<p>Distributing functionality of an application is in common use. Systems that are built with this feature in mind also have to provide high levels of dependability. One way of assuring availability of services is to tolerate faults in the system, thereby avoiding failures. Building distributed applications is not an easy task. To provide fault tolerance is even harder.</p><p>Using middlewares as mediators between hardware and operating systems on one hand and high-level applications on the other hand is a solution to the above difficult problems. It can help application writers by providing automatic generation of code supporting e.g. fault tolerance mechanisms, and by offering interoperability and language independence.</p><p>For over twenty years, the research community is producing results in the area of . However, experimental studies of different platforms are performed mostly by using made-up simple applications. Also, especially in case of CORBA, there is no fault-tolerant middleware totally conforming to the standard, and well studied in terms of trade-offs.</p><p>This thesis presents a fault-tolerant CORBA middleware built and evaluated using a realistic application running on top of it. Also, it contains results obtained after experiments with an alternative infrastructure implementing a robust fault-tolerant algorithm using basic CORBA. In the first infrastructure a problem is the existence of single points of failure. On the other hand, overheads and recovery times fall in acceptable ranges. When using the robust algorithm, the problem of single points of failure disappears. The problem here is the memory usage, and overhead values as well as recovery times that can become quite long.</p> / Report code: LiU-TEK-LIC-2002:55.

This study proposes simulations which present optimized methods for producing fatty acids, fatty alcohols and alkanes using Zymomonas mobilis bacterium by the energy efficient β-oxidation reversal pathway, an eco-friendly alternative to the present petroleum based processes. Zymomonas has advantages of higher carbon intake, higher ethanol tolerance and higher ethanol production efficiency than other organisms. I have improved an earlier Zymomonas genome scale model and used Constraint Based Reconstruction and Analysis (COBRA), a linear optimization based computational tool in Matlab, and to perform flux balance analysis (FBA) based simulations. FBA accounts for formation, consumption, accumulation and removal rate or flux of each metabolite. The results present solution spaces of cell growth rate and product formation rate, which trend with products and their carbon chain length. I have analyzed these solution space trends gaining insight into the Zymomonas’ metabolism, enabling efficient product formation and opening a way for future improvement.

This paper analyzes the theoretical underpinnings and strategic goals of US security strategy with respect to China. It argues that the language used in statements and publications of US strategy demonstrate the development of a strategy of cooperative security. This strategy is dependent on the security environment the United States cultivates with allies and partners in the region. The paper uses evidence from the two largest PACOM military operations--RIMPAC and Cobra Gold-to demonstrate this developing strategy.

Thesis (M.S. in Aeronautical Engineering)--Naval Postgraduate School, June 2005. / Thesis Advisor(s): R.M. Howard, I.M. Ross. Includes bibliographical references (p. 215-217). Also available online.

Made available in DSpace on 2014-08-13T14:50:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-11-27Bitstream added on 2014-08-13T18:01:34Z : No. of bitstreams: 1 000744257.pdf: 1345587 bytes, checksum: 884d34a74775bc0bdd270eedb4458762 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Cryptosporidium serpentis infection is common in reptiles, especially snakes, and is characterized by chronic infection with severe hypertrophic gastritis, which can be lethal. This research aimed to use the real- time polymerase chain reaction (PCR) targeting the heat shock protein gene (Hsp70) for detection of C. serpentis in fecal samples of 503 snakes, and to determine its analytical and epidemiological specificity and sensitivity using, as a gold standard, the nested PCR targeting the 18S rRNA (18S rRNA) gene followed by sequencing of the amplified fragments (nPCR/S). The real-time PCR was positive for C. serpentis in 17 samples (3.37%), and nPCR/S resulted in positive results for C. serpentis in 15 samples (2.98%). It was also observed that the nPCR/S was positive for Cryptosporidium spp. in 60 samples (11.98%). Sequencing of the fragments amplified by nPCR was possible in 38 samples, and resulted in the identification of Cryptosporidium tyzzeri, Cryptosporidium muris, Cryptosporidium varanii and C. serpentis in several species of snakes. The sensitivity and specificity of real-time PCR were, respectively, 93.8% and 99.5%. Although three samples were positive for C. serpentis only by real-time PCR, and were considered as false positive results in the estimation of the epidemiological specificity and sensitivity, the melting curve analysis indicated that these samples had the same melting temperature of the C. serpentis samples. Thus, we conclude that real-time PCR targeting the gene Hsp70 is a sensitive and specific method for the detection of C. serpentis in fecal samples from snakes / FAPESP: 07/54312-2

Orientador: Marcos Roberto de Mattos Fontes / Banca: Pedro de Magalhães Padilha / Banca: Leonardo de Castro Palmieri / Resumo: As fosfolipases A2 (PLA2s) de veneno de serpente são uma das principais toxinas responsavéis pela miotoxicidade e necrose muscular observadas nos acidentes ofídicos. Essas toxinas podem ser separadas em Asp49-PLA2s, cujo mecanismo é catalítico e dependente de cálcio, e as PLA2s homólogas, cuja estrutura é semelhante, porém atividade em mecanismo não catalítico e independente de cálcio. Apesar de os detalhes deste mecanismo não serem bem conhecidos, estudos funcionais ressaltam importância da região do C-terminal e estudos cristalográficos propõem, mais especificamente, um sítio miotóxico composto por resíduos básicos e um hydrophobic knuckle composto por hidrofóbicos, ambos situados na região C-terminal da toxina. O presente trabalho tem objetivo de oferecer mais detalhes acerca do mecanismo de ação miotóxico independente de cálcio. Para tanto, realizamos estudos cristalográficos com miotoxinas botrópicas BthTX-II (uma Asp- PLA2s), BthTX-I e PrTX-I (duas PLA2s homólogas), em presença de íons relevantes para suas atividades. Recentemente, foi demonstrado que íons, tal como manganês, cálcio, zinco entre outros, interferem na atividade biológica de PLA2s e PLA2s homólogas. Assim, estudo cristalográfico da PrTX-I e BthTX-I com íons manganês e zinco foram elucidados no estado nativo e complexado. Experimentos in vivo indicam que tais íons promoveriam efeito inibitório da miotoxicidade. Enquanto os íons manganês não foram localizados no modelo cristalográfico, os íons zinco foram identificados interagindo apenas no modelo nativo com uma His48 e com as His120 de ambos monômeros. Estudos comparativos destas estruturas com a PrTX-II (PLA2s homóloga) com ácidos graxos foi desenvolvido e guiaram para elaboração de nova hipótese do mecanismo de ação independente de... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Phospholipases A2 (PLA2s) from snake venom are among the main toxins responsibles for miotoxicity and muscular necrosis observed in offidic accidents. These toxins can be separated in Asp49-PLA2s, whose catalytic mechanism of action is dependent of calcium, and in homologue PLA2s or PLA2s-like, whose terciary structure is similar, although its activity is not catalytic in a calcium independent mechanism of action. Despite the fact that this calcium independent mechanism is not well known, functional studies highlight the C-terminal region and structural studies points to a myotoxic site, composed by basic residues, and a hydrophobic knuckle, composed by aromatic and hydrophobic, in the C-terminal region. The present study aims to gather more knowledge about this myotoxic calcium independent mechanism of action. For this purpose, the botropic myotoxins BthTX-II (an Asp49- PLA2), BthTX-I and PrTX-I (homologue PLA2s) were studied in the presence of divalent ions by Xray crystallography. Recently, it was demonstrated divalent ions, such as manganese, zinc and calcium, interfere with the biological activity of these toxins. The crystallographic structure of PrTX-I and BthTX-I with manganese and zinc ions in a native and complexed form were elucidated. In vivo studies demonstrated that these ions inhibit the myotoxic activity of these proteins. Although manganese ions were not found in the structures, zinc ions were found interacting with His48 and the C-terminal residue His120. Comparative studies of this structure and PrTX-II (a homologue PLA2) complexed with stearic acid were performed and support a new hypothesis for the myotoxic mechanism of action for homologue PLA2s which includes both myotoxic site and hydrophobic knuckle and, for the first time, His120. Differently from most PLA2s of snake venom... (Complete abstract click electronic access below) / Mestre

Resumo:A infecção por Cryptosporidium serpentis é comum em répteis, em particular em serpentes, e é caracterizada por infecção crônica com presença de gastrite hipertrófica grave, que pode ser letal. Esta pesquisa teve como objetivo utilizar a reação em cadeia da polimerase (PCR) em tempo real, tendo como alvo o gene da proteína do choque térmico (Hsp70), para detecção de C. serpentis em amostras fecais de serpentes, e determinar a sua especificidade e sensibilidade analíticas e epidemiológicas utilizando, como padrão ouro, a nested PCR para amplificação de fragmento parcial do gene da subunidade 18S do rRNA (18S rRNA) seguida de sequenciamento dos fragmentos amplificados (nPCR/S). A PCR em tempo real foi positiva para C. serpentis em 17 amostras (3,37%), enquanto a nPCR/S resultou em positividade para C. serpentis em 15 amostras (2,98%). A nPCR/S resultou em positividade para Cryptosporidium spp. em 60 amostras (11,98%). O seqüenciamento dos fragmentos amplificados pela nPCR foi possível em 38 amostras e resultou na identificação de Cryptosporidium tyzzeri, Cryptosporidium muris, Cryptosporidium varanii e C. serpentis, em diversas espécies de serpentes. Os valores de sensibilidade e especificidade epidemiológicas da PCR em tempo real foram, respectivamente, 93,8% e 99,5%. Embora três amostras tenham apresentado positividade para C. serpentis apenas pela PCR em tempo real, e foram consideradas como resultado falso positivo na estimativa da especificidade e sensibilidade epidemiológicas, a análise da curva de dissociação indicou que essas amostras apresentaram a mesma temperatura de dissociação que as amostras de C. serpentis. Assim, concluiu-se que a PCR em tempo real, visando ao gene Hsp70 é um método sensível e específico para detecção de C. serpentis em amostras fecais de serpentes / Abstract:Cryptosporidium serpentis infection is common in reptiles, especially snakes, and is characterized by chronic infection with severe hypertrophic gastritis, which can be lethal. This research aimed to use the real- time polymerase chain reaction (PCR) targeting the heat shock protein gene (Hsp70) for detection of C. serpentis in fecal samples of 503 snakes, and to determine its analytical and epidemiological specificity and sensitivity using, as a gold standard, the nested PCR targeting the 18S rRNA (18S rRNA) gene followed by sequencing of the amplified fragments (nPCR/S). The real-time PCR was positive for C. serpentis in 17 samples (3.37%), and nPCR/S resulted in positive results for C. serpentis in 15 samples (2.98%). It was also observed that the nPCR/S was positive for Cryptosporidium spp. in 60 samples (11.98%). Sequencing of the fragments amplified by nPCR was possible in 38 samples, and resulted in the identification of Cryptosporidium tyzzeri, Cryptosporidium muris, Cryptosporidium varanii and C. serpentis in several species of snakes. The sensitivity and specificity of real-time PCR were, respectively, 93.8% and 99.5%. Although three samples were positive for C. serpentis only by real-time PCR, and were considered as false positive results in the estimation of the epidemiological specificity and sensitivity, the melting curve analysis indicated that these samples had the same melting temperature of the C. serpentis samples. Thus, we conclude that real-time PCR targeting the gene Hsp70 is a sensitive and specific method for the detection of C. serpentis in fecal samples from snakes / Orientador:Marcelo Vanconcelos Meireles / Banca:Alex Akira Nakamura / Banca:Valéria de Sá Jayme / Banca: Carlos Noriyuki Kaneto / Banca:Roberta Lemos Freire / Doutor

Orientador: Marcos Roberto de Mattos Fontes / Banca: Richard Charles Garrat / Banca: Antonio José da Costa Filho / Resumo: As serpentes do gênero Bothrops são de grande interesse científico, médico e social para o Brasil, visto que este gênero é responsável por cerca de 90% dos acidentes ofídicos que ocorrem em nosso país. Dois dos principais componentes do veneno desses animais são as fosfolipases A2 e as serino proteases. As fosfolipases A2 são enzimas responsáveis pela destruição da membrana celular através da hidrólise de fosfolipídios Ca2+ dependente. Uma classe destas fosfolipases, as fosfolipases homólogas (Lys49-PLA2s), que se caracteriza pela uma substituição natural na posição 49 de um resíduo de Asp para um resíduo de Lys, não apresenta atividade catalítica, mas é capaz de induzir mionecrose por um mecanismo Ca2+ independente devido, provavelmente, à resíduos da região C-terminal. Neste trabalho, através de estudos por cristalografia de raios-X de Lys49-PLA2s botrópicas nativas e quimicamente modificadas pelo brometo de p-bromofenacila (BPB), revisamos a posição da Lys122 - anteriormente apontado como um dos responsáveis ela ausência da atividade catalítica das Lys49-PLA2s por conta da hiperpolarização que causaria na ligação peptídica Cys29/Gly30 - e concluímos que, por conta de esta hiperpolarização ocorrer apenas em alguns monômeros de Lys49-PLA2s complexadas, a Lys122 não deve estar envolvida no "bloqueio" da atividade catalítica. Além disso, a comparação estrutural do loop de ligação de Ca2+ entre as Lys49 e Asp49-PLA2s nos mostra a importância da conservação da Tyr28 dentre as Asp49-PLA2s para a integridade do loop de ligação do Ca2+. Este resíduo estabiliza essa região através de uma ponte de hidrogênio com a Gly35. Nas Lys49-PLA2s, que possuem um resíduo de Asn na posição 28, não ocorre a formação dessa ponte, o que contribuiria para a desestabilização dessa região nessas proteínas ...(Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The snakes from Botrops genus are objects with great scientific, medical and social interesting since that these snakes are responsible of 90% of snakebites in our country. Two of the main components of the venom from these animals are the phospholipases A2 and the serine proteases. The phospholipases A2 are enzymes responsible of cellular membrane disruption through phospholipids hydrolysis Ca2+-dependent. A class of these phospholipases, the homolog phospholipases (Lys49-PLA2s) that underwent a natural substitution Lys to Asp substitution in 49 position, does not show catalytic activity. However, these proteins can perform myonecrosis by a Ca2+-independent mechanism probably, due to action of C-termini region residues. In this work, by x-ray crystallography studies with bothropic Lys49-PLA2s in native and chemically modified by p-bromophenacyl bromide (BPB) forms, we revised the position of Lys122, previously pointed as one of the responsibles of Lys49-PLA2s due to hiperpolarization of its side chain on Cys29/Cys30 peptide bond. Here, we conclude that this hiperpolarization are present only in a few monomers and thus, Lys122 may not be involved in the "blocking" of catalytic activity. Furthermore, structural comparisons of Ca2+ binding loop between Lys49 and Asp49-PLA2s revels the importance of the Tyr28 residue conservation to the integrity of this region. This residue stabilizes the Ca2+ binding loop by a hydrogen bond to Gly35. In Lys49-PLA2s that have an Asn residue in 28 position, does not occur the formation of this bond, contributing to unstabilization of this region and difficulting the binding of Ca2+ cofactor. Phylogenetic studies showed that Asp49- PLA2s with reduced catalytic inactivity and capable to induce myonecrosis are phylogenetic more related to Lys49-PLA2s than to others Asp49-PLA2s, forming a ...(Complete abstract click electronic access below) / Mestre

Orientador: Rui Ferreira Seabra Junior / Resumo: Os acidentes ofídicos constituem um relevante problema de saúde pública, a qual deve receber cuidados rápidos e eficientes. Em relação ao ofidismo, no Brasil, somente há poucos anos foi definida uma política abrangente que enfocasse as múltiplas questões relacionadas aos acidentes humanos provocados por animais peçonhentos. Os venenos de serpentes apresentam uma mistura de compostos inorgânicos (íons metálicos) e orgânicos, sendo ricos em moléculas biologicamente ativas. Dentre essas moléculas, peptídeos, proteínas e compostos de baixa massa molecular são frequentemente estudados por apresentarem grande potencial terapêutico. Essas moléculas, se bem conhecidas, podem ser utilizadas na investigação de mecanismo moleculares e celulares. Além disso, estabelecem interessantes modelos moleculares para o desenvolvimento de estratégias biotecnológicas aplicáveis na criação de ferramentas experimentais e/ou agentes terapêuticos para a pesquisa básica e aplicada. Diante disso, a elucidação dos peptídeos hipotensores presentes no veneno crotálico da subespécie Crotalus durissus terrificus é o objetivo do presente trabalho. Este estudo poderá promover a identificação de outras moléculas hipotensoras podendo conter princípios ativos mais eficientes para o tratamento de quadros clínicos de hipertensão, doença esta que acomete milhares de pessoas no mundo todo. No presente trabalho, a porção peptídica do veneno da serpente C.d.t., apresentou rendimento médio de 12,8% em relação ao veneno b... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The snakebites are an important public health problem, which must receive quick and efficient care. Regarding the ophidism, in Brazil, only a few years ago a comprehensive policy was defined that emphasized multiple issues related to human accidents caused by venomous animals. The snake venoms present a mixture of inorganic and organic compounds, being rich in biologically active molecules. Among these molecules, peptides, proteins and low molecular weight compounds are often studied by their ability therapeutic. Those molecules, when well known, may be used in the investigation of cellular and molecular mechanism. In addition, it provides interesting molecular models for the development of biotechnological strategies applicable in the creation of experimental tools and / or therapeutic agents for basic and applied research. Therefore, the elucidation of hypotensive peptides present in the venom of Crotalus durissus terrificus subspecies is the aim of this study, once this study may promote the identification of other hypotensive molecules may contain more effective active ingredients for the treatment of clinical conditions hypertension, this disease affecting millions of people in the world. In this study, the peptide portion of the venom of the snake Cdt, performed with an average yield of 12.8% compared to the venom under total protein precipitation conditions in the presence of trifluoro acetic acid to 0.1% (v / v) and, when subjected to purification strategy for reverse... (Complete abstract click electronic access below) / Doutor

Orientador: Otavio Augusto Vuolo Marques / Banca: Marcio Roberto Costa Martins / Banca: Ricardo Janinni Sawaya / Resumo: Serpentes dos gêneros Echinanthera e Taeniophallus pertencem à família dipsadidae e estão alocadas na tribo Echinantherini. Esses gêneros possuem características morfológicas similares entre si, incluindo o porte médio (comprimento total < 850 mm) e o corpo delgado, a dentição áglifa e a pupila circular. Além disso, compartilham semelhanças ecológicas como o hábito critozóico e diurno, a dieta baseada em anfíbios anuros e a reprodução, aparentemente restrita à estação chuvosa (setembro a março). O reconhecimento de Echinanthera e Taeniophallus como linhagens filogenéticas distintas tem sido controverso, mas a hipótese mais recente considera a existência de ambos os gêneros. O objetivo do presente trabalho foi caracterizar de forma mais detalhada a história natural de Echinanthera e Taeniophallus para avaliar semelhanças e possíveis diferenças entre esses gêneros. Foram examinados e dissecados espécimes preservados depositados em coleções herpetológicas para coleta de dados de dieta e reprodução. Foi analisado um total de 240 espécimes de E. undulata para caracterização do ciclo reprodutivo e dieta. Outras espécies (T. affinis e T. occipitalis) tiveram exemplares dissecados somente para exame do conteúdo alimentar. Dados da literatura disponíveis para outras espécies também foram incluídos para comparação. Echinanthera undulata apresentou dimorfismo sexual, com fêmeas apresentando comprimento rosto-cloacal maior e tamanho relativo da cauda menor que machos. Duas características (comprimento da cabeça e diâmetro do olho) são similares entre os sexos. Essa serpente apresentou cauda longa, correspondente a cerca de 45% do tamanho total. Com relação à dieta foram encontrados 12 itens, todos anfíbios anuros. A dieta de espécies do gênero Taeniophallus foi mais diversificada. Apenas três... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Dipsadid snakes of the genera Echinanthera and Taeniophallus belong to the Echinantherini tribe. These genera have similar morphological features, including the medium size (total length < 850 mm) and slender body, the aglyph dentition, and round pupil. Furthermore, they share ecological similarities such as the cryptozoic habit and day time activity, diet based on amphibians anurans and reproduction apparently restricted to the rainy season (September to March). The recognition Echinanthera and Taeniophallus as distinct phylogenetic lineages has been controversial, but the most recent hypothesis considers the existence of both genera. The objective of this study was to describe the natural history of Echinanthera and Taeniophallus to evaluate possible similarities and differences between these genera. This study was based on the dissection of preserved specimens from herpetological collections. We analyzed a total of 240 specimens of E. undulata to characterize the reproductive cycle and diet. Individuals of the other species (T. affinis and T. occipitalis) were dissected only to examine gut contents. Literature data for other species were included for comparison. Echinanthera undulata presented sexual dimorphism, females have larger snout vent-length and smaller tail than males. Two variables (head length and eye diameter) are similar between the sexes. This snake had long tail, corresponding to about 45% of the total size. All the prey items (n = 12) found in the gut of E. undulata were anurans. The diet of species from the genus Taeniophallus was more diverse. Only three specimens of T. affinis contained food vestiges (one lizard, one amphibians anurans and one rodent). In T. occipitalis were 12 items (one amphibians anurans and 11 lizards). The reproduction of both genera is similar. Testicular volume... (Complete abstract click electronic access below) / Mestre