Responstider är något som alltid har varit och fortfarande är en viktig del att tänka på vid utveckling av webbapplikationer. Speciellt CMS kan upplevas som väldigt långsamma ibland. En lösning på detta är MVC ramverk, i detta arbete javascript-ramverket backbone. Problemet handlar om att implementera backbone i ett CMS och ta reda på hur prestandan påverkas. För att testa detta skapades två versioner av en sida i wordpress, den ena med en implementation av backbone för att skapa och rendera kommentarer. Tester i olika webbläsare och med olika långa texter på kommentarerna visar på en prestandavinst som ligger omkring 90%.

Unbonded post-tensioned concrete block (UPCB) shear walls are an effective seismic force resisting system due to their ability to contain expected damage attributed to their self-centering capabilities. A few design procedures were proposed to predict the in-plane flexural response of UPCB walls, albeit following only basic mechanics and/or extensive iterative methods. Such procedures, however, may not be capable of capturing the complex nonlinear relationships between different parameters that affect UPCB walls’ behavior or are tedious to be adopted for design practice. In addition, the limited datasets used to validate these procedures may render their accuracy and generalizability questionable, further hindering their adoption by practitioners and design standards. To address these issues, an experimentally-validated nonlinear numerical model was adopted in this study and subsequently employed to simulate 95 UPCB walls with different design parameters to compensate for the lack of relevant experimental data in the current literature. Guided by mechanics and using this database, an evolutionary algorithm, multigene genetic programming (MGGP), was adopted to uncover the relationships controlling the response of UPCB walls, and subsequently develop simplified closed-form wall behavior prediction expressions. Specifically, through integrating MGGP and basic mechanics, a penta-linear backbone model was developed to predict the load-displacement backbone for UPCB walls up to 20% strength degradation. Compared to existing predictive procedures, the prediction accuracy of the developed model and its closed-form nature are expected to enable UPCB wall adoption by seismic design standards and code committees. / Thesis / Master of Applied Science (MASc)

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In practice, graphs often occur as perturbed product structures, so-called approximate graph products. The practical application of the well-known prime factorization algorithms is therefore limited, since most graphs are prime, although they can have a product-like structure. This work is concerned with the strong graph product. Since strong product graphs G contain subgraphs that are itself products of subgraphs of the underlying factors of G, we follow the idea to develop local approaches that cover a graph by factorizable patches and then use this information to derive the global factors. First, we investigate the local structure of strong product graphs and introduce the backbone B(G) of a graph G and the so-called S1-condition. Both concepts play a central role for determining the prime factors of a strong product graph in a unique way. Then, we discuss several graph classes, in detail, NICE, CHIC and locally unrefined graphs. For each class we construct local, quasi-linear time prime factorization algorithms. Combining these results, we then derive a new local prime factorization algorithm for all graphs. Finally, we discuss approximate graph products. We use the new local factorization algorithm to derive a method for the recognition of approximate graph products. Furthermore, we evaluate the performance of this algorithm on a sample of approximate graph products.

The enzyme nitroreductase (NR) catalyzes two-electron reduction of high explosives such as trinitrotoluene (TNT), a wide variety of other toxic nitroaromatic compounds, as well as riboflavin derivatives, using a tightly-bound flavin mononucleotide (FMN) cofactor. It has important environmental and clinical implications. Previous studies have focused on elucidating NRs catalytic mechanism and solving its crystal structure. In this dissertation work, we first develop and implement new strategies for labeling NR with stable isotopes, and report a completely re-designed protocol for NRs purification. Then we report the successful assignment of over half of NRs backbone resonances using 3d-NMR methods. The most significant observation is that we find a well-resolved 2d 1H-15N HSQC NMR spectrum is obtained at 37°C for NR, while the HSQC at 4°C is poorly-dispersed and comprised of sharp overlapped peaks. Thus, it would appear that NR denatures at 4°C. However, as we demonstrate, the non-covalently-bound FMN cofactor is not released at the lower temperature, based on retention of the native flavin visible-CD spectrum. Similarly, far-UV CD spectroscopy shows that the protein retains full secondary structural content at 4C. In addition, near-UV CD and Fluorine-19 NMR experiments demonstrate that under completely native conditions (neutral pH, no additives) NR maintains a high degree of tertiary structure and well-defined hydrophobic side-chain packing, ruling out the possibility of a molten-globule state. Thus, our studies report strong evidence that the dramatic low-temperature (low-T) transition near 20°C observed by NMR is not the result of protein structural changes, but rather, we propose that NR exists as an ensemble of rapidly inter-converting structures, at lower temperature, only adopting a well-defined unique structure above 20°C. Both saturation-transfer from water and solvent proton-exchange measurements support our proposed model in which the unique high-T structure is favored entropically, by release of water molecules; on the other hand, the fluxional low-T state incorporates greater water solvation at 4°C. In the latter part of this study, we present preliminary data suggesting that the flexibility implied by easy water-access to the loosely-structured state plays a role in accommodating binding of diverse substrates. Therefore, the fluxional low-T state may be functionally important. A possible direct link between the enzyme dynamics and its catalytic activity will be an area of future investigation.

Nuclear Magnetic Resonance (NMR) Spectroscopy is a crucial tool for determining the structures of biological molecules. This technique can also be used to extract thermodynamic parameters of these molecules, enhancing our understanding of their biological roles. DNA is analyzed through NMR Spectroscopy in order to identify the effect of sequence on expressivity. DNA predominantly resides in BI orientation, but a second conformation, BII, also exists. DNA can switch between BI and BII backbone conformations and the likelihood of this switching is dependent upon the energetic barrier between these two sub-states. The secondary structure of DNA, and thus its adoption of BI and BII conformation, is sequence-dependent. Therefore, the identity and neighboring base pairs of a segment of DNA have a large effect on the flexibility of the backbone. Methylation also affects backbone structure. The methyl group has been shown to promote either stabilization and/or destabilization on proximate bases. This thesis uses variable temperature NMR and Mathematica modeling to determine the backbone conformations, rate of inter-conversion between BI/BII conformations, and the energetic barrier of this fluctuation for each nucleotide step in DNA dodecamers containing the CRE binding sequence. This has been a long-term goal of the Hatcher-Skeers lab, and the data from this thesis would have been added to years of flanked CRE DNA information to reveal any patterns. In this experiment, 5’-TTTC-3’ CRE DNA dodecamers underwent NMR analyses to extract backbone flexibility parameters. Additionally, the effect of methylation was studied in scans with methylated cytosine in the central CRE sequence. The TRX scale was used to predict the BII character of these sequences. Due to technical errors, the experimental results were not able to accurately represent the specific dynamics of each backbone step. However, general trends were identified, such as adherence to and veracity of the TRX scale and the effect of methylation. It was found that the %BII of the native DNA closely resembled the TRX predictions, whilst the methylated sequence did not. The largest changes in activation energy due to methylation occurred in the central CRE sequence, suggesting methylation is a localized effect. The results reflected several trends from past CRE experiments, but the data cannot be explicitly analyzed due to the technical errors.

Con la finalidad de insertar los genes cry3Ca1 y cry7Aa1 en Ipomoea batatas (L.) Lam. cv. “Huachano” para conferir resistencia a Cylas puncticollis y C. brunneus “gorgojos del camote”, se desarrolló la transformación genética mediada por Agrobacterium tumefaciens, siguiendo dos protocolos de regeneración y transformación. Partiendo de 46 meristemos y 282 hojas con peciolo, se obtuvieron 8 eventos transgénicos de inserción completa del ADN - T (4 por cada protocolo de transformación) y un evento de inserción incompleta. Con una eficiencia de transformación de 8.70%, el protocolo a partir de meristemos demostró ser más eficaz en la obtención de eventos transgénicos de inserciones completas que el protocolo a partir de hojas con peciolo, con el cual se obtuvo una eficiencia de transformación de 1.42%. A su vez, los regenerantes fueron evaluados mediante pruebas in vitro (resistencia a kanamicina) y moleculares (PCR), con los análisis de PCR se confirmó que los 8 regenerantes callo positivos (resistentes a la prueba de kanamicina) también presentaron la inserción de los transgenes de interés “cry3Ca1 y cry7Aa1” y del gen marcador selector “nptII”. Asimismo, se determinó que 4 de los eventos transgénicos integraron secuencias externas al ADN - T “backbone” en el genoma de la planta, uno de los cuales, presentó la inserción del gen bacteriano “virD2”.With the purpose of inserting the genes cry3Ca1 and cry7Aa1 in Ipomoea batatas (L.) Lam. cv. "Huachano" to develop resistance to Cylas puncticollis and C. brunneus “sweet potato weevils”, the genetic transformation was developed using Agrobacterium tumefaciens, following two protocols of regeneration and transformation. Starting from 46 meristems and 282 leaves with petiole, 8 transgenic events were obtained with complete insertion of T - DNA (4 for each transformation protocol) and one event with incomplete insertion. With an efficiency of transformation of 8.70 %, the protocol of meristems proved to be more effective in obtaining transgenic events of complete inserts than the protocol of leaves with petiole, which obtained a efficiency of transformation of 1.42 %. The regenerants were evaluated by testing in vitro (resistance to kanamycin) and molecular (PCR), the PCR analysis confirmed that the 8 regenerants positive callus (resistant to kanamycin test) also presented the insertion of transgenes of interest “cry3Ca1 and cry7Aa1” and selection marker gene “nptII”. Likewise, 4 of the transgenic events integrated sequences outside the T - DNA “backbone” into the plant genome, one of whom, showed the insertion of the bacterial gene “virD2”.

As a result of the recent advances in the computation and communications industries, wireless communications-enabled computing devices are ubiquitous nowadays. Even though these devices are introduced to satisfy the user’s mobile computing needs, they are still unable to provide for the full mobile computing functionality as they confine the user mobility to be within certain regions in order to benefit from services provided by fixed network access points. Mobile ad hoc networks (MANETs) are introduced as the technology that potentially will make the nowadays illusion of mobile computing a tangible reality. MANETs are created by the mobile computing devices on an ad hoc basis, without any support or administration provided by a fixed or pre-installed communications infrastructure. Along with their appealing autonomy and fast deployment properties, MANETs exhibit some other properties that make their realization a very challenging task. Topology dynamism and bandwidth limitations of the communication channel adversely affect the performance of routing protocols designed for MANETs, especially with the increase in the number of mobile hosts and/or mobility rates. The Connected Dominating Set (CDS), a.k.a. virtual backbone or Spine, is proposed to facilitate routing, broadcasting, and establishing a dynamic infrastructure for distributed location databases. Minimizing the CDS produces a simpler abstracted topology of the MANET and allows for using shorter routes between any pair of hosts. Since it is NP-complete to find the minimum connected dominating set, MCDS, researchers resorted to approximation algorithms and heuristics to tackle this problem. The literature is rich of many CDS approximation algorithms that compete in terms of CDS size, running time, and signaling overhead. It has been reported that localized CDS creation algorithms are the fastest and the lightest in terms of signaling overhead among all other techniques. Examples of these localized CDS algorithms are Wu and Li algorithm and its Stojmenovic variant, the MPR algorithm, and Alzoubi algorithm. The designers of each of these algorithms claim that their algorithm exhibits the highest degree of localization and hence incurs the lowest cost in the CDS creation phase. However, these claims are not supported by any physical or at least simulation-based evidence. Moreover, the cost of maintaining the CDS (in terms of the change in CDS size, running time, and signaling overhead), in the presence of unpredictable and frequent topology changes, is an important factor that has to be taken into account -a cost that is overlooked most of the time. A simulation-based comparative study between the performance of these algorithms will be conducted using the ns2 network simulator. This study will focus on the total costs incurred by these algorithms in terms of CDS size, running time, and signaling overhead generated during the CDS creation and maintenance phases. Moreover, the effects of mobility rates, network size, and mobility models on the performance of each algorithm will be investigated. Conclusions regarding the pros and cons of each algorithm will be drawn, and directions for future research work will be recommended.

As a result of the recent advances in the computation and communications industries, wireless communications-enabled computing devices are ubiquitous nowadays. Even though these devices are introduced to satisfy the user’s mobile computing needs, they are still unable to provide for the full mobile computing functionality as they confine the user mobility to be within certain regions in order to benefit from services provided by fixed network access points. Mobile ad hoc networks (MANETs) are introduced as the technology that potentially will make the nowadays illusion of mobile computing a tangible reality. MANETs are created by the mobile computing devices on an ad hoc basis, without any support or administration provided by a fixed or pre-installed communications infrastructure. Along with their appealing autonomy and fast deployment properties, MANETs exhibit some other properties that make their realization a very challenging task. Topology dynamism and bandwidth limitations of the communication channel adversely affect the performance of routing protocols designed for MANETs, especially with the increase in the number of mobile hosts and/or mobility rates. The Connected Dominating Set (CDS), a.k.a. virtual backbone or Spine, is proposed to facilitate routing, broadcasting, and establishing a dynamic infrastructure for distributed location databases. Minimizing the CDS produces a simpler abstracted topology of the MANET and allows for using shorter routes between any pair of hosts. Since it is NP-complete to find the minimum connected dominating set, MCDS, researchers resorted to approximation algorithms and heuristics to tackle this problem. The literature is rich of many CDS approximation algorithms that compete in terms of CDS size, running time, and signaling overhead. It has been reported that localized CDS creation algorithms are the fastest and the lightest in terms of signaling overhead among all other techniques. Examples of these localized CDS algorithms are Wu and Li algorithm and its Stojmenovic variant, the MPR algorithm, and Alzoubi algorithm. The designers of each of these algorithms claim that their algorithm exhibits the highest degree of localization and hence incurs the lowest cost in the CDS creation phase. However, these claims are not supported by any physical or at least simulation-based evidence. Moreover, the cost of maintaining the CDS (in terms of the change in CDS size, running time, and signaling overhead), in the presence of unpredictable and frequent topology changes, is an important factor that has to be taken into account -a cost that is overlooked most of the time. A simulation-based comparative study between the performance of these algorithms will be conducted using the ns2 network simulator. This study will focus on the total costs incurred by these algorithms in terms of CDS size, running time, and signaling overhead generated during the CDS creation and maintenance phases. Moreover, the effects of mobility rates, network size, and mobility models on the performance of each algorithm will be investigated. Conclusions regarding the pros and cons of each algorithm will be drawn, and directions for future research work will be recommended.

RNA backbone is biologically important with many roles in reactions and interactions, but has historically been a challenge in structural determination. It has many atoms and torsions to place, and often there is less data on it than one might wish. This problem leads to both random and systematic error, producing noise in an already high-dimensional and complex distribution to further complicate data-driven analysis. With the advent of the ribosomal subunit structures published in 2000, large RNA structures at good resolution, it became possible to apply the Richardson laboratory's quality-filtering, visualization, and analysis techniques to RNA and develop new tools for RNA as well. A first set of 42 RNA backbone rotamers was identified, developed, and published in 2003; it has since been thoroughly overhauled in conjunction with the backbone group of the RNA Ontology Consortium to combine the strengths of different approaches, incorporate new data, and produce a consensus set of 46 conformers. Meanwhile, extensive work has taken place on developing validation and remodeling tools to correct and improve existing structures as well as to assist in initial fitting. The use of base-phosphate perpendicular distances to identify sugar pucker has proven very useful in both hand-refitting and the semi-automated process of using RNABC (RNA Backbone Correction), a program developed in conjunction with Dr. Jack Snoeyink's laboratory. The guanine riboswitch structure ur0039/1U8D, by Dr. Rob Batey's laboratory, has been collaboratively refit and rerefined as a successful test case of the utility of these tools and techniques. Their testing and development will continue, and they are expected to help to improve RNA structure determination in both ease and quality. / Dissertation