Dans cette thèse, nous présentons des méthodes de calcul (modèles théoriques et algorithmiques) pour effectuer la reconstruction de séquences d'ADN. Il s'agit de l'assemblage de novo de génome à partir de lectures (courte séquences ADN) produites par des séquenceurs à haut débit. Ce problème est difficile, aussi bien en théorie qu'en pratique. Du point de vue théorique, les génomes sont structurellement complexes. Chaque instance d'assemblage de novo doit faire face à des ambiguïtés de reconstruction. Les lectures peuvent conduire à un nombre exponentiel de reconstructions possibles, une seule étant correcte. Comme il est impossible de déterminer laquelle, une approximation fragmentée du génome est retournée. Du point de vue pratique, les séquenceurs produisent un énorme volume de lectures, avec une redondance élevée. Une puissance de calcul importante est nécessaire pour traiter ces lectures. Le séquençage ADN évolue désormais vers des génomes et méta-génomes de plus en plus grands. Ceci renforce la nécessité de méthodes efficaces pour l'assemblage de novo. Cette thèse présente de nouvelles contributions en informatique autour de l'assemblage de génomes. Ces contributions visent à incorporer plus d'information pour améliorer la qualité des résultats, et à traiter efficacement les données de séquençage afin de réduire la complexité du calcul. Plus précisément, nous proposons un nouvel algorithme pour quantifier la couverture maximale d'un génome atteignable par le séquençage, et nous appliquons cet algorithme à plusieurs génomes modèles. Nous formulons un ensemble de problèmes informatiques pour incorporer l'information des lectures pairées dans l'assemblage, et nous étudions leur complexité. Cette thèse introduit la notion d'assemblage localisé, qui consiste à construire et parcourir un graphe d'assemblage partiel. Pour économiser l'utilisation de la mémoire, nous utilisons des structures de données optimisées spécifiquement pour la tâche d'assemblage. Ces notions sont implémentées dans un nouvel assembleur de novo, Monument. Enfin, le dernier chapitre de cette thèse est consacré à des concepts d'assemblage dépassant l'assemblage de novo classique. / In this thesis, we discuss computational methods (theoretical models and algorithms) to perform the reconstruction (de novo assembly) of DNA sequences produced by high-throughput sequencers. This problem is challenging, both theoretically and practically. The theoretical difficulty arises from the complex structure of genomes. The assembly process has to deal with reconstruction ambiguities. The output of sequencing predicts up to an exponential number of reconstructions, yet only one is correct. To deal with this problem, only a fragmented approximation of the genome is returned. The practical difficulty stems from the huge volume of data produced by sequencers, with high redundancy. Significant computing power is required to process it. As larger genomes and meta-genomes are being sequenced, the need for efficient computational methods for de novo assembly is increasing rapidly. This thesis introduces novel contributions to genome assembly, both in terms of incorporating more information to improve the quality of results, and efficiently processing data to reduce the computation complexity. Specifically, we propose a novel algorithm to quantify the maximum theoretical genome coverage achievable by sequencing data (paired reads), and apply this algorithm to several model genomes. We formulate a set of computational problems that take into account pairing information in assembly, and study their complexity. Then, two novel concepts that cover practical aspects of assembly are proposed: localized assembly and memory-efficient reads indexing. Localized assembly consists in constructing and traversing a partial assembly graph. These ingredients are implemented in a complete de novo assembly software package, the Monument assembler. Monument is compared with other state of the art assembly methods. Finally, we conclude with a series of smaller projects, exploring concepts beyond classical de novo assembly.

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A ( diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

This thesis is focused on the preparation of monosubstituted derivatives of -cyclodextrin ( -CD) which can form supramolecular polymers. These polymers can be utilized in capillary electrophoresis. Set of monosubstituted 2I -O-, 3I -O- a 6I -O-(3-(naphthalen-2-yl)prop-2-en-1-yl) derivatives of -CD was prepared (naphthylallyl derivatives). Reaction was performed by cross metathesis of O-allyl derivatives of -CD with a 2-vinylnaphthalene in yields 16 - 25 %. Hoveyda-Grubbs 2nd generation catalyst was used. Alkylation of -CD with 2-(3-bromoprop-1-enyl)naphthalene followed by peracetylation of remaining hydroxyl groups and separation of isomers resulted in the per-O-acetyl-3I -O- a per-O- acetyl-6I -O-(3-(naphthalen-2-yl)prop-2-en-1-yl)- -CD in yields 5 and 1 %. A set of dimers of -CD 1,4-bis( -CD-2I -O-yl)-but-2-ene, 1,4-bis( -CD-3I -O-yl)-but-2-ene and 1,4-bis( - CD-6I -O-yl)-but-2-ene was prepared, too. Reaction was performed by cross metathesis of O-allyl derivatives of -CD in yields 1 - 8 % using again Hoveyda-Grubbs 2nd generation catalyst. The dimers of naphthalene guests (1,2-bis(naphthalen-2-yl)ethene and 1,2-bis(naphthalen-2-yl)ethane) for preparation of complexes with CD dimers were also prepared. Further optimization of synthesis of naphthylallyl derivatives of -CD was carried out. These...

This diploma thesis deals with cooperatives and closely focuses on their bodies. Czech legal order gives only superficial legislation which causes many questions and imperfections to arise. The aim of this thesis is to find solutions to these problems and create an ideal model of cooperative. Following that, the author bases his thoughts on the legal doctrine and Czech court jurisdiction. The introductory part focuses on general questions, i.e. history of cooperatives, legislation and legal characteristics of cooperatives. The author refers to the negative impact of the Communistic Party of Czechoslovakia on cooperativeness between years 1948 - 1989. Such impacts are still present in nowadays legislation. Another imperfections are seen in the starkness and fragmentation of the legislation itself. All these imperfections may be removed by the future law about business cooperatives. The main body of the thesis follows as this describes the cooperative body legislation. Current legislation brings three obligatory bodies - assembly, board and control committee. Next to these, every cooperative may establish optional bodies. The chapter on assembly deals with its status and scope. In connection with assembly's scope the author describes in detail the process of assembly's decisions approving, together...

Proton Lighting AB tillverkar professionell belysning för skola, industri, butiker och offentliga miljöer. Proton Lighting har en årlig tillverkning av 400 000 armaturer i sin fabrik i Värnamo. En ökad global konkurrens medför ökad prispress, samtidigt som Proton Lighting önskar vara flexibla mot sina kunder och erbjuda konkurrenskraftiga leveranstider. För att öka sin konkurrenskraft på marknaden undersöker Proton Lighting möjligheterna till en effektivisering av monteringsprocessen. Monteringen av armaturer utförs idag av montörer självständigt vid enskilda monteringsbänkar. Armaturerna monteras och färdigställs till största del i en sekvens, av en och samma montör. Samarbete och interaktion mellan montörer är minimalt med nuvarande arbetssätt och kompentensvariationer är påtagliga. Montörerna ansvarar också för utförandet av stödjande aktiviteter kopplade till monteringen. Materialförsörjningen utförs idag till stor del av montörerna själva, allt från beställning av material, hämta plockartiklar till retur av material. Syftet med detta arbete är att undersöka möjligheterna till en förändrad monteringsprincip med tillhörande materialförsörjning som effektiviserar monteringsprocessen genom att minimera andelen stödjande aktiviteter kopplade till monteringen. En fallstudie genomfördes på Proton Lighting i syfte att belysa problembilden samt skapa en nulägesbeskrivning av verksamheten. Insamlad data har analyserats tillsammans med studiens teoretiska ramverk kring monteringssystem, materialhantering och produktivitet. Analysen visar att montörerna ägnar stor del av sin arbetstid åt stödjande aktiviteter kopplade till monteringen vilket skapar effektivitetsförluster. Resultatet för studien visar på att med förändrad monteringsprincip med tillhörande materialförsörjning är det möjligt att skapa en effektiviserad monteringsprocess. Utifrån studiens resultat presenteras åtgärdsförslag som adresserar Proton Lightings problembild, främst syftar de till att öka andelen tid som montörerna ägnar åt montering och färdigställande av armaturer. / Proton Lighting is a producer of professional luminaires used in public areas, schools, industry etc. 400 000 luminaires are produced every year at Proton Lightings factory in Värnamo, Sweden. An increased presence by global competitors has induced pressure on prices in the market, while Proton Lighting still wants to offer its costumer a wide variety in products and short lead time delivery. To stay competitive in the luminaire market, Proton Lighting is looking to make their assembly process more cost effective. Today’s assembly of luminaires is performed individually by operators at individual workstations. Each luminaire is assembled in one sequence by a single operator. There is a low presence of co-operation and interaction between operators with the present work procedure, and differences in performance and competence is evident. Operators is also responsible for supportive activities related to the assembling process. Material supply is largely handled by the operators themselves, from ordering material, gather material to returning old material. The purpose of this study is to investigate the possibility of changing the current way of assembling luminaires and supplying material. This will be done to minimize the number of supporting activities connected to the assembling of luminaires, which will result in a more cost-effective assembly. A case study was performed at Proton Lighting to shed light at the existing problems with today’s assembly process. Gathered data was analysed together with the available literature regarding assembly work, material supply and productivity. The analysis showed that the operators spent a lot of time performing supportive activities connected to the assembly work which creates losses in effectiveness. The result of the study shows that with changes to way of assembling luminaires and changing the way of supplying material an increase in effectiveness is generated. The study presents suggestions that addresses Proton Lightings problems related to existing assembly process. The suggestions focus on increasing the time that operators spend assembling luminaire.

DNA-functionalized gold nanoparticles (DNA-NPs) have enormous potential as building blocks for materials due to their ability to specifically recognize and respond to target molecules and surfaces. The ability of DNA aptamers to adopt different conformations and bind either complementary DNA sequences or analyte molecules allows them to mediate nanoparticle assembly or disassembly, generating selective colorimetric responses. Aptamer-mediated nanoparticle assembly and disassembly is sensitive to the nanoparticle ligand shell composition and structure, yet these topics have not been extensively explored. In this dissertation, a method for determining the ligand shell composition of DNA-NPs is described and a framework for understanding the impact of the DNA assembly arrangement and recognition strand density upon aptamer-mediated nanoparticle assembly and disassembly is developed. Design rules for creating sensors with desired properties are elucidated, leading to creation of sensors with improved detection limits and quantification ranges. A technique was needed to determine the number of DNA strands of any base composition attached to gold nanoparticles (AuNPs) of any core size. A rapid, convenient and inexpensive method to quantify the number of label-free DNA strands attached to AuNPs was therefore developed. This technique was extended to determine two different DNA sequences bound to AuNPs using UV-visible and fluorescence spectroscopy. Based on the results of quantifying the ligand shells of DNA-NPs functionalized with two sequences, disulfide-terminated DNA non-specifically adsorbs and then rearranges to specifically bind the gold surface. The position of the AuNPs and DNA strands within DNA-NP assemblies had a profound influence on their ability to assemble and sense adenosine. Assemblies designed for large inter-AuNP spacing were stable but unable to sense adenosine. Assemblies designed for short inter-AuNP spacing were unstable until the DNA ligand shell was diluted. AuNPs functionalized with the fewest number of aptamers produced assemblies with the lowest detection limit and apparent disassociation constant and the largest analyte quantification range. Increasing the number of aptamer strands per AuNP increased the cooperativity of the AuNP disassembly response to adenosine. This dissertation includes previously unpublished co-authored material.

Atualmente, existe um grande número de ferramentas para montagem de fragmentos de DNA disponíveis. Neste trabalho apresentamos um estudo comparativo das ferramentas CAP2, FAKtory, TIGR e PHRAP. Para realizarmos este estudo, primeiramente executamos esses sistemas de montagem sobre 12 casos de testes distintos. Após isso, tomamos os resultados obtidos por cada um deles e os comparamos com as seqüências de onde os fragmentos foram originalmente obtidos. Os testes utilizados avaliam a eficiências dos programas com relação a três problemas associados ao processo de montagem (erros no sequenciamento, fragmentos quimeras e regiões repetidas) e pudemos ver que nenhum dos sistemas é claramente superior aos demais no tratamento de todos eles. Cada ferramenta de montagem parece tratar de melhor forma um problema em especial.Além de avaliarmos os resultados, realizamos também um estudo. / Noways, several peckages for DNA fragment assembly are aviable. In this wok we present a comparative study of the preformances of the programs CAP2, FAKtory, TIGR e PHrap. To get to our objetives, we firt ran each of these programs on twelve intances. After this,we compared the outputs with the sequences from wich the fragments were originally obtained. In this comparison,we took into consideration three problems related to fragments assembly (sequencing errors, chimeric fragments and repeats regions). We conclude that no one of the packages we tested is more efficient than the others when considering all the problems cited above. If we consider a particular problem, the we observed different performances among the programs. Even more, we compare the packages with respect to theirs to CPU times.

Esta tese de doutorado aborda o desenvolvimento de sistemas microfluídicos eletroquímicos ultrassensíveis mediante a integração de eletrodos i) concêntricos e ii) nanoestruturados seletivos à detecção condutométrica sem contato acoplada capacitivamente (capacitively coupled contactless conductivity detection, C4D) e à amperometria, respectivamente. O uso dos eletrodos concêntricos, uma configuração inédita em microdispositivos na qual o filme fino metálico circunda todo o microcanal, se mostrou efetivo na melhora da detectabilidade da C4D para análises em fluxo de soluções padrão de LiClO4. O limite de detecção (LD) para esse sal foi igual a 343 pmol L-1, um valor aproximadamente quatro ordens de grandeza inferior àquele obtido com eletrodos planares. O microchip amperométrico nanoestruturado, por sua vez, consistiu de filmes de Au modificados com nanotubos de carbono de parede única (single-walled carbon nanotubes, SWCNTs) verticalmente alinhados e foi aplicado a padrões do neurotransmissor serotonina. A melhora na detectabilidade do método foi novamente apreciável; os valores de LD foram de 11,8 (Au liso) e 0,2 nmol L-1 (Au modificado com os SWCNTs verticalmente alinhados). Esse último é menor frente à grande maioria dos valores descritos na literatura, para os quais técnicas diversas foram empregadas, incluindo: i) potenciometria com eletrodos modificados (1,0 a 500 nmol L-1), ii) HPLC-MS (18,2 nmol L-1), iii) eletroforese capilar combinada com etapas de extração, empilhamento e préconcentração do analito (7,9 nmol L-1) e iv) sensor químico (200 nmol L-1). Finalmente, objetivando a fabricação de microchips de vidro, condutométricos e amperométricos, incorporando eletrodos concêntricos nanoestrurados, uma nova técnica de selagem foi desenvolvida. Essa técnica, designada como selagem adesiva de sacrifício, baseia-se no uso do resiste negativo SU-8 como camada intermediária de modo a permitir a vedação entre duas lâminas de vidro. Numa etapa posterior, a remoção seletiva do SU-8 sob o microcanal é realizada. Logo, canais microfluídicos com propriedades de superfície similares às do vidro foram obtidos. O protocolo experimental adotado é i) simples, ii) rápido, iii) não envolve níveis de pressão e temperatura elevados e iv) prescinde o uso de salas \"limpas\". Vedações com forças de adesão satisfatórias foram alcançadas, suportando pressões superiores a 4 MPa. / This PhD thesis reports the development of ultrasensitive electrochemical microfluidic systems by integrating concentric and nanostructured electrodes selective to capacitively coupled contactless conductivity detection (C4D) and amperometry, respectively. The use of the concentric electrodes, a new assembly in microdevices with thin films wrapping around the microchannel, showed to be effective towards improvement of the detectability in pressure-driven flow platforms incorporating C4D. The limit-of-detection (LOD) in flow analysis of LiClO4 solutions was 343 pmol L-1, ca. four orders of magnitude lower than to the levels obtained with planar electrodes alone. The nanostructured amperometric microchip, in turn, is related to integration of vertically aligned singlewalled carbon nanotubes (SWCNTs) over Au film. Such platform was applied to determination of serotonin standards. The nanomaterial influenced remarkably the sensitivity and detectability. Our system achieved a LOD of 0.2 nmol L-1, to the best of our knowledge one of the lowest values reported in the literature. Finally, in order to fabricate glass microdevices, conductometric and amperometric, with nanostructured concentric electrodes, we developed a new bonding method. This technique, called as sacrificial adhesive bonding, is based on SU-8 negative resist like intermediate layer so to allow the sealing between two glass slides. Next, the selective removal of the SU-8 under the microchannel is carried out. Thus, microfluidic channels presenting glass-like surface properties were achieved. The experimental protocol is simple and fast. In addition, neither high-pressure and elevated-temperature nor the use of \"clean\" rooms were not required. Bondings with satisfactory adhesion forces were obtained, supporting pressures above 4 MPa.

Advances in engineering polymer technology have created a generation of high strength-to-weight materials for medical applications, with virtually no adverse interactions with body fluids. Polycarbonate is a widely used engineering polymer, and is often used in connection with ultra-violet light (UV) cured adhesives. Because of the chemical complexity of polymers, little is known about their actual aging characteristics. By characterizing the effects of aging, storage environment, and sterilization on medical grade polycarbonate/adhesive system properties, more accurate failure predictions can be made. In this thesis, efforts to better understand the effects of accelerated aging on a medical grade polycarbonate and UV cured adhesive system are presented. A case study in which we applied our findings to improve an existing medical device is also described. The resin investigated was DOW Calibre 2081-15 MFR. The adhesives investigated were Dymax 190-M, Loctite 3311, and Loctite 3921. By adapting ASTM test standards, tests were developed to evaluate the effects one type of accelerated aging method had on the polymers. The polycarbonate resin experienced significant changes in material properties after sterilization. The biggest change was in percent elongation which went from 130% to 40%. The Dymax 190-M had the highest shear break values initially; however, the Loctite 3311 was more consistent. The Loctite material experienced a 15% decrease in shear break value over three years accelerated aging, while the Dymax material experienced a 35% decrease. The use of post sterilization or three year accelerated aging properties for polycarbonate designs is better than using published data. This ensures more accurate evaluation for the safety factor and failure profile. It was found that the accelerated aging method used in this study is reliable for general studies through two years, but accuracy declined significantly after this time. By using our findings we were able to significantly improve the case study assembly. Understanding how material properties change over time helped us identify the major contributors to part failure to create a more robust design and final product.

En l’espace de soixante ans, la Constitution du 4 octobre 1958 a subi de nombreux changements à la fois juridiques et politiques. Une chose a cependant perduré : le parlementarisme rationalisé. Prenant en compte les changements intervenus depuis 1958 et les aspirations des Français à la modernisation et au rééquilibrage des institutions de la Ve République, le Constituant de 2008 a opéré une revalorisation du Parlement et proposé de rendre la fonction parlementaire plus valorisante. Mais à l’aune de dix années d’expérience, force est de constater que les améliorations attendues n’ont pas véritablement eu lieu. Dans le même temps, les exigences démocratiques des Français ont évolué. De ce fait, ce qui était acceptable hier, à défaut d'être accepté, ne l'est plus aujourd'hui. Il en est ainsi des avantages, des pratiques, des comportements individuels ou collectifs de responsables politiques.On peut dès lors s’interroger sur ce que devrait être le député de la Ve République tant au niveau de son statut que de son rôle. Il ressort de cette étude que l’actuel statut du député est appelé à se renforcer, notamment, s’agissant des moyens alloués au député, ainsi que des droits et garanties afin de permettre une plus grande mobilité entre le mandat et l’activité professionnelle de l’élu, et d’améliorer la représentativité du député par l’ouverture de l’Assemblée à un nouveau public. Le cadre institutionnel dans lequel s’exerce le travail parlementaire doit également être assoupli pour rétablir le député dans ses fonctions de collaborateur du Gouvernement pour la confection des lois et de contrôleur de l’action gouvernementale. Enfin, le travail en circonscription ne doit pas être négligé car il permet à l’élu de mieux exercer ses missions législatives et de contrôle. / In the space of sixty years, the Constitution of 4th October 1958 has undergone many legal and political changes. However, one thing has remained: streamlined parliamentarianism. Considering the changes since 1958 and the aspirations of the French people for the modernisation and the rebalancing of the institutions of the Fifth Republic, in 2008 the constituent power worked on upgrading the role of the Parliament and proposed to improve the attractiveness of the parliamentarian function. After ten years of experience, it is clear that the potential improvements have not taken place. At the same time, the democratic requirements of the French have evolved. Hence, what was acceptable yesterday may not be today. This is true for the advantages, traditional practices, individual or collective behaviours of policy makers. Consequently, it may be asked what an MP of the Fifth Republic should be, in both status and function.This study shows that the status of the MP should be strengthened, notably with regard to the resources allocated to the MP, as well as rights and guarantees to allow greater mobility between the mandate and the professional activity of the elected representative, and to improve the representativeness of the MP through the opening up of the Assembly to a new audience. Also, the institutional system within which parliamentary work is performed must be more flexible to return the MP to his/her role as a legislator and overseer of government action. Finally, constituency work must not be neglected because it allows the MP to better carry out his/her legislative and overseeing missions.