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Onischenko, Evgeny. "Disassembly and reassembly of the nuclear pore complex /". Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-929-7/.
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Schermer, Ulrike. "Mechanism of chromatin reassembly at the yeast PHO5 promoter upon repression". Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-64228.
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Shimanskaya, Elena Mikhaylovna. "Feature reassembly of semantic and morphosyntactic pronominal features in L2 acquisition". Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/1902.
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Previous research in Second Language Acquisition (SLA) has shown that some of the systematic errors of second language (L2) learners can be attributed to the influence of the native language (L1). In fact, many hypotheses in generative SLA have focused on the role of L1 transfer ranging the spectrum from No Transfer to Full Transfer. The goal of this dissertation was to investigate L1 transfer by focusing on L1-L2 differences in terms of linguistic features; specifically, how differences in the featural and morpholexical organization of L1 and L2 pronominal paradigms affect SLA.
In this work I operationalize L1 transfer in terms of the Feature Reassembly Hypothesis (FRH; Lardiere, 2009). The hypothesis pioneers conceptualization of L1 transfer as an initial attempt by L2 learners to establish a direct mapping between L1 and L2 forms. The FRH is particularly suitable to the study of L2 development because it predicts that when a one-to-one initial mapping is unsuccessful, L2 learners will gradually reorganize the L1 grammatical system until they attain (possibly complete) convergence. Empirical testing of the hypothesis is critical since determining when and why transfer occurs opens numerous possibilities to predict transfer errors and to develop pedagogical approaches to tackle negative transfer.
In the current study I focus on the L2 acquisition of four 3rd person singular French object pronouns in the interlanguage of native speakers of English. Difficulties in the acquisition of Romance object pronouns have been amply documented in L2 research. However, most of the previous studies of the topic have focused on L2 acquisition of clitic pronouns and their syntactic properties. The present study takes a novel approach investigating the acquisition of strong as well as clitic pronouns. In my dissertation I test different kinds of knowledge including learners' comprehension of different kinds of pronouns. Going beyond production data, my experimental tasks include a grammaticality judgment task with correction, a picture selection task, and a self-paced reading task. The experimental tasks were administered to a group of native speakers (n=43) and L2 learners of French (n=87). The overall picture that emerges from the current study allows unveiling the initial mapping and subsequent reassembly of the semantic and morphosyntactic features implicated in the acquisition process of the four forms under investigation.
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Kumas, Gozde. "Detecting G-protein Coupled Receptor Interactions Using Enhanced Green Fluorescent Protein Reassembly". Master's thesis, METU, 2012. http://etd.lib.metu.edu.tr/upload/12614136/index.pdf.
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The largest class of cell surface receptors in mammalian genomes is the superfamily of G protein-coupled receptors (GPCRs) which are activated by a wide range of extracellular responses such as hormones, pheromones, odorants, and neurotransmitters. Drugs which have therapeutic effects on a wide range of diseases are act on GPCRs. In contrast to traditional idea, it is recently getting accepted that G-protein coupled receptors can form homo- and hetero-dimers and this interaction could have important role on maturation, internalization, function or/and pharmacology.
Bimolecular fluorescence complementation technique (BiFC)is an innovative approach based on the reassembly of protein fragments which directly report interactions. In our study we implemented this technique for detecting and visualizing the GPCR interactions in yeast cells. The enhanced green fluorescent protein (EGFP) fractionated into two fragments at genetic level which does not possess fluorescent function. The target proteins which are going to be tested in terms of interaction are modified with the non-functional fragments, to produce the fusion proteins. The interaction between two target proteins, in this study Ste2p receptors which are alpha pheromone receptors from Saccharomyces cerevisiae, enable the fragments to come in a close proximity and reassemble. After reassembly, EGFP regains its fluorescent function which provides a direct read-out for the detection of interaction. Further studies are required to determine subcellular localization of the interaction. Moreover, by using the fusion protein partners constructed in this study, effects of agonist/antagonist binding and post-translational modifications such as glycosylation and phosphorylation can be examined. Apart from all, optimized conditions for BiFC technique will guide for revealing new protein-protein interactions.
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Kennan, Mary Anne, i Fletcher T. H. Cole. "Institutional repositories as portents of change: Disruption or reassembly? Conjectures and reconfigurations". Richard B. Hill, 2008. http://hdl.handle.net/10150/105838.
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This paper reviews how Open Access policies (OA) and Institutional Repositories (IR) might be portrayed as agents of change within the realm of scholarly publishing. Using commentary on academic publishing as background, commentary that sees OA and IR as optimal and inevitable, and beneficially disruptive of the existing system, two theoretical approaches are presented as ways of providing a more detailed and explicit analysis of OA/IR dynamics. Both theories to varying degrees derive their inspiration from an exploration of the nature of change. The first â disruptive technology/disruptive innovationâ approach (Christensen) specifies change in market theory terms, a re-structuring "driven" by innovation within, and possibly disruptive of, existing market arrangements. The second approach views change as a process of "reassembling" and reconfiguring of relationships between elements of a network (Actor-Network Theory). The application of both approaches to OA/IR is explored, including reference to a case study on a university institutional repository implementation. While "disruption" and similar terms might be in common and casual use, the basic idea gains greater clarity in these theories, and in doing so promotes greater awareness of the assumptions being made, and the aspirations being pursued.
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Yarashus, Heather R. "Stripping and Reassembly of the Yeast Vacuolar H+-ATPase Peripheral Protein Subunits". W&M ScholarWorks, 1993. https://scholarworks.wm.edu/etd/1539625807.
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Mendes, Luis Felipe Santos. "Structural and dynamic characterization of the Golgi Reassembly and Stacking Protein (GRASP) in solution". Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/59/59135/tde-18042018-094959/.
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The Golgi complex is an organelle responsible for receiving synthesized cargo from the endoplasmic reticulum for subsequent post-translations modifications, sorting and secretion. A family of proteins named Golgi Reassembly and Stacking Proteins (GRASP) is essential for the correct assembly and laterally tethering of the Golgi cisternae, a necessary structuration to keep this organelle working correctly. The GRASP structure is mainly composed of two regions: an N-terminal formed by two PDZ domains connected by a short loop (GRASP domain) and a non-conserved C-terminal region, rich in serine and proline residues. Although there are now a few crystal structures solved for the N-terminal domain, it is surprising to notice that no information is currently available regarding a full-length protein or even about dynamic and structural differences between the two PDZs in solution, which is the main functional region of this protein. Using a full-length GRASP model, we were capable of detecting the coexistence of regular secondary structures and large amounts of disordered regions. The overall structure is less compact than a regular globular protein and the high structural flexibility makes its hydrophobic core more accessible to solvent. GRASP coexist in a dynamic conformational ensemble of a µs-ms timescale. Our results indicate an unusual behavior of GRASP in solution, closely resembling a class of collapsed intrinsically disordered proteins called molten globule. We report here also the disorder-to-order transition propensities for a native molten globule-like protein in the presence of different mimetics of cell conditions. Changes in the dielectric constant (such as those experienced close to the membrane surface) seem to be the major factor capable of inducing several disorder-to-order transitions in GRASP, which seems to show very distinct behavior when in conditions that mimic the vicinity of the membrane surface as compared to those found when free in solution. Other folding factors such as molecular crowding, counter ions, pH and phosphorylation exhibit lower or no effect on GRASP secondary structure and/or stability. This is the first study focusing on understanding the disorder-to-order transitions of a molten globule structure without the need for any mild denaturing condition. Regarding the PDZs that form the GRASP domain, we observed that GRASPs are formed by a more unstable and flexible PDZ1 and much more stable and structurally well-behaved PDZ2. More than that, many of the unstable regions found in PDZ1 are in the predicted binding pocket, suggesting a structural promiscuity inside this domain that correlates with the functional promiscuity of interacting with multiple protein partners. This thesis presents the first structural characterization of a full-length GRASP, the first model of how GRASPs (or any molten globule-like protein) can be modulated by the cell during different cell functionalities and the first work in the community proving that the established idea that both PDZs are structurally equivalent is not completely rightO complexo de Golgi é um organela responsável pela recepção de carga sintetizada no retículo endoplasmático e por subsequente modificações pós-traducionais, classificação e secreção. Uma família de proteínas chamada Golgi Reassembly and Stacking Proteins (GRASP) é essencial para o correto empilhamento das cisternas e conexões laterais das pilhas do complexo de Golgi, uma estruturação necessária para manter essa organela funcionando corretamente. A estrutura das GRASPs é composta de duas regiões principais: uma extensão N-terminal formado por dois domínios PDZ conectados por um loop (domínio GRASP) e uma região C-terminal não conservada, rica em resíduos de serina e prolina. Embora existam algumas estruturas cristalográficas resolvidas para o domínio N-terminal, é surpreendente notar que não havia nenhuma informação na literatura sobre a construção inteira de um GRASP, ou mesmo um estudo detalhado sobre os PDZs no N-terminal em solução, que é a principal região funcional dessa proteína. Usando um modelo de GRASP em sua construção completa, fomos capazes de detectar a coexistência de estruturas secundárias regulares e grandes quantidades de regiões desordenadas. A estrutura é menos compacta do que uma proteína globular e a alta flexibilidade estrutural torna o seu núcleo hidrofóbico mais acessível ao solvente. GRASPs coexistem em um conjunto conformacional dinâmico numa escala de tempo característico de s-ms. Nossos resultados indicam um comportamento incomum da GRASP em solução, similar à de uma classe de proteínas intrinsicamente desordenadas colapsadas conhecidas como glóbulos fundidos. Nós relatamos também as propensões de transição estrutural do tipo desordem-ordem para uma proteína glóbulo fundido nativa, induzidas pela presença de diferentes miméticos de condições celulares especificas. A mudança na constante dielétrica do meio (como as experimentadas próximas à superfície da membrana biológica) é o principal modulador estrutural, capaz de induzir múltiplas transições desordem-ordem na GRASP, sugerindo um comportamento muito distinto quando em condições que imitam a vizinhança da superfície da membrana em comparação com os encontrados quando livre em solução. Outros fatores de enovelamento, tais como o molecular crowding, contra-ions, pH e a fosforilação exibem efeitos menores (ou nenhum) na estrutura secundária e/ou estabilidade da GRASP. Este é o primeiro estudo focado na compreensão das transições desordem-ordem em uma estrutura do tipo glóbulo fundido sem que houvesse a necessidade de qualquer condição desnaturante. Em relação aos PDZs que formam o domínio GRASP, observamos que as GRASPs são formadas por um PDZ1 mais instável e flexível e um PDZ2 muito mais estável e estruturalmente bem comportado. Mais do que isso, muitas das regiões instáveis encontradas no PDZ1 estão no predito bolsão de ligação, sugerindo uma promiscuidade estrutural dentro desse domínio que se correlaciona com a promiscuidade funcional de interação com múltiplos parceiros proteicos. É apresentado nesta tese a primeira caracterização estrutural de uma GRASP em sua forma completa, o primeiro modelo de como as GRASPs (ou qualquer proteína em forma de glóbulo fundido) pode ser modulada estruturalmente pela célula durante diferentes funcionalidades e o primeiro trabalho na comunidade provando que a estabelecido ideia de que ambos os PDZs são estruturalmente equivalentes não é completamente correta
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Shekhawat, Sujan Singh. "Genetically Encoded Sensors for Detection of Proteases Utilizing Auto-Inhibited Coiled Coils and Split-Protein Reassembly". Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205209.
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The detection of cellular events is central to understanding biomoleculer processes as well as aid in therapeutic intervention strategies. One of the most fascinating biomoleculer events during the life cycle of a cell is proteolytic cleavage of proteins by enzymes known as proteases. Proteases are ubiquitous and participate in essential functions such as fertilization, embryo development, cell cycle regulation, immune response, tissue remodeling and programmed cell death. As proteases are involved in fundamental cellular processes any dysregulation of protease activity is usually associated with a diseased state. Thus methods for detection of protease activity are desirable as it may facilitate the identification of many pathological conditions which are associated with the aberrant expression and activity of proteases.Towards the goal of a general and modular strategy we have utilized split protein reassembly and coiled coils to develop genetically encoded sensors for detection of proteases. We established our first generation protease design utilizing split firefly luciferase and anti-parallel coiled coils and detected Tobacco Etch Virus (TEV) as a model protease. Two further iterations of the coiled-coil design led to the development of second and third generation of protease sensors which showed substantial improvement in the sensor response and was applied towards detection of therapeutically relevant proteases such as caspase-3, prostate specific antigen (PSA), ß-secretase and calpain-1.We applied our methodolgy to develop protease biosensors for the detection of a family of cysteine protease known as caspases. Caspases are involved in programmed cell death and their misregulation is implicated in cancer as well as neurodegenerative disorders. The panel of caspase biosensors was utilized to investigate caspase cleavage specificity as well as caspase activation in mammalian cytosolic extracts and live mammalian cells. Perhaps more importantly, we discovered cross talk between members of the caspase family which perform different biological functions.Finally, we detail our progress towards mimicking a naturally occurring multicomponent complex formed during programmed cell death, known as the apoptosome which leads to the activation of caspases. We have successfully utilized principles of self assembly and multivalency to assemble multi component complexes which exhibit proteolytic activity similar to the natural apoptosome.
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Porter, Jason Robert. "SPLIT-PROTEIN REASSEMBLY METHODS FOR THE DETECTION AND INTERROGATION OF BIOMOLECULAR INTERACTIONS AND MODULATORS THEREOF". Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/194359.
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The interactions between protein-protein, protein-nucleic acid, and protein-small molecules are central to biological processes and are key for the design of new therapeutics. Rapid and easy to implement methodologies are needed that enable the interrogation of these interactions in a complex cellular context. Towards this goal, I have utilized the concept of split-protein reassembly, also called protein complementation, for the creation of a variety of sensor architectures that enable the interrogation of protein-nucleic acid, protein-protein, and protein-small molecule interactions. Utilizing the enzymatic split-reporter β-lactamase and existing zinc finger design strategies we applied our recently developed technology termed SEquence-Enabled Reassembly (SEER) towards the creation of a sensor capable of the specific detection of the CryIA transgene. Additionally, the split β-lactamase reporter was utilized for the sitespecific determination of DNA methylation at cytosine residues that is involved in epigenetic regulation. This method, dubbed mCpG-SEER, enabled the direct detection of femtomole levels of dsDNA methylation in sequence specific manner. In a separate endeavor, we have developed and optimized the first cell-free split-reporter systems for GFP, split β-lactamase, and firefly luciferase for the successful dsDNA-dependent reassembly of the various reporters. Our cell free in vitro translation systems eliminates previous bottlenecks encountered in split-reporter technologies such as laborious transfection/cell culture or protein purification. Capitalizing on the ease of use and speed afforded by this new technology we describe the sensitive detection of protein-protein, protein-nucleic acid, and protein-small molecule interactions and inhibitors thereof. In a related area, we have applied this rapid cell-free split-firefly luciferase assay to the specific interrogation of a large class of helix-receptor protein-protein interactions. We have built a panel consisting of the clinically relevant Bcl-2 family of proteins, hDM2, hDM4, and p53 and interrogated the specificity of helix-receptor interactions as well as the specificity of peptide and small-molecule inhibitors of these interactions. Finally, we describe the further applications of our cell-free technology to the development of a large number of general split-firefly luciferase sensors for the detection of ssRNA sequences, the detection of native proteins, the evaluation of protease activity, and interrogation of enzyme-inhibitor interactions. The new methodologies provided in this study provides a general and enabling methodology for the rapid interrogation of a wide variety of biomolecular interactions and their antagonists without the limitations imposed by current in vitro and in vivo approaches.
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Furman, Jennifer Lynn. "IN VITRO AND IN VIVO DETECTION OF NUCLEIC ACIDS AND PROTEINS USING SPLIT-PROTEIN REASSEMBLY". Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/195828.
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The ability to directly monitor the presence of specific proteins or nucleic acids in a variety of in vitro and in vivo contexts has great utility for understanding biology as well as for the development of diagnostic agents. Herein I describe several methodologies, utilizing split-protein reassembly, which provides potentially general strategies for sequence-specific detection of DNA and RNA sequences as well as poly(ADP-ribose). I also provide a new split-protein approach for the direct detection of native proteins, such as the cancer marker HER2.The green fluorescent protein (GFP) provides a convenient sensor for reporting on a variety of cellular events. A series of spectroscopically distinct GFP variants was developed for sequence-specifically reporting on DNA. Each of these variants was demonstrated to provide a sensitive readout for the presence of a particular DNA sequence. Furthermore, utilizing a method of mixed split-protein complementation, I was able to simultaneously report on the presence of two distinct DNA sequences in the same solution.To provide a general solution for reporting on the presence of particular RNA sequences, a method was developed that utilized elements from a hybridization-based detection strategy coupled with split-protein reassembly. Specifically, DNA guide sequences complementary to an intended target were attached to hairpin sites that served as binding sites for high-affinity zinc fingers. Localization of the zinc fingers allowed for reassembly of the attached split enzyme, providing a sensitive readout for the presence of potentially any RNA sequence of interest. This methodology was applied to the detection of mRNA encoding VEGF, hDM2, and HER2, each of which may be overexpressed in cancer.A method was established for reporting on the presence of modifications to DNA and proteins that are elicited in response to DNA damage. Specifically, sensors were designed, which incorporated endogenous damage-recognition domains, to report on the global presence of particular DNA modifications, including the formation of 8-oxoguanine and pyrimidine dimers. Furthermore, to provide a technique for monitoring the general accrual of DNA damage and to interrogate the DNA damage response in cells, a sensor was developed which reported on the accrual of a posttranslational protein modification, poly(ADP-ribosyl)ation.Finally, I describe advances toward the adaptation of our protein-based biosensors for use in living cells, utilizing both GFP-based approaches for live cell imaging as well as luminescent-based strategies for reporting on proteins and nucleic acids following cell lysis.
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Schäfer, Anja [Verfasser], i Hans Georg [Akademischer Betreuer] Bock. "An optimizational approach for an algorithmic reassembly of fragmented objects / Anja Schäfer ; Betreuer: Hans Georg Bock". Heidelberg : Universitätsbibliothek Heidelberg, 2015. http://d-nb.info/1180301536/34.
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Wibranek, Bastian [Verfasser], Oliver [Akademischer Betreuer] Tessmann i Anna-Maria [Akademischer Betreuer] Meister. "Robotic Digital Reassembly: Towards physical editing of dry joined architectural aggregations / Bastian Wibranek ; Oliver Tessmann, Anna-Maria Meister". Darmstadt : Universitäts- und Landesbibliothek, 2021. http://d-nb.info/1237050030/34.
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Sahu, Bijay Kumar. "Aeromagnetics of selected continental areas flanking the Indian Ocean : with implications for geological correlation and reassembly of Central Gondwana". Doctoral thesis, University of Cape Town, 2000. http://hdl.handle.net/11427/10718.
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Reassembling continental fragments of Gondwana has been a subject of interest to many since almost the beginning of the last century. As a result, the broad relative position of the major continental fragments and their dispersal history is well understood using marine magnetic anomalies, coastline geometry, surface geology and limited geophysics. Uncertainty still prevails in reassembly of central Gondwana fragments flanking the Indian Ocean. This thesis aims at utilising geophysical constraints to corroborate an fine-tune the reconstruction of these fragments supported by geological evidence.
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Watts, Corinne Hannah. "Invertebrate community reassembly and altered ecosystem process rates following experimental habitat restoration in a mined peat bog in New Zealand". Thesis, University of Canterbury. Biological Sciences, 2006. http://hdl.handle.net/10092/1481.
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I investigated the effects ofhabitat loss and subsequent restoration on invertebrate community structure and ecosystem functioning in a mined peat bog in the North Island, New Zealand. In an experimental trial, the impact of peat bog habitat loss and isolation on the invertebrate community associated with Sporadanthus ferrugineus (Restionaceae) was investigated. Potted S. ferrugineus plants were exposed to invertebrates at various distances up to 800 m from an intact habitat (the presumed source population) over 18 weeks. Invertebrates rapidly colonised the experimental plants, with all major Orders and trophic groups present on Sc ferrugineus within 6 weeks. However. with increasing distance away from the undisturbed habitat, there was a significant decrease in total richness and abundance of invertebrates associated with the potted plants. Additional tests showed that even a moderate degree of isolation (i.e. greater than 400 m) from the intact habitat caused an almost complete failure of 'Batrachedra' sp. to colonise its host plant, at least in the short-term, The density of eggs and larvae, and the average larval size of 'Batrachedra' sp. (Lepidoptera: Coleophoridae) colonising Si ferrugineus plants, as well as the proportion of Si ferrugineus stems damaged by 'Batrachedra' sp. herbivory, all decreased logarithmically with increasing distance from the intact habitat. Surprisingly, though, the rate of recovery of the insect-plant interaction following experimental habitat restoration was remarkably rapid (i.e. between 3Y2 and 6 years). After just 6 years there was no significant difference in insect-plant interactions between the intact peat bog sites and any of the experimentally restored sites up to 800 m away. These results suggest that the degree of isolation from undisturbed habitat has a major impact on the rate and patterns of restoration recovery in the invertebrate community and that some insect-plant interactions can recover rapidly from habitat loss with restoration management. Restoration of mined peat bogs in northern New Zealand is initiated by establishing a native vegetation cover to minimize further peat degradation. The effects of various restoration techniques on litter decomposition, microbial community activity and beetle community composition were investigated within an experimental trial, These treatments included translocation ofpeat bog habitat (direct transfer of islands), milled peat islands with no seed and milled peat islands with seed, and were compared with an unrestored mined site and an undisturbed peat bog. In all the response variables measured, the undisturbed peat bog sites had significantly higher decomposition rates and microbial respiration rates, and significantly higher abundance and species richness of beetles than any of the restoration treatments. Inaddition, the technique used to restore mined peatlands had a significant effect on the beetle community composition and litter decomposition processes. Despite a rapid initial change in the beetle community following habitat translocation, the direct transfer islands were still the most similar in beetle species composition to the undisturbed peat bog. Microbial activity and decomposition rates were higher in the direct transfer and mined peat surface after 6 months. However, even after 12 months, decomposition rates in the restored habitats were still far from reaching the levels recorded in the undisturbed peat bog. The results suggest that beetle community structure and ecosystem processes such as decomposition and microbial activity rates may be able to recover faster with certain restoration techniques, such as direct transfer of intact habitat islands. Subsequently, I examined long-term beetle community reassembly on islands that had been restored by creating raised areas ofprocessed peat with the addition of Leptospermum scoparium seed. Monitoring of different-aged restored islands representing the full range of restoration ages (up to 6 years) available at the peat mine, indicated that as the peat islands became older and the vegetation structure became more complex, the abundance, species richness and composition of the beetle community became increasingly similar to the community in the undisturbed peat bog. Despite this, distinct differences between the intact peat bog and older restored peat islands still persisted, even after 6 years, particularly at an individual species level. However, it is predicted that within 12 years the restored peat islands will share 100% ofbeetle species in common with the undisturbed peat bog. Taken together, these results indicate that restoration is effective in initiating the recovery of beetle assemblages and ecosystem processes (such as litter decomposition and microbial community activity) in cut-over peat bogs. However, it is estimated to take at least 12 years before pre-mining communities and functions are attained, and ongoing monitoring to develop an understanding of the longer-term dynamics of such ecosystems and processes is clearly required.
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Ooi, Aik Teong. "Sequence-Specific DNA Detection Utilizing Custom-Designed Zinc Finger Proteins". Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/194236.
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DNA diagnostics are important technologies in molecular and cellular biology. By allowing identification of specific sequences, DNA-based diagnostics potentially provide more accurate and rapid results than protein- or antigen-based diagnostics, primarily because phenotypic changes come much later than changes in genotype. Despite this advantage, there are fewer diagnostic or imaging systems that target DNA than those targeting proteins, antibodies, or antigens.Each type of DNA-based diagnostic has its own, unique set of limitations; however, most can be attributed to issues related to sequence restriction, signal detection, specificity, or some combination thereof. For example, while PCR-based methods allow amplification and assessment of specific DNA sequences, they lack the ability to report information of specific cells, or cell types, within the heterogeneous pool of cells typically found in a tumor biopsy. In addition, none of the currently available DNA detection methods has the potential to be utilized in living cells, a disadvantage which limits the potential applications.The work presented here describes the design and development of a new methodology for the detection of specific double-stranded DNA sequences. This detection method is based on the concept that two inactive fragments of a reporter protein, each coupled to engineered zinc finger DNA-binding motifs, are able to reassemble and form an active complex in the presence of a predefined DNA sequence. This system, designated sequence-enabled reassembly (SEER), can achieve single base-pair specificity, and has the potential to be utilized in living cells.In this dissertation, we discuss the efforts from constructing to refining the system, as well as the future applications of SEER in diagnostics and therapeutics. Chapter I will provide an introduction to DNA detection methods, on which the principles of the SEER system are based. Chapter II describes the design and construction of an enzymatic SEER system, SEER-LAC, using beta-lactamase as the enzyme. In Chapter III, we outline the in vitro characterization of the SEER-LAC system, followed by its optimization in Chapter IV. Chapter V illustrates the efforts to develop SEER system for mammalian cell culture applications. In the final chapter, the future developments and applications of SEER are discussed.
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Ducki, Luisa C. "Soil fungi, but not bacteria, track vegetation reassembly across a 30-year restoration chronosequence in the northern jarrah forest, Western Australia". Thesis, Ducki, Luisa C. (2020) Soil fungi, but not bacteria, track vegetation reassembly across a 30-year restoration chronosequence in the northern jarrah forest, Western Australia. Honours thesis, Murdoch University, 2020. https://researchrepository.murdoch.edu.au/id/eprint/64708/.
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Plant communities have been the primary focus of ecological restoration initiatives; however, the integration of the soil microbiome has become of interest to restoration practice and theory. The inter-dependent nature of the above- and belowground biological environments has led to assumptions that reciprocal shifts in community compositions will occur in response to disturbance and restoration. Ecological restoration of post-mining landscapes within the northern jarrah forest re-instates vegetation communities that are representative of those in adjacent reference forest. The limited studies of soil microbial communities have not addressed whether these communities recover along similar trajectories to plant communities aboveground. Here, a 30-year restoration chronosequence of vegetation development was compared with that of the belowground assemblages of bacteria and fungi, identified using environmental DNA methods. Novel findings of this study highlight similarities between restoration trajectories of fungal and vegetation assemblages, though both remained distinct from reference jarrah forest compositions after 27-years. In contrast, soil bacterial assemblages in restored jarrah forest re-assembled rapidly, with substrate depth being a greater driver of composition than vegetation. Explanatory environmental variables, such as litter cover and initial fertiliser application, were significantly associated with vegetation composition. High covariance among physico-chemical factors made it difficult to establish influences of individual variables on bacterial and fungal communities. Litter depth was significantly associated with fungal composition across the restoration chronosequence, whilst available potassium was associated with both bacterial and fungal community composition. My findings add to a growing body of literature which acknowledges the rich diversity of the belowground microbial community, and the potential for their use as predictors of restoration trajectories. Future research could focus on direct associations between fungi and plant communities, such as potential for fungal inoculation to assist in the rapid reinstatement of missing plants which rely on symbiotic associations with the belowground microbiome.
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Pocock, Melissa. "An Examination of the Need for Legislative Reform Arising from the 'Holdout' Phenomena in the Reassembly and Termination of Community Titles Schemes". Thesis, Griffith University, 2016. http://hdl.handle.net/10072/365465.
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A significant number of Queenslanders reside in community titles schemes, and this figure is increasing annually as a result of population growth, changes in planning policies and economic opportunities. Many buildings constructed since the introduction of community titles legislation in the 1960s are now reaching or have exceeded their economic lifespan. Despite this, termination and redevelopment of schemes has received little attention until recently.
Section 78(1) of the Body Corporate and Community Management Act 1997 (Qld) requires the passage of a resolution without dissent – unanimous approval by lot owners – to terminate a scheme, a necessary prerequisite to redevelopment of the scheme land. The requirement for unanimity prevents the termination of a scheme where a single dissenting owner exists. This inability to overcome what may be a single owner’s dissent, when the vast majority of other owners support the termination, is problematic. This is particularly the case in circumstances where a dissenting owner is engaging in strategic holdout behaviour with a view to extracting the best financial and non-financial terms for a sale. Self-interested holdout behaviour, together with the economic and social impact discontinuation of a redevelopment proposal may have on the wider community, is a justification for reforming the termination provisions of the Body Corporate and Community Management Act to better balance the rights and interests of stakeholders.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith Law School
Arts, Education and Law
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Förderer, Steffen-Marc. "Converting Network Media Data into Human Readable Form : A study on deep packet inspection with with real-time visualization". Thesis, Linnéuniversitetet, Institutionen för datavetenskap, fysik och matematik, DFM, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-18289.
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A proof of concept study into the working of network media capture and visualization through the use of Packet Capture in real-time. An application was developed that is able to capture tcp network packets; identify and display images in raw HTTP network traffic through the use of search, sort, error detection, timeout failsafe algorithms in real time. The application was designed for network administrators to visualize raw network media content together with its relevant network source \& address identifiers. Different approaches were tried and tested such as using Perl with GTK+ and Visual Studio C\# .Net. Furthermore two different types of image identification methods were used: raw magic string identification in pure tcp network traffic and HTTP Mime type identification. The latter being more accurate and faster. C# was seen as vastly superior in both speed of prototyping and final performance evaluation. The study presents a novel new way of monitoring networks on the basis of their media content through deep packet inspection
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SARKAR, RAJARSHI. "Design and Synthesis of Heteroleptic and Heterometallic Metallo-Supramolecular Terpyridine Architectures". University of Akron / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=akron1444660678.
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Karresand, Martin. "Completing the Picture : Fragments and Back Again". Licentiate thesis, Linköping : Department of Computer and Information Science, Linköpings universitet, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-11752.
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Yan, Shanshan. "Chinese sentence-final particles and their behaviours in English speakers' L2 Chinese". Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275336.
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This study investigates how seven Chinese sentence-final particles (SFP le, ne1, ma, ne2, ba1, ba2 and a; hereafter SFP) and their features are represented in English speakers’ L2 Chinese. In this research, SFPs are analysed as heads instantiating different positions in the CP domain (Paul 2009, 2014, 2015), which are head-final, and in particular, they are considered to carry semantic, syntactic and discourse features. As there is no SFP in English, the features on Chinese SFPs are realised by a variety of syntactic means. Through a proficiency test and six experimental tasks, data from 76 participants (including 18 Chinese native speakers, 20 low-intermediate learners, 20 high-intermediate learners and 18 advanced learners) were collected. Results show that English-speaking L2 learners can easily establish the basic syntactic structure of Chinese SFPs and successfully acquire the features attached to SFPs ma, ba1 and a. However, they have significant difficulty in acquiring the features attached to SFPs le, ne1, ne2 and ba2. In general, syntactic features on Chinese SFPs are intact in L2 grammars, whereas semantic features (i.e. syntax-semantics interfaces) are very vulnerable. In addition, it is found that not all discourse features (syntax-discourse interfaces) are problematic. Findings indicate that both L1 grammar (i.e. L1 transfer) and L2 input (frequency, saliency and complexity) play important roles in affecting learners’ acquisition of the features attached to Chinese SFPs. In particular, learners seem to transfer all feature sets from their L1 English. Semantic features that have been transferred from their L1 English but that are neither confirmed nor disconfirmed by the Chinese input have become dormant in the L2 Chinese, which complements the Dormant Feature Hypothesis (Yuan 2014). Furthermore, the homomorphous SFPs which exhibit a ‘one-to-many’ form-meaning connection are believed to complicate learners’ recognition and acquisition of relevant features on SFPs. It is also demonstrated that the mapping of a feature across CP domains (i.e. from a two-CP structure to a one-CP structure) can be problematic and difficult. The discourse feature needs to be reassembled in L2 grammars, which advances the arguments of the Feature Reassembly Hypothesis (Lardiere 2008, 2009a,b).
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Ciavatta, Emiliano. "Analisi e ricostruzione di flussi TCP con il software Caronte". Master's thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amslaurea.unibo.it/23321/.
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Al giorno d'oggi la maggior parte delle applicazioni che utilizziamo sono connesse a Internet. Le aziende hanno iniziato a fornire i servizi su cloud, spostando la computazione e i dati dai dispositivi dei clienti a server raggiungibili attraverso Internet. Questo fenomeno ha causato un aumento esponenziale del traffico di rete. Esponendo però i servizi su Internet sono aumentate le minacce alla sicurezza che provengono dall'esterno e che passano attraverso la rete. Per questo motivo analizzare il traffico di rete è diventata un'attività fondamentale. I volumi di traffico generati però dalle applicazioni moderne sono elevati: servono quindi strumenti automatici che siano in grado di filtrare il traffico di rete per individuare e isolare le minacce. Esistono diversi strumenti automatici che sono in grado di rilevare e prevenire minacce di rete che funzionano analizzando i pacchetti catturati su interfacce di rete. Questi strumenti sono molto efficaci nell'individuare tentativi d'intrusione, ma non permettono di effettuare una post-analisi manuale delle minacce individuate per capire come gli utenti malevoli abbiano sfruttato le vulnerabilità e i problemi del software. La maggior parte di questi strumenti effettuano un'analisi a livello di rete, andando a ispezionare il contenuto dei pacchetti. Per capire come degli avversari sfruttano eventuali vulnerabilità del software molte volte però è necessario ricostruire il flusso logico delle conversazioni di rete. L'obiettivo di questo progetto di tesi è quindi quello di realizzare uno strumento che sia in grado d'individuare le minacce analizzando il traffico di rete e ricostruendo i protocolli utilizzati. Lo strumento sarà in grado di analizzare e ricostruire le connessioni TCP presenti in flussi di rete e tutti i protocolli basati su questo. Il processo di ricostruzione consiste nell'individuare tutti i pacchetti che formano una stessa connessione logica ed estrarre da questi il contenuto della conversazione effettuata.
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Tybon, Robert, i n/a. "Generating Solutions to the Jigsaw Puzzle Problem". Griffith University. School of Management, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20041101.085937.
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This thesis examines the problem of the automated re-assembly of jigsaw puzzles. The objectives of this research are as follows: to provide a clear statement of the jigsaw puzzle re-assembly problem; to find out which solution technique is best suited to this problem; to determine the level of sensitivity of the proposed solution technique when solving different variations of this problem; and to explore solution methods for solving incomplete jigsaw puzzles (puzzles with missing pieces). The jigsaw puzzle re-assembly problem has been investigated only intermittently in the research literature. This work presents an extensive examination of the suitability and efficiency of the standard solution techniques that can be applied to this problem. A detailed comparison between different solution methods including Genetic Algorithms, Simulated Annealing, Tabu Search and Constraint Satisfaction Programming, shows that a constraint-based approach is the most efficient method of generating solutions to the jigsaw puzzle problem. The proposed re-assembly algorithm is successful. Consequently, it can be used in development of automated solution generators for other problems in the same domain, thus creating new theoretical and applied directions in this field of research. One potential theoretical line of research concerns jigsaw puzzles that do not have a complete set of puzzle pieces. These incomplete puzzles represent a difficult aspect of this problem that is outlined but can not be resolved in the current research. The computational experiments conducted in this thesis demonstrate that the proposed algorithm being optimised to re-assemble the jigsaw puzzles is not efficient when applied to the puzzles with missing pieces. Further work was undertaken to modify the proposed algorithm to enable efficient re-assembly of incomplete jigsaw puzzles. Consequently, an original heuristic strategy, termed Empty Slot Prediction, was developed to support the proposed algorithm, and proved successful when applied to certain sub-classes of this problem. The results obtained indicate that no one algorithm can be used to solve the multitude of possible scenarios involved in the re-assembly of incomplete jigsaw puzzles. Other variations of the jigsaw puzzle problem that still remain unsolved are presented as avenues for future research. The solution of this problem involves a number of procedures with significant applications in other computer-related areas such as pattern recognition, feature and shape description, boundary-matching, and heuristic modelling. It also has more practical applications in robotic vision and reconstruction of broken artefacts in archaeology.
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Tybon, Robert. "Generating Solutions to the Jigsaw Puzzle Problem". Thesis, Griffith University, 2004. http://hdl.handle.net/10072/366062.
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This thesis examines the problem of the automated re-assembly of jigsaw puzzles. The objectives of this research are as follows: to provide a clear statement of the jigsaw puzzle re-assembly problem; to find out which solution technique is best suited to this problem; to determine the level of sensitivity of the proposed solution technique when solving different variations of this problem; and to explore solution methods for solving incomplete jigsaw puzzles (puzzles with missing pieces). The jigsaw puzzle re-assembly problem has been investigated only intermittently in the research literature. This work presents an extensive examination of the suitability and efficiency of the standard solution techniques that can be applied to this problem. A detailed comparison between different solution methods including Genetic Algorithms, Simulated Annealing, Tabu Search and Constraint Satisfaction Programming, shows that a constraint-based approach is the most efficient method of generating solutions to the jigsaw puzzle problem. The proposed re-assembly algorithm is successful. Consequently, it can be used in development of automated solution generators for other problems in the same domain, thus creating new theoretical and applied directions in this field of research. One potential theoretical line of research concerns jigsaw puzzles that do not have a complete set of puzzle pieces. These incomplete puzzles represent a difficult aspect of this problem that is outlined but can not be resolved in the current research. The computational experiments conducted in this thesis demonstrate that the proposed algorithm being optimised to re-assemble the jigsaw puzzles is not efficient when applied to the puzzles with missing pieces. Further work was undertaken to modify the proposed algorithm to enable efficient re-assembly of incomplete jigsaw puzzles. Consequently, an original heuristic strategy, termed Empty Slot Prediction, was developed to support the proposed algorithm, and proved successful when applied to certain sub-classes of this problem. The results obtained indicate that no one algorithm can be used to solve the multitude of possible scenarios involved in the re-assembly of incomplete jigsaw puzzles. Other variations of the jigsaw puzzle problem that still remain unsolved are presented as avenues for future research. The solution of this problem involves a number of procedures with significant applications in other computer-related areas such as pattern recognition, feature and shape description, boundary-matching, and heuristic modelling. It also has more practical applications in robotic vision and reconstruction of broken artefacts in archaeology.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Management
Faculty of Commerce and Management
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Sarkar, Mohosin M. "Engineering Proteins with GFP: Study of Protein-Protein Interactions In vivo, Protein Expression and Solubility". The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261418776.
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Perônico, Phamela Bernardes. "Estrutura taxonômica e funcional da assembleia de peixes no Rio Tocantins, antes e após a formação do reservatório de Peixe Angical, região do Alto Rio Tocantins, TO". Universidade Federal do Tocantins, 2017. http://hdl.handle.net/11612/414.
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Análises baseadas em traços funcionais descrevem as espécies em relação às suas características biológicas e assim complementam as informações taxonômicas. Ainda que diversos trabalhos sejam realizados visando descobrir impactos ambientais após a criação de usinas hidrelétricas, poucos são voltados para investigar padrões de estabilização da estrutura da ictiofauna em termos taxonômicos e funcionais; a resposta funcional em longo prazo, em particular, é totalmente desconhecida. Neste estudo buscamos investigar padrões de reestruturação da assembléia de peixes em termos taxonômicos e funcionais nas zonas de transição, fluvial e lacustre, ao longo de dez anos, englobando momentos anteriores e posteriores à construção da UHE Peixe Angical, rio Tocantins. Nossos resultados revelaram indícios de estabilização taxonômica e funcional dentro da primeira década do reservatório, nas diferentes zonas. Tanto a riqueza taxonômica quanto a riqueza funcional apresentaram declínio progressivo após a instalação da barragem, atingindo níveis mais estáveis após seis anos. Conforme esperado, o aumento na abundância registrado no primeiro ano do reservatório não se manteve ao longo do tempo e foi possível notar um decréscimo acentuado em todos os pontos amostrais. Houve evidente alteração na composição taxonômica e funcional ao longo dos anos, com menor taxa de mudança a partir do 6º ano. Espécies registradas na fase Rio com maiores abundâncias praticamente deixaram de ser registradas após a criação da barragem, enquanto outras espécies com características que lhes permitiram resistir aos filtros ambientais do reservatório se destacaram em número de indivíduos. Espacialmente, foi possível notar diferentes padrões de composição tanto para a estrutura taxonômica quanto para a estrutura funcional da assembléia. Além disso, nossos resultados apontam que a perda de diversidade funcional se dá por fatores estocásticos; e que, apesar de haverem perdas de perfis funcionais através da perda de espécies, ainda não foi possível constatar uma convergência funcional. Portanto, dez anos de represamento foi suficiente para observarmos fortes padrões de alteração sobre a ictiofauna afetada pelo represamento da UHE Peixe Angical, além da eminente estabilização dos atributos taxonômicos e funcionais nas diferentes zonas do reservatório ao longo do tempo.Functional traits describe species in respect to functional characteristics and therefore complement taxonomic information. Although several studies investigate environmental impacts caused by hydropower dams, few have focused on long-term patterns of functional and taxonomic fish diversity; changes in functional structure, in particular, are largely unknown. In this study, we investigated long-term changes (10 years) in taxonomic and functional diversity across environmental gradients created by the construction of Peixe Angical hydropower dam, Tocantins River, Amazon Basin. Our results revealed trends of functional and taxonomic stabilization 10 years after river regulation, in the different zones of the reservoir. Both the functional and taxonomic diversity showed progressive decrease over time, reaching more stable levels after 6 years. As expected, the increase in fish abundance registered soon after damming was followed by a marked decrease in all sites. We observed strong alteration in functional and taxonomic composition over the years, with more stable values after the sixth year. The most abundant species in the river period virtually disappeared after river damming, replaced by species with adaptations to cope with the environmental filters created by the impoundment. In addition, our results showed that the loss of functional diversity occurred stochastically; despite the loss of functional profiles with the loss of species, it was not possible to determine functional convergence. In conclusion, Peixe Angical hydropower dam induced strong changes in the taxonomic and functional structure of fish assemblages, with trends of stabilization ten years after river impoundment, in the different zones of the reservoir.
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Rodovalho, Beatriz. "Amateur d’amateurs : enjeux esthétiques et historiques du remontage de films de famille à travers l’œuvre de Péter Forgács". Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCA057.
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À partir de l’œuvre du cinéaste et artiste hongrois Péter Forgács, la thèse aborde plus généralement la question du remontage de films amateurs dans le documentaire contemporain et examine les enjeux esthétiques, historiques et politiques du remploi des films de famille. Les concepts de déterritorialisation et de reterritorialisation développés par Gilles Deleuze et Félix Guattari nous permettent d’interroger la manière dont la pratique « archéologique » du remontage ouvre les films de famille à de multiples resignifications. Comment traversent-ils des territoires esthétiques, géographiques, institutionnels et politiques, de mémoire, d’histoire et de pensée ? Comment, à travers le temps, les histoires que contiennent ces rouleaux des pellicules substandard sont-elles traversées par l’Histoire ? Comment ces films peuvent-ils, rétrospectivement, subvertir la construction officielle de l’histoire et de la mémoire et renégocier la perception du temps historique ? Quelle métahistoire construisent-ils ?L’analyse de la déterritorialisation et de la reterritorialisation des films de famille par le remploi, nous permet d’interroger la manière dont la pratique du remontage crée un nouveau territoire cinématographique, où la mémoire et l’histoire du passé comme de l’avenir peuvent être creusées dans et par l’image. Ici apparaissent les enjeux poét(h)iques et politiques du remploiThrough the work of Hungarian artist and filmmaker Péter Forgács, the thesis addresses the question of the reuse (remontage) of amateur films in contemporary documentary and examines the aesthetic, historical and political implications of the appropriation of home movies. The concepts of deterritorialization and reterritorialization developed by Gilles Deleuze and Félix Guattari allow us to question how the “archeological” practice of reassembly exposes home movies to multiple significations. How can they traverse aesthetic, geographical, institutional and political territories as well as territories of memory, history and thought? How are the stories contained in these rolls of substandard film traversed by History? How can these films subvert the official construction of history and memory and renegotiate the perception of historical time? What metahistory do they establish?The analysis of deterritorialization and reterritorialization of home movies allows us to question how the practice of reassembly creates a new cinematographic territory, in which memory and history of the past, as of the future, can be mined in and by the image. Thus remontage implicates poet(h)ical and political issues
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Indi, S. S. "Structural studies of in situ, reassembled and extracted microtubules in insect ovaries". Thesis, University of Exeter, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376836.
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Marulanda, Dabeiba. "Structural studies of reassembled and intact thioredoxin by high-resolution solid-state NMR magic angle spinning spectroscopy". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 13.72 Mb., 213 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3205438.
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Hwang, Chun-Hui, i 黃純慧. "Improvement of TCP Packet Reassembly in Libnids". Thesis, 2009. http://ndltd.ncl.edu.tw/handle/14433139325143622152.
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碩士元智大學
資訊工程學系
97
Internet’s growing quickly makes the monitor and protect about the Internet security have become more important. The most important thing about monitor system design is to protect the internet security, so there is a lot of tool and software that we can use to monitor the internet. Most of these monitoring systems are designed basis on the API’s library, such as the libcap to capture the packets and the libnids to reassemble packets. Most of the monitoring system usually use the libnids to capture the packet, IP defragmentation, and TCP stream reassembly. When using the libnids to reassembly the TCP data stream, if the situation about packet loss and capture unsuccessful happened, that will fail to continue analyzing following packets. So, we will improve the procedure of libnids in TCP stream reassembly by add a interrupt waiting mechanism. Packet dispatch mechanism make the libnids been waiting for a period of time, it can continue o analyze following packets. In addition, libnids will avoid consuming a lot of memory to store following packets that can’t be reassembly. Finally, we will deliver packets with packet header informations to the application layer for get more useful network information to make the network management.
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Chen, Yueh-Hao, i 陳岳豪. "Promotion Effect of MST3 on Tight Junction Reassembly". Thesis, 2015. http://ndltd.ncl.edu.tw/handle/rx8wq6.
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碩士中華醫事科技大學
醫學檢驗生物技術系碩士班
103
Part1 All epithelial cells form adherent junctions that provide structural integrity to the epithelium. Cell polarization and the formation of cell–cell junctions are coupled processes that are essential to tissue morphogenesis. The blood-brain barrier and blood-testis-barrier belong to tight junction. In our previous study, MST3 inhibits the cell polarity and migration. Tight junction disruption was required to migration process. However, the requirement for MST3 in tight junction assembly and has not been clearly demonstrated .So we examined the tight junction assembly of MST3 in MDCK stable clone by calcium switch method which withdrawal of calcium from the medium cause rapid loss of cell-cell junction, and then be reversed by re-addition of calcium. We reported that the tight junction reassembly after calcium recovery in WT-MST3-MDCK was earlier than that in KD-MST3-MDCK. Part 2 MST3 (mammalian-Ste20-kinase 3) is a member of the Ste20 (sterile-20) kinase family. Earlier we showed it inhibiting cell migration. Recent studies indicate other Ste20 types like proline-alanine-rich Ste20-related kinase (PASK) and oxidative stress-response protein 1 (OSR1) as conserved regulators of cell volume, ion transport, and hypertension. We reported that MST3 may involve in pathogenesis of hypertension through inhibiting Na reabsorption in renal collecting duct of medulla prinicapal cells. We try to further know the MST3 renal distribution to investigate the role of MST3 regulation. Immunohistochemistry revealed MST3 was expressed in part of the Distal Convoluted Tubule (DCT) by using of NCC protein as the DCT marker. In addition, we tried to clone 、、subunit ofENaC to understand the mechanism of MST3 related regulation of ENaC.
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Chen, Sue Train, i 陳書川. "VLSI Design of the Reassembly Management for ATM/AAL". Thesis, 1995. http://ndltd.ncl.edu.tw/handle/61249748301537774139.
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Lovas, Jonathan Roek. "Hierarchical Modularity in the Reassembly of Hydra’s Nervous System". Thesis, 2020. https://doi.org/10.7916/d8-4wy9-eg37.
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Modularity plays a pivotal role in evolution, as the compartmentalization of components of a system allows their independent optimization in isolation, minimizing the effect on the system as a whole. As a manifestation of this universal design principle, evidence suggests modularity plays a key role in the function of the brain as well, allowing the compartmentalization of specific structural and functional units before their integration. Despite this, it’s unknown how modularity arises during the development of neural circuits. Accordingly, observing the development of the modularity of the nervous system and correlating this with the emergence of specific behaviors has the potential to highlight features of the functional role of modularity in the mature nervous system.
To explore this issue, we work with the small cnidarian Hydra vulgaris, a representative of some of the simplest nervous systems in evolution. Depending on the size of the animal, Hydra’s isometrically scaling nervous system of 300-2,000 neurons is organized in two independent nerve nets in its ectoderm and endoderm and is distributed through the body of the animal without any cephalization or ganglia. Moreover, under the right conditions Hydra can reassemble itself into a normal animal after complete dissociation into individual cells. Using transgenic Hydra which express the calcium sensor GCaMP6s in every neuron (Dupre and Yuste, 2017) we have imaged the neuronal activity of dissociated preparations as they re-aggregate then regenerate over a period of several days. We demonstrate the robust synchronization of Hydra’s neural nets during the process. Of the possible routes toward synchronization, we observe that an initially random structure takes on a hierarchical organization as small groups of neurons synchronize. As these proto-circuits further synchronize, the modularity of the system increases, accompanied by a loss of the hierarchical depth of the network structure as normal behavioral rhythms resume during regeneration.
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Shou-Jung, Peng, i 彭首榮. "FPGA-Based MPEG Reassembly Chip Design for ATM Networks". Thesis, 1998. http://ndltd.ncl.edu.tw/handle/32706430397316981400.
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碩士大同工學院
資訊工程研究所
86
ATM-based broadband services has been key to the next-generationtelecommunication applications. In particular, the use of ATM to transportreal-time, high quality video has been standardized by international bodiesincluding DAVIC, ATM-Forum, ATSC and ITU. Among all the applications, videotransport based AAL-5 processing must be dealt with in a unique way due tothe necessity of handling clock-recovery at the receiver end, and also to keepthe buffer at a minimum size. In this thesis research, a hardware based MPEGre-assembly circuit is designed. The design starts with an analysis offunctional requirements imposed by ATM-Forum, and then comes up with an MPEGre-assembly algorithm at AAL-5 layer. The design is further implemented byusing an FPGA tool. Simulations are conducted to show the usefulness of thedesign. The resulting system can be applied to a wide variety of networksincluding ADSL, VDSL, Fiber-to-the-Curb and BISDN. The key advantages includecompliance with open standard for network interface with customer premisesequipment, cost effectiveness, and flexibility in functional expansion.
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Cordero, Guzmán Gustavo Segundo. "Reassembly and biochemical characterization of the human Smc5/6 complex". Thèse, 2017. http://hdl.handle.net/1866/20396.
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Dráb, Martin. "Určování genetických variant z masivně paralelních sekvenačních dat pomocí lokálních reassembly". Master's thesis, 2017. http://www.nusl.cz/ntk/nusl-365074.
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Despite active development during past years, the task of sequencing a genome still remains a challenge. Our current technologies are not able to read the whole genome in one piece. Instead, we shatter the target genome into a large amounts of small pieces that are then sequenced separately. The process of assembling these small pieces together, in order to obtain sequence of the whole genome, is painful and rsource-consuming. Multiple algorithms to solve the assembly problem were developed. This thesis presents yet another assembly algorithm, based on the usage of de Bruijn graphs, and focusing on sequencing short genome regions. The algorithm is compared to well-known solutions in the field. 1
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Wibranek, Bastian. "Robotic Digital Reassembly: Towards physical editing of dry joined architectural aggregations". Phd thesis, 2021. https://tuprints.ulb.tu-darmstadt.de/18578/1/Wibranek_Robotic%20Digital%20Reassembly.pdf.
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The accelerating changes in how people use and occupy buildings, coupled with humanity’s growing consciousness towards the climate impact of construction, impose reconsideration of existing patterns in the built environment. Most buildings today are planned to resemble a fixed shape, binding their material into a static assemblage. In contrast, computerization in many fields of everyday life shifts our imagination to an editable world. While the digital world is constantly evolving and changes can be instantly programmed, changes in the physical world require immense labor, manpower, and machinery. However, the fast technological advances in digital design and fabrication are challenging the economies of static composition of buildings. Digital design tools offer access to the broad space of design alternatives on all scales, from building topologies to the single building element. By changing a few parameters, designers can reconfigure a design almost automatically. At the same time, architectural research on Digital Materials, Discrete Design, and robotic construction holds the potential to transport these digital qualities into the physical world. As a result, buildings can be thought of as material resources, can be reassembled, and their building elements might flow back into the industry for future building, contributing to the built environment’s shift towards circular economy. Combining digital design tools, detachable building elements, and robotic skills is worth exploring to understand their potential and qualities for an editable built environment.
This thesis presents a combinatorial modeling framework for robotic assembly and reassembly of buildings. The applicability of the framework is demonstrated in four case studies employing strategies of robotic programming linked with digital design tools for dry-fitted and interlocking building elements. The use of tactile robotic skills is discussed in a comprehensive case study, utilizing machine learning for the design and robotic control of an interlocking assembly. The robot-oriented design focuses on building elements with quantities, geometries, and connections suitable for handling by a robot.
This shift, in turn, enables architects not only to produce changeable structures but also to gain control and thoroughly explore the design space resulting from elements that can be reassembled. In Robotic Digital Reassembly, materialization and production of architecture are not a one-off process. They rather become a series of instances shifting and adapting into an ever-unfolding future.
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Chiu, Yi-hsien, i 邱議賢. "Real-Time Packet Tracing & Reassembly Utilizing Session Analysis and Hash Function". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/43692971184962850277.
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碩士國立雲林科技大學
資訊管理系碩士班
93
Network packet tracing is one of the most common evidence acquisition methods. However, the complexity of relative analysis makes packet tracing and evidence preservation incompetent to match the ever-increasing network speed. While distributed-system and multi-processor solutions are available, it is considered inappropriate to businesses with strained budget. This study designs a low-cost and space-efficient packet trace mechanism for long-term real-time evidence gathering. The proposed method utilizes session analysis and hash functions as means of compression and as support to digital forensics in evidence examination. As a proof of concept, a prototype system is developed, on a low-end optimized Linux PC, and tested. The result shows that this mechanism is able to perform real-time packet tracing and reassembly using single low-end PC on T3 networks.
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Cheng, Ming-Li, i 鄭名利. "Design and Implementation of a Hardware Accelerated IP Layer Packet Reassembly Module". Thesis, 2009. http://ndltd.ncl.edu.tw/handle/24614380699784722132.
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碩士國立臺灣大學
電機工程學研究所
97
In modern designs of network appliances, an IP offload engine is used essentially in a Network Intrusion Detection System (NIDS) or an Intrusion Prevention System (IPS). An IP packet reassembly module provides high-speed and efficient reassembly of IP fragments received at an intermediate station in a computer network. Traditionally, software reassembles the IP fragments received from the MAC layer to a TCP packet. In order to achieve multi-gigabit per second data rates, the IP packet reassembly hardware module is configured to replace the reassembly task of IP fragments. This thesis addresses the design of a hardware implementation of an IP reassembly module. The IP reassembly module utilizes a synchronous timer to do time work for each fragment group. The synchronous timer resolves the occupied issue in the memory resource. The IP reassembly module is equipped with a hash table having a plurality of entries for maintaining status information for each received fragment and for each original packet being reassembled from the fragments. The proposed hash table accelerates searching and achieves the balance between speed, memory size and cost in the system. We implemented the proposed hashing approach IP packet reassembly module in a Xilinx ML507 FPGA development platform and obtained an estimated throughput of 3.2 Gbps.
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Chang, Bo-Yi, i 張柏毅. "Study of Algorithm and Hardware Design for Genome Reassembly by Short Reads". Thesis, 2012. http://ndltd.ncl.edu.tw/handle/14864492249561925423.
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碩士國立臺灣大學
電子工程學研究所
100
Genome governs the behavior and traits of a being. It is the DNA sequence in cell nuclei. DNA sequences consist of four types of nucleobases - A, C, G and T. A DNA sequence can be regarded as a long string constructed by these four alphabets. By the DNA sequences of an individual, we can analyze potential hereditary diseases it may have. Human DNA sequence is surely the most popular topic. DNA sequencing machine can decode the alphabet on a DNA sequence. However, contemporary DNA sequencing machines have a length limit for incoming DNA sequences(about 20~1000 nucleobases). The total length of human DNA sequences is about 3×〖10〗^9 nucleobases, which can not be directly decoded by DNA sequencing machines. So, to decode the alphabet of the DNA sequence of a human, we need to extract multiple copies of the DNA sequences from him/her, and then randomly cut the sequences into small pieces with length under 1000 nucleobases for DNA sequencing machines to decode. These small pieces are called short reads. After the alphabet on short reads is decoded, we reconstruct the original DNA sequence by these short reads. Since the DNA sequences between two different human are very similar, we can refer to a reconstructed DNA sequence of another human(which is called reference sequence). For each short read, find the most similar subsequence and the location of the most similar subsequence (which is called best mapping location) on the reference sequence. The original DNA sequence can be reconstructed by putting each short read to the best mapping location. The process of finding the most similar subsequence on the reference sequence is called short read alignment. Currently, short read alignment algorithms are mostly done in software. After genome reassembly become a popular medical service in hospitals, the speed of software is not enough for huge amount of needs. Short read alignment contains candidate mapping location(CML) generator and similarity score with actual alignment computation. State-of-the-art CML generators consumes too much memory when implemented in hardware. We propose Bloom filter-based CML generator, which has much lower memory consumption than state-of-the-art solutions. Similarity score computation and actual alignment computation are usually done with Smith-Waterman algorithm, which is implemented in systolic array for hardware implementations. We propose a modified processing element in the systolic array to have a smaller area and shorter critical path.
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Gong, Yu-Cheng, i 龔育正. "Chip Design and Implementation of ATM/AAL5 Reassembly Processor with Hashing Searching Technique". Thesis, 1999. http://ndltd.ncl.edu.tw/handle/02418171915322587520.
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碩士國立中正大學
電機工程研究所
87
Today, as the demand of network bandwidth keeps growing, ATM technology is being considered as a suitable platform. Many R&D organizations and network companies have invested the research on developing the ATM NIC for the PC host. In these few years, we have developed several versions of ATM NIC for the PC. We have also devoted our efforts on the development of next generation ATM NIC. This new version of the ATM NIC improves the performance significantly. We extend such performance to handle 128 connections simultaneously. Furthermore, we have included the ABR traffic management function to this ATM NIC. Due to these changes, the architecture becomes more complicated, and therefore makes the system more practical. In this thesis, we first introduce the new version of the ATM NIC, then we describe the Reassembly Processor. We explain our design consideration in details. Considerations include the environment that the Reassembly Processor is formed. We discuss the reassembly functions and structure used by some other high performance ATM NICs. We adopt the Xilinx XC4000 series FPGA chips. The design flow is based on the Top-Down approach. First, we decide what are the specifications required for the chip. We write the FSM and associated modules by using Verilog HDL. We use the Synopsis FPGA Express to synthesize our codes. We use the Xilinx tool to convert and PAR (Place and Route) the circuit, and then download the design into FPGA chip to do the tests. Finally, we design a test board to verify our designed FPGA. We have successfully realized this implementation.
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Qi, Dake. "Myosin light chain phosphorylation facilitates in vivo myosin filament reassembly after mechanical perturbation". Thesis, 2002. http://hdl.handle.net/2429/12293.
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It is generally believed that the myosin thick filaments in smooth muscle are
structurally less stable than those in striated muscle. In vitro studies have shown that
phosphorylation of the 20-kD myosin light chain (MLC) facilitates formation of the thick
filaments from monomeric myosins in solution. It appears that the structural integrity of
the thick filaments can be enhanced by phosphorylation of the MLC. It is however not
known whether the transition from monomeric to filamentous myosin occurs in intact
smooth muscle when the light chains are phosphorylated during muscle activation. The
physiological significance of the thick filament lability and the role of MLC
phosphorylation in modulating the filament integrity in intact smooth muscle are still
being debated. It has been shown in our laboratory that mechanical strain is able to
induce partial dissolution of unphosphorylated myosin thick filaments in intact smooth
muscle; repolymerization of the thick filaments occurs when the muscle is subjected to
cycles of contraction and relaxation. The objective of my thesis research is to determine
whether MLC phosphorylation is required for repolymerization of the thick filaments
after they have been partially disassembled by mechanical agitation.
We used the conventional electron microscopy to quantify the cross-sectional
density of myosin thick filaments in airway smooth muscle; partial dissolution of the
thick filaments was induced by applying length oscillations to the muscle preparation;
recovery of the thick filament density after oscillation was examined in the presence and
absence of wortmannin, a potent inhibitor of myosin light chain kinase (MLCK). The
results showed that isometric force production in airway smooth muscle was totally
dependent on MLC phosphorylation. The inhibition of MLC phosphorylation alone did
not cause disassembly of myosin filaments. The unphosphorylated thick filaments
however partially dissolved when the muscle was subjected to oscillatory strains, as
evidenced by a 25% decrease in the filament density. The post-oscillation filament
density did not recover when wortmannin was present; it recovered to the pre-oscillation
level when wortmannin was removed. Based on the above findings, we conclude that
thick filament formation in vivo is MLC phosphorylation dependent.
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Ji-XuanXu i 徐繼煊. "Activation of PKCα and Rac1 promotes invadopodia reassembly through optogenetically engineered Ca2+ oscillations". Thesis, 2019. http://ndltd.ncl.edu.tw/handle/u54va4.
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碩士國立成功大學
生物醫學工程學系
107
Calcium (Ca2+) plays an important role in the signal transduction of cells, regulating the physiological activities of cells such as fertilization, cell proliferation, cell contraction, cell migration, and apoptosis. Invadopodia is a protrusion on the cell membrane that uses metalloproteinases to degrade the extracellular matrix. Invadopodia plays an important role in the invasion and metastasis of cancer cells. Ca2+ has also been shown to be important for the formation of invadopodia and the disintegration of extracellular matrices by cancer cells. However, in the previous literature on this topic, there has been no precise study to indicate what kind of Ca2+ signal causes invadopodia assembly. Optogenetic technology is a research method that provides high temporal and spatial resolution and has been developed and applied to many precise biological and medical studies. Therefore, we use optogenetic techniques combining 470 nm of blue light to activate light-sensitive channels (Ca2+ translocating channelrhodopsin, CatCh) expressed on human melanoma cancer cells (A375) to create different oscillating waves, so that Ca2+ signals can flow into cells in different oscillating waves. In this study, we explore how Ca2+ signals affect the formation of invadopodia. Our research showed that low frequency (0.01 Hz, 0.1 Hz) Ca2+ oscillations promoted reassembly of invadopodia, while high frequency (1 Hz) Ca2+ oscillations caused the collapse of invadopodia. In addition, we also found that low frequency Ca2+ oscillation caused by light stimulation promotes the reassembly of invadopodia by activating PKCα (protein kinase C alpha) and Rac1 (Ras-related C3 botulinum toxin substrate 1). As for the role of RhoA (Ras homolog gene family, member A) and Cdc42 (Cell division control protein 42 homolog) in this process, we need further research to prove it.
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Frazer, Lynn V. "Paleolimnological reconstruction of cladoceran community reassembly following experimental manipulation of two boreal shield lakes". 2009. http://hdl.handle.net/1993/21339.
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Barra, Cabello Marcos Patricio [Verfasser]. "Disassembly and reassembly of the manganese complex of photosystem II / by Marcos Patricio Barra Cabello". 2007. http://d-nb.info/989257436/34.
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Schermer, Ulrike [Verfasser]. "Mechanism of chromatin reassembly at the yeast PHO5 promoter upon repression / vorgelegt von Ulrike Schermer". 2007. http://d-nb.info/983072876/34.
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Ma, Jaw-Woei, i 馬兆緯. "JPANDDR–Implementation of a JAVA based tool for Protocol Analysis,Network Diagnose and Data Reassembly". Thesis, 2007. http://ndltd.ncl.edu.tw/handle/j9jyg7.
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碩士國立臺北科技大學
資訊工程系研究所
95
With the popularity of Internet applications, more and more protocols emerge. Various protocols make the communication among different systems possible. Although layering concept simplifies the design and implementation of protocol architecture, to understand the details of the cooperation of between protocols is still a complicated work. One thing that people agreed is that realizing a single packet thoroughly over a network will be definitely a basic starting point. Based on that, properly reassembling the related packets may tell more information and the interactions among networking protocols. To do so, a convenient tool would be helpful. The objective of this research is to design a network tool that provides not only the basic capability such as header parsing, protocol tracking and monitoring, and analyzing and diagnosing network condition, but also the information recovery and replay of the reconstructed messages from the captured data packets in a network. We abbreviated the system as JPANDDR, which is based upon the JAVA-language, incorporating with JPcap and JMF. In addition, the system also provides a friendly graphical user interface (GUI) ease the operation and presents various reports via individual graphical window to help understand the results. With the development of the system functions, it facilitates the user understanding the analysis and the design of network protocols, interactions between adjacent and peer layers, the network operation from a top-level, and the diagnosis and troubleshooting of the networks.
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Lin, Wen-Zhi, i 林文智. "The Role of PYK2/Src in Calcitonin-induced Podosome Reassembly and Sealing Zone Detachment in Osteoclasts". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/96009504852448586015.
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碩士國防醫學院
生物及解剖學研究所
93
Osteoclasts (OCs) are multinucleated, terminally differentiated cells which play an essential role in bone resorption. To resorb bone, OCs attach to extracellular matrix or the bone surface via specialized attachment structures called podosomes, which form a prominent F-actin-rich ring that is thought to correspond to the sealing zone of resorbing OCs. It had been showed that Pyk2/Src/Cbl complex is critical to the αvβ3 integrin-mediated signaling in podosome. The concept of outside-in and inside-out of integrin-mediated signaling has been elucidated in depth through the study of Pyk2/Src/Cbl complex. Calcitonin (CT) is a 32-amino acid polypeptide which inhibits OC motility, induces OC retraction, and disrupts the actin-ring structure of OCs. Thus it is reasonable to assume that the Pyk2/Src/Cbl complex in podosome could be the potential target for the CT-induced signaling. In isolated authentic rabbit OCs cultured on extracellular matrix-coated Petri dish, we previously showed that CT induced dephosphorylation and redistribution of Pyk2. The dephosphorylation of Pyk2 would be expected to prevent the formation of Pyk2/Src/Cbl complex and therefore inhibit OC motility and attachment. However, the effects of CT on Pyk2/Src/Cbl complex function and their distribution in OCs are not clear. We therefore investigated whether CT affects Pyk2/Src association and Src phosphorylation in OCs by using the immunoprecipitation and Western blot methods. The result showed that CT induced an increase of Src tyrosine phosphorylation and Pyk2/Src association. Using immunofluorescent confocal analysis, we showed that CT induces dephosphorylation of Pyk2 in the sealing zone and increase Src tyrosine phosphorylation and Pyk2/Src association in the central region of OCs. Further examination using specific Y416 and Y527 phosphorylation antibodies of Src showed that CT induced increase of Y416 but not Y527 phosphorylation. The increase of Y416 and decrease of Y527 phosphorylation were found in the central region of OCs after CT stimulation. In conclusions, CT may induce podosome reassembly and sealing zone detachment by decrease Pyk2 phosphorylation in the sealing zone and increase Y416 phosphorylation of Src and Pyk2/Src association in the central region of OCs.
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Chen, Chun-Yeh, i 陳俊曄. "An FPGA Implementation of a 40Gbps Ultra High Speed FIFO Queue - Dump Process, Segmentation and Reassembly". Thesis, 2008. http://ndltd.ncl.edu.tw/handle/29502868111400146381.
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Seepany, Harshika. "Chromatin Reassembly following a DNA Double-Strand Break Repair: The Ctf18-complex and Ctf4 work in concert with H3K56 Acetylation". Thesis, 2011. http://hdl.handle.net/1807/29616.
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The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.