Dissertations / Theses on the topic 'Interval Sequences'

Finding matches, both exact and approximate, between a sequence of symbols A and a pattern P has long been an active area of research in algorithm design. Some of the more well-known byproducts from that research are the diffprogram and grep family of programs. These problems form a sub-domain of a larger area of problems called discrete pattern matching which has been developed recently to characterize the wide range of pattern matching problems. This dissertation presents new algorithms for discrete pattern matching over sequences and develops a new sub-domain of problems called discrete pattern matching over interval sets. The problems and algorithms presented here are characterized by three common features: (1) a "computable scoring function" which defines the quality of matches; (2) a graph based, dynamic programming framework which captures the structure of the algorithmic solutions; and (3) an interdisciplinary aspect to the research, particularly between computer science and molecular biology, not found in other topics in computer science. The first half of the dissertation considers discrete pattern matching over sequences. It develops the alignment-graph/dynamic-programming framework for the algorithms in the sub-domain and then presents several new algorithms for regular expression and extended regular expression pattern matching. The second half of the dissertation develops the sub-domain of discrete pattern matching over interval sets, also called super-pattern matching. In this sub-domain, the input consists of sets of typed intervals, defined over a finite range, and a pattern expression of the interval types. A match between the interval sets and the pattern consists of a sequence of consecutive intervals, taken from the interval sets, such that their corresponding sequence of types matches the pattern. The name super-pattern matching comes from those problems where the interval sets corresponds to the sets of substrings reported by various pattern matching problems over a common input sequence. The pattern for the super-pattern matching problem, then, represents a "pattern of patterns," or super-pattern, and the sequences of intervals matching the super-pattern correspond to the substring of the original sequence which match that larger "pattern."

Une séquence est une suite d’éléments ordonnés comme par exemple les trajectoires de déplacement ou les séquences d’achats de produits dans un supermarché. La fouille de séquences est un domaine de la fouille de données qui vise à extraire des motifs séquentiels fréquents à partir d’un ensemble de séquences, où ces motifs sont le plus souvent des sous-séquences. Plusieurs algorithmes ont été proposés pour l’extraction des motifs séquentiels fréquents. Avec l’évolution des capacités de calcul, la tâche d’extraction des motifs séquentiels fréquents est devenue plus rapide. La difficulté réside alors dans le trop grand nombre de motifs séquentiels extraits, qui en rend difficile la lisibilité et donc l’interprétation. On parle de déluge de motifs. L’Analyse Formelle de Concepts (AFC) est un domaine d’analyse de données permettant d’identifier des relations à partir d’un ensemble de données binaires. Les structures de motifs étendent l’AFC pour traiter des données complexes comme les séquences. La plateforme GALACTIC implémente l’algorithme Next Priority Concept qui propose une approche d’extraction de motifs pour des données hétérogènes et complexes. Il permet un calcul de motifs génériques à travers des descriptions spécifiques d’objets par des prédicats monadiques. Il propose également de raffiner un ensemble d’objets à travers des stratégies d’explorations spécifiques, ce qui permet de réduire le nombre de motifs. Dans ce travail, nous nous intéressons à l’analyse de données séquentielles en utilisant GALACTIC. Nous proposons plusieurs descriptions et stratégies adaptées aux séquences. Nous proposons également des mesures de qualité non supervisées pour pouvoir comparer entre les motifs obtenus. Une analyse qualitative et quantitative est menée sur des jeux de données réels et synthétiques afin de montrer l’efficacité de notre approche
A sequence is a sequence of ordered elements such as travel trajectories or sequences of product purchases in a supermarket. Sequence mining is a domain of data mining that aims an extracting frequent sequential patterns from a set of sequences, where these patterns are most often common subsequences. Support is a monotonic measure that defines the proportion of data sharing a sequential pattern. Several algorithms have been proposed for frequent sequential pattern extraction. With the evolution of computing capabilities, the task of frequent sequential pattern extraction has become faster. The difficulty then lies in the large number of extracted sequential patterns, which makes it difficult to read and therefore to interpret. We speak about "deluge of patterns". Formal Concept Analysis (FCA) is a field of data analysis for identifying relationships in a set of binary data. Pattern structures extend FCA to handle complex data such as sequences. The GALACTIC platform implements the Next Priority Concept algorithm which proposes a pattern extraction approach for heterogeneous and complex data. It allows a generic pattern computation through specific descriptions of objects by monadic predicates. It also proposes to refine a set of objects through specific exploration strategies, which allows to reduce the number of patterns. In this work, we are interested in the analysis of sequential data using GALACTIC. We propose several descriptions and strategies adapted to sequences. We also propose unsupervised quality measures to be able to compare between the obtained patterns. A qualitative and quantitative analysis is conducted on real and synthetic datasets to show the efficiency of our approach

This thesis consists of five articles mainly devoted to problems in dynamical systems and ergodic theory. We consider non-uniformly hyperbolic two dimensional systems and limit distributions of point measures which are absolutely continuous with respect to the Lebesgue measure. Let $f_{a_0}(x)=a_0-x^2$ be a quadratic map where the parameter $a_0\in(1,2)$ is chosen such that the critical point $0$ is pre-periodic (but not periodic). In Papers A and B we study skew-products $(\th,x)\mapsto F(\th,x)=(g(\th),f_{a_0}(x)+\al s(\th))$, $(\th,x)\in S^1\times\real$. The functions $g:S^1\to S^1$ and $s:S^1\to[-1,1]$ are the base dynamics and the coupling functions, respectively, and $\al$ is a small, positive constant. Such quadratic skew-products are also called Viana maps. In Papers A and B we show for several choices of the base dynamics and the coupling function that the map $F$ has two positive Lyapunov exponents and for some cases we further show that $F$ admits also an absolutely continuous invariant probability measure. In Paper C we consider certain Bernoulli convolutions. By showing that a specific transversality property is satisfied, we deduce absolute continuity of the to these Bernoulli convolutions associated distributions. In Papers D and E we consider sequences of real numbers in the unit interval and study how they are distributed. The sequences in Paper D are given by the forward iterations of a point $x\in[0,1]$ under a piecewise expanding map $T_a:[0,1]\to[0,1]$ depending on a parameter $a$ contained in an interval $I$. Under the assumption that each $T_a$ admits a unique absolutely continuous invariant probability measure $\mu_a$ and that some technical conditions are satisfied, we show that the distribution of the forward orbit $T_a^j(x)$, $j\ge1$, is described by the distribution $\mu_a$ for Lebesgue almost every parameter $a\in I$. In Paper E we apply the ideas in Paper D to certain sequences which are equidistributed in the unit interval and give a geometrical proof of an old result by Koksma.

O termo Coal Bed Methane (CBM) refere-se ao metano gerado nas camadas de carvão e é um alvo exploratório na indústria do petróleo. Desde os anos setenta quando o CBM foi visto como uma fonte de energia economicamente viável estudos foram direcionados no entendimento de sua ocorrência, distribuição, viabilidade, produtividade e recuperação (Flores, 1997). Atualmente o CBM é produzido economicamente e investigado em diversas bacias carboníferas do mundo. No Brasil as principais acumulações de carvão são de idade Permiana e fazem parte da Formação Rio Bonito da Bacia do Paraná. De várias jazidas de carvão conhecidas a Jazida de Santa Terezinha, nordeste do estado do Rio Grande do Sul, é a que certamente apresenta o maior potencial para CBM. Seu condicionamento como um baixo estrutural com camadas de carvão de espessuras significativas ocorrendo entre 400m e 1000m de profundidade conferiram a jazida uma situação favorável para geração de metano. Uma boa quantidade de dados geológicos provenientes de diversos poços testemunhados foi utilizada para caracterização estratigráfica do intervalo carbonoso da jazida. A descrição detalhada de testemunhos deu embasamento para análise de fácies e sistemas deposicionais permitindo o reconhecimento de parasseqüências, cujo empilhamento evidenciou uma seqüência deposicional dominantemente transgressiva apresentando na base depósitos aluviais, na porção intermediária sistemas lagunares/paludais com formação de turfeiras, e no topo depósitos marinhos. A análise estrutural revelou uma forte compartimentação tectônica das camadas de carvão, deslocadas por falhamentos normais de alto rejeito. A integração de dados estratigráficos com a determinação do padrão de estruturação atual e demais complexidades forneceu elementos para o reconhecimento de uma zona com melhores condições para exploração de CBM na Jazida de Santa Terezinha.
Coal bed methane (CBM0 refers to the methane gas generated in coal beds and is a worldwide target in the petroleum industry. Since the Seventies when CBM was seen like a economically viable energy source studies had been directed to understand it’s occurrence pattern, distribution, viability, productivity and recovery (Flores, 1997). Nowadays CBM is economically produced and investigated in several coaly basins around the world (USA, China). In Brazil the main coal accumulations are of Permian age being part of the Rio Bonito Formation of Parana Basin. From all known coalfields the Santa Terezinha coalfield, in the northeastern region of Rio Grande do Sul state, certainly is the one that presents greater potential to CBM. The structural conditioning and the good thickness of coal beds occurring in depths between 400m and 1000m emplaced the coalfield in a favorable situation to methane generation. Tens of cored wells were utilized to the stratigraphic characterization of the coal bearing interval. A detailed description of cores supplied informations to facies and depositional environments analysis allowing the recognition of parasequences with a dominant retrogradational pattern characterizing a manly transgressive depositional sequence showing aluvial deposits at the base, marsh and lacustrine deposits in middle portion and marine strata on top. The structural analysis revealed a strong tectonic compartmentation of coal beds, displaced by normal faults with high slip. The integration of stratigraphic data with the determination of actual structural patterns and other complexities allowed the recognition of a zone with better conditions to CBM exploration in the Santa Terezinha coalfield.

Data mining is increasingly becoming important tool in extracting interesting knowledge from large databases. Many industries are now using data mining tools for analysing their large collections of databases and making business decisions. Many data mining problems involve temporal aspects, with examples ranging from engineering to scientific research, finance and medicine. Temporal data mining is an extension of data mining which deals with temporal data. Mining temporal data poses more challenges than mining static data. While the analysis of static data sets often comes down to the question of data items, with temporal data there are many additional possible relations. One of the tasks in temporal data mining is the pattern discovery task, whose objective is to discover time-dependent correlations, patterns or rules between events in large volumes of data. To date, most temporal pattern discovery research has focused on events existing at a point in time rather than over a temporal interval. In comparison to static rules, mining with respect to time points provides semantically richer rules. However, accommodating temporal intervals offers rules that are richer still. This thesis addresses several issues related to the pattern discovery from interval sequence data. Despite its importance, this area of research has received relatively little attention and there are still many issues that need to be addressed. Three main issues that this thesis considers include the definition of what constitutes an interesting pattern in interval sequence data, the efficient mining for patterns in the data, and the identification of interesting patterns from a large number of discovered patterns. In order to deal with these issues, this thesis formulates the problem of discovering rules, which we term richer temporal association rules, from interval sequence databases. Furthermore, this thesis develops an efficient algorithm, ARMADA, for discovering richer temporal association rules. The algorithm does not require candidate generation. It utilizes a simple index, and only requires at most two database scans. In this thesis, a retrieval system is proposed to facilitate the selection of interesting rules from a set of discovered richer temporal association rules. To this end, a high-level query language specification, TAR-QL, is proposed to specify the criteria of the rules to be retrieved from the rule sets. Three low-level methods are developed to evaluate queries involving rule format conditions. In order to improve the performance of the methods, signature file based indexes are proposed. In addition, this thesis proposes the discovery of inter-transaction relative temporal association rules from event sequence databases.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
O trabalho consiste na análise estratigráfica do intervalo siluro-devoniano da Bacia do Amazonas utilizando como base os conceitos da Estratigrafia Moderna, mais especificamente a sequência estratigráfica genética, proposta por Galloway (1989), a qual utiliza as superfícies de inundação marinha como os limites de uma sequência sedimentar. A principal razão para a utilização desta metodologia deve-se ao fato que o conteúdo rochoso compreendido no intervalo estudado teve a sua sedimentação relacionada às transgressões marinhas que faziam parte do contexto paleogeográfico da bacia durante o Siluriano e Devoniano. Desta forma, as superfícies de inundação máxima, representativas de eventos cronoestratigráficos, destacam-se nos perfis de raios gama e são tomadas como datum de correlação em treze poços exploratórios, os quais foram distribuídos em quatro seções (A-A, B-B, C-C e D-D) pela bacia. A análise destas seções permitiu a identificação de quatro sequências de terceira ordem (AB, BC, CD e DE), limitadas no topo e na base por superfícies de inundação marinha. Cada sequência é constituída por ciclos regressivo-transgressivos assimétricos, representados pelo trato de sistemas de mar alto e pelo trato de sistemas transgressivo. A análise destas seções integrada à interpretação de mapas estratigráficos (isópacas, isólitas e porcentagem de areias) possibilitou identificar o depocentro da bacia, bem como duas áreas principais como fonte de sedimentos arenosos (uma a oeste e outra a sul). Além disto, foi possível inferir que a comunicação marinha com o continente, durante as transgressões paleozoicas, responsável pela deposição de sedimentos pelíticos, seguiu uma orientação de norte para sul, evoluindo obliquamente em direção ao continente num trend nordeste para sudoeste. Por fim, a partir da análise cíclica em perfis de raios gama, as superfícies de inundação marinha, do intervalo Devoniano, das bacias do Amazonas e Parnaíba foram correlacionadas.

Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 2006.
Includes bibliographical references (p. 85-86).
Many manufacturing companies wrestle with managing in-house manufactured inventories especially in the climate of Just-in-Time (JIT) manufacturing and with constant pressure to reduce inventory levels. One popular self-managing approach to controlling inventory levels while being responsive to customer demand is implementing a 'Pull' system. A Pull system is one that takes production signals from the downstream process and is based on true customer demand. This is in contrast to a 'Push' system that takes the production signal from the upstream schedule. This thesis will explore inventory management strategies at 3WA Powertrain Operation (PTO) as they approach plant wide implementation of 'Pull-to-Assembly'. 3WA PTO is working to completely link each of their in-house component (parts) production processes to the scheduled Assembly process such that component production signals will each 'pull' from the following process step and ultimately from the Powertrain Assembly schedule. The tested hypotheses include: 1) For 'Pull-to-Assembly' to be successful, a highly synchronized and visible in-house inventory management structure must first be in-place.
(cont.) Successful inventory management requires that inventory levels for each component must be completely understood and tuned to the variety of the component, process lead time, demand and variability in both lead time and demand. 2) A Pull system, like any other manufacturing process or technology, requires effective integration of the human, organizational, and technical system features. 3) Transitioning from a primarily Push to a Pull system as well as implementing new inventory strategies requires effective management of change. This thesis leads with the analysis of technical features required to implement a Pull system at 3WA as well as to improve in-house inventory management methods. Included within this technical analysis is the presentation of a 'calculator' tool that allows the user to determine initial inventory levels appropriate for a given part based on the demand/lead time scenario. Following the more technical analysis, this thesis examines the organizational change and human elements needed to transition to and sustain a Pull system in this organization. The following overarching conclusions were developed based on observations, research and experimentation at 3WA PTO.
(cont.) More specific conclusions related to the topics of 'Pull-to-Assembly, inventory management, data driven decision making, 'pulling' change in a tribal knowledge culture and the "demographic cliff' are presented within the thesis. Standardized processes and system stability along with accurate, knowledgeable and visible inventory management must be in-place before an extensive 'Pull' system will be successful.
(cont.) There is no 'one-size fits all' for inventory management. Inventory management depends primarily on expected demand, lead time and the variability in both. Equally important to choosing an inventory strategy, however, is having a solid understanding of true customer needs including how they will signal demand, how often and how fast the product is needed. Change must be 'Pulled' from an organization for 'True Change' to happen. The 'demographic cliff' is approaching for many traditional manufacturing companies like 3WA and the right employee skills profiling, retirement policies, and knowledge retention/sharing strategies must be in place for both short-term and long-term company success.
by Aimee L. Vessell.
S.M.
M.B.A.

The contributions of the present thesis are in the domain of Pattern Mining and Knowledge Discovery, being of particular relevance for the sequential pattern mining and time-interval related pattern mining fields. In this thesis, a new efficient sequential pattern mining algorithm called VEPRECO is introduced, the contributions of which are: (i) a new representation, (ii) pre-pruning strategies and (iii) candidate selection policies which reduce the number of iterations of the algorithm. In this thesis, a new efficient algorithm for mining time interval patterns, called vertTIRP, has also been presented, combining an efficient representation of these patterns with a pairing strategy to accelerate the mining process. And finally, to open the door of mining of time interval patterns to multivariate time series, the TA4L algorithm has been introduced. TA4L transforms time series into interval-based sequences suitable for feeding time interval algorithms
Les contribucions d'aquesta tesi estan en el domini de la mineria de patrons i el descobriment del coneixement, sent de particular rellevància pels camps de mineria de patrons seqüencials i els patrons d'intervals temporals. En aquesta tesi, s'ha presentat un nou algoritme eficient de mineria de patrons seqüencials anomenat VEPRECO, les contribucions del qual són: (i) una nova representació, (ii) unes estratègies de prepoda i (iii) unes polítiques de selecció de candidats que redueixen el nombre d'iteracions de l'algoritme. En aquesta tesi, també s'ha presentat un nou algoritme eficient per minar patrons d'intervals temporals, denominat vertTIRP, el qual combina una representació eficient d'aquests patrons amb una estratègia d'aparellament per tal d’accelerar el procés de la mineria. I finalment, per obrir la porta de la mineria de patrons d'intervals temporals a sèries temporals multivariades, s'ha presentat l'algoritme TA4L. TA4L transforma sèries temporals en seqüències d’intèrvals aptes per alimentar algoritmes d'intervals temporals
Programa de Doctorat en Tecnologia

Within Big Bend National Park, the unconformable contact between the Buda Limestone and the overlying Boquillas Formation represents the Commanchean-Gulfian boundary. Previous studies of the geochronology of this interval have relied primarily on provincial ammonite faunas rather than foraminifera, and place the Buda and basal Boquillas in the Lower Cenomanian. Because of its indurated nature, a comprehensive foraminiferal biozonation has not been acquired for the Buda Limestone. Recent revisions to Cretaceous foraminiferal biozonations and taxonomies necessitates a new biostratigraphic study of the Buda - Boquillas interval. The overlapping ranges of F. washitensis, G. bentonensis, G. caseyi, P. appenninica, P. delrioensis, P. stephani, and R. montsalvensis place the Buda within the upper portion of the Early to Middle Cenomanian Th. globotruncanoides Zone. Microkarst found on the surface of the Buda Limestone has been interpreted as representing a subaerial exposure and sequence boundary. However, microkarst-like features can result from subaqueous or intrastratal processes. Carbon and oxygen stable isotope analysis of the lower and middle Buda has indicated a mean δ13C value of 1.73‰ VPDB, which is in line with other values reported from the Lower Cenomanian. The top 2.6m of Buda contains a 0.62‰ negative δ13C shift from 1.88‰ VPDB to 1.26‰ VDPB in a 40 cm interval, expected if subaerial exposure occurred. Higher variation in measured carbon isotope values beneath the contact also lend evidence for meteoric alteration. The standard deviation in δ13C values from the top 2.8 m of the Buda is 0.207, which is 2.16 times larger than the rest of the studied section at 0.096. The Buda contains a shallow pelagic-dominated fauna of heterohelicids (45-90%), globigerinellids (3-37%), and hedbergellids (4-22%). Intermediate-depth globigerinellids display an initial increase followed by a marked decrease in abundance upsection, interpreted as sea level transgression and regression, respectively. The lower contact of the Buda with the Del Rio Clay has been previously interpreted as a subaerial exposure, and a P:B break from ~0% planktonics in the upper Del Rio to ~80% in the Buda supports this claim. This study therefore interprets both the upper and lower contacts of the Buda as sequence boundaries. The overlying 1.2 m Boquillas is nearly devoid of benthics and represents a deeper assemblage including the double-keeled Dicarinella sp., as well as several Upper Cenomanian (D. algeriana Subzone) species. Based on foraminiferal data, the duration of the Buda - Boquillas unconformity is roughly equivalent to the missing Th. reicheli and Th. greenhornensis Biozones, or a sizable portion of the Middle Cenomanian.
Systematic paleontology -- Biostratigraphy of the Buda Limestone -- Biostratigraphy of the lowermost Boquillas Formation -- Stable isotope geochemistry.
Department of Geological Sciences

Dans la plupart des eucaryotes, il n’existe qu’une seule région centromérique par chromosome et celle-ci est capable d’être liée au fuseau mitotique via le complexe du kinétochore. Dans ce contexte, la présence de deux centromères est un défi pour une séparation normale. Au cours de la mitose, la capture des deux centromères de la même chromatides vers les pôles opposés génère un pont d’anaphase résultant en une rupture entre les centromères. Les extrémités libérées peuvent être fusionnées bout à bout recréant ainsi un dicentrique. Le chromosome entre alors dans un cycle de Rupture Cassure Pont, capable quelques cycles d’entrainer des modifications profondes du nombre de copies de gène qui peuvent contribuer à l'oncogenèse et résistance à la chimiothérapie. Malgré son importance, le mécanisme de rupture reste pour une grande partie inexploré. Ce projet permet l’analyse de la rupture des chromosomes dicentriques en utilisant le modèle de la levure bourgeonnante, Saccharomyces cerevisiae. Nous utilisons des souches dicentriques conditionnelles dans lequelles un chromosome, portant un centromère conditionnel sous le contrôle de deux promoteurs inductibles au galactose, est fusionné à un autre chromosome natif par recombinaison homologue. Nous avons observé que les chromosomes dicentriques ont tendance à casser dans le voisinage des deux centromères. La région de la rupture se répand sur ~ 30 kb vers l'autre centromère. Une insertion d’un fragment d’ADN 1-kb possédant un centromère ectopique dans un chromosome avec un centromère conditionnelle établit un point chaud d’environs 30 kb indiscernables des points chauds à centromères natifs. En outre, la taille de zone de rupture n’est pas corrélée à la distance intercentromerique (des intervalles de 30-600 kb ont été testés). Cela indique que la plus forte propension à rompre est une conséquence de la structure ou de la fonction des centromères et est sans rapport avec les séquences environnantes des chromosomes. Il est encore difficile de savoir si la rupture aux centromères a une fonction physiologique, mais nous pouvons supposer que ce point chaud peut favoriser les réarrangements d'ADN dans ces régions permettant ainsi l’inactivation du centromère et donc le retour à un caryotype stable. Globalement dans la S.cerevisiae, les dicentriques cassent dans les régions péricentromériques ou dans les fusions de télomères quand ils sont présents. Fait intéressant, les séquences télomériques internes, à savoir les répétitions TG₁₋₃, établissent plusieurs points chauds de rupture à une fréquence similaire. En perspective, il serait intéressant d'aborder les questions suivantes : 1) Quelles sont les caractéristiques qui rendent une région plus sujette à la casse ? 2) Quelles sont les positions de rupture au niveau des nucléotides ? 3) Existe-t-il un contrôle de la cassure des chromatides exercé dans la cellule ? 4) Quelle peut être la fonction biologique des points chauds de cassures ?
In most eukaryotes, there is one defined centromeric region per chromosome that links it to the spindle apparatus via the kinetochore complex. In this context, the presence of two centromeres is a challenge for an accurate segregation. During mitosis, the capture of the two centromeres of the same chromatid to opposite poles generates anaphase bridges that results in breakage between the centromeres. The released ends can be fused end-to-end thus recreating dicentric. It enters breakage-fusion-bridge cycles that, in multiple rounds, can result in large gene copy number alterations that can contribute to oncogenesis and chemotherapy resistance. Despite of its significance, the mechanism of breakage remains for a large part unexplored. This project adresses the dicentric breakage using a budding yeast, Saccharomyces cerevisiae. We use conditional dicentric strains, where a chromosome, bearing a conditional centromere under the control of two galactose-inducible promoters, is fused to another native chromosome by homologous recombination. We observed that dicentric chromosomes tend to break in the vicinity of the two centromeres. The breakage region spreads over ~30 kb towards the other centromere. An insertion of a 1-kb ectopic centromere in a chromosome with a conditional centromere establishes a ~30 kb hot spot indistinguishable from the hot spots at native centromeres. Furthermore, the size of breakage region is unrelated to an intercentromeric distance (30-600 kb intervals were tested). This indicates that the higher propensity to break is a consequence of centromere structure or function and is unrelated to the native surrounding sequences. It is yet unclear whether breakage at centromeres has a physiological function but we can speculate that this hot spot may favour local DNA rearrangements that result in centromere inactivation and thus the return to a stable karyotype. Overall in budding yeast, dicentrics break at pericentromeric regions or at the telomere fusions when they are present. Interestingly, internal telomeric sequences, i.e. TG₁₋₃ repeats, establish several breakage hot spots with a similar frequency. In perspective, it would be interesting to address the following questions: 1) What are features that make a region more prone to breakage? 2) What are the positions of breakage at nucleotide level? 3) Is there a coordination of dicentric chromatid breakage? 4) What can be the biological function of dicentric breakage hot spots?

The aim of this project is to develop and perform a first evaluation of a software, based on the active contour, which automatically computes the cross-section area of the internal jugular veins through a sequence of 90 ultrasound images. The software is intended to be useful in future research in the field of intra cranial pressure and its associated diseases. The biomechanics of the internal jugular veins and its relationship to the intra cranial pressure is studied with ultrasound. It generates data in the form of ultrasound sequences shot in seven different body positions, supine to upright. Vein movements in cross section over the cardiac cycle are recorded for all body positions. From these films, it is interesting to know how the cross-section area varies over the cardiac cycle and between body positions, in order to estimate the pressure. The software created was semi-automatic, where the operator loads each individual sequence and sets the initial contour on the first frame. It was evaluated in a test by comparing its computed areas with manually estimated areas.  The test showed that the software was able to track and compute the area with a satisfactory accuracy for a variety of sequences. It is also faster and more consistent than manual measurements. The most difficult sequences to track were small vessels with narrow geometries, fast moving walls, and blurry edges. Further development is required to correct a few bugs in the algorithm. Also, the improved algorithm should be evaluated on a larger sample of sequences before using it in research.

Interest in the architecture and fluid flow potential of fault zones in basalt sequences has intensified over recent years, due to their applications in the hydrocarbon industry and CO₂ storage. In this study, field mapping is combined with micro-structural analyses and flow modelling to evaluate fault growth, evolution, fluid-rock interactions, and permeability changes over time in faults in basalt sequences. Twelve brittle fault zones cutting basalt sequences in the North Atlantic Igneous Province were studied. This study finds that fault architecture is ultimately controlled by displacement and juxtaposition. Self-juxtaposed faults (i.e. basalt faulted against itself) are characterised by wide zones of brecciation, cataclasis, fracturing, mineralisation and alteration. Non self-juxtaposed faults (i.e. basalt faulted against an inter-lava unit) are characterised by relatively narrow principal slip zones, filled with clay smears or clay-rich gouge derived from inter-lava beds. This study also finds that brittle deformation of basalts at the grain scale is mineralogy dependent. Fe-Ti oxides and pyroxenes deform by intragranular fracturing and grain size reduction, whereas olivines and feldspars are susceptible to replacement by clay and zeolites. Fault rock bulk chemistries are likely to differ from their host rocks, and this is controlled by secondary mineral formation, with zeolite and clay minerals playing an important role. Flow modelling in this study shows that controls on along- and across-fault fluid flow can significantly change fault zone bulk permeability over time, as a result of mineralisation and alteration of the fault zone as it evolves. The results from this study are used to propose a model for how fault strength, fault-related alteration, and permeability change over time in fault zones in basalt sequences. Results highlight the impact that fault-related alteration could have on CO₂ storage. A predictive model for fault structure at depth, developed from this study's findings, is presented for fault zones in basalt sequences, which has particular relevance to the hydrocarbon and CO₂ industry.

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This research takes as an object of reflection and analysis the classroom environment and more specifically, the 'class', the moment the teacher puts the teaching work in practice. Based on studies and empirical knowledge about the subject, some questions stand out as guiding elements of the present investigation: how the teacher imagines his classroom and where that imaginary comes from, what he teaches beyond systematized knowledge and if he passes value judgments in this activity. In order to deal with this problematization, it is sought to investigate some conceptions that guide the teacher formation process towards the concepts about "class", "student" and "content". The general objective is to see if there is any gap between what theachers say that a lesson would be and what, in recorded lessons, these teachers have performed as practice. In the perspective of reaching the proposed objective, the research is based on the conception that every sequence of statements offers possibilities of interpretation. Having as theoretical reference the Discourse Analysis of the French Line, the analyzes are based on these theoretical assumptions, such as the notions of Subject and Social, Ideological and Discursive Formation, among others, that are brought to the discussion. The corpus of the research consists of discursive sequences resulting from interviews and class recordings of six teachers from an educational institution. In general, the teacher and the student are considered as representatives of determined places in the structure of a social formation, which allows constructing interpretations without the pretension of generalizations.
Esta pesquisa toma como objeto de reflexões e análise o ambiente da sala de aula e mais especificamente, a „aula‟, momento em que o professor coloca em prática o trabalho docente. A partir de estudos e de conhecimento empírico sobre a temática, alguns questionamentos se destacaram como elementos norteadores da presente investigação: como o professor imagina sua aula e de onde vem esse imaginário, o que ele ensina para além dos conhecimentos sistematizados e se ele passa juízos de valor nesta atividade. Com o intuito de trabalhar esta problematização, busca-se investigar algumas concepções que norteiam o processo de formação do professor, no que diz respeito aos conceitos sobre “aula”, “aluno” e “conteúdo”. O objetivo geral é investigar se há algum intervalo entre o que dizem os professores sobre o que seria uma aula e o que, em aulas gravadas, esses professores realizam como prática. Na perspectiva de alcançar o objetivo proposto, a pesquisa baseia-se na concepção de que toda sequência de enunciados oferece lugar à interpretação. Tendo como referencial teórico a Análise do Discurso de Linha Francesa, pautam-se as análises nestes pressupostos teóricos, como as noções de Sujeito e de Formação Social, Ideológica, Discursiva e Imaginária, dentre outros, que são trazidos para a discussão. O corpus da pesquisa constitui-se de sequências discursivas resultantes de entrevistas e gravações de aula de seis professores de uma instituição de ensino superior privada, de um curso de Administração. De modo geral, consideram-se o professor e o aluno como representantes de lugares determinados na estrutura de uma formação social, o que permite construir interpretações sem a pretensão de generalizações.

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This study has as a main objective to make a detailed stratigraphic analysis of the Aptian-Albian interval in the east part of Araripe Basin, NE of Brazil which correspond, litostratigraphically, to Rio Da Batateira, Crato, Ipubi and Romualdo formations. The stratigraphic analysis was based on three different stages, the 1D, 2D and 3D analysis; these ones were adapted to the sequence stratigraphy concepts in order to create a chronostratigraphic framework for the study area within the basin. The database used in the present study contains field and well information, wells that belong to Santana Project, carried out by the Minist?rio de Minas e Energia- DNPM- CPRM from 1977 to 1978. The analysis 1D, which was done separately for each well and outcrop allowed the recognition of 13 sedimentary facies, mainly divided based on predominant litologies and sedimentary structures. Such facies are lithologically represented by pebble, sandstones, claystones, margas and evaporates; these facies are associated in order to characterize different depositional systems, that integrate from the continental environment (fluvial system and lacustre), paralic system (delta system and lagunar) to the marine environment (shelfenvironment). The first one, the fluvial system was divided into two subtypes: meandering fluvial system, characterized by fill channel and floodplain deposits; the facies of this system are associated vertically according to the textural thinning upward cycles (dirting-up trend pattern in well logs). Lacustrine environment is mainly related with the lithotypes of the Crato Formation, it shows a good distribution within the basin, been composed by green claystone deposits and calcareous laminated. Deltaic System represented by prodelta and delta front deposits which coarsening upward tendency. Lagunar system is characterised by the presence of anhydrite and gypsum deposits besides the black claystone deposits with vegetal fragments which do not contain a fauna typically marine. The marine platform system is composed by successions of black and gray claystone with fossiliferous fauna of Dinoflagellates (Spiniferites Mantell, Subtilisphaera Jain e Subtilisphaera Millipied genre) typical of this kind of depositional system. The sedimentary facies described are vertically arranged in cycles with progradational patterns which form textural coersening upward cycles and retrogradational, represented by textural thinning dowward cycles. Based in these cycles, in their stack pattern and the vertical change between these patterns, the systems tracks and the depositional sequences were recognized. The Low System Track (LST) and High System Track (HST) are composed by cycles with progradational stack pattern, whereas the Trangessive System Track (TST) is composed by retrogradational stack pattern cycles. The 2D stratigraphic analysis was done through the carrying out of two stratigraphic sections. For the selection of the datum the deepest maximum flooding surface was chosen, inside the Sequence 1, the execution of these sections allowed to understand the behaviour of six depositional systems along the study area, which were interpreted as cycles of second order or supercycles (cycles between 3 and 10 Ma), according to the Vail, et al (1977) classification. The Sequence 1, the oldest of the six identified is composed by the low, transgressive and high systems tracks. The first two system tracks are formed exclusively by fluvial deposits of the Rio da Batateira Formation whereas the third one includes deltaic and lacustrine deposits of the Crato Formation. The sequences 2 and 3 are formed by the transgressive systems tracks (lake spreading phase) and the highstand system track (lake backward phase). The TST of these sequences are formed by lacustrine deposits whereas HST contains deltaic deposits, indicating high rates of sedimentary supply at the time of it s deposition. The sequence 4 is composed by LST, TST and HST, The TST4 shows a significant fall of the lake base level, this track was developed in conditions of low relation between the creation rate of space of accommodation and the sedimentary influx. The TST4 marks the third phase of expansion of the lacustrine system in the section after the basin?s rift, the lacustrine system established in the previous track starts a backward phase in conditions that the sedimentary supply rate exceeds the creation rate of space accommodation. The sequence 5 was developed in two different phases, the first one is related with the latest expansion stage of the lake, (TST5), the basal track of this sequence. In this phase the base level of the lake rose considerably. The second phase (related to the TST5) indicates the end of the lacustrine domain in the Araripe Basin and the change to lagunar system ant tidal flat, with great portions in the supratidal. These systems were formed by restricted lagoons, with shallow level of water and with intermittent connections with the sea. This, was the phase when the Araripe Basin recorded the most several arid conditions of the whole interval studied, Aptian Albian, conditions that allow the formation of evaporitic deposits. The sequence 6 began its deposition after a significant fall of the sea (LST6). The sequence 6 is without any doubtlessly, the sequence that has deposits that prove the effective entrance of the sea into the Araripe Basin. The TST6, end of this sequence, represents the moment which the sea reaches its maximum level during the Aptian Albian time. The stratigraphic analysis of the Aptian Albian interval made possible the understanding that the main control in the development of the depositional sequences recognized in the Araripe Basin were the variations of the local base level, which are controlled itself by the climate changes
O presente trabalho tem como objetivo principal realizar uma an?lise estratigr?fica detalhada do intervalo Aptiano ao Albiano na parte leste da Bacia do Araripe, NE do Brasil, o qual corresponde, litoestratigraficamente, ?s forma??es Rio da Batateira, Crato, Ipub? e Romualdo. A an?lise estratigr?fica envolveu tr?s etapas distintas, a an?lise 1D, 2D e 3D, nas quais foram adaptados os conceitos da estratigrafia de seq??ncias visando elaborar um arcabou?o de car?ter cronoestratigr?fico para a por??o estudada da bacia. Tal estudo contou com uma base de dados integrada por informa??o de campo e de po?os pertencentes ao projeto Santana, realizado pelo Minist?rio de Minas e Energia- DNPM- CPRM nos anos de 1977 e 1978. A an?lise 1D, por meio da an?lise individual de cada afloramento e po?o, permitiu o reconhecimento de 13 f?cies sedimentares, individualizadas com base principalmente nas litologias predominantes e nas estruturas sedimentares. Tais f?cies s?o representadas litologicamente por conglomerados, arenitos, pelitos, calc?rios, margas e evaporitos. As mesmas se associam de forma a caracterizar diferentes sistemas deposicionais, que integram desde o ambiente continental (sistemas fluvial e lacustre), ambiente par?lico (sistemas deltaico e lagunar) at? o ambiente marinho (sistema plataformal). O primeiro deles, o sistema fluvial, foi dividido em dois sub-tipos: o sistema fluvial meandrante, caracterizado por dep?sitos de preenchimento de canal e dep?sitos de plan?cie de inunda??o, e o sistema fluvial entrela?ado formado principalmente por dep?sitos de preenchimento de canal; as f?cies deste sistema se associam verticalmente segundo ciclos de afinamento textural para o topo (padr?o em sino nos perfis geof?sicos). O sistema lacustre, relacionado principalmente aos lit?tipos da Forma??o Crato, apresenta uma boa distribui??o na bacia, sendo composto por dep?sitos de pelitos verdes e calc?rios laminados. O sistema deltaico, representado por dep?sitos de prodelta e de frente deltaica, os quais se disp?em verticalmente em ciclos com granocresc?ncia para o topo (padr?o em sino invertido nos perfis geof?sicos). O sistema lagunar caracteriza-se pela presen?a de dep?sitos de anidrita e gipsita, al?m dos dep?sitos de pelitos negros com restos vegetais, os quais n?o cont?m uma fauna tipicamente marinha. O sistema de plataforma marinha ? composto por sucess?es de pelitos pretos e cinza com faunas fossiliferas de Dinoflagelados (g?neros Spiniferites Mantell, Subtilisphaera Jain e Subtilisphaera Millipied), t?picas de este tipo de sistema deposicional. As f?cies sedimentares descritas se arranjam verticalmente de forma a compor ciclos com padr?es de empilhamento progradacional, os quais formam ciclos com engrossamento textural para o topo, e retrogradacional, representados por ciclos com afinamento textural para o topo. Com base nestes ciclos, em seus padr?es de empilhamento e na mudan?a verticais entre estes padr?es, foram reconhecidos os tratos de sistemas e as seq??ncias deposicionais. Os tratos de sistemas de N?vel Baixo e o de N?vel Alto s?o compostos por ciclos com padr?o de empilhamento progradacional; o Trato de Sistemas Transgressivo, por sua vez, ? formado por ciclos com padr?o de empilhamento retrogradacional. A an?lise estratigr?fica 2D foi elaborada por meio da realiza??o de duas se??es estratigr?ficas. Para a escolha do datum foi privilegiada a superf?cie de m?xima inunda??o mais basal, interna ? Seq??ncia 1. A elabora??o destas se??es possibilitou compreender o comportamento de seis seq??ncias deposicionais ao longo da ?rea de estudo, as quais foram interpretadas como ciclos de segunda ordem ou superciclos (ciclos com dura??es entre 3 e 10 Ma), segundo a classifica??o de Vail, et al (1977). A Seq??ncia 1, mais antiga das seis seq??ncias identificadas, ? composta pelos tratos de sistemas de N?vel Baixo, Transgressivo e de N?vel Alto. Os dois primeiros tratos s?o formados exclusivamente pelos dep?sitos fluviais da Forma??o Rio da Batateira, ao passo que o terceiro inclui dep?sitos deltaicos e lacustres da Forma??o Crato. As seq??ncias 2 e 3 s?o formadas pelos tratos de sistemas Transgressivo (TST; fase de expans?o do lago) e de N?vel Alto (TSNA; fase retra??o do lago). Os TST s destas seq??ncias s?o formados por dep?sitos lacustres, ao passo que os TSNA s cont?m dep?sitos deltaicos, indicando assim condi??es de alta taxa de suprimento sedimentar na ?poca da deposi??o deste. A seq??ncia 4 ? formada pelos tratos de sistemas de N?vel Baixo (TSNA), Transgressivo e de N?vel Alto. O TSNB registra uma queda importante do n?vel base do lago; este trato se desenvolveu em condi??es de baixa raz?o entre a taxa de cria??o de espa?o de acomoda??o e a taxa de influxo sedimentar. O TST marca a terceira fase de expans?o do sistema lacustre na se??o p?s rifte da bacia; o sistema lacustre implantado no trato anterior inicia uma fase de retra??o em condi??es em que a taxa de aporte sedimentar passa a suplantar a de cria??o de espa?o de acomoda??o. A seq??ncia 5 desenvolveu-se em duas fases distintas. A primeira relaciona-se com a ?ltima etapa de expans?o do lago, (TST), trato basal desta seq??ncia. Nesta fase, o n?vel base do lago subiu consideravelmente. A segunda fase, relacionada ao TSNA), indica o final do dom?nio lacustre na Bacia do Araripe e a mudan?a para sistemas lagunares e de plan?cie de mar?, com grande desenvolvimento das por??es de supramar?. Estes sistemas eram formados por lagunas restritas, com l?mina de ?gua rasa, e com conex?o intermitente com o mar. Esta foi a fase em que a Bacia do Araripe registrou as mais severas condi??es de aridez de todo intervalo estudado, Aptiano ao Albiano, condi??es estas que propiciaram a forma??o de dep?sitos evapor?ticos. A seq??ncia 6 iniciou sua deposi??o ap?s uma queda significativa do incipiente mar (TSNB). Esta seq??ncia ?, indubitavelmente, a que cont?m os dep?sitos que comprovam a efetiva entrada do mar na Bacia do Araripe. O TST, trato final desta seq??ncia, representa o momento em que o n?vel do mar atingiu o seu m?ximo durante todo o intervalo Aptiano ao Albiano. A an?lise estratigr?fica do intervalo Aptiano ao Albiano permitiu compreender que o controle principal no desenvolvimento das seq??ncias deposicionais reconhecidas na Bacia do Araripe foram ?s varia??es do n?vel de base local, as quais s?o controladas, por sua vez, pelas mudan?as clim?ticas

Cladophora is a widespread freshwater filamentous cholorophyte genus and is frequently observed in eutrophic waters where it can produce large nuisance blooms. These blooms can have direct impacts on water intake for power generation, irrigation canals and can be aesthetically unpleasant. Much of the ecological and physiological studies on Cladophora have assumed that the populations of this genus in North America belong to the species Cladophora glomerata. However, this has never been tested despite that it is well documented that identifying freshwater Cladophora to the species level is difficult due morphological variability under different ecological conditions. In addition, the species epithets for freshwater Cladophora are based on European collections and it is not clear if these should be applied to North America. This study examines approximately 40 collections of Cladophora from the Laurentian Great Lakes and 43 from various locations in North America ranging from the Northwest Territories to Puerto Rico. Initially we determined the nucleotide sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal cistron and observed sequence divergence to be low (0-3%), demonstrating an inability for this marker to resolve species delineation as divergence of this region was low. Amplification of the inter-simple sequence repeat (ISSR) regions were used to analyze microsatellite motif frequency throughout the genome to evaluate the biogeography relationships, including diversity, of freshwater Cladophora sp. five different primers were used on 70 individuals. UPGMA analyses of the presence/absence of bands demonstrate that each of the Great Lake populations separate into groups according to the Lake they were initially sampled from. However, collections from North America are highly variable and do not form well supported biogeographic clades. In addition, these collections appear to be distinct from type cultures of freshwater Cladophora from Europe. Supplementary morphological analysis using suggested taxonomically valid criterion (length and diameter of main axis, ultimate branch, and apical cell) none were able to differentiate Great Lake populations.

In cancer research, class discovery is the first process for investigating a new dataset for which hidden groups there are by similar attributes. However datasets from gene expressions, RNA microarray or RNA-sequence, are high-dimensional. Which makes it hard to perform clusteranalysis and to get clusters that are well separated. Well separated clusters are wanted because that tells that objects are most likely not placed in wrong clusters. This report investigate in an experiment whether using K-Means and hierarchical are suitable for clustering gene expressions in RNA-sequence data from various tumors. Dimensionality reduction methods are also applied to see whether that helps create well-separated clusters. The results tell that well separated clusters are only achieved by using PCA as dimensionality reduction and K-Means on correlation. The main contribution of this paper is determining that using K-Means or hierarchical clustering on the full natural dimensionality of RNA-sequence data returns unwanted silhouette average width, under 0,4.

Molecular and morphologic studies were used to determine the evolution, classification and differentiation of Nymphaea odorata. Molecular analyses of the nuclear internal transcribed spacer (ITS) region, the chloroplast trnL-F region, and inter-simple sequence repeat (ISSR) markers determined the variation present between and within two species of Nymphaea. The ITS region resulted in a phylogeny depicting strong separation between species (N. mexicana and N. odorata) and some separation between N. odorataâ s subspecies. The ITS region contained polymorphisms, which upon SAHN clustering and principle coordinate (PCOA) and minimum spanning tree (MST) analyses produced groups similar to the clades in the ITS phylogeny. Sixteen accessions were chosen for trnL-F analysis, where a subspecies-specific molecular marker was found. In most accessions the marker confirmed the original subspecies classification. Molecular analyses using ISSRs characterized among population variation in N. odorata and N. mexicana using five primers. ISSR markers among populations were highly variable within a species and were used in UPGMA, PCOA and MST analysis, which resulted in separation between the subspecies. Both univariate and multivariate analyses were performed on quantitative and qualitative morphological characters. An analysis of variance resulted in six morphological characteristics that were statistically significant (P< 0.05), the majority being leaf blade characteristics. Multivariate statistics of principle component analysis and discriminate analysis resulted in groups for each subspecies, both emphasized the importance of quantitative leaf blade characteristics. Overall, both morphology and molecular characteristics supported the classification of subspecies for ssp. odorata and ssp. tuberosa, due a lack of strong segregation of characteristics.
Master of Science

ABSTRACT COMPARATIVE SEQUENCE ANALYSIS OF THE INTERNAL TRANSCRIBED SPACER 2 REGION OF TURKISH RED PINE (Pinus brutia TEN.) AND NATURAL ALEPPO PINE (Pinus halepensis MILL.) POPULATIONS FROM TURKEY Tozkar, Ö
zge M.S., Department of Biology Supervisor: Prof. Dr. Zeki Kaya April, 2007, 107 pages Turkish red pine (Pinus brutia) is wide-spread and an important forest tree species in Turkey, occurring mainly in southern, western and north-western Turkey and as small isolated populations in the Black Sea region. Aleppo pine (Pinus halepensis) has naturally found only in Adana and Mugla provinces as small population in mixture with Turkish red pine. Although Turkish red pine and Aleppo pine are morphologically different, Turkish red pine has been regarded as subspecies of Aleppo pine by some taxonomists due to occurrence of natural hybridization between these two species. However, the phylogenic relationship between these species needs to be explored further. In the present study, by sampling overlapped populations of both species from Mugla and Adana provinces (4 populations of Turkish red pine and 3 populations of Aleppo pine), internal transcribed spacer (ITS) region of ribosomal DNA were comparatively studied with sequence analysis. Although ITS1, 5.8s and ITS2 regions of ribosomal DNA were studied with ITS primers, only ITS2 region was successfully amplified with polymerase chain reaction (PCR). The complete data set for this region was analysed using MEGA3.1 and Arlequin softwares. Analysis of molecular variance (AMOVA) demonstrated the highest genetic differentiation between Turkish red pine and Aleppo pine in Mugla with 100 percentage of variation. AMOVA analysis also indicated the possibility of low-level migration of genes between Turkish red pine and Aleppo pine populations in Adana with 50.65 percent of molecular variance. Haplotype comparison revealed that two major haplotypes were represented Based on the results of ITS2 region sequence analysis, Turkish populations of Aleppo pine and Turkish red pine populations could not be fully differentiated. In Mugla province Turkish red pine and Aleppo pine revealed more differentiation due to reproductive isolation. But in Adana province, two species shared more common genetic background due to possible hybridization. Since ITS2 region of nuclear ribosomal DNA revealed a few variable and parsimony informative sites for both species, thus, only ITS2 region of ribosomal DNA does not appear to be sufficient for fully resolving genetic relationships between Turkish red pine and Aleppo pine populations. Further studies including ITS1 and 5.8s regions of ribosomal DNA and populations included from major Aleppo pine distribution areas will be useful to understand the evolutionary relationship between Aleppo pine and Turkish red pine populations in Turkey.

Wilson’s disease is a rare inborn error of metabolism caused by a defect in ATP7B, a protein necessary for proper copper excretion into bile. It is characterised by copper accumulation with hepatic and central nervous system dysfunction.

We investigated 24 Swedish families with Wilson’s disease by sequencing the entire coding sequence using a new technique called manifold sequencing. Disease causing mutations were found in 44 out of 48 alleles.

From data obtained in the first study, the two most common mutations (C3207A and C2930T) were sought in 2640 anonymous DNA samples from a Swedish population, using a pooling strategy and solid-phase minisequencing. Four C3207A and one C2930T were found. From the number of C3207A, a prevalence of Wilson’s disease in Sweden of about 1 in 110,000 could be estimated.

Four groups with three patients each had four different genotypes concerning mutations in ATP7B. The patients’ psychopathological symptoms were investigated, using the Karolinska Scales of Personality rating (KSP) and Comprehensive Psychopathological Rating Scale (CPRS). A trend towards lower CPRS scores was seen in the groups with mutations known to render ATP7B completely without activity.

Using ⁶¹Cu liver PET in patients homozygous for mutations in ATP7B, heterozygotes, normal individuals and two patients with alcoholic liver cirrhosis, significantly slower uptake was seen in the homozygotes as compared to the heterozygotes and normal individuals. The patients with cirrhosis had values in between. This implies that ⁶¹Cu liver PET might be used as an additional rapid and little invasive diagnostic tool in Wilson’s disease.

In a retrospectively studied cohort consisting of 363 patients followed in Sweden and the UK, nine cases of aggressive intra-abdominal malignancies were seen, which is more than expected. Caution should be taken in the follow-up of Wilson’s disease patients.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
The aim of this study was to evaluate the effectiveness of two procedures, Discrete Trial (DT) and Discrete Trial with Interresponse Interval (DT/IRI), on the production of behavioral variability in different conditions (directly reinforced and induced) and determine what condition, in each procedure, would facilitate the selection of an initial sequence of low probability. Were selected 18 college students with baseline performance measured by U-valeu, that was equal or less than 0,5. They were divided into the two procedures and subdivided into three groups with three participants (VAR, YOKE and CON). The task was to form images on the computer screen by pressing two keys (left and right) on lateral keyboards. The unit was four responses to the keys. In both procedures, a piece of the image, a tone and 0,5 seconds was used to reinforce sequences that attended the contingency s criterion, and a timeout of 1,0 second, if not. Only the DT/IRI had a 0,5 second interval after the first three responses of the sequence. The experiment had three phases. In Phase I, baseline, sequences was continuous reinforced (CRF). For two groups (DT- VAR and DT/IRI-VAR) in Phase 2, variability was direct reinforced on 15 sequences, mean that the less frequent and less recent sequence had more probability of been reinforced than the others, and a target sequence (less frequent sequence at baseline) was reinforced in CRF. In Phase 3, the distribution of reinforcement of the prior phase was yoked for the 15 sequences and another target sequence was reinforced in CRF. For the groups DT-YOKE and DT/IRI-YOKE, the phase s exposure was reversed, whereas in Phase 2 the distribution of reinforcement was yoked to the performance of the VAR groups. In groups DT-CON and DT/IRI-CON, only the target sequence was reinforced in both phases. The results showed that variability increased in the first session of Phase 2 for all participants. The DT-YOKE group showed the highest levels of variability within this procedure. In the DT/IRI procedure, this was true for the group DT/IRI-VAR. With regard to the selection of the target sequence the groups that had higher percentages of selection in all sessions were DT-CON and DT/IRI-VAR, respectively within each procedure. It was noted that both procedures produced the selection of the target sequence, but is seems that the use of IRI produced a more variable performance, when it was directly reinforced, allowing the selection of the target sequence to occur more rapidly
O objetivo do estudo foi avaliar a efetividade de dois procedimentos, Tentativa Discreta (TD) e Tentativa Discreta com Intervalo entre as Respostas (TD/IRI), na produção da variabilidade comportamental em diferentes condições (diretamente reforçada e induzida) e averiguar que condição, em cada procedimento, mais facilitaria a seleção de uma sequência de baixa probabilidade inicial. Selecionou-se 18 universitários com um desempenho na linha de base, medido pelo índice U, igual ou inferior a 0,5. Estes foram divididos nos dois procedimentos e subdivididos em três grupos com três participantes (VAR, ACO e CON). A tarefa consistia em formar figuras na tela do computador pressionando duas teclas (direita e esquerda) de teclados laterais. A unidade comportamental era quatro respostas às teclas. Nos dois procedimentos apresentava-se um pedaço da figura, um tom e 0,5 segundo, caso a sequência fosse passível de reforço, e um timeout de 1,0 segundo, caso não fosse. Somente no TD/IRI havia um IRI de 0,5 segundo após as três primeiras respostas da sequência. O experimento continha três fases. Na Fase 1, linha de base, vigorava o reforçamento contínuo (CRF) das 16 sequências. Para dois grupos (TD-VAR e TD/IRI-VAR) na Fase 2 havia o reforçamento direto da variabilidade, para 15 sequências, no qual a sequência menos frequente e menos recente teria maior probabilidade de ser reforçada, e CRF de uma sequência alvo (sequência menos frequente na linha de base). Na Fase 3, havia a distribuição acoplada dos reforços da fase anterior para as 15 sequências e CRF de outra sequência alvo. Para os grupos TD-ACO e TD/IRI-ACO a ordem de exposição às fases foi inversa, visto que na Fase 2 a distribuição de reforços foi acoplada ao desempenho dos participantes dos grupos VAR. Nos grupos TD-CON e TD/IRI-CON havia somente o CRF da sequência alvo nas duas fases. Os resultados mostraram que a variabilidade aumentou na primeira sessão da Fase 2 para todos os participantes. O grupo TD-ACO foi o que apresentou maior índices de variabilidade dentro deste procedimento. Já no TD/IRI, isto foi verdadeiro para o grupo TD/IRI-VAR. Com relação à seleção da sequência alvo, os grupos que apresentaram maiores porcentagens de seleção em todas as sessões foram TD-CON e TD/IRI-VAR, respectivamente dentro de cada procedimento. Notou-se que os dois procedimentos produziram seleção da sequência alvo, mas parece que o uso do IRI produziu um responder mais variável, quando este foi diretamente reforçado, o que possibilitou que a seleção da sequência alvo ocorresse mais rapidamente

This thesis is devoted to two $\mathcal{NP}$-complete combinatorial optimization problems arising in computational biology, the well-studied \emph{multiple sequence alignment} problem and the new formulated \emph{interval constraint coloring} problem. It shows that advanced mathematical programming techniques are capable of solving large scale real-world instances from biology to optimality. Furthermore, it reveals alternative methods that provide approximate solutions. In the first part of the thesis, we present a \emph{Lagrangian relaxation} approach for the multiple sequence alignment (MSA) problem. The multiple alignment is one common mathematical abstraction of the comparison of multiple biological sequences, like DNA, RNA, or protein sequences. If the weight of a multiple alignment is measured by the sum of the projected pairwise weights of all pairs of sequences in the alignment, then finding a multiple alignment of maximum weight is $\mathcal{NP}$-complete if the number of sequences is not fixed. The majority of the available tools for aligning multiple sequences implement heuristic algorithms; no current exact method is able to solve moderately large instances or instances involving sequences exhibiting a lower degree of similarity. We present a branch-and-bound (B\&B) algorithm for the MSA problem.\ignore{the multiple sequence alignment problem.} We approximate the optimal integer solution in the nodes of the B\&B tree by a Lagrangian relaxation of an ILP formulation for MSA relative to an exponential large class of inequalities, that ensure that all pairwise alignments can be incorporated to a multiple alignment. By lifting these constraints prior to dualization the Lagrangian subproblem becomes an \emph{extended pairwise alignment} (EPA) problem: Compute the longest path in an acyclic graph, that is penalized a charge for entering ``obstacles''. We describe an efficient algorithm that solves the EPA problem repetitively to determine near-optimal \emph{Lagrangian multipliers} via subgradient optimization. The reformulation of the dualized constraints with respect to additionally introduced variables improves the convergence rate dramatically. We account for the exponential number of dualized constraints by starting with an empty \emph{constraint pool} in the first iteration to which we add cuts in each iteration, that are most violated by the convex combination of a small number of preceding Lagrangian solutions (including the current solution). In this \emph{relax-and-cut} scheme, only inequalities from the constraint pool are dualized. The interval constraint coloring problem appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy is a method used to obtain information about protein tertiary structure. The output of these experiments provides aggregate data about the exchange rate of residues in overlapping fragments of the protein backbone. These fragments must be re-assembled in order to obtain a global picture of the protein structure. The interval constraint coloring problem is the mathematical abstraction of this re-assembly process. The objective of the interval constraint coloring problem is to assign a color (exchange rate) to a set of integers (protein residues) such that a set of constraints is satisfied. Each constraint is made up of a closed interval (protein fragment) and requirements on the number of elements in the interval that belong to each color class (exchange rates observed in the experiments). We introduce a polyhedral description of the interval constraint coloring problem, which serves as a basis to attack the problem by integer linear programming (ILP) methods and tools, which perform well in practice. Since the goal is to provide biochemists with all possible candidate solutions, we combine related solutions to equivalence classes in an improved ILP formulation in order to reduce the running time of our enumeration algorithm. Moreover, we establish the polynomial-time solvability of the two-color case by the integrality of the linear programming relaxation polytope $\mathcal{P}$, and also present a combinatorial polynomial-time algorithm for this case. We apply this algorithm as a subroutine to approximate solutions to instances with arbitrary but fixed number of colors and achieve an order of magnitude improvement in running time over the (exact) ILP approach. We show that the problem is $\mathcal{NP}$-complete for arbitrary number of colors, and we provide algorithms that, given an instance with $\mathcal{P}\neq\emptyset$, find a coloring that satisfies all the coloring requirements within $\pm 1$ of the prescribed value. In light of our $\mathcal{NP}$-completeness result, this is essentially the best one can hope for. Our approach is based on polyhedral theory and randomized rounding techniques. In practice, data emanating from the experiments are noisy, which normally causes the instance to be infeasible, and, in some cases, even forces $\mathcal{P}$ to be empty. To deal with this problem, the objective of the ILP is to minimize the total sum of absolute deviations from the coloring requirements over all intervals. The combinatorial approach for the two-color case optimizes the same objective function. Furthermore, we use this combinatorial method to compute, in a Lagrangian way, a bound on the minimum total error, which is exploited in a branch-and-bound manner to determine all optimal colorings. Alternatively, we study a variant of the problem in which we want to maximize the number of requirements that are satisfied. We prove that this variant is $\mathcal{APX}$-hard even in the two-color case and thus does not admit a polynomial time approximation scheme (PTAS) unless $\mathcal{P}=\mathcal{NP}$. Therefore, we slightly (by a factor of $(1+\epsilon)$) relax the condition on when a requirement is satisfied and propose a \emph{quasi-polynomial time approximation scheme} (QPTAS) which finds a coloring that ``satisfies'' the requirements of as many intervals as possible.

Les nouvelles technologies de séquençage (NGS) ont révolutionné nos approches de la génomique.De nombreux génomes d'organismes ont été séquencés et assemblés.Le décryptage de l'information qu'ils contiennent (annotation) est plus que jamais une étape cruciale.Dans ce manuscrit, je vais me focaliser sur l’impact qu'ont eu les NGS sur l'annotation des génomes de paramécies, et notamment l'annotation de gènes et d'éléments transposables (ET).La paramécie est un eucaryote unicellulaire possédant deux types de noyaux. Un noyau germinal (MIC) utilisé pour transmettre l'information génétique à la génération sexuelle suivante, et un noyau somatique (MAC) assurant l'expression des gènes.Les caractéristiques particulières des gènes de paramécies m'ont incité à développer une chaîne de procédures dédiée à leur annotation, utilisant des données ARN-seq.A chaque cycle sexuel, le MAC parental est perdu et un nouveau MAC est généré à partir d'un MIC impliquant des réarrangements programmés de génome et notamment de l'élimination d'ADN portant des ET et de petites séquences à copie unique appelées IES (Internal Eliminated Sequence). Nous avons développé le logiciel ParTIES, utilisant des données ADN-seq, pour identifier les ~45 000 IES du génome de Pararamecium tetraurelia et montré que les IES sont des reliques d'ET.Une série de trois duplications globales de génome (WGD) anciennes mais encore visible, pendant l'histoire évolutive de la lignée, nous a permis de décrire la dynamique d'invasion et d'évolution des ET à l'origine des IES
The next generation sequencing technologies (NGS) have revolutionized genomics.Genomes of numerous organisms have been sequenced and assembled.Deciphering the encoded information (annotation) has more than ever become crucial. In this thesis manuscript, I focus on the impact of NGS on the annotation of Paramecium genomes, in particular the annotation of genes and transposable elements (TE).Paramecia is a unicellular eukaryote possesses two types of nuclei. A germline nucleus (MIC) transmits the genetic information to the next sexual generation, and a somatic nucleus (MAC) is responsible for gene expression.Special genes caracteristics of paramecia stimulated me to develop a workflow dedicated to their annotation, using RNA-seq data.At each sexual cycle, the parental MAC is lost and a new MAC develops from a copy of the MIC, through programmed genome rearrangements, notably the elimination of DNA corresponding to TE and short unique copy sequences called IES (Internal Eliminated Sequence).I developed the ParTIES software, using DNA-Seq data, to identify the ~45,000 IESs in the germline genome of Paramecium tetraurelia and to show that the IESs are remnants of TE.A series of three whole genome duplications (WGD) in the evolutionary history of the lineage, ancient but still visible, allow us to describe the dynamics of the invasion and evolution of TE that decay to become IES

Le travail produit s'inscrit dans un cadre industriel piloté par la société 2MoRO Solutions. La réalisation présentée dans cette thèse doit servir à l'élaboration d'un service à haute valeur, permettant aux exploitants aéronautiques d'optimiser leurs actions de maintenance. Les résultats obtenus permettent d'intégrer et de regrouper les tâches de maintenance en vue de minimiser la durée d'immobilisation des aéronefs et d'en réduire les risques de panne.La méthode que nous proposons comporte trois étapes : (i) une étape de rationalisation des séquences afin de pouvoir les combiner [...]
The present work is part of an industrial project driven by 2MoRO Solutions company.It aims to develop a high value service enabling aircraft operators to optimize their maintenance actions.Given the large amount of data available around aircraft exploitation, we aim to analyse the historical events recorded with each aircraft in order to extract maintenance forecasting. Theresults are used to integrate and consolidate maintenance tasks in order to minimize aircraft downtime and risk of failure. The proposed method involves three steps : (i) streamlining information in order to combinethem, (ii) organizing this data for easy analysis and (iii) an extraction step of useful knowledgein the form of interesting sequences. [...]

Most evolutionary analyses are based upon pre-estimated multiple sequence alignment models. From a computational point of view, it is too complex to estimate a correct alignment, as it is to derive a correct tree from that alignment. Several works have recently reported on the influence of alignment on downstream analysis, and on the uncertainty inherent to their estimation. Chapter 1 develops the notion of alignment uncertainty as either inherent to the data (internal) or resulting from methodological biases (external). Chapter 2 presents two contributions of mine for the improvement of MSA methods through the use of homology extension (TM-Coffee) and thanks to an improved word-matching algorithm (SymAlign). In Chapter 3, I show how alignment uncertainty can be used to improve the trustworthiness of phylogenetic analysis. Chapter 4 shows how a similar improvement can be obtained through a simple adaptation of the T-Coffee transitive score, thus allowing downstream analysis to take into account internal alignment uncertainty. The final chapter contained a discussion of our current results and possible future work.
La mayoría de los análisis evolutivos están basados en modelos establecidos de alineamiento de secuencia múltiple. Desde un punto de vista computacional, es igual de complejo la estimación de un alineamiento correcto, como la obtención de un árbol correcto a partir del alineamiento. Recientemente varios trabajos han informado sobre la influencia del alineamiento en los análisis posteriores, y en la incertidumbre inherente a su estimación. El Capítulo 1 desarrolla el concepto de incertidumbre de alineación, tanto inherente a los datos (internos), como resultante de los sesgos metodológicos (externo). El Capítulo 2 presenta dos contribuciones mías para la mejora de los métodos de MSA a través del uso de la extensión de homología (TM‐Coffee) y gracias a un algoritmo de coincidencia de palabra mejorado (SymAlign). En el capítulo 3, se muestra cómo la incertidumbre de alineación puede ser utilizada para mejorar la confiabilidad del análisis filogenético. El capítulo 4 nos muestra como se puede obtener una mejora similar por medio de una simple adaptación de la puntuación transitiva del T-- Coffee, lo cual permite un análisis posterior para tener en cuenta la incertidumbre de alineación interna. El último capítulo contiene un análisis de los resultados actuales y los posibles futuros trabajos.

Робота полягає у розробленні методів визначення інтервалів між калібруваннями (міжкалібрувальних інтервалів) робочих еталонів та засобів вимірювальної техніки, які застосовуються у випробувальних та калібрувальних лабораторіях, спрямована на забезпечення метрологічної простежуваності, точності та достовірності результатів вимірювань. У роботі досліджено можливість контролю відповідності метрологічних характеристик еталонів та засобів вимірювальної техніки встановленим нормам із застосуванням контрольних карт накопичених сум (CUSUM-карт). Проведені дослідження показали, що, незважаючи на здатність CUSUM-карт виявляти навіть незначні зміни метрологічних характеристик засобів вимірювальної техніки, час отримання сигналів може бути досить тривалим. Проаналізувавши затримку сигналів на CUSUM-картах та недоліки, що їх спричинюють, було запропоновано новий метод ковзної регресії на CUSUM-карті. Метод заснований на порівнянні кута нахилу регресійної лінії, проведеної за кількома послідовними точками на карті, з розрахованим гранично допустимим. Показано теоретично та доведено експериментально, що застосування методу ковзної регресії дозволяє зменшити час затримки сигналу про вихід метрологічних характеристик еталонів чи засобів вимірювальної техніки за встановлені границі. Представлено новий підхід до контролю стану засобів вимірювальної техніки шляхом аналізу СКВ результатів спостережень, що вказує на зменшення їх чутливості. Підхід заснований на ймовірнісному аналізі потрапляння СКВ результатів спостережень в певні діапазони розподілу Пірсона. Введено поняття критичної послідовності точок, виникнення якої вказує на зміну чутливості з часом засобу вимірювальної техніки, та коефіцієнт ефективності, який вказує на доцільність застосування того чи іншого підходу. На основі проведених розрахунків та досліджень запропоновано адаптивний алгоритм виявлення критичної послідовності СКВ-точок, який дозволяє контролювати стан робочих еталонів та засобів вимірювальної техніки, спираючись на отримані СКВ результатів спостережень у контрольних точках. Наведено теоретичне та експериментальне обґрунтування розроблених методів, показано в якому випадку необхідно застосовувати той чи інший метод.

Cette thèse s'inscrit dans le domaine de l'apprentissage statistique. Le cadre principal est celui de la prévision de suites déterministes arbitraires (ou suites individuelles), qui recouvre des problèmes d'apprentissage séquentiel où l'on ne peut ou ne veut pas faire d'hypothèses de stochasticité sur la suite des données à prévoir. Cela conduit à des méthodes très robustes. Dans ces travaux, on étudie quelques liens étroits entre la théorie de la prévision de suites individuelles et le cadre statistique classique, notamment le modèle de régression avec design aléatoire ou fixe, où les données sont modélisées de façon stochastique. Les apports entre ces deux cadres sont mutuels : certaines méthodes statistiques peuvent être adaptées au cadre séquentiel pour bénéficier de garanties déterministes ; réciproquement, des techniques de suites individuelles permettent de calibrer automatiquement des méthodes statistiques pour obtenir des bornes adaptatives en la variance du bruit. On étudie de tels liens sur plusieurs problèmes voisins : la régression linéaire séquentielle parcimonieuse en grande dimension (avec application au cadre stochastique), la régression linéaire séquentielle sur des boules L1, et l'agrégation de modèles non linéaires dans un cadre de sélection de modèles (régression avec design fixe). Enfin, des techniques stochastiques sont utilisées et développées pour déterminer les vitesses minimax de divers critères de performance séquentielle (regrets interne et swap notamment) en environnement déterministe ou stochastique.

Today, the main research field for the automotive industry is to find solutions for active safety. In order to perceive the surrounding environment, tracking nearby traffic objects plays an important role. Validation of the tracking performance is often done in staged traffic scenarios, where additional sensors, mounted on the vehicles, are used to obtain their true positions and velocities. The difficulty of evaluating the tracking performance complicates its development. An alternative approach studied in this thesis, is to record sequences and use non-causal algorithms, such as smoothing, instead of filtering to estimate the true target states. With this method, validation data for online, causal, target tracking algorithms can be obtained for all traffic scenarios without the need of extra sensors. We investigate how non-causal algorithms affects the target tracking performance using multiple sensors and dynamic models of different complexity. This is done to evaluate real-time methods against estimates obtained from non-causal filtering. Two different measurement units, a monocular camera and a LIDAR sensor, and two dynamic models are evaluated and compared using both causal and non-causal methods. The system is tested in two single object scenarios where ground truth is available and in three multi object scenarios without ground truth. Results from the two single object scenarios shows that tracking using only a monocular camera performs poorly since it is unable to measure the distance to objects. Here, a complementary LIDAR sensor improves the tracking performance significantly. The dynamic models are shown to have a small impact on the tracking performance, while the non-causal application gives a distinct improvement when tracking objects at large distances. Since the sequence can be reversed, the non-causal estimates are propagated from more certain states when the target is closer to the ego vehicle. For multiple object tracking, we find that correct associations between measurements and tracks are crucial for improving the tracking performance with non-causal algorithms.

Калашников, К. О. Зменшення втрат електроенергії в тяговій мережі постійного струму шляхом вибору раціональної дислокації тягових навантажень : авт. дис. к. т. н. / К. О. Калашников ; Дніпропетр. нац. ун-т залізн. трансп. ім. акад. В. Лазаряна. - Д. : Вид-во Дніпропетр. нац. ун-ту залізн. трансп. ім. акад. В. Лазаряна, 2014. - 20 с. : іл. ГРНТИ 73.29.71 УДК 621.331:621.311.024(043.3) Захист – 6 березня 2014 р.
UK: АНОТАЦІЯ Дисертація присвячена вирішенню актуальної науково-технічної задачі зменшення втрат електроенергії в тяговій мережі постійного струму шляхом вибору раціональної дислокації тягових навантажень. На основі аналізу існуючих методів зменшення втрат електроенергії в тяговій мережі встановлено, що існують додаткові резерви зменшення втрат шляхом вибору раціональної дислокації тягових навантажень, послідовності відправлення поїздів різних категорій, інтервалів між поїздами. Сформульовано принцип зменшення втрат електроенергії в тяговій мережі на основі методу деформованого багатогранника, який дозволяє розраховувати оптимальні відстані між тяговими навантаженнями для побудови енергоефективних ГРП. Розглянуто ситуації для різної кількості поїздів між ТП. Запропоновано принцип зменшення втрат електроенергії в тяговій мережі на основі евристичного алгоритму пошуку мінімуму функції списку шляхом вибору оптимальної послідовності відправлення та інтервалів між поїздами. При цьому послідовність поїздів різних категорій представляється як список, а кожній послідовності відправлення поїздів різних категорій відповідає певне значення втрат електроенергії в тяговій мережі. Розроблено програмний комплекс для складання енергоефективних ГРП. Проведено експериментальну перевірку теоретичних положень дисертації з використанням програмного комплексу «Поток». Чистий дисконтований дохід для електрифікованих ділянок Придніпровської залізниці за 1 рік становить 1,4 млн грн.
RU: АННОТАЦИЯ Диссертация посвящена решению актуальной научно-технической задачи уменьшения потерь электроэнергии в тяговой сети постоянного тока путем выбора рациональной дислокации тягових нагрузок. На основе анализа существующих методов уменьшения потерь электроэнергии в тяговой сети установлено, что существуют дополнительные резервы снижения потерь путем выбора рациональной дислокации тяговых нагрузок, последовательности отправления поездов различных категорий, интервалов между поездами. Выделены факторы, которые влияют на величину потерь электроэнергии в тяговой сети постоянного тока: параметры СТЭ – схемы питания контактной сети, длина фидерной зоны, мощность и напряжение на шинах ТП; параметры пути – сопротивление движению, уклоны; технические данные ЭПС – максимальная скорость, масса, мощность, потребляемый ток; параметры транспортного потока – дислокация поездов между ТП, размеры движения, интервалы между поездами, последовательность отправления поездов различных категорий; прочие факторы – квалификация машинистов, погодные условия. Установлен потенциал уменьшения потерь электроэнергии в тяговой сети путем уменьшения неравномерности транспортного потока: для схемы двухстороннего питания величина потерь изменяется на 18,9 %; для узловой схемы питания – на 11,1 %. Разработаны модели СТЭ и транспортного потока, в которых ж.д. станция представлена как трансформатор транспортного потока с возможностью учета влияния показателей транспортного потока на величину потерь электроэнергии в тяговой сети. Установлены предельные показатели транспортного потока по условиям работы СТЭ для электрифицированного участка Приднепровской ж.д.: максимальная интенсивность транспортного потока – , максимальная плотность транспортного потока – . Разработана математическая модель энергооптимальной дислокации тяговых нагрузок между ТП, позволяющая выбирать схемы расположения тяговых нагрузок между ТП на каждом шаге времени, при которых потери электроэнергии в тяговой сети минимальны. Предложен подход, при котором расстояния между тяговыми нагрузками представлены как ребра многогранника. Ограничения по безопасности движения поездов учитываются следующим образом: минимальная длина ребра должна быть не меньше длины блок-участка устройств СЦБ, максимальная – не более длины рассматриваемого участка. Сформулирован принцип уменьшения потерь электроэнергии в тяговой сети на основе метода деформируемого многогранника, который позволяет рассчитывать оптимальные расстояния между тяговыми нагрузками для построения энергоэффективных ГДП. Рассмотрены ситуации для различного количества поездов между ТП. Предложен принцип уменьшения потерь электроэнергии в тяговой сети на основе эвристического алгоритма поиска минимума функции списка путем выбора оптимальной последовательности отправления и интервалов между поездами. При этом последовательность поездов различных категорий представляется как список, а каждой последовательности отправления поездов различных категорий поставлено в соответствие определенное значение потерь электроэнергии в тяговой сети. Разработан программный комплекс для составления энергоэффективных ГДП. Проведена экспериментальная проверка теоретических положений диссертации с использованием программного комплекса «Поток» путем имитационного моделирования. Установлены пределы изменения величины потерь электроэнергии в зависимости от: последовательности отправления поездов для различных схем питания – 20-23 % (двухсторонняя – 20 %, узловая и параллельная – 23 %); дислокации и интервалов между тяговыми нагрузками – 23–27 % (двухсторонняя – 23 %, узловая и параллельная – 27 %). Проведены технико-экономические расчеты, подтверждающие эффективность применения методов уменьшения потерь электроэнергии в тяговой сети путем выбора рациональной дислокации тяговых нагрузок. Чистый дисконтированный доход для электрифицированных участков Приднепровской ж.д. за 1 год составляет 1,4 млн грн.
EN: ABSTRACT The dissertation is devoted to the solution of the important scientific and technical tasks - decreasing energy losses in traction line by choosing a rational dislocation traction loads. Based on the analysis of existing methods of reducing electricity losses in traction lines it’s established that there are additional reserves of decreasing losses by choosing a rational dislocation of the traction loads, sequence of departure of trains with different categories, intervals between trains. It’s formulated the principles of reducing electric power losses in traction lines based on the method of strain of the polytope, which allows to calculate the optimal distance between traction loads for building energy-efficient schedule of trains. The author proposed the principle of reduction of electricity losses in traction line on the basis of the heuristic algorithm for finding the minimum of the function list by selecting the optimal sequence of departure and intervals between trains. The sequence of trains with various categories is represented as a list, and each sequence of trains with different categories corresponds to a certain value of electricity losses in traction lines. It’s developed a software package designed to compute energy-efficient train schedule. An experimental verification of theoretical propositions in dissertation using software complex «Potok» on the basis of simulation showed a positive economice effect.The net product value for electrified sections of Pridneprovskaya railway for 1 year is 1.4 million UAH.

碩士
元智大學
工業工程與管理學系
98
To survive in current competitive and fast-changed business environment, enterprises need to know their customers behavior in depth to provide the right services to customers at right time. However, the customer databases in enterprises are usually large and disordered which makes customer behavior analysis difficult. Sequential pattern mining and sequence classification are two popular data mining methods to explore customer behavior. The former can discover frequent occurring patterns, while the latter can assign a most probable class label to a given sequence based on the characteristics of the sequence. However, previous researches seldom discussed sequence classification problem related to time information. Without time information, two sequences with the same itemsets but different time-intervals will be classified as the same class, which is inappropriate in customer behavior analysis. For this reason, this research presents a time-interval sequence classification methodology to help decision makers make better business strategies to satisfy their various customers. The proposed sequence classification methodology includes two main stages. The first stage is time-interval sequential pattern mining, which employs I-PrefixSpan algorithm to discover time-interval sequential patterns in the large database. The second stage is time-interval sequence classification method, which contains sequence similarity measure, time-interval sequence classification model establishment, and model optimization procedure. A simple case and NorthWind database which is a large scale database are employed to test the classification method. The experiment results indicate the proposed time-interval sequence classification method is feasible and efficient.

碩士
東海大學
資訊工程與科學系碩士在職專班
96
Facing competitively intense era, the enterprise adopts the computer to enhance the benefit all. Using data mining technique can help enterprise to mine useful information in huge databases. Data mining is a popular domain of research in resent years, and sequential pattern mining is one of the popular techniques. Sequential pattern mining is used to disclose frequent sequential patterns in databases. This technique has broad applications, including marketing and behavior analysis of customer purchasing, web browsing, and time series analysis and so on. However, researches about the sequence of consumers’ shopping behaviors are mostly in producing frequent sequential patterns by generating and verifying candidates of sequential patterns. Recent years, some scholars proposed closed partial order method in place of finding sequential patterns, which can find accurate and interesting information in sequence database. Nevertheless, the closed partial order can display the ordering relationship of items, but it can’t discover the detailed information of times. In this paper, our research focuses on finding closed time-interval partial orders in item-interval sequence databases. In addition, we develop an efficient algorithm to reveal closed time-interval partial orders.

博士
國立中央大學
企業管理研究所
98
This research models the sequences and time-intervals of network intrusion. In order to maintain network security, common intrusion detection systems have to monitor the entire network environment. However, most traditional detection methods generate too many intrusion alerts, which forces network administrators to conduct numerous investigations of suspicious incidents to determine potential intrusion behavior. To solve this problem, this research combines specific time-interval clustering analysis of online user’s behaviors with sequential pattern analysis to provide specific rules of intrusion behaviors. The acquired sequential pattern of the intrusion events lists the ordered relationship of all intrusion related events. In addition, the possible time-intervals between events are analyzed and clustered to indentify exact frequent time-intervals. The proposed method can provide specific intrusion information to the network administrator, which effectively helps him to monitor and maintain network security with less time and effort.

碩士
國立中央大學
資訊管理研究所
96
Sequential pattern mining can reveal the behaviors of events along the time, and it is one of the most important approaches in data mining. In sequence data, events can be classified into two major types, where one is point-based events and the other is interval-based events. When a data sequence can contain both types of events, we say this data sequence has hybrid events. Recently, the work of Wu and Chen has proposed algorithms to discover sequential patterns of hybrid events, called hybrid temporal patterns. Although hybrid temporal patterns can reveal the temporal relationships among hybrid events, they can not tell us the time intervals among events. Therefore, this thesis extends hybrid temporal patterns so that the time intervals among events can be revealed. We call this type of extended patterns as time-interval hybrid temporal patterns. In the thesis, we proposed two algorithms, ti-HPrefixSpan and ti-HTPM, to discover time-interval hybrid temporal patterns by modifying traditional PrefixSpan and GSP algorithms, respectively. In the experiments, we evaluate the proposed methods’ performance using synthetic data and real stock price data. The results of the experiments show that the performances of the two proposed algorithms are quite satisfactory. Besides, we also show that time-interval hybrid temporal patterns can obtain higher prediction accuracy than hybrid temporal patterns.

碩士
國立中央大學
資訊管理研究所
92
Sequential pattern mining is of great importance in many applications including computational biology study, consumer behavior analysis, system performance analysis, etc. Recently, an extension of sequential patterns, called time-interval sequential patterns, is proposed by Chen, Jiang, and Ko, which not only reveals the order of items but also the time intervals between successive items. For example: having bought a laser printer, a customer returns to buy a scanner in three months and then a CD burner in six months. Although time-interval sequential patterns are useful in predicting when the customer would take the next step, it can not determine when the next k steps will be taken. Hence, we present two efficient algorithms, MI-Apriori and MI-PrefixSpan to solve this problem. The experimental results show that the MI-PrefixSpan algorithm is faster than the MI-Apriori algorithm but the MI-Apriori algorithm has a better scalability.