Using design patterns is a widely accepted method to improve software development. There are many benefits of the application of patterns claimed in the literature. The most cited claim is that design patterns can provide a common design vocabulary and therefore improve greatly communication between software designers. Most of the claims are supported by experiences reports of practitioners, but there is a lack of quantitative research concerning the actual application of design patterns and about the realization of the claimed benefits. In this paper we analyze the development process of over 1000 open source software projects using version control information. We explore this information to gain an insight into the differences of software development with and without design patters. (author's abstract) / Series: Working Papers on Information Systems, Information Business and Operations

Abstract <br /><br /> Coordination models and languages are relatively new methods in modeling component-based software systems. These models and languages separate the communication aspect of systems from their computation aspect, and hence enable the modeling of concurrent, distributed, and heterogeneous systems. In this thesis, our goal is to show that Reo, a channel-based exogenous coordination language, is powerful enough to be used in the area of workflow management. In order to achieve this goal, we consider a set of workflow control patterns. We implement each of these patterns in terms of a Reo circuit and show that these Reo circuits capture the behavior of the corresponding workflow control patterns. We believe that the patterns we choose in this thesis are enough to show the strength of Reo as a workflow language. <br /><br /> We explain our approach in four steps. In the first step, we specify the general definition of workflow control patterns in terms of some Point Interval Temporal Logic formulas. In the second step, we convert each PITL formula to a constraint automaton. In the third step, we implement each workflow control pattern by a Reo circuit; each Reo circuit consists of a set of <em>components</em> and a set of <em>connectors</em> that connect and coordinate those components and provide its behavior as a relation on <em>timed data streams</em>; a timed data stream is a twin pair of a data stream and a time stream. In the forth step, we compositionally derive the constraint automata of that Reo circuit and finally, in the fifth step, we show the equivalence of the two constraint automata.

Analysis of gene expression microarray data has traditionally been conducted using hierarchical clustering. However, such analysis has many known disadvantages and pattern discovery (PD) has been proposed as an alternative technique. In this work, three similar but different PD algorithms Teiresias, Splash and Genes@Work were benchmarked for time and memory efficiency on a small yeast cell-cycle data set. Teiresias was found to be the fastest, and best over-all program. However, Splash was more memory efficient. This work also investigated the performance of four methods of discretizing microarray data: sign-of-the-derivative, K-means, pre-set value, and Genes@Work stratification. The first three methods were evaluated on their predisposition to group together biologically related genes. On a yeast cell-cycle data set, sign-of-the-derivative method yielded the most biologically significant patterns, followed by the pre-set value and K-means methods. K-means, preset-value, and Genes@Work were also compared on their ability to classify tissue samples from diffuse large b-cell lymphoma (DLBCL) into two subtypes determined by standard techniques. The Genes@Work stratification method produced the best patterns for discriminating between the two subtypes of lymphoma. However, the results from the second-best method, K-means, call into question the accuracy of the classification by the standard technique. Finally, a number of recommendations for improvement of pattern discovery algorithms and discretization techniques are made.

This descriptive study was done 1) to explore and describe the proportional distribution of breast, cervical and colorectal cancers by stage (a proxy measure of availability, access, and utilization of secondary prevention strategies) in northern Saskatchewan First Nations and non-First Nations in comparison to southern Saskatchewan First Nations and non-First Nations; 2) to assess the impact of stage and age on the survival patterns for these cancers in northerners and First Nations whose survival patterns have been shown by previous research to be equal or poorer in comparison to southerners. Univariate and multivariate survival analyses were carried out to ascertain the impact of the different proportions of stage for each study group on survival. Stage at time of diagnosis is a proxy assessment of secondary prevention services, which include formal screening programs.<p> Data for this study was obtained from the Saskatchewan Cancer Registry, which has been maintaining cancer data since 1932. Cancer stage at time of diagnosis information is complete in the registry for different years for each cancer site. Hence data for breast cancer was for the years 1970 to 1995; cervical cancer data for the years 1980 to 1995; colorectal cancer data for the years 1990 to 1995. <p> The proportion of cancer cases for each site by TNM stage and age were compared among the four study groups. First Nation and northern populations were found to have a larger proportion of diagnoses at a later stage in comparison to the southern non-First Nation group. <p> Using Cox's proportional hazards model, both stage and age at time of diagnosis were found to be significant predictors of survival for all study groups. Age and stage adjusted relative risks were calculated and found to be significant in comparison to the southern non-First Nation group for cancer of the breast (RR =1.81 P=0.013). For cervical cancer the relative risk of dying of cervical cancer for southern First Nations in comparison to southern non­-First Nations was found to be 1.38 but this was not statistically significant (p = 0.097). For colorectal cancer, the relative risk of dying of colorectal cancer was found to be better for northern First Nations in comparison to southern non-First Nations (RR = 0.59), however this was not statistically significant (p = 0.45).<p> This study showed that despite adjusting for stage and age at time of diagnosis, there were still some unexplained differences in the survival pattern of northern First Nations, northern non-First Nations and southern First Nations in comparison to southern non-First Nations. Hypotheses as to what these unexplained differences are have been offered. These include differences in socio-economic status as well as availability, accessibility, attitudes towards and knowledge of secondary prevention strategies. Further study into these unexplained differences should be carried out.

The interaction in massively multiplayer online role-playing games¡]MMORPGs¡^form a considerable component in enjoyment of playing¡]Kerr, 2006¡FCole & Griffiths, 2007¡^. So player is attracted by the more interactive online gaming. Therefore interaction is extremely important for MMORPGs. However, according to Freeman (2004), much of the research focused on individual behavior, but ignored the social dimensions of the influence between relationships and individual behavior. The research of online gaming has neglected that too. Therefore, the purpose of this study is to explore how is the social network of MMORPGs players in the game¡HAnd what effect will social network have on players¡¦ interaction patterns¡H In this paper, the survey has been completed online by 337 players, who reported on their buddy list, ego-centered network, and interaction patterns. This study explored that male role is more skilled in technical behavior¡Fthe social capital of players involved in online gaming communities is more prosperous. It is found that the ego-centered network of players positively affects players¡¦ interaction patterns. Friendships are connected with strong ties, but acquaintances are connected with weak ties. Both of them could affect players¡¦ interaction patterns, but the influence of friendship is relatively higher than that of acquaintance on players¡¦ interaction patterns.

In this dissertation we used tunable particle-particle and particle-substrate attraction to achieve reversible two-dimensional crystallization of colloids on homogeneous and patterned substrates. Total internal reflection and video microscopy techniques were used to quantify the interparticle and particle-substrate interactions in these colloidal systems. Equilibrium and dynamic simulations were then utilized to link these colloidal interactions to the experimental colloidal phase behaviour. The importance of the nature of the attractive interaction in successfully crystallizing colloids has also been documented. The first set of experiments demonstrates the use of temperature and specific ion effects to reversibly control the net particle-substrate van der Waals (vdW) attraction. Colloidal stabilization was achieved via the use of adsorbed polymer brush layers. By using evanescent wave microscopy, we directly and precisely measured how temperature and specific ion effects control the dimensions of adsorbed polymer layers and hence the net van der Waals attraction in between the colloids and the substrate. However, the magnitude of the van der Waals attraction decays very rapidly with increasing surface separation and is therefore not conducive to the self assembly of colloidal crystals. We successfully used thermoresponsive polymer nanoparticles to control the depletion attraction between micron sized silica particles and thereby induced reversible crystallization of the micron sized silica colloids on homogeneous substrates. Video and evanescent wave microscopy techniques were used to measure the nanoparticle-induced attractive interaction as a function of temperature. The experimentally observed phase behaviour was verified via simulations that utilized knowledge of the measured colloidal depletion interactions. Finally, patterned surface topologies were used to position attractive colloidal crystals. Simulations were used to link the measured colloidal interactions to experimental phase behaviour as well as substrate topology. An extension of the concepts developed in this dissertation might suggest a general strategy to assemble colloidal particles into robust and annealable crystals contributing to the fabrication of photonic bandgap materials.

No description available.

Certain scientific application domains, such as High-Energy Physics or Earth Observation, are expected to produce several Petabytes (220 Gigabyes) of data that is analyzed and evaluated by the scientists all over the world. In the context of data grid technology, data replication is mostly used to reduce access latency and bandwidth consumption. In this thesis, we adopt the typical Data Grid architecture, three kinds of nodes: server, cache, and client nodes. A server node represents a main storage site. A client node represents a site where data access requests are generated, and a cache node represents an intermediate storage site. However, the access latency of the hierarchical storage system may be of the order of seconds up to hours. The static replication strategy can be used to improve such long delay; however, it cannot adapt to changes of users¡¦ behaviors. Therefore, the dynamic data replication strategy is used in Data Grids. Three fundamental design issues in a dynamic replication strategy are: (1) when to create the replicas, (2) which files to be replicated, and (3) where the replicas to be placed. Two of well known replication strategies are Fast-Spread and Cascading, which can work well for different kinds of access patterns individually. For example, the Fast-Spread strategy works well for random access patterns, and the Cascading strategy works well for the patterns with the properties of localities. However, for so many different access patterns, if we use a strategy for one kind of access patterns and another strategy for another kind of access patterns, the system may become too complex. Therefore, in this thesis, we propose one strategy which can work for any kind of access patterns. We propose a replication approach, a Different Threshold (DT) approach to data replication in Data Grids, which can be dynamically adapted to several kinds of access patterns and provide even better performance than Cascading and Fast-Spread strategies. In our approach, there are different thresholds for different layers. Based on this approach, first, we propose a static DT strategy in which the threshold at each layer is fixed. So, by carefully adjusting the difference between the thresholds Ti, where i is the i-th layer of the tree structure, we can even provide the better performance than the above two well-known strategies. Moreover, among large amount of different data files, there may exist some hot data files. Those files which have been mostly requested are hot data files. To reduce the number of requests for the hot files, next, we propose the dynamic DT strategy. In the dynamic DT strategy, each data file even has its own threshold. We let data replication of hot files occur earlier than others by decreasing the thresholds of hot files earlier than the normal ones. From our simulation results, we show that the response time in our static DT strategy is less than that in the Cascading and the Fast-Spread strategies. Moreover, we can show that the performance of the dynamic DT strategy is better than that of the static DT strategy.

Proteins are the structural components of living cells and tissues, and thus an important building block in all living organisms. Patterns in proteins sequences are some subsequences which appear frequently. Patterns often denote important functional regions in proteins and can be used to characterize a protein family or discover the function of proteins. Moreover, it provides valuable information about the evolution of species. Patterns contain gaps of arbitrary size. Considering the no--gap--limit sequential pattern problem in a protein database, we may use the algorithm of mining sequential patterns to solve it. However, in a protein database, the order of segment appearing in protein sequences is important and it may appear many times repeatedly in a protein sequence. Therefore, we can not directly use the traditional sequential pattern mining algorithms to mine them. Many algorithms have been proposed to mine sequential patterns in protein databases, for example, the SP-index algorithm. They enumerate patterns of limited sizes (segments) in the solution space and find all patterns. The SP-index algorithm is based on the traditional sequential pattern mining algorithms and considers the the problem of the multiple--appearances of segments in a protein sequence. Although the SP-index algorithm considers the characteristics of bioinformatics, it still contains a time--consuming step which constructs the SP-tree to find the frequent patterns. In this step, it has to trace many nodes to get the result. Therefore, in this thesis, we propose a Bit--Pattern--based (BP) algorithm to improve the disadvantages of the SP-index algorithm. First, we transform the protein sequences into bit sequences. Second, we construct the frequent segments by using the AND operator. Because we use the bit operator, it is efficient to get the frequent segments. Then, we prune unnecessary frequent segments, which results in the case that we do not have to test many frequent segments in the following step. Third, we use the OR operator to get the longest pattern. In this step, we test whether two segments can be linked together to construct a long segment, and we get the result by testing once. Because we focus on which position the segment appears on, we can use the OR operator and then judge the bit sequences to get the result. Thus, we can avoid many testing processes. From our performance study based on the biological data, we show that we can improve the efficiency of the SP-index algorithm. Moreover, from our simulation results, we show that our proposed algorithm can improve the processing time up to 50\% as compared to the SP-index algorithm, since the SP--index algorithm has to trace many nodes to construct the longest pattern.

Thèse doctorat : Informatique : Nantes : 2007. / Bibliographie p. 151-159.