Evaluating and improving the performance of video content distribution in lossy networks

The contributions in this research are split in to three distinct, but related, areas. The focus of the work is based on improving the efficiency of video content distribution in the networks that are liable to packet loss, such as the Internet. Initially, the benefits and limitations of content distribution using Forward Error Correction (FEC) in conjunction with the Transmission Control Protocol (TCP) is presented. Since added FEC can be used to reduce the number of retransmissions, the requirement for TCP to deal with any losses is greatly reduced. When real-time applications are needed, delay must be kept to a minimum, and retransmissions not desirable. A balance, therefore, between additional bandwidth and delays due to retransmissions must be struck. This is followed by the proposal of a hybrid transport, specifically for H.264 encoded video, as a compromise between the delay-prone TCP and the loss-prone UDP. It is argued that the playback quality at the receiver often need not be 100% perfect, providing a certain level is assured. Reliable TCP is used to transmit and guarantee delivery of the most important packets. The delay associated with the proposal is measured, and the potential for use as an alternative to the conventional methods of transporting video by either TCP or UDP alone is demonstrated. Finally, a new objective measurement is investigated for assessing the playback quality of video transported using TCP. A new metric is defined to characterise the quality of playback in terms of its continuity. Using packet traces generated from real TCP connections in a lossy environment, simulating the playback of a video is possible, whilst monitoring buffer behaviour to calculate pause intensity values. Subjective tests are conducted to verify the effectiveness of the metric introduced and show that the results of objective and subjective scores made are closely correlated.

Dapsone induces oxidative stress and impairs antioxidant defenses in rat liver

Dapsone (DDS) is currently used in the treatment of leprosy, malaria and in infections with Pneumocystis jirovecii and Toxoplasma gondii in AIDS patients. Adverse effects of DDS involve methemoglobinemia and hemolysis and, to a lower extent, liver damage, though the mechanism is poorly characterized. We evaluated the effect of DDS administration to male and female rats (30 mg/kg body wt, twice a day, for 4 days) on liver oxidative stress through assessment of biliary output and liver content of reduced (GSH) and oxidized (GSSG) glutathione, lipid peroxidation, and expression/activities of the main antioxidant enzymes glutathione peroxidase, superoxide dismutase, catalase and glutathione S-transferase. The influence of DDS treatment on express ion/activity of the main DDS phase-II- metabolizing system, UDP-glucuronosyltransferase (UGT), was additionally evaluated. The involvement of dapsone hydroxylamine (DDS-NHOH) generation in these processes was estimated by comparing the data in male and female rats since N-hydroxylation of DDS mainly occurs in males. Our studies revealed an increase in the GSSG/GSH biliary output ratio, a sensitive indicator of oxidative stress, and in lipid peroxiclation, in male but not in female rats treated with DDS. The activity of all antioxidant enzymes was significantly impaired by DDS treatment also in male rats, whereas UGT activity was not affected in any sex. Taken together, the evidence indicates that DDS induces oxidative stress in rat liver and that N-hydroxylation of DDS was the likely mediator. Impairment in the activity of enzymatic antioxidant systems, also associated with DDS-NHOH formation, constituted a key aggravating factor.

Connection of Network Sensors to Distributed Information Measurement and Control System for Education and Research

The development of the distributed information measurement and control system for optical spectral research of particle beam and plasma objects and the execution of laboratory works on Physics and Engineering Department of Petrozavodsk State University are described. At the hardware level the system is represented by a complex of the automated workplaces joined into computer network. The key element of the system is the communication server, which supports the multi-user mode and distributes resources among clients, monitors the system and provides secure access. Other system components are formed by equipment servers (CАМАC and GPIB servers, a server for the access to microcontrollers MCS-196 and others) and the client programs that carry out data acquisition, accumulation and processing and management of the course of the experiment as well. In this work the designed by the authors network interface is discussed. The interface provides the connection of measuring and executive devices to the distributed information measurement and control system via Ethernet. This interface allows controlling of experimental parameters by use of digital devices, monitoring of experiment parameters by polling of analog and digital sensors. The device firmware is written in assembler language and includes libraries for Ethernet-, IP-, TCP- и UDP-packets forming.

Characterization of the amp genes involved in the regulation of beta-lactamase expression in Pseudomonas aeruginosa

Antibiotic resistance, production of alginate and virulence factors, and altered host immune responses are the hallmarks of chronic Pseudomonas aeruginosa infection. Failure of antibiotic therapy has been attributed to the emergence of P. aeruginosa strains that produce β-lactamase constitutively. In Enterobacteriaceae, β-lactamase induction involves four genes with known functions: ampC, ampR, ampD, and ampG, encoding the enzyme, transcriptional regulator, amidase and permease, respectively. In addition to all these amp genes, P. aeruginosa possesses two ampG paralogs, designated ampG and ampP. In this study, P. aeruginosa ampC, ampR, ampG and ampP were analyzed. Inactivation of ampC in the prototypic PAO1 failed to abolish the β-lactamase activity leading to the discovery of P. aeruginosa oxacillinase PoxB. Cloning and expression of poxB in Escherichia coli confers β-lactam resistance. Both AmpC and PoxB contribute to P. aeruginosa resistance against a wide spectrum of β-lactam antibiotics. The expression of PoxB and AmpC is regulated by a LysR-type transcriptional regulator AmpR that up-regulates AmpC but down-regulates PoxB activities. Analyses of P. aeruginosa ampR mutant demonstrate that AmpR is a global regulator that modulates the expressions of Las and Rhl quorum sensing (QS) systems, and the production of pyocyanin, LasA protease and LasB elastase. Introduction of the ampR mutation into an alginate-producing strain reveals the presence of a complex co-regulatory network between antibiotic resistance, QS alginate and other virulence factor production. Using phoA and lacZ protein fusion analyses, AmpR, AmpG and AmpP were localized to the inner membrane with one, 16 and 10 transmembrane helices, respectively. AmpR has a cytoplasmic DNA-binding and a periplasmic substrate binding domains. AmpG and AmpP are essential for the maximal expression of β-lactamase. Analysis of the murein breakdown products suggests that AmpG exports UDP-N-acetylmuramyl-L-alanine-γ-D-glutamate-meso-diaminopimelic acid-D-alanine-D-alanine (UDP-MurNAc-pentapeptide), the corepressor of AmpR, whereas AmpP imports N-acetylglucosaminyl-beta-1,4-anhydro-N-acetylmuramic acid-Ala-γ-D-Glu-meso-diaminopimelic acid (GlcNAc-anhMurNAc-tripeptide) and GlcNAc-anhMurNAc-pentapeptide, the co-inducers of AmpR. This study reveals a complex interaction between the Amp proteins and murein breakdown products involved in P. aeruginosa β-lactamase induction. In summary, this dissertation takes us a little closer to understanding the P. aeruginosa complex co-regulatory mechanism in the development of β-lactam resistance and establishment of chronic infection. ^

An approach for design and analysis of User-centric Communication Middleware

Today, the development of domain-specific communication applications is both time-consuming and error-prone because the low-level communication services provided by the existing systems and networks are primitive and often heterogeneous. Multimedia communication applications are typically built on top of low-level network abstractions such as TCP/UDP socket, SIP (Session Initiation Protocol) and RTP (Real-time Transport Protocol) APIs. The User-centric Communication Middleware (UCM) is proposed to encapsulate the networking complexity and heterogeneity of basic multimedia and multi-party communication for upper-layer communication applications. And UCM provides a unified user-centric communication service to diverse communication applications ranging from a simple phone call and video conferencing to specialized communication applications like disaster management and telemedicine. It makes it easier to the development of domain-specific communication applications. The UCM abstraction and API is proposed to achieve these goals. The dissertation also tries to integrate the formal method into UCM development process. The formal model is created for UCM using SAM methodology. Some design errors are found during model creation because the formal method forces to give the precise description of UCM. By using the SAM tool, formal UCM model is translated to Promela formula model. In the dissertation, some system properties are defined as temporal logic formulas. These temporal logic formulas are manually translated to promela formulas which are individually integrated with promela formula model of UCM and verified using SPIN tool. Formal analysis used here helps verify the system properties (for example multiparty multimedia protocol) and dig out the bugs of systems.

Streaming di immagini via ethernet con Zynq con sistemi operativi Standalone e Linux

Il seguente lavoro di tesi si inserisce all'interno di un progetto accademico volto alla realizzazione di un sistema capace elaborare immagini utilizzando una rete FPGA, acquisite da un sensore. Ogni scrittura di un nuovo frame in memoria RAM genera un interrupt. L'obiettivo della tesi è creare un sistema client/server che permetta il trasferimento del flusso di frame dalla ZedBoard a un PC e la visualizzazione a video. Il progetto eseguito sulla ZedBoard è proposto in due versioni: la prima in assenza di sistema operativo (Standalone) e una seconda implementata su Linux. Il progetto eseguito sul PC è compatibile con Linux e Windows. La visualizzazione delle immagini è implementata utilizzando la libreria OpenCV.

Interfaccia utente per assegnamento missioni e monitoraggio di un trattore automatico

Il presente lavoro consiste nella realizzazione di un'interfaccia utente adibita all'assegnamento di missioni e al monitoraggio remoto di un rover agricolo autonomo. Sfruttando l'informatica per la sua implementazione, tale interfaccia trova invece applicazione nel campo dell'automazione e dell'agricoltura di precisione. L'utilizzatore ha perciò la facoltà di muovere il rover in campo aperto e di demandargli missioni specifiche, ricevendo allo stesso tempo un feedback continuo sul suo operato. L'applicativo software comunica quindi in maniera bidirezionale con il veicolo controllato ed è predisposto per sfruttare diversi canali di comunicazione (antenne seriali, pacchetti udp, socket tcp). La scrittura del codice è stata seguita da una serie di prove di comunicazione con il veicolo, effettuate indoor, e infine da alcuni test completi effettuati outdoor, con il rover in movimento.

Bounds on end-to-end performance of networks employing erasure control coding

Erasure control coding has been exploited in communication networks with an aim to improve the end-to-end performance of data delivery across the network. To address the concerns over the strengths and constraints of erasure coding schemes in this application, we examine the performance limits of two erasure control coding strategies, forward erasure recovery and adaptive erasure recovery. Our investigation shows that the throughput of a network using an (n, k) forward erasure control code is capped by r =k/n when the packet loss rate p ≤ (te/n) and by k(l-p)/(n-te) when p > (t e/n), where te is the erasure control capability of the code. It also shows that the lower bound of the residual loss rate of such a network is (np-te)/(n-te) for (te/n) < p ≤ 1. Especially, if the code used is maximum distance separable, the Shannon capacity of the erasure channel, i.e. 1-p, can be achieved and the residual loss rate is lower bounded by (p+r-1)/r, for (1-r) < p ≤ 1. To address the requirements in real-time applications, we also investigate the service completion time of different schemes. It is revealed that the latency of the forward erasure recovery scheme is fractionally higher than that of the scheme without erasure control coding or retransmission mechanisms (using UDP), but much lower than that of the adaptive erasure scheme when the packet loss rate is high. Results on comparisons between the two erasure control schemes exhibit their advantages as well as disadvantages in the role of delivering end-to-end services. To show the impact of the bounds derived on the end-to-end performance of a TCP/IP network, a case study is provided to demonstrate how erasure control coding could be used to maximize the performance of practical systems. © 2010 IEEE.

A Scalable Synthesis of the Difluoromethyl-allo-threonyl Hydroxamate-Based LpxC Inhibitor LPC-058.

The difluoromethyl-allo-threonyl hydroxamate-based compound LPC-058 is a potent inhibitor of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) in Gram-negative bacteria. A scalable synthesis of this compound is described. The key step in the synthetic sequence is a transition metal/base-catalyzed aldol reaction of methyl isocyanoacetate and difluoroacetone, giving rise to 4-(methoxycarbonyl)-5,5-disubstituted 2-oxazoline. A simple NMR-based determination of enantiomeric purity is also described.

Genetic and Molecular Basis of Encapsulation and Capsule Diversity in Kingella kingae

Kingella kingae is a bacterial pathogen that is increasingly recognized as an etiology of septic arthritis, osteomyelitis, bacteremia, and endocarditis in young children. The pathogenesis of K. kingae disease starts with bacterial adherence to the respiratory epithelium of the posterior pharynx. Previous work has identified type IV pili and a trimeric autotransporter protein called Knh (Kingella NhhA homolog) as critical factors for adherence to human epithelial cells. Additional studies established that the presence of a polysaccharide capsule interferes with Knh-mediated adherence. Given the inhibitory role of capsule during adherence we sought to uncover the genes involved in capsule expression to understand how capsule is elaborated on the cell surface. Additionally, this work aimed to further characterize capsule diversity among K. kingae clinical isolates and to investigate the relationship between capsule type and site of isolation.

We first set out to identify the carbohydrates present in the K. kingae capsule present in the prototype strain 269-492. Glycosyl composition and NMR analysis of surface extractable polysaccharides demonstrated two distinct polysaccharides, one consisting of GalNAc and Kdo with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and the other containing galactose alone with the structure →5)-β-Galf-(1→.

To discern the two polysaccharides we disrupted the ctrA gene required for surface localization of the K. kingae polysaccharide capsule and observed a loss of GalNAc and Kdo but no effect on the presence of Gal in bacterial surface extracts. In contrast, deletion of the pamABCDE locus involved in production of a reported galactan exopolysaccharide eliminated Gal but had no effect on the presence of GalNAc and Kdo in surface extracts. These results established that K. kingae strain KK01 produces a polysaccharide capsule with the structure →3)-β-GalpNAc-(1→5)-β-Kdop-(2→ and a separate exopolysaccharide with the structure →5)-β-Galf-(1→.

Having established that K. kingae produces a capsule comprised of GalNAc and Kdo, we next set out to identify the genetic determinants of capsule through a transposon mutagenesis screen. In addition to the previously identified ctrABCD operon, lipA, lipB, and a putative glycosyltransferase termed csaA (capsule synthesis region A gene A) were found to be essential for the production of surface-localized capsule. The ctr operon, lipA, lipB, and csaA were found to be present at unlinked locations throughout the genome, which is atypical for gram-negative organisms that elaborate a capsule dependent on an ABC-type transporter for surface localization. Through examining capsule localization in the ctrA, lipA, lipB, and csaA mutant strains, we determined that the ctrABCD, lipA/lipB, and csaA gene products respectively function in capsule export, assembly, and synthesis, respectively. The GalNAc transferase and Kdo transferase domains found in CsaA further support its role in catalyzing the synthesis of the GalNAc-Kdo capsule in the K. kingae prototype strain.

To investigate the capsule diversity that exists in K. kingae we screened a panel of strains isolated from patients with invasive disease or healthy carriers for the csaA capsule synthesis locus. We discovered that Kingella kingae expresses one of 4 capsule synthesis loci (csa, csb, csc, or csd) associated with a capsule consisting of Kdo and GalNAc (type a), Kdo and GlcNAc (type b), Kdo and ribose (type c), and GlcNAc and galactose (type d), respectively. Cloning of the csa, csb, csc, or csd locus into the empty flanking gene region in a non-encapsulated mutant (creation of an isogenic capsule swap) was sufficient to produce either the type a, type b, or type c capsule, respectively, further supporting the role of these loci in expression of a specific polysaccharide linkage. Capsule type a and capsule type b accounted for 96% of invasive strains. Conversely, capsule type c and capsule type d were found disproportionately among carrier isolates, suggesting that capsule type is important in promoting invasion and dissemination.

In conclusion, we discovered that Kingella kingae expresses a polysaccharide capsule and an exopolysaccharide on its surface that require distinct genetic loci for surface localization. Further investigation into genetic determinants of encapsulation revealed the loci ctrABCD, lipA/lipB, and a putative glycosyltransferase are required for capsule expression, with the gene products having roles in capsule export, assembly, and synthesis, respectively. The putative glycosyltransferase CsaA was determined to be a bifunctional enzyme with both GalNAc-transferase and Kdo-transferase activity. Furthermore, we discovered a total of 4 capsule types expressed in clinical isolates of K. kingae, each with a distinct capsule synthesis locus. The variation in the proportion of capsule types found between invasive strains and carriage strains suggest that capsule type is important in promoting invasion and dissemination. Taken together, this work expands our knowledge of the capsule types expressed among K. kingae carrier and invasive isolates and provides insights into the common genetic determinants of capsule expression. These contributions may lead to selecting clinically relevant capsule types to develop into a capsule based vaccine to prevent K. kingae colonization.

Civic Humanism and the Classical Tradition in the Early Republic of Chile

The first decades of the 19th century constituted a period of profound change for Chile, the principal results of which were to be seen in the consolidation of the process of independence from Spanish dominion in 1818. The consequences were not limited to a revolution of military and political nature; they also included a renovation of the cultural panorama -at least among the educated patriots who made an effort to distance themselves ideologically from the Monarchy-, with the implicit challenge of establishing a new order for Chile, based on legitimate and universally recognizable foundations. The inspirational framework for these efforts is usually associated with other revolutionary examples -France and the United States- that preceded the emancipation processes in Spanish America, as well as with the discourses of illustrated liberalism. As we will attempt to demonstrate in this study, a new reading of the texts written by the Creoles that lead the Chilean independence process may, nonetheless, also reveal the relevance of the classical tradition as a model for the configuration and legitimization of the first Republican projects that especially admired the ideals of Republicanism.

An IP capable data link layer protocol for narrow band half-duplex packet data radio networks

The wide adaptation of Internet Protocol (IP) as de facto protocol for most communication networks has established a need for developing IP capable data link layer protocol solutions for Machine to machine (M2M) and Internet of Things (IoT) networks. However, the wireless networks used for M2M and IoT applications usually lack the resources commonly associated with modern wireless communication networks. The existing IP capable data link layer solutions for wireless IoT networks provide the necessary overhead minimising and frame optimising features, but are often built to be compatible only with IPv6 and specific radio platforms. The objective of this thesis is to design IPv4 compatible data link layer for Netcontrol Oy's narrow band half-duplex packet data radio system. Based on extensive literature research, system modelling and solution concept testing, this thesis proposes the usage of tunslip protocol as the basis for the system data link layer protocol development. In addition to the functionality of tunslip, this thesis discusses the additional network, routing, compression, security and collision avoidance changes required to be made to the radio platform in order for it to be IP compatible while still being able to maintain the point-to-multipoint and multi-hop network characteristics. The data link layer design consists of the radio application, dynamic Maximum Transmission Unit (MTU) optimisation daemon and the tunslip interface. The proposed design uses tunslip for creating an IP capable data link protocol interface. The radio application receives data from tunslip and compresses the packets and uses the IP addressing information for radio network addressing and routing before forwarding the message to radio network. The dynamic MTU size optimisation daemon controls the tunslip interface maximum MTU size according to the link quality assessment calculated from the radio network diagnostic data received from the radio application. For determining the usability of tunslip as the basis for data link layer protocol, testing of the tunslip interface is conducted with both IEEE 802.15.4 radios and packet data radios. The test cases measure the radio network usability for User Datagram Protocol (UDP) based applications without applying any header or content compression. The test results for the packet data radios reveal that the typical success rate for packet reception through a single-hop link is above 99% with a round-trip-delay of 0.315s for 63B packets.

Dual Roles of Diadenosine Polyphosphates in Corneal Epithelial Cell Migration

Purpose. To investigate the influence of diadenosine polyphosphates on the rate of corneal epithelial cell migration. Methods. Primary corneal epithelial cell cultures were obtained from New Zealand White rabbits. Immunocytochemical experiments were performed by fixing the cells with 4% paraformaldehyde (PFA) and incubated with cytokeratin 3 primary antibody, which was subsequently incubated with a secondary IgG mouse labeled with FITC, and the cells were observed under confocal microscopy. Migration studies were performed by taking confluent monolayers that were wounded with a pipette tip and challenged with different di- and mononucleotides with or without P2 antagonist (n = 8 each treatment). For concentration–response analysis, compounds were tested in doses ranging from 10−8 to 10−3 M (n = 8). The stability of the dinucleotides was assayed by HPLC, with an isocratic method (n = 4). Results. Cells under study were verified as corneal epithelial cells via the immunocytochemical analysis. Cell migration experiments showed that Ap4A, UTP, and ATP accelerated the rate of healing (5, 2.75, and 3 hours, respectively; P < 0.05; P < 0.001), whereas Ap3A, Ap5A, and UDP delayed it (6.5, 10, and 2 hours, respectively; P < 0.05). ADP did not modify the rate of migration. Antagonists demonstrated that Ap4A and Ap3A did activate different P2Y receptors mediating corneal wound-healing acceleration and delay. Concerning the possible degradation of the dinucleotides, it was almost impossible to detect any products resulting from their cleavage. Conclusions. Based on the pharmacological profile of all the compounds tested, the two main P2Y receptors that exist in these corneal cells are a P2Y2 receptor accelerating the rate of healing and a P2Y6 receptor that delays this process.

Sampling bloom filter-based detection of unknown RFID tags

Unknown RFID tags appear when the unread tagged objects are moved in or tagged objects are misplaced. This paper studies the practically important problem of unknown tag detection while taking both time-efficiency and energy-efficiency of battery-powered active tags into consideration. We first propose a Sampling Bloom Filter which generalizes the standard Bloom Filter. Using the new filtering technique, we propose the Sampling Bloom Filter-based Unknown tag Detection Protocol (SBF-UDP), whose detection accuracy is tunable by the end users. We present the theoretical analysis to minimize the time and energy costs. SBF-UDP can be tuned to either the time-saving mode or the energy-saving mode, according to the specific requirements. Extensive simulations are conducted to evaluate the performance of the proposed protocol. The experimental results show that SBF-UDP considerably outperforms the previous related protocols in terms of both time-efficiency and energy-efficiency. For example, when 3 or more unknown tags appear in the RFID system with 30 000 known tags, the proposed SBF-UDP is able to successfully report the existence of unknown tags with a confidence more than 99%. While our protocol runs 9 times faster than the fastest existing scheme and reducing the energy consumption by more than 80%.

Metabolic consequences of knocking out UGT85B1, the gene encoding the glucosyltransferase required for synthesis of dhurrin in Sorghum bicolor (L. Moench)

Many important food crops produce cyanogenic glucosides as natural defense compounds to protect against herbivory or pathogen attack. It has also been suggested that these nitrogen-based secondary metabolites act as storage reserves of nitrogen. In sorghum, three key genes, CYP79A1, CYP71E1 and UGT85B1, encode two Cytochrome P450s and a glycosyltransferase, respectively, the enzymes essential for synthesis of the cyanogenic glucoside dhurrin. Here, we report the use of targeted induced local lesions in genomes (TILLING) to identify a line with a mutation resulting in a premature stop codon in the N-terminal region of UGT85B1. Plants homozygous for this mutation do not produce dhurrin and are designated tcd2 (totally cyanide deficient 2) mutants. They have reduced vigor, being dwarfed, with poor root development and low fertility. Analysis using liquid chromatography-mass spectrometry (LC-MS) shows that tcd2 mutants accumulate numerous dhurrin pathway-derived metabolites, some of which are similar to those observed in transgenic Arabidopsis expressing the CYP79A1 and CYP71E1 genes. Our results demonstrate that UGT85B1 is essential for formation of dhurrin in sorghum with no co-expressed endogenous UDP-glucosyltransferases able to replace it. The tcd2 mutant suffers from self-intoxication because sorghum does not have a feedback mechanism to inhibit the initial steps of dhurrin biosynthesis when the glucosyltransferase activity required to complete the synthesis of dhurrin is lacking. The LC-MS analyses also revealed the presence of metabolites in the tcd2 mutant which have been suggested to be derived from dhurrin via endogenous pathways for nitrogen recovery, thus indicating which enzymes may be involved in such pathways.