International Telemetering Conference Proceedings / October 22-25, 2001 / Riviera Hotel and Convention Center, Las Vegas, Nevada / The Range Instrumentation and Control System (RICS) is a PC-based client/server application designed to collect time-space position information (TSPI) from remote radar test sites and distribute it in real-time across a wide area network (WAN). The system architecture is composed of two main parts - the Data Interface Adapter (or DIA, which runs under VxWorks and is implemented using C/C++) and the RICS console PC (which runs under Windows 2000 and is implemented in Java). CORBA is used to provide communication between the RICS console and DIA. This paper describes the design of the system, focusing primarily on the DIA software.

Approved for public release; distribution is unlimited / Virtual Private Networks (VPNs) are designed to use the Transmission Control Protocol (TCP) or User Datagram Protocol (UDP) to establish secure communication tunnels over public Internet. Multipath TCP (MPTCP) extends TCP to allow data to be delivered over multiple network paths simultaneously. This thesis first builds a testbed and investigates the potential of using MPTCP tunnels to increase the goodput of VPN communications and support seamless mobility. Based on the empirical results and an analysis of the MPTCP design in Linux kernels, we further introduce a full-multipath kernel, implementing a basic Multipath UDP (MPUDP) protocol into an existing Linux MPTCP kernel.We demonstrate the MPUDP protocol provides performance improvements over single path UDP tunnels and in some cases MPTCP tunnels. The MPUDP kernel should be further developed to include more efficient scheduling algorithms and path managers to allow better performance and mobility benefits seen with MPTCP. / Outstanding Thesis / Lieutenant, United States Navy

Master of Science / Department of Computing and Information Sciences / Gurdip Singh / As the network bandwidth and delay increase, TCP becomes inefficient. Data intensive applications over high-speed networks need new transport protocol to support them. This project describes a general purpose high performance data transfer protocol as an application level solution. The protocol Reliable UDP-based data transfer works above UDP with reliability. Reliable Data Transfer protocol provides reliability to applications using the Sliding Window protocol (Selective Repeat). UDP uses a simple transmission model without implicit handshaking techniques for providing reliability and ordering of packets. Thus, UDP provides an unreliable service and datagrams may arrive out of order, appear duplicated, or go missing without notice. Reliable UDP uses both positive acknowledgements and negative acknowledgements to guarantee data reliability. Both simulation and implementation results have shown that Reliable UDP provides reliable data transfer. This report will describe the details of Reliable UDP protocol with simulation and implementation results and analysis.

This thesis examines the current implementations for the distribution of real-time GNSS data over IP networks such as the public Internet, focusing on two essential components of the system, data format and transport protocol. The provision of a suitable data format will allow users to take full advantage of the real-time GNSS data distribution system. Types of GNSS supported, message sizes, data rates, data precision levels, hardware and software support and possible future developments are investigated. An analysis is carried out on commonly known GNSS data formats, highlighting the most suitable standard for each evaluation criterion. A similar investigation is carried out on the transport protocols. An analysis is conducted on various design aspects of NTRIP and RT-IGS protocols, covering factors such as data latency, integrity, firewalls and proxy server compatibility and scalability. The analysis also covers the design aspects of the new draft Version 2 of NTRIP. The latter parts of this thesis report on the experiment results aimed at providing assessment of the current level of implementation of NTRIP. Data latency and integrity using NTRIP over the Internet are examined. Their impacts on users applications as the quality of real-time kinematic positioning is assessed. The results show that the performance of the system satisfies the rigorous requirement of the end-user application. The draft version of the new NTRIP indicates that UDP will be also supported. A similar investigation is carried out, providing the first experiment results on the new option. Tests using similar metrics, data latency and integrity, were carried out to verify the inherent differences between TCP and UDP. It was ascertained that, in most cases, UDP does offer improvement in terms of reduced latency over TCP. However this improvement is not significant enough to affect the performance of users applications tested. Compatibility tests were also carried out and the test results show that the new option experiences some compatibility issues with firewalls and wireless networks.

The UDP-glucuronosyltransferases (UGTs) are a superfamily of enzymes that glucuronidate small, lipophilic molecules, thereby altering their biological activity and excretion. In humans, important examples of UGT substrates include molecules of both endogenous and xenobiotic origin; thus, UGTs are considered essential contributors to homeostatic regulation and an important defence mechanism against chemical insult. In keeping with both roles, UGTs are most strongly expressed in the liver, a predominant organ involved in detoxification. Rates of glucuronidation in humans are neither uniform among individuals, nor constant in an individual over time. Genetic determinants and non-endogenous signals are both known to influence the expression of UGTs, which in turn may affect the efficacy of certain pharmaceutical treatments or alter long-term risk of developing disease. Thus, this thesis focuses on the transcriptional regulation of UGT genes in humans, particularly on mechanisms that are likely to be relevant to their expression and variation in the liver. Two major approaches were used: firstly, extensive studies of several UGT promoters were performed to identify and characterise transcriptional elements that are important for UGT expression; and secondly, important hepatic transcription factors were investigated as potential regulators of UGT genes. UGT1A3, UGT1A4 and UGT1A5 are a subset of highly related, but independently regulated, genes of the human UGT1 subfamily. UGT1A3 and UGT1A4 are expressed in the liver, whereas UGT1A5 is not. The presented analysis of the UGT1A3, UGT1A4 and UGT1A5 proximal promoters demonstrates that a hepatocyte nuclear factor (HNF)1-binding site common to all three promoters is important for UGT1A3 and UGT1A4 promoter activity in vitro, but is insufficient to drive UGT1A5 expression. Two additional elements required for the maximal activity of the UGT1A3 promoter were also identified that may distinguish this gene from UGT1A4. UGT1A3 was investigated further, focusing on mechanisms that may contribute to interindividual variation in UGT1A3 expression. Polymorphisms in the UGT1A3 proximal promoter were identified and their functional consequences tested. Known variants of HNF1alpha were also tested for altered activity towards the UGT1A3 gene. UGT1A9 is the only hepatic member of the UGT1A7-1A10 subgroup of UGT1 enzymes. Previous work had identified HNF1-binding sites in all four genes, and HNF4alpha as an UGT1A9-specific regulator. The work presented herein extends these findings to show that HNF1 factors and HNF4alpha synergistically regulate UGT1A9, and that HNF4alpha is not the only transcription factor responsible for the unique presence of UGT1A9 in the liver. Liver-enriched transcription factors screened as potential UGT regulators were chosen from the HNF1, HNF4, HNF6, FoxA and C/EBP protein families. Functional interactions newly identified by this work were HNF4alpha with UGT1A1 and UGT1A6, HNF6 with UGT1A4 and UGT2B11, FoxA1 and FoxA3 with UGT2B11, UGT2B15 and UGT2B28 and C/EBPalpha with UGT2B17. Observations were also made regarding different patterns of interaction between each UGT and the transcription factors tested, particularly HNF1alpha.

Over the last 35 years many adaptive traffic signal control systems have been developed presenting alternative strategies to improve traffic signal operations. However, less than 1% of all traffic signals in the United States are controlled by adaptive systems today. The extensive infrastructure necessary including reliable communication and complex calibration leads to a time consuming and costly process. In addition, the most recent National Traffic Signal Report Card indicated an overall grade of D for the nation’s traffic signal control and operations. Recent economic adversity adds to the already difficult task of proactively managing aged signal timing plans. Therefore, in an attempt to escape the status quo, a flow based adaptive split signal control model is presented, having the principal objective of updating the split table based solely on real-time traffic conditions and without disrupting coordination. Considering the available typical traffic signal control infrastructure in cities today, a non centralized system is proposed, directed to the improvement of National Electrical Manufacturers Association (NEMA) based systems that are compliant with the National Transportation Communications for Intelligent Transportation System Protocol (NTCIP) standards. The approach encompasses the User Datagram Protocol (UDP) for system communication allowing an external agent to gather flow information directly from a traffic signal controller detector status and use it to better allocation of phase splits. The flow based adaptive split signal control was not able to consistently yield significant lower average vehicle delay than a full actuated signal controller when evaluated on an intersection operating a coordinated timing plan. However, the research proposes the ability of an external agent to seamless control a traffic signal controller using real-time data, suggesting the encouraging results of this research can be improved upon.

UDP-galactopyranose mutase (UGM) is a flavoenzyme which catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDPGalf). UDP-Galf is the active precursor of Galf residues. Glycoconjugates of Galf residues are found in the cell wall of bacteria and on the cell surface of higher eukaryotes. Galf residues have not been found in humans and the fact that they are essential for the growth of pathogenic bacteria makes UGM a potential antibacterial target. In the present study, crystal structures of UGM from Deinocococcus radiodurans (drUGM) in complex with substrate (UDP-Galp) were determined. UDP-Galp is buried in the active site and bound in a U-shaped conformation. The binding mode and active site interactions of UDP-Galp are consistent with the previous biochemical and mechanistic studies. The mobile loops in the substrate complex structures exist in a closed conformation and Arg198 on one of the mobile loops stabilizes the phosphate groups of the substrate. The anomeric carbon of galactose is 2.8 Å from the N5 of FAD (in the reduced complex) favorable to form FAD-galactosyl adduct. In addition to substrate complex structures, the crystal structures of drUGM in complex with UDP, UMP, and UDP-Glc have been determined. The mobile loops in all these complexes exist in a closed conformation. Inhibitors for UGM were identified by ligand-based and structure-based methods. The phosphonate analog of UDP-Galp (GCP) showed only weak inhibition against various bacterial UGMs. The structure of drUGM in complex with GCP provided a basis for its inhibitory activity. Poor stabilization of the phosphate groups by conserved arginines (Arg198 and Arg305) and altered sugar binding mode account for its activity. Novel indole-based (LQ1, LQ6 and LQ10) inhibitors of UGM were identified through structure-based virtual screening (SBVS) of a chemical library. Inhibition studies also allowed the identification of an active site aspartic acid that plays role in inhibitor binding. The structural studies on drUGM provided a basis for understanding substrate binding to UGM. In vitro enzyme inhibition studies allowed the identification of novel indole-based inhibitors. The structural and inhibition studies reported here enhance the understanding of UGM-ligand interactions and will assist in the development of more potent inhibitors of UGM.

UDP-galactopyranose mutase (UGM) is a flavoenzyme which catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDPGalf). UDP-Galf is the active precursor of Galf residues. Glycoconjugates of Galf residues are found in the cell wall of bacteria and on the cell surface of higher eukaryotes. Galf residues have not been found in humans and the fact that they are essential for the growth of pathogenic bacteria makes UGM a potential antibacterial target. In the present study, crystal structures of UGM from Deinocococcus radiodurans (drUGM) in complex with substrate (UDP-Galp) were determined. UDP-Galp is buried in the active site and bound in a U-shaped conformation. The binding mode and active site interactions of UDP-Galp are consistent with the previous biochemical and mechanistic studies. The mobile loops in the substrate complex structures exist in a closed conformation and Arg198 on one of the mobile loops stabilizes the phosphate groups of the substrate. The anomeric carbon of galactose is 2.8 Å from the N5 of FAD (in the reduced complex) favorable to form FAD-galactosyl adduct. In addition to substrate complex structures, the crystal structures of drUGM in complex with UDP, UMP, and UDP-Glc have been determined. The mobile loops in all these complexes exist in a closed conformation. Inhibitors for UGM were identified by ligand-based and structure-based methods. The phosphonate analog of UDP-Galp (GCP) showed only weak inhibition against various bacterial UGMs. The structure of drUGM in complex with GCP provided a basis for its inhibitory activity. Poor stabilization of the phosphate groups by conserved arginines (Arg198 and Arg305) and altered sugar binding mode account for its activity. Novel indole-based (LQ1, LQ6 and LQ10) inhibitors of UGM were identified through structure-based virtual screening (SBVS) of a chemical library. Inhibition studies also allowed the identification of an active site aspartic acid that plays role in inhibitor binding. The structural studies on drUGM provided a basis for understanding substrate binding to UGM. In vitro enzyme inhibition studies allowed the identification of novel indole-based inhibitors. The structural and inhibition studies reported here enhance the understanding of UGM-ligand interactions and will assist in the development of more potent inhibitors of UGM.

Nowadays, the methods of improving the Reliability of network packets are existent. Some start with the software and others with the hardware. For example, like the Dual System, Redundancy or Fault Tolerant Network, etc. However, it costs a lot to construct the required mechanism, and these methods are not reliable for some special network packets, like the UDP packet. Is there a method to raise the reliability of UDP packet just to increase the software equipments or hardware equipments? The network controller that improves the Reliability of UDP Packets in this thesis uses the same two packets, and it transfers the two packets into different network paths to the same destination workstation. This mechanism can avoid the network accidents causing by the network wires breaking or the network switch machine turn-off, and the destination workstation can¡¦t be hurt from the damage of losing the information carried by UDP packets. Moreover, this method can detect the network accidents as the function of the Fault Tolerant Network by using the dual packets, and send signals to alert the network manager ahead of time. In addition, by using the network controller, network manager or constructor mentioned in this thesis, the RNP topology can be easily built, just by connecting the RNP type wires to the network switches or network bridges.

<p>Distribution of information across IP based networks is today part of our everyday life. IP is the backbone of the Internet and most office networks. We use IP to access web pages, listen to radio, and to create computation clusters. All these examples use bandwidth, and bandwidth is a limited resource.</p><p>Many applications distribute the same information to multiple receivers, but in many cases the same information is sent to a single receiver at a time, thus multiple copies of the same information is sent, thus consuming bandwidth.</p><p>What if the information could be broadcasted to all the clients at the same time, similar to a television broadcast. TCP/IP provides some means to do that. For example UDP supports broadcasting; the problem faced when using UDP is that it’s not reliable. There is no guarantee that the information actually reaches the clients.</p><p>This Bachelor thesis in Computer Science aims to investigate the problems and solutions of how to achieve reliable distribution of fixed size data sets using a non reliable multicast communication channel, like UDP, in a LAN environment.</p><p>The thesis defines a protocol (Almost Reliable Multicast Protocol – Arm-P) that provides maximum scalability for delivery of versioned data sets that are designed to work in a LAN-environment. A proof-of-concept application is implemented for testing purposes.</p>