Dissertations / Theses on the topic 'Clonky'

The first part of the thesis deals with electron microscopy and physical model fluid flow. In the next part, a three-dimensional model is created in programme SolidWorks. It is the model of scintilating detector with aperture or screen with three hundred little apertures. These models are submitted to analysis focusing on investigation of the gas flow at different pressure in chamber of specimen ESEM using Cosmos FloWorks system. The results of the analysis of both apertures variants are compared with the request to minimize the pressure in the trajectory of the secondary electrons as well as in the chamber of specimen.

This diploma thesis deals with electron microscopy. Examined equipment is environmental scanning electron microscope (ESEM), namely scintillation a detector of the microscope. There is solved the influence of the profile of holes in diaphragms to the resulting pressure and gas flow on the path of secondary electrons at the detector. Introductory part of thesis informs about microscopy in general, with concentration on electron microscopy; especially on scanning microscope, because research is taken just on the environmental scanning electron microscope. Another part informs about both general principles of dynamics of gases and with finite volume method. Another part deals with concrete used software and with setting of individual parameters for calculation. At the beginning of calculation are used five basic profiles of holes in diaphragms for pressure 1000 Pa in the chamber of the sample. For modelling individual shapes is used 3D parametric modeller SolidWorks. Analysis of circulation of secondary electrons through detector is made by using Cosmos FloWorks module. The most suitable type of diaphragms is chosen from measured models. Another part of diploma thesis deals with measuring of chosen types of diaphragms for more pressures in the chamber of the sample; the pressure is 200, 400, 600, 800 and 1000 Pa. The outcomes of this research are both models of pressure and speed of circulation inside the detector and graphically processed values by using different diaphragms, respectively one type of a diaphragm in different pressures. Production drawings of each diaphragm, together with calculated models, are enclosed.

Les études d’amélioration génétique du Terminalia superba par voie asexuée ont été entreprises au CONGO, dans le cadre d’un projet de reboisement industriel de cette espèce. Une centaine de Limba d’élite sélectionnés dans les forêts du sud du Congo, ont été clonés et font l’objet depuis 1976 de plusieurs expérimentations et observations. Si actuellement, le bouturage est acquis et la croissance des clones encourageante, il n’en est pas de même de la réjuvénilisation qui ne semble pas encore satisfaisante, en particulier pour les caractères de branchaison. En conclusion, nous suggérons un schéma d’amélioration qui concilie la méthode asexuée et sexuée à partir des tests de provenances qui viennent d’être mis en place à NGOUA 2
Asexual propagation and morphogenetic clonal variability of Terminalia superba Engler and Diels (Limba) in South Congo. Genetic improvement of Terminalia superba by asexual propagation has been studied in Congo as part of an industrial reforestation project. One hundred elite Limba, selected in South Congo forests, were cloned and since 1976 have been studied in several trials. A technique of establishing cuttings is now well understood and the growth of clones is encouraging, but rejuvenation remains unsatisfactory, particularly as it affects branching. This thesis concludes with a suggested breeding scheme involving both sexual and asexual propagation of material being tested in recently established provenance trials

The development of radiata pine (Pinus radiata D. Don.) clones was compared in monoclonal and clonal mixture plots planted in an experiment established at Dalethorpe, Canterbury, New Zealand with ten radiata pine clones in September 1993. Clones were deployed in a randomised complete block plot design with three replications. Each replication contained ten treatments of monoclonal plots and one in which all the clones were intimately mixed in equal proportions. Clones significantly differed in initial morphologies, survival and stem slenderness. Sturdiness and initial heights were found to be the best predictors of initial survivals. The study revealed that mode of deployment did not affect overall productivity, but individual clones exhibited significantly different productivities between modes of deployment. All clones contributed similarly to overall productivity in the monoclonal mode of deployment, whereas the contribution of clones in the clonal mixture mode of deployment was disproportionate. A minority of the clones contributed a majority of overall productivity in the clonal mixture mode of deployment. The inclusion of competition index as an independent variable in a distance-dependent individual tree diameter increment model explained a significant amount of variability in diameter growth. The use of an inverse-squared distance to neighbouring plants in the competition index provided a slightly superior fit to the data compared to one that employed a simple inverse of distance. Addition of genotype information in the competition index further improved the fit of the model. Clones experienced different levels of competition in monoclonal and clonal mixture modes of deployment. Competition in monoclonal plots remained uniform over time, whereas some clones experienced greater competition in clonal mixture plots which led to greater variability in their tree sizes. This study indicated that single tree plot progeny test selections and early selections may miss out some good genotypes that can grow rapidly if deployed monoclonally. Stand level modelling revealed that clones differed significantly in modeled yield patterns and model asymptotes. Clones formed two distinct groups having significantly different yield models. The study also demonstrated that models developed from an initial few years’ data were biased indicators of their relative future performances. Evaluation of effectiveness of the 3-PG hybrid model using parameter values obtained from destructive sampling and species-specific values from different studies revealed that it is possible to calibrate this model for simulating the productivity of clones, and predictions from this model might inform clonal selections at different sites under differing climatic conditions. Destructive sampling at age 5 years revealed that clones significantly differed in foliage and stem biomass. The differences in productivities of clones were mainly due to differences in biomass partitioning and specific leaf areas. Clones significantly differed in dynamic wood stiffness, stem-slenderness, branch diameter, branch index and branch angle at an initial stocking of 1250 stems/ha. Mode of deployment affected stem slenderness, which is sometimes related to stiffness. Although dynamic stiffness was correlated with stem slenderness and stem slenderness exhibited a significant influence on stiffness, clones did not exhibit statistically significant differences in dynamic stiffness. Increasing initial stocking from 833 stems/ha to 2500 stems/ha resulted in a 56 % decrease in branch diameter and a 17 % increase in branch angle. Trees in the monoclonal mode of deployment exhibited greater uniformity with respect to tree size, stem-slenderness, and competition experienced by clones compared to those in the clonal mixture mode of deployment. Susceptibility of one clone to Woolly aphid suggested that greater risks were associated with large scale deployment of susceptible clones in a monoclonal mode of deployment. This study also indicated that if the plants were to be deployed in a monoclonal mode then block plot selections would have greater potential to enhance productivity.

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The objective was to rescue, preserve and multiply the genetic material of the best species/origins selected Eucalyptus spp., to southern Brazil and select the best clones for propagation in Commercial level. The forest Eucalyptus spp. the study is located in the city of Rio Negrinho, SC. The forest was planted in December 1999. The species of the gender Eucalyptus sp. present in the experimental area are grown from seeds, from different locations. For selection of the best sources, subjects were evaluated for survival, height, diameter at breast height, volume, and features like the trunk tortuosity and fork. For vegetative material rescue experiment was applied the techniques of annealing and semi-annealing nine potential species, where individuals were evaluated number of shoots, number of cutting, survival and rooting. The same was evaluated according to the youthfulness through different heights from the ground for E. benthamii. The potential species for quantitative and qualitative variables, as well as the ranking used to select the best species, three species that stood out were E. dunni, E. benthamii and E. dorrigoensis. Regarding the origins for E. smithii the origin Wilson Promontorj to E.benthamii Australia, as well as E. viminalis and E. deanei the origin Manville SC and E. macarthurii Pieter Maritz. Among the vegetative recovery methods tested, the girdling showed better results due to the issuance of shoots. For the survival and 12 13 rooting of seedlings it is necessary to further study since only E. deanei embedded material obtained using IBA at 3000 mg L-¹. As for the issue of shoots depending on the degree of youthfulness to E. benthamii is recommended to perform the incision in the trees at the height of 20 and 50 cm above the ground, and new studies because not yielded results as the survival and rooting of cuttings
O objetivo do estudo foi resgatar, conservar e multiplicar o material genético das melhores espécies/procedências selecionadas de Eucalyptus spp., para a região norte de Santa Catarina e selecionar os melhores clones para a propagação em nível comercial. O povoamento de Eucalyptus spp. do estudo está localizada no município de Rio Negrinho, SC. O talhão foi plantado em dezembro de 1999. As espécies do gênero Eucalyptussp. presentes na área experimental são oriundas de sementes, provenientes de diversos locais. Para seleção das melhores procedências, os indivíduos foram avaliados quanto à sobrevivência, altura, diâmetro à altura do peito, volume, e características qualitativas como tortuosidade do tronco e bifurcação. Para o experimento de resgate de material vegetativo foramaplicadas as técnicas de anelamento e semianelamento em nove espécies potenciais, onde os indivíduos foram avaliados em termos de número de brotações, número de estacas, sobrevivência e enraizamento. O mesmo foi avaliado em função da juvenilidade através das diferentes alturas em relação ao solo para a E. benthamii. As espécies potencias em relação às variáveis quantitativas e qualitativas, assim como o ranking utilizado para selecionar as melhores espécies, as três espécies que se destacaram foram E. dunni. E. benthamiie E. dorrigoensis. Em relação as procedências para E. smithii a procedência de Wilson Promontorj, para E.benthamii a Austrália, assim como para E. deanei e E. viminalis a procedência Manville SC, e para E. macarthuriiPieter Maritz. Dentre os métodos de resgate vegetativo testados, o anelamento apresentou melhores resultados em função da emissão de brotações. Para a sobrevivência e o enraizamento dos propágulos torna-se necessário novos estudos uma vez que apenas E. deanei obteve 8 9 material enraizado com a utilização de AIB na concentração de 3.000 mg L-¹. Quanto a emissão de brotos em função do grau de juvenilidade para E. benthamii, recomenda-se realizar a incisão nas árvores na altura de 20 e 50 cm acima do solo, e a realização de novos estudos pois não obteve-se resultado quanto a sobrevivência e enraizamento das estacas

This work deal with the analysis of influence of pressure‘s sizes in vacuum chamber of specimen Evironmental Scanning Electron Microscope and the influence of sizes of aperture diaphragm by scintillation detector. The analysis proceeds in detector of secondary electrons. The detector is modelled by system 3D CAD SolidWorks with the help of system CAE Cosmos FloWorks.

In this dissertation I present experimental results obtained on the mercury optical clock project in the research group of Jason Jones at the University of Arizona. The project began in 2008 with the purpose of investigating the feasibility of neutral mercury as an optical clock species. The first series of investigations involved building the essential apparatus and scanning the doppler-broadened 6¹S₀ - 6³P₀ clock transition in ¹⁹⁹Hg. Here I present significant modifications to the cooling and trapping laser, improvements to the spectroscopy laser linewidth, and attempts to measure the 2-photon transition in ¹⁹⁹Hg. After previously demonstrating spectroscopy of the mercury clock transition using an optically-pumped semiconductor laser for the cooling and trapping source (OPSL), we replaced the OPSL with a a fiber-amplified ECLD system. We custom built a fiber amplifier to provide gain at 1015 nm, demonstrating the system can yield up to 5 W of signal power with excellent suppression of the ASE power. We find that the ASE is well suppressed by using a two-stage configuration and short sections of gain fiber. The linewidth of our original spectroscopy laser was over 10 kHz, which is unsuitable to resolve of sub-Doppler features. To enhance the performance of our spectroscopy system, we integrated faster feedback bandwidth using AOMs, and incorporated derivative gain into the system. This resulted in a feedback bandwidth for our spectroscopy laser of over 200 kHz. With this system, we demonstrate anactively stabilized linewidth of 525 Hz for our spectroscopy system. Using the upgraded cooling and spectroscopy laser systems, we demonstrate spectroscopy of the clock system and confirm temperature measurements derived from the transition linewidth. We also describe attempts to detect the recoil shift and 2-photon transition in neutral mercury.

Fragmentos de código duplicado, ou clones, são inseridos em aplicativos por serem uma maneira simples de reúso, dentre outros motivos. Clones são, portanto, comuns em programas. No entanto, a atividade de manutenção pode ficar custosa se o código do programa analisado possuir muitos clones, principalmente os semânticos, os quais podem possuir códigos distintos, mas realizam tarefas similares. Nesse sentido, a utilização de ferramentas que automatizam a tarefa de detectar clones é desejável. Ferramentas atuais de detecção de clones semânticos são capazes de identificar esses clones com altas taxas de acerto. No entanto, elas não são capazes de identificar clones semânticos considerando também os fluxos dos procedimentos ou funções que são invocados dentro dos fragmentos de código comparados. Essa limitação pode levar as ferramentas a indicarem clones semânticos falso positivos. Este trabalho apresenta uma técnica de detecção de clones semânticos que considera as chamadas de procedimentos presentes nos programas. Essa técnica apresentou uma taxa de acertos 2,5% maior do que técnicas convencionais de acordo com um benchmark, também desenvolvido neste trabalho. Esse benchmark foi criado com base nas classificações de clones fornecidas por programadores da indústria e da academia. A técnica interprocedimental de detecção de clones semânticos pode ser utilizada para evolução, manutenção, refatoração e entendimento de programas.
Fragments of duplicated code, or clones, are embedded in applications as they are a simple way to reuse code, among other reasons. Clones are therefore common in programs. However, the maintenance activity may be costly if the program code has many clones to analyze, specially semantic clones, which are semantically similar but may have different syntax. In this regard, the use of tools that automate the task of detecting clones is desirable. Current tools for detecting semantic clones are able to identify those clones with high hit rates. However, they are not able to detect semantic clones also considering the flow of procedures or functions that are invoked within the compared code fragments. This limitation can lead the tools to indicate false positive semantic clones. This paper presents a technique that takes into account the procedure calls in programs to detect semantic clones. This technique showed a 2.5% higher hit rate than conventional techniques according to a benchmark also developed in this work. This benchmark was created based on evaluations provided by programmers from academic and industrial settings. The interprocedural semantic clone detection technique can be used for evolution, maintenance, refactoring and understanding of programs.

In recent years, it has been observed that software clones and plagiarism are becoming an increased threat for one?s creativity. Clones are the results of copying and using other?s work. According to the Merriam – Webster dictionary, “A clone is one that appears to be a copy of an original form”. It is synonym to duplicate. Clones lead to redundancy of codes, but not all redundant code is a clone.On basis of this background knowledge ,in order to safeguard one?s idea and to avoid intentional code duplication for pretending other?s work as if their owns, software clone detection should be emphasized more. The objective of this paper is to review the methods for clone detection and to apply those methods for finding the extent of plagiarism occurrence among the Swedish Universities in Master level computer science department and to analyze the results.The rest part of the paper, discuss about software plagiarism detection which employs data analysis technique and then statistical analysis of the results.Plagiarism is an act of stealing and passing off the idea?s and words of another person?s as one?s own. Using data analysis technique, samples(Master level computer Science thesis report) were taken from various Swedish universities and processed in Ephorus anti plagiarism software detection. Ephorus gives the percentage of plagiarism for each thesis document, from this results statistical analysis were carried out using Minitab Software.The results gives a very low percentage of Plagiarism extent among the Swedish universities, which concludes that Plagiarism is not a threat to Sweden?s standard of education in computer science.This paper is based on data analysis, intelligence techniques, EPHORUS software plagiarism detection tool and MINITAB statistical software analysis.

Conservation and restoration of quaking aspen in the western United States requires an understanding of how and when aspen clones became established, how clones adapt to environmental challenges, and how individual clones interact within stands. I used molecular tools to identify individual clones in a natural population of aspen in southern Utah and detected high and low levels of clonal diversity within stands. Stands with high clonal diversity were located in areas with a more frequent fire history, indicating that fires may have prepared sites for seed germination and establishment over time. Conversely, areas of low clonal diversity corresponded to areas with less frequent fire. The same molecular tools were then used to investigate clonal interactions/succession over relatively recent time. For this portion of the study I sampled small, medium, and large aspen ramets (stems) at 25 subplots within spatially separated one-hectare plots, and mapped the clonal identities. I found that approximately 25% of the clones appeared to be spreading into adjacent clones, while 75% of the clones had a stationary pattern. In the final portion of the study, I again used molecular tools to identify aspen clones and investigated tradeoffs between growth and defense chemistry in mature, naturally-occurring trees. Growth was estimated using a ten-year basal area increment, and the percent dry weight of salicortin, tremulacin, and condensed tannins was measured in the same trees. Overall I discovered evidence for a tradeoff between growth and salicortin/tremulacin, and a marginally significant but positive relationship between growth and condensed tannins.

Os fatores de crescimento vascular endotelial (VEGF) e o fibroblástico básico (bFGF) são reguladores importantes do desenvolvimento e função placentária. Os efeitos destes na expressão da enzima esteroidogênica aromatase P450 (P450arom) na placenta bovina em diferentes estágios gestacionais (90 a 270 dias) foram avaliados através de imunocitoquímica. Além disso, comparou-se a influência destes entre células placentárias de bovinos clonados e não clonados aos 270 dias. A aromatase P450 foi localizada exclusivamente no citoplasma das células trofoblásticas gigantes e sua expressão foi menor aos 150 dias de gestação, em relação às demais idades (p<0,05). O VEGF (50 ng/ml) influenciou significativamente a expressão da P450arom aos 150 e 270 dias, enquanto o bFGF (10 ng/ml) foi efetivo em estimular essa expressão particularmente no final da gestação (270 dias). Os dois fatores combinados (bFGF+VEGF) inibiram a expressão da P450arom no terço inicial (90 dias), mas, por outro lado, estimularam-na aos 150 e 270 dias (p<0,05). Nos clones, a expressão da P450arom, nos grupos controle e VEGF, foi semelhante a dos animais não clonados aos 270 dias de gestação, porém, o bFGF e os dois fatores combinados inibiram-na significativamente (p<0,05). Em todos os grupos analisados, a expressão da P450arom apresentou característica ascendente em função dos dias de cultivo, atingindo concentração máxima após 96 horas de incubação. Assim, o presente estudo demonstrou efeitos distintos e estágio-específicos dos fatores de crescimento bFGF e VEGF na secreção de estrógenos na placenta bovina via modulação da expressão da aromatase P450 in vitro. Conclui-se que estes fatores de crescimento agem como potentes moduladores de enzimas esteroidogênicas e que, sob as condições de cultivo estabelecidas, as células placentárias de bovinos clonados apresentam padrão de resposta distinto quando comparadas com células de bovinos não clonados de mesma idade gestacional.
Vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) are important regulators of placental development and function. Their effects on the steroidogenic enzyme aromatase P450 (P450arom) expression from bovine placenta at different gestational stages (90 - 270 days) were evaluated by immunocytochemistry. Moreover, we compared the effects of these growth factors on P450arom expression between cloned and non cloned bovine placental cells. P450arom was localized exclusively in trophoblast giant cells cytoplasm, and its expression reached lowest levels at day 150 of gestation in comparison to the remaining evaluated gestational stages. VEGF (50 ng/mL) influenced significantly P450arom expression at days 150 and 270, whereas bFGF (10 ng/mL) was effective in stimulating P450arom expression particularly during late gestation (day 270). The two factors combined (bFGF+VEGF) inhibited P450arom expression during early gestation (day 90), but, in contrast, stimulated it at days 150 and 270 of pregnancy (P<0.05). In cloned bovine placental cells, P450arom expression was similar to non-cloned cells in the control and VEGF groups, however, bFGF and both factors together inhibited it significantly (P<0.05). In all groups analyzed, P450arom expression presented rising pattern over the duration of the culture, reaching maximal values at 96 hours of incubation. Thus, the present study demonstrated distinct and stage-specific effects of these growth factors on bovine placenta P450arom expression in vitro. We concluded that these growth factors act as potent steroidogenic enzymes regulators, and, under the established culture conditions, placental cells from cloned bovines presented distinct answer pattern compared to non cloned placental cells at the same gestational stage.

Les donnees de cette these montrent que des lymphocytes t cd4+ et cd8+ specifiques d'antigenes de la tumeur infiltrent la plupart des melanomes humains. L'un de ces clones de til (cd8+) reconnaissant 12 lignees de melanomes hla-a2 sur 15 testees a ete utilise pour rechercher l'antigene partage par ces lignees et reconnu dans le contexte hla-a2. Le gene codant pour cet antigene a ete identifie par co-transfection d'une bibliotheque de cdna tumoral et du gene hla-a2 dans des cellules cos-7. Il s'agit du gene de la n-acetylglucosaminyltransferase v. De facon originale, la region codant pour le peptide antigenique se trouve localisee dans un intron de ce gene. L'expression de cet antigene a ete analysee par rt-pcr. Il est exprime dans 50% des melanomes, 5% des sarcomes et 10% des tumeurs du cerveau mais n'est pas exprime de facon significative dans les tissus sains, dont la peau. L'expression de cet antigene semble donc essentiellement specifique de tumeurs. Par ailleurs une analyse fonctionnelle in-vitro de clones de til cd4+ et cd8+ specifiques de melanomes humains a ete realisee. Elle nous a permis de montrer qu'en reponse a la cellule tumorale autologue, la majorite de ces clones produit du tnf, mais ne secrete pas les lymphokines majeures telles que l'il-2, l'il-4 et l'ifn-g. Ce defaut de production ne provient pas d'une alteration fonctionnelle des til puisqu'un anticorps anti-cd3 immobilise induit la production d'il-2 et qu'une augmentation de la densite du peptide antigenique sur les cellules tumorales restaure la secretion d'il-2 par deux clones cd8+. Le niveau d'expression des antigenes de tumeurs semble donc determiner le niveau d'activation des til specifiques

This thesis deals with the production of a plastic body of the aperture by the method of injection moulding. The work includes a design of the injection mould for the given component. First, an appropriate material for the moulded piece was chosen and then the necessary calculations for the injection mould were made. A quadruplex injection mould with a heated inlet nozzle and pullout cores was designed based on these calculations. Modular components were chosen when designing the injection mould. The next part of the thesis contains the selection of the injection moulding machine for the given mould. The conclusion contains a technical-economical evaluation including the cost estimating for the injection mould and cost estimating for one moulded piece.

Le declenchement par une hormone steroide, la 20-hydroxyecdysone, de la formation d'une aile a partir d'un massif de cellules indifferenciees, le disque imaginal, est etudie chez le lepidoptere bombyx mori comme un modele de differenciation d'un organe. Notre objectif est de determiner comment est hierarchisee et coordonnee la cascade d'activation genique a l'origine de cette differenciation. La realisation puis le criblage differentiel d'une banque adnc de disques alaires de bombyx mori en cours de differenciation ont permis d'isoler un certain nombre de clones correspondant a des genes exprimes dans un contexte hormonal eleve et pendant le processus de morphogenese de l'aile. L'analyse des patrons d'expression au cours du developpement des arnm correspondant a quelques uns de ces clones permet de suggerer que la morphogenese de l'aile nymphale d'un lepidoptere commence deja lors de la derniere mue larvaire. Le clone bmcoll correspond a un arnm codant pour une proteine de la superfamille des collagenes. Il represente la premiere molecule de ce type decrite chez bombyx mori. La frequence des interruptions de la serie des triplets gly-xaa-yaa codant pour la triple helice collagenique lui confere un caractere de collagene non fibrillaire, mais les comparaisons avec les banques de donnees ne permettent pas d'identification formelle. Les acides amines representes aux positions xaa et yaa des triplets gly-xaa-yaa sont dans la majorite des cas la glutamine et la proline respectivement et la region ncl, completement originale, ne presente aucune homologie avec les regions c-terminales deja decrites. L'accumulation des messagers de bmcoll varie dans le meme sens que le taux de 20-hydroxyecdysone chez la larve. In vitro, le blocage de la synthese proteique par la cycloheximide provoque, comme avec la 20-hydroxyecdysone, l'accumulation des transcrits de bmcoll sous un delai d'une heure. Le modele de regulation qui est propose dans cette these suggere que les messagers de bmcoll, intrinsequement instables dans le disque pendant les phases de croissance lente de l'ebauche, sont stabilises en presence d'hormone par la disparition d'une proteine destabilisatrice hormone sensible. Cette hypothese est en accord avec la presence dans la region 3' non traduite de sequences responsables de l'instabilite de certains messagers de mammiferes. A notre connaissance, un tel mode de regulation n'a jamais ete decrit dans les modeles rendant compte de l'action de la 20-hydroxyecdysone sur le controle de l'activite genique

[eng] Chronic respiratory infection (CRI) by Pseudomonas aeruginosa is the main cause of morbidity and mortality in cystic fibrosis (CF). During the progression from early infection to chronic non-eradicable colonization P. aeruginosa undergoes a complex evolutionary adaptation and diversification process which eventually leads to a mixed and persistent infecting population in which multidrug resistant variants frequently rise compromising the selection of appropriate antibiotic therapies. In this work the interplay between three key microbiological aspects of these infections was investigated: the occurrence of transmissible and persistent strains, the emergence of variants with enhanced mutation rates (mutators) and the evolution of resistance to antibiotics. Clonal epidemiology, antibiotic susceptibility profiles, contribution of P. aeruginosa classical resistance mechanisms and the role of mutator variants were investigated in two large collections of CF P. aeruginosa isolates from the Balearic Islands and Spain. As well, whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, within-host evolution, WGS mutator genotypes (mutome) and resistome of widespread P. aeruginosa clonal complex 274 (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. Finally, due to the Chronic respiratory infection (CRI) by Pseudomonas aeruginosa is the main cause of morbidity and mortality in cystic fibrosis (CF). During the progression from early infection to chronic non-eradicable colonization P. aeruginosa undergoes a complex evolutionary adaptation and diversification process which eventually leads to a mixed and persistent infecting population in which multidrug resistant variants frequently rise compromising the selection of appropriate antibiotic therapies. In this work the interplay between three key microbiological aspects of these infections was investigated: the occurrence of transmissible and persistent strains, the emergence of variants with enhanced mutation rates (mutators) and the evolution of resistance to antibiotics. Clonal epidemiology, antibiotic susceptibility profiles, contribution of P. aeruginosa classical resistance mechanisms and the role of mutator variants were investigated in two large collections of CF P. aeruginosa isolates from the Balearic Islands and Spain. As well, whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, within-host evolution, WGS mutator genotypes (mutome) and resistome of widespread P. aeruginosa clonal complex 274 (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. Finally, due to the relevance of aminoglycosides in the management of CF-CRI, the dynamics of P. aeruginosa resistance development to aminoglycosides was also studied in vitro by WGS approaches. Despite discrepancies between molecular genotyping methods, a high degree of genetic diversity was documented among CF isolates from the Balearic Islands and Spain with scarce representation of CF epidemic strains. However, for the first time in Spain, we documented a superinfection with the multidrug resistant Liverpool Epidemic Strain (LES) in a chronically colonized patient. As well, P. aeruginosa CC274, previously detected in several CF individuals from Austria, Australia and France, was detected in 5 unrelated chronically colonized patients from the Balearic Islands and, therefore, this clone-type should be added to the growing list of CF epidemic clones. Subsequent analysis of the whole genomes sequences of P. aeruginosa isolates from the CC274 P. aeruginosa collection provides evidence of interpatient dissemination of mutator sublineages and denotes their potential for unexpected short-term sequence type (ST) evolution and antibiotic resistance spread, illustrating the complexity of P. aeruginosa population biology in CF. As well, epidemiological studies demonstrated the coexistence of two divergent lineages but without evident geographical barrier. Antibiotic resistance significantly accumulated overtime accompanied by hypersusceptibility to certain antibiotics such as aztreonam, which can be explained in terms of collateral susceptibility. Correlation between phenotypes and WGS genotypes of clonal isolates from the CC274 collection allowed us to define the mutational resistome of CF P. aeruginosa which extends beyond the classical mutational resistance mechanisms. Among the new chromosomic resistance determinants encountered, mutations within the penicillin-binding-protein 3 (PBP3), shaping up beta-lactam resistance, are noteworthy as well as mutations within the fusA1 gene, coding for elongation factor G, which along with MexXY overexpresion contribute to high-level aminoglycoside resistance. Strikingly, we encountered that MexXY overexpression is dispensable for in vitro resistance development to aminoglycosides which suggests an evolutionary advantage of its overexpression in the CF respiratory tract. Altogether this work demonstrates that clonal epidemiology and antibiotic resistance evolution in the CF setting results from the complex interplay among mutation-driven resistance mechanisms, within host diversification and interpatient transmission of epidemic strains.
[spa] La infección respiratoria crónica por P. aeruginosa es la principal causa de morbilidad y mortalidad en pacientes con fibrosis quística (FQ). Durante la progresión desde la infección temprana a la colonización crónica, P. aeruginosa experimenta un complejo proceso adaptativo y de diversificación que resulta en una población heterogénea y persistente en la que la aparición de resistencias a los antibióticos comprometen la selección de terapias apropiadas. En este trabajo se investigó la interacción entre tres aspectos microbiológicos clave de estas infecciones: la presencia de cepas transmisibles y persistentes, la aparición de variantes con tasas de mutación incrementadas y la evolución de la resistencia a los antibióticos. La epidemiología clonal, los perfiles de sensibilidad antibiótica, la contribución de los mecanismos clásicos de resistencia de P. aeruginosa y el papel de las variantes hipermutadoras se estudiaron en dos grandes colecciones de aislados procedentes de pacientes con fibrosis quística de las Islas Baleares y España. Asimismo, mediante secuenciación de genoma completo, se determinó la filogenia, diseminación interpaciente, evolución intrapaciente, genotipo hipermutador y resistoma de una colección de aislados clonales pertenecientes al complejo clonal 274 (CC274), proviniendo dichos aislados de dos países muy distantes, Australia y España, y cubriendo un período de 18 años. Finalmente, dada la relevancia de los aminoglucósidos en el manejo de estos pacientes, se estudió la dinámica del desarrollo de resistencia a aminoglucósidos in vitro mediante secuenciación de genoma completo. A pesar de encontrarse discrepancias entre los métodos de genotipado molecular, se documentó un alto grado de diversidad genética en las colecciones de las Islas Baleares y España, siendo escasa la representación de cepas epidémicas. No obstante, por primera vez en España, se documentó un caso de sobreinfección con el clon epidémico multirresistente de Liverpool. Además, en 5 pacientes de Baleares, crónicamente colonizados y sin aparente relación epidemiológica, se detectó el CC274. Puesto que este complejo clonal también ha sido detectado en pacientes de países como Austria, Australia y Francia, éste debería incluirse en la creciente lista de cepas epidémicas. El análisis posterior de las secuencias de genoma completo de los aislados del CC274 evidenció la diseminación interpaciente de un sublinaje hipermutador, denotando además el potencial de estas variantes para la inesperada evolución a corto plazo del secuenciotipo y la rápida diseminación de resistencias. Además, los estudios epidemiológicos demostraron la coexistencia de dos linajes divergentes, no evidenciándose barrera geográfica. Asimismo se documentó una tendencia generalizada a la acumulación de resistencias a los antibióticos en el tiempo, acompañada de hipersensibilidad a ciertos antibióticos como aztreonam, lo cual se puede explicar en términos de sensibilidad colateral. La correlación entre los fenotipos y genotipos determinados mediante secuenciación del genoma completo de los aislados pertenecientes al CC274 nos permitió definir el resistoma mutacional de P. aeruginosa en la FQ, el cual se extiende más allá de los mecanismos mutacionales clásicos. Entre los nuevos determinantes de resistencia cromosómica encontrados caben destacar tanto las mutaciones en la proteína fijadora de penicilina PBP3, que confieren resistencia a betalactámicos, como las mutaciones en fusA1, que codifica para el factor de elongación G, y que junto con la hiperexpresión de MexXY contribuyen a la resistencia de alto nivel a aminoglucósidos. Paradójicamente, encontramos que la hiperexpresión de MexXY es prescindible para el desarrollo de resistencia in vitro a aminoglucósidos, lo que sugiere que dicha hiperexpresión confiere una ventaja evolutiva in vivo. En conjunto, este trabajo demuestra que, en la FQ, la epidemiología clonal y la evolución de la resistencia a los antibióticos son el resultado de una compleja interacción entre los mecanismos de resistencia mutacionales, la diversificación de la población infectante y la transmisión interpaciente de cepas epidémicas.
[cat] La infecció respiratòria crònica per P. aeruginosa és la principal causa de morbiditat i mortalitat en els pacients amb fibrosi quística (FQ). Durant la progressió des de la infecció primerenca a la colonització crònica, P. aeruginosa experimenta un complexe procés adaptatiu i de diversificació que resulta en una població heterogènia i persistent en la qual l'aparició de variants resistents a múltiples antibiòtics comprometen la selecció de teràpies antibiòtiques apropiades. En aquest treball es va investigar la interacció entre tres aspectes microbiològics clau: la presència de soques transmissibles i persistents, l'aparició de variants amb taxes de mutació incrementades i l'evolució de la resistència als antibiòtics. L'epidemiologia clonal, els perfils de sensibilitat antibiòtica, la contribució dels mecanismes clàssics de resistència i el paper de les variants hipermutadores es van estudiar en dos grans col·leccions d'aïllats procedents de pacients amb FQ de les Illes Balears i Espanya. Així mateix, mitjançant seqüenciació del genoma complet, es va determinar la filogènia, disseminació interpacient, evolució intrapacient, genotip hipermutador i resistoma d'una col·lecció d'aïllats pertanyents al complexe clonal 274 (CC274), provenint de dos països molt distants, Austràlia i Espanya, i cobrint un període de 18 anys. Finalment, donada la rellevància dels aminoglicòsids en el maneig d’aquests pacients, es va estudiar la dinàmica del desenvolupament de resistència a aminoglicòsids in vitro mitjançant seqüenciació de genoma complet. Tot i trobar discrepàncies entre els mètodes de genotipat molecular, es va documentar un alt grau de diversitat genètica en les col·leccions de les Illes Balears i Espanya, sent escassa la representació de soques epidèmiques. No obstant això, per primera vegada a Espanya, es va documentar un cas de sobreinfecció amb el clon epidèmic multiresistent de Liverpool. A més, en 5 pacients de les Illes Balears, crònicament colonitzats i sense aparent relació epidemiològica, es va detectar el CC274. Ja que aquest complexe clonal també ha estat detectat en països com Àustria, Austràlia i França, aquest clon hauria d'incloure a la creixent llista de soques epidèmiques. L'anàlisi posterior de les seqüències de genoma complet dels aïllats pertanyents al CC274, va evidenciar la disseminació interpaciente d'un subllinatge hipermutador, denotant a més el potencial d'aquestes variants per a la inesperada evolució a curt termini del sequenciotip i per a la ràpida disseminació de la resistència antibiòtica. A més, els estudis epidemiològics van demostrar la coexistència de dos llinatges divergents, no existint barrera geogràfica. Així mateix es va evidenciar una tendència generalitzada a l'acumulació de resistències en el temps, acompanyada d'hipersensibilitat a certs antibiòtics com l’aztreonam, la qual cosa es pot explicar en termes de sensibilitat col·lateral. La correlació entre els fenotips i genotips determinats mitjançant seqüenciació del genoma complet dels aïllats pertanyents al CC274 ens va permetre definir el resistoma mutacional de P. aeruginosa en la FQ, el qual s'estén més enllà dels mecanismes de resistència mutacionals clàssics. Entre els nous determinants de resistència cromosòmica trobats cal destacar tant les mutacions en la proteïna fixadora de penicil·lina PBP3, que confereixen resistència a betalactàmics, així com les mutacions en fusA1, que codifica per al factor d'elongació G, i que juntament amb la hiperexpressió de MexXY contribueixen a la resistència d'alt nivell a aminoglucòsids. Paradoxalment, vam trobar a més que la hiperexpressió de MexXY és prescindible per al desenvolupament de resistència in vitro a aminoglucòsids, el que suggereix que aquesta hiperexpressió suposa un avantatge evolutiu in vivo. En conjunt, aquest treball demostra que l'epidemiologia clonal i l'evolució de la resistència als antibiòtics en el context de la FQ són el resultat d'una complexa interacció entre els mecanismes de resistència mutacionals, la diversificació de la població infectant i la transmissió interpaciente de ceps epidèmiques.

Circadian rhythms are endogenous cycles that control physiological and behavioral changes that can be affected by environmental factors which allow most eukaryotic organisms to synchronize their daily activities with the 24-hour day. Parasteatoda tepidariorum,the common house spider, demonstrates a short-period circadian clock averaging 21.6 hours when left in constant darkness, yet they are able to entrain to a 24-hour light cycle. We tested whether these spiders were able to use non-photic Zeitgebers to entrain to the 24-hour day. Periodic presentation of food and disturbance were not found to be effective cues for the spiders’ entrainment. A few individuals were clearly able to entrain to an 8 oC amplitude temperature cycle, while most did not.

The dissertation thesis deals with the application of absorption methods for the separation of gaseous pollutants from polluted gaseous mixtures using a pilot plant scrubber. The efficiency of the gaseous pollutant removal was determined based on the hydrodynamic distribution of fluids inside the spray chamber. A TF-28 150 spiral nozzle, which was used to spray the absorption liquid, was experimentally characterized. Specifically, the pressure impact pattern of the liquid produced by the nozzle was investigated using intrusive methods and the effective spray angles, the modes of primary and secondary atomization, the droplet size and liquid velocity distributions were determined using non-intrusive optical methods. Numerical simulations of flow of model gas phase inside the sprinkler head and spraying of the liquid through the spiral nozzle were also carried out. The obtained data can be applied to estimate the interface area and together with the determination of the coefficient of total mass transfer thus define the kinetics of chemisorption for a given absorbent/absorbate combination.

A restricted version of the Galois connection between polymorphisms and invariants, called Pol−CInv, is studied, where the invariant relations are restricted to so-called clausal relations. In this context, the relationship of maximal C-clones and maximal clones is investigated. It is shown that, with the exception of one special case occurring for Boolean domains, maximal C-clones are never maximal clones
Wir untersuchen eine eingeschränkte Variante der Galoisverbindung zwischen Polymorphismen und invarianten Relationen, bezeichnet mit Pol−CInv, wobei die invarianten Relationen auf sogenannte klausale Relationen beschränkt werden. In diesem Zusammenhang wird die Beziehung zwischen maximalen C-Klonen und maximalen Klonen betrachtet. Es wird gezeigt, daß, mit Ausnahme eines Spezialfalles für Boolesche Grundmengen, maximale C-Klone niemals maximale Klone sind

The essays featured in this collection highlight the gaps, as well as parallels, between mental illness and the human condition. In "Appearances," the narrator struggles with her own visual identity especially after reflecting on her Mom's own lengthy history with the mirror. In "Migrations," the lyrical voice of the narrator carries the reader through the typical day of a clinically depressed female character. Lastly, "Attempting the Fall," addresses the issues society has with mental illness by following the narrator from her suicide attempt to the mental ward.

This report discusses clones with nullary operations and the corresponding relational clones, both defined on arbitrary non-empty sets. The relationship between such clones and clones in the usual sense, i.e. without nullary operations, is investigated, and in particular the latter type of clones is located in the lattice of all clones. By means of two pairs of kernel and closure operators, a framework is developed that allows to transfer statements about usual clones to statements about clones with nullary constants. In this respect, familiar operators and constructions from clone theory, like the operators Pol and Inv, the closure operators belonging to the clone lattices, and the different variants of local closure operators on sets of relations and operations, respectively, are translated from the usual setting to the more general one and vice versa. The applicability of the presented machinery is demonstrated using the example of the theorem characterising Galois closed sets w.r.t. Pol-Inv as local closures of clones and relational clones, respectively.

The determination of semantic equivalence is an undecidable problem; however, this dissertation shows that a reasonable approximation can be obtained using a combination of static and dynamic analysis. This study investigates the detection of functional duplicates, referred to as semantic method clones (SMCs), in Java code. My algorithm extends the input-output notion of observable behavior, used in related work [1, 2], to include the effects of the method. The latter property refers to the persistent changes to the heap, brought about by the execution of the method. To differentiate this from the typical input-output behavior used by other researchers, I have coined the term method IOE-Behavior; which means its input-output and effects behavior [3]. Two methods are defined as semantic method clones, if they have identical IOE-Behavior; that is, for the same inputs (actual parameters and initial heap state), they produce the same output (that is result- for non-void methods, and final heap state). The detection process consists of two static pre-filters used to identify candidate clone sets. This is followed by dynamic tests that actually run the candidate methods, to determine semantic equivalence. The first filter groups the methods by type. The second filter refines the output of the first, grouping methods by their effects. This algorithm is implemented in my tool JSCTracker, used to automate the SMC detection process. The algorithm and tool are validated using a case study comprising of 12 open source Java projects, from different application domains and ranging in size from 2 KLOC (thousand lines of code) to 300 KLOC. The objectives of the case study are posed as 4 research questions: 1. Can method IOE-Behavior be used in SMC detection? 2. What is the impact of the use of the pre-filters on the efficiency of the algorithm? 3. How does the performance of method IOE-Behavior compare to using only input-output for identifying SMCs? 4. How reliable are the results obtained when method IOE-Behavior is used in SMC detection? Responses to these questions are obtained by checking each software sample with JSCTracker and analyzing the results. The number of SMCs detected range from 0 45 with an average execution time of 8.5 seconds. The use of the two pre-filters reduces the number of methods that reach the dynamic test phase, by an average of 34%. The IOE-Behavior approach takes an average of 0.010 seconds per method while the input-output approach takes an average of 0.015 seconds. The former also identifies an average of 32% false positives, while the SMCs identified using input-output, have an average of 92% false positives. In terms of reliability, the IOE-Behavior method produces results with precision values of an average of 68% and recall value of 76% on average. These reliability values represent an improvement of over 37% (for precision) of the values in related work [4]. Thus, it is my conclusion that IOE-Behavior can be used to detect SMCs in Java code with reasonable reliability.
Ph.D.
Doctorate
Computer Science
Engineering and Computer Science
Computer Science

As principais causas de morte perinatal em bezerros estão de alguma forma relacionadas a problemas cardiorrespiratórios. A maior parte de morte de bezerros ocorre justamente no período de até 48h após o nascimento, quando ainda estão sendo feitos os ajustes fisiológicos necessários à vida extrauterina. Com o aumento de animais advindos das técnicas de produção in vitro, também aumentaram os problemas de sobrevivência e sobrevida dos recém nascidos. Este estudo teve como objetivo geral padronizar valores de referência de hemogasometria e espirometria de bezerros a termo, nascidos por parto espontâneo, e prematuros, nascidos por cesariana, da raça Nelore concebidos por inseminação artificial (IA), assim como estabelecer protocolos de cuidados intensivos neonatais aos animais prematuros. Objetivamente, o estudo compreendeu: 1. A avaliação dos valores de pressão invasiva de átrio direito, ventrículo direito, artéria pulmonar e artéria pulmonar ocluída, hemogasometria, espirometria e capnografia de bezerros da raça Nelore, a termo, nascidos por parto espontâneo; 2. A avaliação e padronização da hemogasometria arterial de bezerros raça Nelore, a termo, nascidos de partos espontâneos; 3. A avaliação da pressão invasiva da artéria pulmonar e dos efeitos do sildenafil sobre os valores de pressão de artéria pulmonar em bezerros da raça Nelore, prematuros, nascidos por cesariana; 4. Diferenças hemodinâmicas (utilizando o cateter de Swan-Ganz), na função pulmonar e nas trocas gasosas entre bezerros a termo nascidos por parto espontâneo e prematuros nascidos por cesariana; 5. O estabelecimento de protocolos de cuidados neonatais para bezerros advindos de gestações complicadas com risco de morte neonatal prematura, onde foram realizadas 3 cesarianas em bezerros concebidos por IA e 16 concebidos por transferência nuclear por de células somática (clonagem), sendo estabelecidos protocolos de terapia neonatal com sildenafil, surfactante e oxigenoterapia. Bezerros da raça Nelore a termo nascidos por parto espontâneo estabilizam seus parâmetros de hemogasometria a valores de animais adultos em até 48 horas após o nascimento e têm valores de hemogasometria mais próximos dos valores normais para a espécie, enquanto os bezerros prematuros, nascidos por cesariana, têm valores mais deslocados em relação a normalidade. A padronização da hemogasometria de bezerros da raça Nelore nascidos por eutocia, pode fomentar as pesquisas com animais advindos de técnicas de PIV, assim como aumentar a sobrevida e sobrevivência além de diminuir a mortalidades desses animais. Já o sildenafil não apresenta efeitos adversos significativos quanto a oxigenação dos bezerros em que foi usado, mesmo quando houve alterações não desejadas da PAP. Dessa forma, quando não existe a possibilidade de se aferir a PAP e suspeita-se de hipertensão, o sildenafil é pode ser usado sem maiores consequências para a saúde do paciente.
The main causes of perinatal death in cattle are frequently related to cardiorespiratory distress. A great number of losses are placed during the first 48h after birth, when important physiological adjustments to the extra-uterine life are still in progress. Recent increase of offspring derived from assisted reproductive in vitro biotechnologies resulted in diminished survival rates of the newborn. The present study aimed to obtain standard values of hemodynamic evaluation, blood gas and spirometry of Nelore calves conceived by artificial insemination (AI) born at term, spontaneously, or from premature calves born by cesarean delivery, as well as to establish protocols of neonatal intensive care focusing on premature animals. Objectively, the study comprised: 1. The evaluation of invasive pressure values from right atrium, right ventricle, pulmonary artery and pulmonary wedge pressure, blood gas, spirometry and capnography of Nelore calves born spontaneously; 2. Evaluation and standardization of arterial blood gas of Nelore calves born at term spontaneously; 3. Evaluation of invasive pressure of pulmonary artery (PAP) and effects of sildenafil administration on its values from Nelore premature calves born by cesarean; 4. The comparison of hemodynamic, blood gas and spirometry of calves born at term spontaneously or premature calves born by cesarean delivery, during the first 30 days of life; 5. The establishment of neonatal care protocols focusing on complicated pregnancies at risk of premature neonatal death, when 3 cesarean sections of calves conceived by AI and 16 conceived by nuclear transfer of somatic cells (cloning) were monitored, and therefore protocols involving neonatal therapy with sildenafil, surfactant and oxygen therapy were established. Nelore calves born at term spontaneously have their blood gas stabilized in values similar to adult cattle until 48 hours after birth, and present a blood gas profile more similar to the expected for the species, whereas premature calves born from cesarean delivery present values different from normality. The standardization of blood gas of Nelore calves born at term from eutocic deliveries may promote better perinatal survival rates in offspring derived from in vitro production. The treatment with sildenafil does not present adverse effects related to the oxygen levels of calves even when adverse alterations were observed in PAP. Therefore, whenever hypertension is suspected and measurement of PAP is impaired, the sildenafil treatment may be used without major consequences to the patient health

O VEGF é um fator mitogênico específico de células endoteliais que promove diferenciação celular materno-fetal placentária quando ligado a seus receptores (Flt-1 e KDR). Sua expressão é controlada por mecanismos autócrinos e parácrinos e está associada ao desenvolvimento da placenta. A placenta bovina foi utilizada como modelo de estudo por apresentar a facilidade de se avaliar os componentes do sistema VEGF em diferentes fases gestacionais. Como objetivo este estudo buscou analisar o fator de crescimento vascular endotelial (VEGF) e seus receptores através da técnica de PCR em tempo real no início, meio e fim de gestação. Para tanto, amostras de placentomas, região interplacentomal e corpo lúteo foram coletadas em diferentes fases gestacionais. Foram utilizados placentomas de animais clonados obtidos apenas aos 270 dias de gestação e estas amostras foram comparadas aos animais não clonados na mesma fase. A expressão do VEGF no placentoma apresentou um decréscimo (p < 0.05) no final da gestação (270 dias) em relação à expressão do VEGF aos 90 dias. A expressão do Flt-1 e do KDR na região interplacentomal foi semelhante desde os 45 até 90 dias de gestação e apresentou um aumento significativo (p < 0.05) aos 150 dias. No corpo lúteo gestacional, a expressão do VEGF aos 210 dias foi maior (p ≤ 0.05) em relação a 90 e 150 dias; observou-se também baixa expressão do KDR aos 90 dias de gestação (p < 0.05) em relação aos 210 dias. Pode-se concluir que a regulação da expressão do VEGF variou em relação aos seus receptores nos três tecidos avaliados. Placentomas de bovinos clonados não apresentaram diferenças significativas em relação à expressão do sistema VEGF se comparados aos placentomas de animais não clonados sugerindo ser esta expressão equivalente em placentas de animais clonados que vieram a termo.
The VEGF is a specific endothelial mitogenic factor that promotes feto-maternal cell differentiation in placenta through binding to its receptors (Flt-1 and KDR). Their expression is controlled by autocrine and paracrine mechanisms that are associated to placenta development. The bovine placenta was used in this study as a model due to easiness of evaluation of VEGF system components in different phases of pregnancy. The objective of this study was to analyze the vascular endothelial growth factor (VEGF) and its receptors expression using the real time PCR technique in the beginning, half and end of pregnancy. Furthermore, placentome samples, interplacentomal areas and corpus luteum were collected in different gestational phases for comparative studies. Placentome of cloned animals were analyzed at 270 days of pregnancy and compared to non-cloned animals in the same phase. The expression of VEGF in the placentome presented a decrease of expression (p < 0.05) in the end of the gestation (270 days) in relation to 90 days. The expression of Flt-1 and of KDR in interplacentomal area was similar from 45 to 90 days of pregnancy with a significant increase (p <0.05) observed at 150 days. In the gestational corpus luteum, the expression of VEGF at 210 days was higher (p ≤ 0.05) in comparison to 90 and 150 days. In the same tissue KDR expression at 90 days was lower (p < 0.05) in relation to 210 days. In conclusion the regulation VEGF varied in relation to its receptors expression in all three studied tissues. Cloned placentomes showed no significant differences in VEGF system expression compared to the placentome of non-cloned animals, suggesting there is an equivalent expression in placentas from cloned animals that came to term.

Background: Clonal competition in cancer describes the process in which the progeny of a cell clone supersedes or succumbs to other competing clones due to differences in their functional characteristics, mostly based on subsequently acquired mutations. Even though the patterns of those mutations are well explored in many tumors, the dynamical process of clonal selection is underexposed. Methods: We studied the dynamics of clonal competition in a BcrAbl-induced leukemia using a γ-retroviral vector library encoding the oncogene in conjunction with genetic barcodes. To this end, we studied the growth dynamics of transduced cells on the clonal level both in vitro and in vivo in transplanted mice. Results: While we detected moderate changes in clonal abundancies in vitro, we observed monoclonal leukemias in 6/30 mice after transplantation, which intriguingly were caused by only two different BcrAbl clones. To analyze the success of these clones, we applied a mathematical model of hematopoietic tissue maintenance, which indicated that a differential engraftment capacity of these two dominant clones provides a possible explanation of our observations. These findings were further supported by additional transplantation experiments and increased BcrAbl transcript levels in both clones. Conclusion: Our findings show that clonal competition is not an absolute process based on mutations, but highly dependent on selection mechanisms in a given environmental context.

This diploma thesis deals with cavitation flow in the microscale, which remains an area with a lack of sufficient description of this phenomenon. At the same time, microfluidics is a field experiencing a dramatic rise in numerous biochemical applications, which underlines the relevance of researches of this type. In theoretical part of the thesis, cavitation was described in detail. In the practical part, a microfluidic device with a cavitation orifice was designed and manufactured. The ANSYS program was used for this design. An experiment was performed with the designed microchip, the aim of which was to observe a cavitating flow on the orifice. This measurement took place at the microfluidic laboratory at Victor Kaplan Department of Fluid Engineering. Due to the failure of the experiment, a CFD model of two-phase cavitation flow was built. The conclusions of the thesis were compiled from the findings of measurement and the results of modeling.

For this project I was planning to construct a clock that could be synchronized with an external source. The clock should be able to keep the time between synchronizations as these may be sparse. It also needed to be able to store the current time in a memory and keep a register of stored times. The current time and the register must be viewable by the user and the clock must also have the ability to count down the last five seconds prior to a minute selected by the user. I have performed this work at home with my own equipments.

As an external source for the synchronization I have chosen the DCF-77 clock signal broadcasted from Germany. To receive this signal I used a cheap AM receiver built specifically for this purpose. For the actual clock I used a PIC microcontroller which I programmed in C. The chip had all I needed including an oscillator and a RAM memory. I also connected a 3x16 character LCD display to the clock as well as 4 1-pole buttons for the user interface.

The program is built upon an interrupt routine that with help of an internal timer is set to execute once every hundreds of a second. During this interrupt routine all other functions are executed. These functions include a DCF decoder, an internal clock to keep the time, an LCD driver and a user interface.

I have managed to read the clock signal from the receiver but due to interferences from the computer I used to program the PIC chip, I have not been able to get any good reception close to the computer. Apart from this setback the clock works as it should and it meets all other criteria.

We introduce a special set of relations on a finite set, called clausal relations. A restricted version of the Galois connection between polymorphisms and invariants, called Pol-CInv, is studied, where the invariant relations are clausal relations. Clones arising from this Galois connection, so-called C-clones, are investigated. Finally, we show that clausal relations meet a sufficient condition that is known to ensure polynomial time solvability of the corresponding CSP.

Activation of a5??1 integrin potentiates L-type calcium current in vascular smooth muscle, which is partly mediated by tyrosine phoshorylation of the a1c channel subunit. Expressed rabbit VSM and neuronal isoforms are also potentiated by a5??1 integrin activation and require dual phosphorylation of a1c by PKA and c-Src. To explore common mechanisms of regulation by a5??1 integrin, whole cell patch clamp experiments were used to investigate the effects of a5??1 integrin antibody on expressed cardiac calcium channels. In HEK cells transfected with a1c, ??2a and a2-d1 subunits alone, currents increased 1.8 ?? 2.0 fold on application of a5??1 antibody. The potentiation was almost completely abolished on the application of PKI, a highly specific Protein Kinase A (PKA) inhibitor. The expressed currents increased 2.0 ?? 2.2 fold on application of PKA activator 8-Br-cAMP, and abolished by PKI. Our results suggest that regulation of L-type calcium channels by a5??1 integrin is a general mechanism shared by VSM, neuronal and cardiac channels. However, in the cardiac isoform, only PKA phosphorylation is involved.

We assessed clonal development and extent of progression of hemopoietic malignancies (dysmyelopoietic syndrome (DMPS) and acute myelogenous leukemia) by examining in vitro growth patterns of their normal and leukemic progenitors. Additional phenotypic and cytogenetic analysis of an in vitro human myeloid leukemia model (HL-60) and its variant sublines were performed. These were aimed at determining cytogenetic abnormalities associated with phenotypic changes which accompany the derivation of these variant sublines. Our findings indicate that in vitro bone marrow cultures can be used clinically to rule out preleukemia, and that quantitations of bone marrow culture (CFU-C) can determine the potential for the development of acute leukemia in the DMPS patients. Acute leukemia developed in 48% of DMPS patients with a median transformation of 10 months.
In acute leukemia, there was a preferential growth of normal karyotype in the in vitro cultures even among the phenotypically specified "blast" colonies.
Analysis of HL-60 variant sublines demonstrated the development of specific chromosomal abnormalities (1q+, iso8q, iso17q) in two cell lines (clones resistant to chemical induction) in association with loss of differentiation. These specific chromosomal abnormalities are known to be associated with tumor progression. The development of 1q+ abnormality was associated with loss of myeloperoxidase reaction and persistence of primary granules in that specific variant. A group of variant subclones was also associated with loss of differentiation, cytogenetically however, they demonstrated a revert to near diploid near normal karyotypes.

Introduction: Barrett’s oesophagus (BO) is a metaplastic premalignant disease which can undergo a metaplasia-­‐dysplasia-­‐adenocarcinoma pathway. It represents an example of field cancerization by which an area occupied by BO can undergo molecular and genetic changes associated with carcinogenesis without being phenotypically cancerous. Previous work suggested that non-­‐cancerous BO contains a monoclonal population. More recent work demonstrated that premalignant Barrett’s fields are polyclonal suggesting that clonal interactions may be important in carcinogenesis. It is the aim of this thesis to further investigate clonal interactions in BO by understanding the effects of therapy in altering the relationships of clonal populations in BO, by assessing the relationship of clonal populations in dysplasia as compared with the associated cancer, and by attempting to elucidate a potential molecular mechanism of clonal interactions. Results: The overall results can be summarised as follows: 1.Premalignant clonal populations are well mixed allowing for clonal interactions. However, the adenocarcinoma associated with high grade dysplasia is monoclonal and derived from clonal populations found in the dysplasia, indicating possible clonal interactions during carcinogenesis. 2. Patients with persistent disease after endoscopy retain the same clonal populations. However, the clonal populations of recurrent disease changes such that new clonal populations arise or may benefit from the extinction of others. 3. These clonal populations may be derived from deep submucosal glands or may be found in phenotypically normal squamous epithelium indicating a common stem cell origin. 4. A possible mechanism of clonal interaction may be the senescence associated secretory phenotype: senescence is abundant in BO and can cause proliferation in neighbouring cells in vitro. Conclusion: This thesis has investigated the implications of clonal interactions in BO. The demonstration of temporal clonal heterogeneity as a result of endoscopic therapy, as well as spatial clonal heterogeneity possibly resulting in carcinogenesis, asks for a mechanistic explanation of clonal interactions. The consequences of senescence may well provide one such mechanism.

Temporal binding refers to the perceptual attraction of causally related events, which are perceived as closer together in time than unrelated events. This effect is not only characterised by the perceived attraction of cause and effect, but also by a contraction of the interval separating the events. Since the original article on temporal binding (Haggard, Clarke, & Kalogeras, 2002), research has identified the conditions necessary for the effect to occur. While predictability and contiguity are both necessary, it is causality and not intentional action that is the root of the effect (Buehner, 2012). Despite this fruitful work, little is known about how temporal binding is realised. Event perception approaches suggest that binding arises as a realignment of sensory streams. Time perception approaches, in contrast, suggest that binding arises due to a changes in temporal perception during the interval. Given the precedence for the latter approach in the literature (Humphreys & Buehner, 2009; Wenke & Haggard, 2009), I therefore applied an internal clock model of time perception to temporal binding. In Experiments 1 – 4 (Chapter 3), I explored whether binding is effected by the general slowing of a rate of an internal clock. Participants made verbal estimates of either an interval (in causal and noncausal conditions), or of an unrelated event embedded either before or during the interval. I hypothesised that changes in a general clock rate would both affect intervals and embedded events, such that events embedded during causal intervals would be judged as shorter than those embedded during noncausal intervals. The results revealed that causal trial intervals were judged as shorter than noncausal intervals, while no effect was found for embedded events. These results suggested that binding is effected by clock processes specific to cause-effect intervals. Experiments 5 - 8 (Chapter 4) examined whether binding might arise either due to changes 1 in a specific clock rate or to differential timing latencies. Using a temporal discrimination procedure, participants judged whether a variable duration interval was shorter or longer than a reference interval. The point of subjective equality (PSE) was computed for each reference duration, and then modelled using regression. The results revealed a significant binding effect, but more importantly, significant differences in regression slopes between causal and noncausal conditions in three out of four experiments. These results supported the hypothesis of a slower clock rate in temporal binding. In Experiments 9 - 10 (Chapter 5) I verified the results of Chapter 4 by examining discrimination thresholds between two causal and two noncausal intervals. In both experiments (Chapter 5), higher just-noticeable- difference (JND) thresholds were found in causal conditions, supporting the notion of a slower clock rate in cause-effect intervals. Taken together, the present body of work supports the notion that temporal binding is effected by a slower internal clock rate. Future experiments might investigate whether clock slowing in binding is driven by causality or predictability.

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Comunicação e Expressão. Programa de Pós-Graduação em Literatura.
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A televisão, o vídeo e o cinema são hoje a cultura global, e há bastante tempo eles utilizam a matéria-prima literária para o seu fazer. Outrossim, resta indagar se essas mídias, tão presentes nas relações sociais contemporâneas, assim como as novas tecnologias da comunicação, como o computador e o ciberespaço, podem constituir intertextos para a literatura. As relações entre tecnologia - notadamente a eletrônica - e literatura podem ser verificadas tanto na questão temática, de que é exemplo a literatura cyberpunk, como na estrutura (hipertexto) e na forma dos textos, que às vezes faz lembrar o pulsar tecnológico. Neste trabalho, apresento relações entre literatura e tecnologia a partir da análise de cinco contos de autores contemporâneos da literatura brasileira, incluindo, ao final, comentários sobre blogs, a partir da obra impressa Wunderblogs.com.

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We have investigated the rate of substitution of advantageous mutations in populations of haploid organisms where the rate of recombination can be controlled. We have verified that in all the situations recombination speeds up adaptation through recombination of beneficial mutations from distinct lineages in a single individual, and so reducing the intensity of clonal interference. The advantage of sex for adaptation is even stronger when deleterious mutations occur since now recombination can also restore genetic background free of deleterious mutations. However, our simulation results demonstrate that evidence of clonal interference, as increased mean selective effect of fixed mutations and reduced likelihood of fixation of small-effect mutations, are also present in sexual populations. What we see is that this evidence is delayed when compared to asexual populations.
Nós investigamos a taxa de substituição de mutações vantajosas em populações de organismos haplóides, assumindo que o mecanismo de recombinação está fixo, com a ocorrência de mutações benéficas e deletérias. Propomos um modelo de população finita de indivíduos em que permitiu a recombinação com taxa r e quantificamos o sexo no modelo. Verificamos que o sexo e a recombinação aumentam a taxa de adaptação por permitir a recombinação das mutações originalmente benéficas em linhagens distintas da população e, assim, reduz a intensidade da interferência clonal. A vantagem do sexo é maior até quando ocorrem mutações deletérias, pois a recombinação possui um papel importante, porque eliminam as mutações deletérias com maior eficiência. Porém, nossos resultados de simulação demonstram também a ocorrência de evidências da interferência clonal em populações sexuadas. Observamos que, comparando a população sexuada com a assexuada, a interferência clonal ocorre para taxas mais elevadas de mutação benéfica. Notamos claramente a redução no ritmo de crescimento da taxa de fixação das mutações benéficas juntamente com o aumento do efeito médio seletivo das mutações que se fixam. E determinamos as distribuições que melhor descrevem a distribuição do efeito seletivo das mutações benéficas que conseguem se fixar em uma população.

Cavitating flow through five perforated plates with different number of holes with preserved constant flow cross-section area in sum were experimentally examined. Dynamic characteristics such as dependence of pressure amplitudes and dominant frequencies on cavitation number in all regimes of cavitating flow: incipient cavitation, partial cavitation, fully developed cavitation and supercavitation are obtained. For determination of dominant frequencies several pressure transducers in two regimes of measurement were used. Results were validated with frequency spectra obtained from picture analysis based on high-speed camera records.

Malhas de relógio são arquiteturas de rede de relógio adequadas para distribuir confiavelmente o sinal de relógio na presença de variações de processo e ambientais. Tal propriedade se torna muito importante nas tecnologias submicrônicas onde variações têm um papel importante. A confiabilidade da malha de relógio é devido aos caminhos redundantes conectando o sinal de relógio até os receptores de forma que variações afetando um caminho possam ser compensadas pelos outros caminhos. A confiabilidade vem ao custo de mais consumo de potência e fiação. Desta forma fica claro o balanceamento necessário entre distribuir confiavelmente o sinal de relógio (mais redundância) e o consumo de potência e aumento de fiação. O clock skew é definido como a diferença entre os tempos de chegada do sinal de clock nos seus receptores. Quanto maior é o clock skew, mais lento o circuito precisa operar. Além de diminuir a velocidade do circuito, um valor alto de clock skew aumenta a probabilidade de o circuito não funcionar devido às variações. Neste trabalho, nos focamos no problema de clock skew. Inicialmente extraímos informações úteis de como o comprimento da fiação e a capacitância variam a medida que o tamanho da malha varia. São apresentadas fórmulas analíticas que encontram o tamanho ótimo para ambos objetivos e é apresentado um estudo de como o clock skew varia a medida que nos afastamos do tamanho ótimo da malha de relógio. Um método para a redução de clock skew através do deslocamento dos buffers também é apresentado. Tal melhoria no clock skew não afeta o consumo de potência já que o tamanho dos buffers e a malha não são alterados.
Clock meshes are a suitable clock network architecture for reliably distributing the clock signal under process and environmental variations. This property becomes very important in the deep sub-micron technology where variations play a main role. The clock mesh reliability is due to redundant paths connecting clock buffers to clock sinks, so that variations affecting one path can be compensated by other paths. This comes at cost of more power consumption and wiring resources. Therefore it is clear the tradeoff between reliably distributing the clock signal (more redundancy) and the power and resource consumption. The clock skew is defined as the difference in the arrival time of clock signal at clock sinks. The higher is the clock skew, the slower is the circuit. Besides slowing down the circuit operation, a high clock skew increases the probability of circuit malfunction due to variations. In this work we focus on the clock skew problem. We first extract some useful information on how the clock wirelength and capacitance change as the mesh size changes. We present analytical formulas to find the optimum mesh size for both goals and study how the clock skew varies as we move further away from the optimum mesh size. We also present a method for reducing the clock mesh skew by sliding buffers from the position where they are traditionally placed. This improvement comes at no increasing cost of power consumption since the buffer size and the mesh capacitance are not changed.

Orientadores: Valéria Maia Merzel, Suzan Pantaroto de Vasconcellos
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A poluição é um problema mundial amplamente discutido, incluindo os derramamentos de petróleo ocorridos através de acidentes ou por atividades humana, os quais acarretam grande impacto ambiental e econômico. O processo de biorremediação utiliza micro-organismos, associados ou não a outros compostos como biossurfactantes e até mesmo enzimas, com o objetivo de transformar compostos orgânicos em inorgânicos, levando à formação de compostos inertes ou não tóxicos. Deste modo, a biorremediação representa um modo efetivo e sustentável para se tratar áreas contaminadas. Neste trabalho foi possível avaliar o potencial de clones metagenômicos obtidos a partir da construção de uma biblioteca fosmidial e de linhagens de bactérias, todos provenientes de amostras de petróleo de reservatórios brasileiros em escala de microcosmos e mesocosmos, visando futura aplicação em processos de biorremediação. Em um primeiro ensaio os micro-organismos foram avaliados na forma livre, em 50 mL de água do mar artificial e petróleo bruto como única fonte de carbono, a cada sete dias durante 21 dias. Posteriormente, os micro-organismos com melhor potencial de biodegradação foram selecionados e aprisionados em esferas de quitosana e testados novamente em microcosmos, em diferentes escalas, durante 21 e 30 dias. Com base nos resultados observados nos ensaios de degradação em microcosmos, um último ensaio foi realizado empregando-se um consórcio contendo quatro clones metagenômicos e uma linhagem de Bacillus subtilis, o qual foi avaliado em ensaio de mesocosmos em 3000 litros de água do mar não-estéril. Nesta etapa, parâmetros como a contagem total dos micro-organismos (DAPI) e a demanda biológica de oxigênio (DBO) foram avaliados, e a cromatografia gasosa (CG) foi empregada para avaliar a degradação de hidrocarbonetos do petróleo. Os resultados demonstraram a capacidade desses micro-organismos em degradar compostos do petróleo bruto, tanto hidrocarbonetos alifáticos como aromáticos. Em microcosmos, na forma livre, as linhagens de Dietzia maris e Micrococcus sp. apresentaram o melhor desempenho, alcançando ao final de 21 dias 99% de degradação de hidrocarbonetos alifáticos e de 63-99% de degradação de aromáticos (fenantreno e metilfenantreno). Dentre os clones, o clone 2B apresentou o melhor desempenho para degradar tanto hidrocarbonetos alifáticos (47%) como aromáticos (94%). Na forma aprisionada, os micro-organismos também apresentaram capacidade para degradar petróleo bruto em mesocosmos, exibindo valores de degradação de 90 a 100 % para hidrocarbonetos saturados e 70 a 100% para aromáticos, ao final de 30 dias de avaliação. Os resultados indicam um resultado promissor e inédito, onde um consórcio combinado contendo clones metagenômicos e Bacillus subtillis pode ser futuramente utilizado em estratégias de bioaumento, em sistemas de contenção, como ferramenta para biorremediação de ambientes contaminados com hidrocarbonetos
Abstract: Pollution is a global environmental problem widely discussed, including oil spills that occur accidentally or due to human activities, which cause huge environmental and economic impacts. Bioremediation process uses biological agents, associated or not to other compounds like biosurfactants or even their enzymes, to mineralize or complex organic and inorganic pollutant compounds, transforming them into inert or non-toxic compounds. Thus, bioremediation represents an ecofriendly and effective way to treat impacted areas. In this work, the biodegradation potential of clones obtained from metagenomic libraries and bacterial isolates, all originated from Brazilian petroleum reservoirs, was evaluated in microcosm and mesocosm scale aiming at a future application in bioremediation process. In the first assay, microorganisms were evaluated as free cells, in 50 mL-volume of artificial seawater and using crude oil as sole carbon source. The experiment was monitored each seven days during 21 days. Further, the best performing microorganisms were selected, immobilized in chitosan beads and evaluated in microcosm assays, at different scales, during 21 and 30 days. Finally, in the last experiment, one consortium containing four metagenomic clones and a Bacillus subtilis strain was evaluated in mesocosmos assay in 3000 L-volume of non-sterile seawater. Parameters such as total counting of microorganisms by DAPI and biological oxygen demand (BOD) were evaluated, and petroleum degradation was monitored by chromatographic analysis. Results demonstrated the ability of the microorganisms to degrade aliphatic and aromatic hydrocarbons. In microcosms, using free cells, the strains of Dietzia maris and Micrococcus sp. showed the best performance, reaching 99% of aliphatic hydrocarbon degradation and 63-99% of aromatic compound degradation in 21 days. Among metagenomic clones, clone 2B presented the best performance to degrade aliphatic (47%) and aromatic hydrocarbons (94%). In chitosan beads, the microorganisms were also able to degrade crude petroleum, showing percentages between 90 and 100% for aliphatic hydrocarbons and 70 and 100% to aromatic. The results gathered in this work demonstrate that a microbial consortium containing metagenomic clones and one bacterial strain is able to achieve high extents of hydrocarbon degradation, offering a promising tool to be further used in bioaugmentation approaches for treating contaminated environments
Doutorado
Genetica de Microorganismos
Doutora em Genética e Biologia Molecular

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Os plantios clonais são comumente utilizados para obter ganhos na produtividade. No entanto, a uniformidade genética, quando em extensas áreas, pode comprometer o desempenho silvicultural do eucalipto. Uma alternativa seria o emprego da mistura de clones em áreas comerciais. Este trabalho foi realizado com o objetivo de comparar a auto e alocompetição entre clones comerciais de Eucalyptus spp., e estimar as capacidades de exercer ou sofrer competição. O experimento foi implantado em delineamento de blocos casualizados, com 12 clones comerciais no espaçamento de 3,6 m x 2,5 m, com 5 plantas por parcela e 3 repetições. Foram avaliados aos 3 e 5 anos os caracteres altura de planta, diâmetro à altura do peito, volume e incremento médio anual. Com os dados médios da parcela foram efetuadas as análises estatísticas e estimados os parâmetros de competição. Houve diferenças entre a auto e a alocompetição para incremento médio anual e volume em ambas as idades avaliadas. O desempenho médio dos clones em auto e alocompetição foram semelhantes, não ocasionando prejuízos para a produção de madeira. A mistura clonal pode ser empregada sempre que for vantajosa do ponto de vista de manejo ou industrial. Os clones diferiram quanto à sua capacidade de exercer ou sofrer competição.
Clonal plantations are commonly used for gains in productivity. However, the genetic uniformity when in extensive areas, can compromise the silvicultural performance of Eucalyptus. An alternative would be the use a mixture of clones in commercial areas. This study was conducted in order to compare auto and allocompetition between commercial clones of Eucalyptus spp., and estimate the capacity to exercise or tolerate competition. The experiment was established in a randomized block design, with 12 commercial clones in the spacing of 3.6 m x 2.5 m, and consists of 5 plants per experimental plot in 3 repetitions. Each clone was evaluated exercising and tolerating competition in all the others, at 3 and 5 years. With the average data were performed statistical analysis and estimated parameters of competition. There were differences between auto and allocompetition the two ages evaluated for annual volume and average increment. The average performance of clones auto and allocompetition were similar, not causing damage to the production of the timber could be used to mix clonal whenever advantageous from the standpoint of handling or manufacturing. Clones differed in their ability to tolerate or exercise competition.