in silico estimated size. The phylogenetic tree built has 40 sequences, from which 38 are from insects and 2 are from mammals (external group). The tree follows the insect evolution patterns and a new organism containing two potential UAP coding genes was identified. This work presents the first evidence that Jbtx is able to interfere in the gene expression in R. prolixus. The results obtained through phylogenetic analysis shows that UAP is an enzyme ancestral to the diversification in Insecta.