The Protist EST program (PEP) aims to explore the diversity of eukaryotic genomes, in a systematic and comprehensive way. A main element of the PEP initiative is to establish a database, the Protist EST Database (PEPdb), which is the centerpiece of the PEP collaboration. The major functions of the PEPdb are management of the data generated by PEP, analysis of these data, and to allow collected sequence information to be accessed via the Internet by PEP members or other users. In this project, a consistent and easy to use relational database was implemented. All information about PEP members, Publications, Libraries and ESTs can be stored in the database system. The operations are achieved by a friendly user interface. This database stores about 10000 records and is displayed on the web site "http://info.biology.mcmaster.ca/ling/estHome.html" for demonstration. An analysis of ESTs from the ciliated protozoan Tetrahymena thermophila was undertaken. A total of 3740 non-redundant gene assemblies and singletons from TIGR were analyzed. These sequences have been compared against the NCBI non-redundant protein and nucleotide databases using BLASTX and BLASTN to identify putative genes. Of 850 highly significant matches with an expect value cut-off of 10^-20 , 35.5% represent genes previously cloned from T. thermophila, and 64.5% had significant similarity to genes from other organisms deposited in the NCBI. There are 26 sequences (3.1%) that matched signal transduction proteins, including Rac, Ras, MAPK, ERK1, PKC, cAMP and 14-3-3 (a protein involved in signal transduction, exocytosis and cell cycle regulation). This result indicates that T. thermophila likely encodes the MAPK/ERK signaling pathway. About 53 sequences (6.2%) matched to cytoskeleton proteins which were divided into two groups. The first group matched genes coding for microtubules, especially to tubulin genes. The other group matched to microfilament genes including one actin, three actin-related and one profilin proteins. There were no sequences similar to intermediate filaments. Comparison of the EST counts from one gene provide absolute estimates of mRNA expression levels. The most abundant genes represented are enolase, SerH3 and Tubulin. Among 850 highly significant similarities, 196 were restricted to the ciliophora. GRL and SerH are ciliate-specific genes. There were 508 sequences that had highly significant matches (expect value < 10^-20) to human genes. Approximately 189 of them were present in humans but not found in the completely sequenced Saccharomyces cerevisiae. Based on Venn diagram analysis, T. thermophila contains abundant Eukaryotic specific proteins and many prokaryotic-like genes, and some metabolic enzymes in T. thermophila are also present in plants. These results support the fact that T. thermophila is an excellent unicellular model system for gene discovery and functional analysis. / Thesis / Master of Science (MS)

Technological advances have allowed to collect and store large volumes of data over the years. Besides, it is significant that today's applications have high performance and can analyze these large datasets effectively. Today, it remains a challenge for data mining to make its algorithms and applications equally efficient in the need of increasing data size and dimensionality [1]. To achieve this goal, many applications rely on parallelism, because it is an area that allows the reduction of cost depending on the execution time of the algorithms because it takes advantage of the characteristics of current computer architectures to run several processes concurrently [2]. This paper proposes a parallel version of the FuzzyPred algorithm based on the amount of data that can be processed within each of the processing threads, synchronously and independently.

BACKGROUND: Clostridium sordellii can cause severe infections in animals and humans, the latter associated with trauma, toxic shock and often-fatal gynaecological infections. Strains can produce two large clostridial cytotoxins (LCCs), TcsL and TcsH, related to those produced by Clostridium difficile, Clostridium novyi and Clostridium perfringens, but the genetic basis of toxin production remains uncharacterised. RESULTS: Phylogenetic analysis of the genome sequences of 44 strains isolated from human and animal infections in the UK, US and Australia placed the species into four clades. Although all strains originated from animal or clinical disease, only 5 strains contained LCC genes: 4 strains contain tcsL alone and one strain contains tcsL and tcsH. Four toxin-positive strains were found within one clade. Where present, tcsL and tcsH were localised in a pathogenicity locus, similar to but distinct from that present in C. difficile. In contrast to C. difficile, where the LCCs are chromosomally localised, the C. sordellii tcsL and tcsH genes are localised on plasmids. Our data suggest gain and loss of entire toxigenic plasmids in addition to horizontal transfer of the pathogenicity locus. A high quality, annotated sequence of ATCC9714 reveals many putative virulence factors including neuraminidase, phospholipase C and the cholesterol-dependent cytolysin sordellilysin that are highly conserved between all strains studied. CONCLUSIONS: Genome analysis of C. sordellii reveals that the LCCs, the major virulence factors, are localised on plasmids. Many strains do not contain the LCC genes; it is probable that in several of these cases the plasmid has been lost upon laboratory subculture. Our data are consistent with LCCs being the primary virulence factors in the majority of infections, but LCC-negative strains may precipitate certain categories of infection. A high quality genome sequence reveals putative virulence factors whose role in virulence can be investigated.

No description available.

This thesis focuses on the evolution of the Internet system. It examines the dynamics of competing and collaborating technologies in the invention and development of computer networking technologies in general. In particular, it examines the negotiations among social groups with different economic and political interests in designing the Internet system. This system has been shaped by competition and collaboration between the US and other countries (other regions) reflecting their different institutional arrangements in the telecommunications sector and the dynamics of uneven power relationships. Population dynamics, i.e. similarities and differences in the growth and pervasiveness of the Internet system between regions and countries, are also examined to uncover how the co-evolution between technological system and social, cultural, and economic systems countries influenced by global and local interplay. This thesis combines techno-economic and socio-technological approaches in technology studies to address the 'localisation' of a technological system, how a system adapted to or was influenced by the local context of its application. This research focuses on empirical evidence about the evolution of the Internet system, recognizing that the Internet system is one instance of a large technological system. In addition, the political economy perspective provides a foundation for an integrated analysis of the local situation and the wider power structure which illustrates the economic and political interests that are embedded in the design and development of the Internet system. The main research questions are how have political and economic interests shaped the evolution of the Internet system and why does the outcome of the Internet system's development vary across countries? The Internet system emerged from one of the early experimental computer networks in the US, the UK and France during the development of packet switching technology and it involved mainly computer scientists. The development of packet switching technologies has been shaped by battles for control between network operators and computer manufacturers as a consequence of technological convergence; and between telecommunication operators and advanced users (e.g. computer engineers and scientists in the case of the Internet system) in the process of institutional change in telecommunications sector. The analysis shows how these battles were guided by different interests and strategies between, notably, the US and European countries. The analysis of the population dynamics of Internet system development confirms its uneven development between countries following regional, economic and cultural routes. It also confirms that the international spread of the Internet network is influenced by different choices of ICTs and non-linear relationships between competing technologies. The sources of uneven development of the Internet system are founded in the global expansion of the Internet system. These sources are shown to include: asymmetric development of research networks between regions and countries, the effects of the different economic and political interests of the US (and European countries) in connecting the Internet to other countries and regions, the US-centered network design and the international financial settlement regime for the Internet in addition to the existing technological and economic gaps and cultural differences between countries that influence the localisation of the Internet system. The empirical findings that emerge from the econometric modelling demonstrate that knowledge production and distribution capabilities, global integration efforts, economic strength and equality of income distribution, size of social system, telecommunication policies, science and technology policies, prices for access and using of the Internet, all influence the localisation of the Internet system. The thesis contests many accounts of the diffusion of the Internet that are based on 'technological inevitability' and the 'universality' of the technical methods chosen.

Large deviation theory has experienced much development and interest in the last two decades. A large deviation principle is the exponential decay of the probability of increasingly rare events and the computation of a rate or entropy function which measures the rate of decay. Within the probability literature there has been much use made of these rates in diverse applications. These large deviation principles have been discovered for independent and identically distributed random variables, as well as random vectors and these have been extended to some cases of weak dependence. In this thesis we prove large deviation principles for finite dimensional distributions of scaling limits of random measures. Functional approaches to large deviation theory using test functions as dual objects to random measures are also developed. These results are applied to some important classes of models, in particular Poisson point processes, Poisson center cluster processes and doubly stochastic point processes. / Graduation date: 1991

No description available.

No description available.

The main objectives of this dissertation are the following. The first objective is concerned with the stabilization of large-scale systems by a decentralized control. The fundamental idea behind this type of control is the stabilization of the isolated subsystems of a large-scale system in such a way that the global stability requirement is also satisfied. For this purpose, a new stability criterion is introduced to identify a class of interconnected systems that can be stabilized by local state feedback. In addition to this, two specific classes of interconnections are presented for which the overall system stability can be ensured by a decentralized approach. A new constructive procedure for the design of decentralized controllers for the identified classes of large-scale systems is discussed. The principal advantages of this design procedure are that it requires a minimal amount of computation and is a systematic procedure eliminating the trial and error arguments as in the earlier methods. The second objective of the dissertation is to investigate the problem of the stabilization of a class of large-scale systems which are composed of identical subsystems and identical interconnections. For this class of systems, certain significant theorems, concerning the qualitative properties are introduced. Following the guidelines set forth by the above theorems, a few different schemes for the decentralized and multilevel control of the aforementioned class of large-scale interconnected systems are presented. The third objective concerns the development of a few different schemes for the design of an asymptotic state estimator for large-scale systems described as interconnections of several low-order subsystems. The most attractive feature of the present schemes is that the majority of the necessary computations are performed at the subsystem level only, thereby leading to a simple and practicable estimator design. Finally, all the above results are illustrated by numerical examples. Further, a comparison study is conducted to show the advantages of the methods and the results in this dissertation in comparison with some results available in the literature.

In the design of large-scale systems the problem is often too large to be approached by a single group. Then the system design problem must be resolved into component subproblems with different groups assigned to work on each subproblem. A. Wayne Wymore's "Tricotyledon Theory of Systems Design" (T3SD) provides a general system theoretic framework for the statement of large-scale system design problems. In this paper some results are developed for the extension of T3SD to the problem of the resolution of system design problems into system component design problems. Initially resolutions with respect to I/O specifications and technologies are defined and examined. Following this, resolutions with respect to merit orderings in which the merit orderings on the component problems have a specified relation with the merit orderings on the original problem are discussed. Ideal, strong and perfect resolutions with respect to merit orderings are defined and relationships among these types of resolutions are discussed. It is shown that trivial strong and ideal resolutions can always be developed from simple resolutions. Perfect resolutions are always ideal resolutions and ideal resolutions are always strong resolutions. Finally it is shown that given a class of simple resolutions there always exists a maximal ideal resolution for that class.