Anotação proteogenômica é uma abordagem que une a análise proteômica com a anotação genômica. O intuito de tal abordagem é prover uma anotação mais detalhada ao gene. Intuito esse, que nem sempre é possível quando se trata apenas de genes, uma vez que produtos gênicos, com funções importantes preditas, somente passam a ter papel na fisiologia do organismo quando expressos e traduzidos. Com todo o avanço atual de estudos na área proteogenômica, a geração de dados tem crescido de modo exponencial e, com esse crescimento, nota-se a necessidade cada vez maior da criação de sistemas capazes de processar, armazenar e gerenciar essas novas informações produzidas. Assim, é descrito nesse trabalho o desenvolvimento do ProGen AP , sendo constituído de uma interface web construída em HTML/PHP5, um banco de dados cujo SGBD é o mySQL e de módulos de processamento de dados proteômicos, neste caso o LabKey (com o core Xtandem!) e o QuickMod. Todos os módulos são open source e comunicam entre si através de scripts PERL. Nesse sistema, o pesquisador fornece dados de experimentos proteômicos e o sistema, então, os processa e retorna ao usuário informações sobre o gene expresso, a localização dos peptídeos dentro do gene aos quais pertencem e, ainda, informações quantitativas sobre o peptídeo e a proteína identificados. Além disso, o uso de um processamento esquematizado reduz a possibilidade de erro de entrada/saída de dados nos módulos intermediários do processamento. Aqui, o ProGen AP foi aplicado no estudo proteômico do Mycobacterium tuberculosis (MTb). Na literatura, o genoma do MTb cepa H37Rv contém apenas 4062 open reading frames (ORFs) preditos e o complemento funcional desse genoma, o proteoma, ainda não está totalmente elucidado. A análise do proteoma do MTb, com o uso do ProGen AP, resultou em uma lista total de 154.982 identificações de peptídeos, representando um total de 147.334 peptídeos únicos. Até o momento, foram identificadas 2.369 proteínas, cobrindo aproximadamente 58% de todo o genoma do MTB. É importante ressaltar que, dentre todas as proteínas identificadas até o momento, a maioria delas está anotada como proteinas hipotéticas em seu genoma, e, por consequência, os resultados obtidos nesse projeto confirmam e validam a existência de tais produtos gênicos. Além disso, 567 peptídeos foram identificados como N-terminal e 1229 como C-terminal, o que indica a correta predição do início e do término da tradução de tais genes. Todos esses resultados positivos confirmam que a abordagem utilizada no ProGen AP é eficiente e pode ser usada em vários outros organismos de interesse do pesquisador. / Proteogenomic annotation is an approach that combines proteomic analysis and genomic annotation. The aim of this approach is to provide a more detailed annotation, which is not possible in most of the times when dealing mostly with genes, once that genomic products, with important predicted functions are only important in the organism physiology when they are expressed and translated. There have been occurring several advances in proteogenomic studies and the generation of new data sets has been growing in an exponential wave. With all this growth, the creation of systems able to storing, processing and analyzing all the new knowledge produced is eminent. This study presents the deployment of ProGen AP, a system built with a HTML/PHP5 web interface, a mySQL data management system to store the data and two processing modules (LabKey, with core X!Tandem and QuickMod). In this system, the researcher provides a data set from a proteomic experiment and then the system processes it and returns to the researcher information about the expressed gene, the peptides localization inside the gene that they belong and, also, quantitative information about the peptide and the protein that were identified. Also, the use of an automated pipeline reduces the possibility of making mistakes in input/output of the data when using the intermediate modules. Here, the ProGen AP were applied to perform a proteogenomic annotation of Mycobacterium tuberculosis (MTb). In literature, the MTb genome, strain H37RV, have only 4062 predicted open reading frames (ORFs) and the functional complement of this genome is not completely known. The MTb analysis using ProGen AP, resulted in a list of 154.982 peptides identification, representing a total of 147.334 single peptides. Until now, were identified 2.369 proteins, covering nearly of 58% of the whole MTb genome. Is very important to highlight that, among all the identified proteins until now, most of them are annotated as hypothetical proteins in the MTb genome, so can be affirmed that the results of this project can confirm and validate the existence of all these genomic products. Beside this, 567 peptides were identified as been an N-terminal peptide and 1229 were identified as been a C-terminal, this fact indicates that the prediction of the beginning and the end of translation of those genes are right. All these positive results corroborate that the approach utilized in the ProGen AP is efficient and can be used in studies of other organisms.

Denna uppsats handlar om programmering av autoriggningsverktyg för Maya 2013 som skulle effektivisera animeringsproduktionspipelinen genom att spara tid vid riggningsdelen av animeringspipelinen. Vidare handlar denna uppsats om utvärdering av tiden som man kan spara vid användningen av detta autoriggningsverktyg. Verktyget är flexibelt på det sätt att den stödjer humanoida karaktärer och är användbar för mer än mänskliga karaktärer. Tiden som spenderas att manuellt rigga samma typ av karaktärrigg varierar från person till person och det kan ta väldigt lång tid, därför gjordes en enkät som delades ut till deltagare som är erfarna inom riggningsområdet. Resultaten av denna enkät hjälper vid beräkningen av tiden som kan sparas med autoriggningsverktyg i en animeringspipeline. Resultatet av undersökningen visar att man kan spara tid genom att använda sig ut av ett autoriggningsverktyg istället för att rigga manuellt. Tiden som kan sparas med detta autoriggningsverktyg är nästan sju timmar för mänskliga karaktärer och nästan 8 timmar för kentaur.

Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the energy industries around the world because it causes a huge economic loss due to not only frequent replacements of the parts of pipelines and tanks but also potential damage of the entire fields of crude oil. Previous studies have revealed that corrosions are generated mainly by microbial activities and they are now called as Microbial Influenced Corrosion (MIC) or simply bio-corrosion. Bacterial species actually causing bio-corrosion is crucial for the suppression of the corrosion. To diagnose and give proper treatment to pipelines in industrial plants, it is essential to identify the bacterial species responsible for bio-corrosions. For attaining at this aim, I conducted an analysis of the microbial community at the corrosion sites in pipelines of oil plants, using the comparative metagenomic analysis along with bioinformatics and statistics. In this study, I collected and analyzed various bio-corrosion samples from four different oil fields. First, I collected samples from the seawater pipelines that are essential in the oil fields to maintain seawater injection system (field#1), and then I conducted the metagenomic analysis of these samples. The metagenomes obtained revealed that samples in both sites contain a wide range of bacterial taxa. However, the comparative analysis of the microbial community with statistics in the comparison between sites with corrosion and without corrosion revealed the presence of microorganisms whose abundances were significantly higher in sites with corrosion. Some of these microbes can be sulfate reducers and sulfur oxidizers of which are considered to be casual agents in recent bio-corrosion models. In addition to the seawater pipelines, I also collect samples from corrosion sites in oil pipelines at Field #2 and #3. My metagenomic analysis combined with statistics showed that several microorganisms are speculated to be very active at the corrosion sites in the oil pipeline. Although biological mechanisms of forming bio-corrosion in the oil pipelines still remain unclear, these microbial species are suggested to be some of the responsible bacteria for bio-corrosion in the oil pipelines. Besides seawater injection systems, groundwater injection systems are often used, especially in inland oil fields. Therefore, more detailed understanding of biocorrosion in the groundwater injection system is also required in oil industries. In the present studies, I then analyzed the microbial communities in pipelines in the oil field where groundwater is used as injection water (field #4). I collected samples from four different facilities in the field #4. Metagenome analysis revealed that microbial community structures were largely different even among samples from the same facility. Treatments such as biocide and demineralization at each location in the pipeline may affect the microbial communities independently. The results indicated that microbial inspection throughout the pipeline network is important to protect industrial plants from bio-corrosions. Identifying the bacterial species responsible to bio-corrosion, this study provides us with information on bacterial indicators that will be available to classify and diagnose bio-corrosions. Furthermore, these species may be available as biomarkers to detect the events of bio-corrosion at an early stage. Then, any appropriate care such as the appropriate choice of biocides can be taken immediately and appropriately. Thus, my study will provide a platform for obtaining microbial information related to bio-corrosion that enables us to obtain a practical approach to protect them from bio-corrosion.

This thesis is focused on a crudeoil pipeline repair technology at the dead plate. The thesis is devided into 4 basic parts (chapters). The openning chapter describes reasons for performing regular pipeline inspections regarding pipeline's defects and technology of defects repair. The second chapter is devoted to the particular repair technology - cut out of a damaged pipeline part and its replacement by a new pipeline piece - with a detail description of preliminary and consenquential assembly activities (safety and environmental aspects). This chapter also comprises a list of documents confirming technical qualification and readiness for repairs execution. The third chapter is aimed at proposition and verification of the welding method by means of non-destructive and destructive testing of a test circumferential weld according to the proposed weld procedure specification – WPS. There are presented the results of particular tests and complex evaluation of the welding process design by the inspection organization. The last, fourth chapter deals with a calculation of general costs of repair execution which is an important part of a final pricing.

The task of the diploma thesis ‚‚Adjustment of the pumping station and delivery pipeline of the raw water to location of JETE for considered building up of new nuclear sources‘‘ is to figure out a capability of the pumping station Hněvkovice to draw a sufficient capacity of a raw water to the Temelín nuclear power plant. In case of necessity, it designs useful adjustment of a pumping station and deliver pipeline for increasing the raw water delivery rate.

This thesis describes issues related to design and structural analysis of steam pipeline. Analysis are done by using two different software program – AutoPIPE and Ansys. Issues related to pipeline support system and thermal expansion are solved by using AutoPIPE. Structural analysis results are evaluated in accordance with ČSN EN 13 480 code.

In the field of apparatus engineering and pipeline construction wall thicknesses of 100 mm are processed and joined with heated tool butt welding. The welding procedure is regarded as well-understood. However, there are no systematic experimental investigations into the wall thicknesses above 30 mm published. The welding parameters for high wall thicknesses of PE (polyethylene) and PP (polypropylene) are extrapolated as it is given in the guidelines of DVS (Deutscher Verband für Schweißen und verwandte Verfahren e.V.). However, cases of damage to welded pipelines show that not enough understanding of the process management and the weld properties is available for the welding of large pipe dimensions. The present study investigates the welding behaviour of semi- finished products (plates and pipes) with wall thicknesses up to 100 mm. The mechanical properties are tested in short-term tests and in long-term tensile creep tests. The results relating to the fusion behaviour basically show a curved melt profile which influences the mechanical behaviour of the welded components. The tensile creep tests establish a tendency towards the premature failure of the peripheral regions.

The problem of energy saving during overhaul of a linear part of gas trunkline is regarded in this paper. This issue has been analyzed from different perspectives. Thermodynamic analysis of gas evacuation from a string that is off operation for the overhaul to a parallel or adjacent string with the use of mobile compressor systems was made. Economical attractiveness of mobile compressor systems applications was proved. Various methods of gas trunklines linear parts overhaul have been considered. For each of the methods problems of minimization of necessary for the overhaul amount of energy consuming machines have been solved. The results can be used in the development of overhaul projects of the gas trunklines linear parts.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24295号 / 工博第5068号 / 新制||工||1791(附属図書館) / 京都大学大学院工学研究科都市社会工学専攻 / (主査)教授 CRUZ Ana Maria, 教授 渦岡 良介, 教授 肥後 陽介 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

In this theses techniques for high-speed digital delta-sigma modulator(DDSM) structures are considered. Four techniques are applied andevaluated: unfolding, increasing the number of delay elements in theinner loop, pipelining/retiming, and optimizations provided by thesynthesis tool. Of interest is to see the speed-area-power trade-offs.For implementation, three different modulators meeting the samerequirements are implemented. Each modulator has a 16-bit input andresults in a 3-bit output. The baseline case is a second-ordermodulator, which has one delay element in its inner loop. Throughoptimization, two new structures are found: to provide two delayelements in the inner loop, a fourth-order modulator is required,while to provide three delay elements, a thirteenth-order modulator isobtained.The results show that in general it is better to unfold the modulatorthan to obtain the speed-up through optimizing the arithmeticoperators with the synthesis tool. Using correct pipelining/retimingis also crucial. Finally, for very high-speed implementation, usingthe structures with more delay elements is required. Also, in manycases these are more area and power efficient compared to usingoptimized arithmetic operators, despite their higher computationalcomplexity.