No description available.

Currently, the design model for flexural rupture of an eccentrically loaded bracket plate is based on the material tensile rupture strength times the net elastic section modulus. Different bolt and plate sizes were tested to determine if this model is correct. It was found that the current model is conservative and that the material tensile rupture strength times the net plastic section modulus is a superior design model. Also, limited finite element modeling was performed to predict the elastic stiffness of such connections. The resulting data correlates well with test results, and confirms that most of the connection ductility comes from bolt plowing. These results can be used for splice plate connections in cantilever construction, as well. / Master of Science

Dermicidina (DCD) é um gene mapeado no cromossomo 12, lócus 12q13.1, e codifica uma proteína de 110 aminoácidos, que sofre um processamento proteolítico, gerando peptídeos ativos. O peptídeo C-terminal (DCD-1L) de 48 aminoácidos tem uma carga -2, e exerce função antibacteriana e antifúngica, e o peptídeo C-terminal splice variante, denominado DCD-SV de 59 aminoácidos, tem carga neutra, e suas propriedades ainda não foram estabelecidas. Neste trabalho são apresentados os resultados da expressão, purificação e sequenciamento da DCD nativa produzida em E. coli BL21 transformada com o vetor pAE-DCD. Na segunda parte são descritas as análises físico-químicas e bioquímicas da interação dos peptídeos sintéticos DCD-1L e DCD-SV com vesículas lipídicas gigantes e vesículas unilamelar grandes sintetizadas com palmitoil-oleoil-fosfatidilcolina. As preferenciais estruturais dos peptídeos foram investigadas por espectroscopia de Dicroísmo Circular. Nossos resultados sugerem que a DCD-SV tem alta propensão para adotar uma estrutura helicoidal permitindo sua inserção e oligomerização em membranas biomiméticas, e possível formação de canais de condutância molecular. / Dermicidin (DCD) is mapped a gene on chromosome 12, locus 12q1.13 whose 110 amino acids protein is proteolytically processed to N and C-terminal peptides. The 48-amino acid C-terminal peptide (DCD-1L) has -2 net charges and display antibacterial and antifungal properties and the 59-amino acid splice variant C-terminal peptide (DCD-SV) has neutral net charge; however, its structure and biological function are unknown. Here we show the results of expression, purification and amino acid sequencing of recombinant DCD protein produced in E.coli transformed with pAE-DCD vector. We also describe the results of physical-chemical and biochemical analyses showing the visible differences between the interactions of DCD-1LL and DCD-SV synthetic peptides with giant unilamellar vesicles and large unilamellar vesciles made of palmitoyl-oleoyl phosphatidylcholine, used as biomimetic membranes. The structural preferences of peptides were analyzed by circular dichroism spectroscopy. Our results suggest that DCD-SV peptide has higher propensity to adopt helicoidal structure enabling it to insert into mimetic membranes, undergo oligomerization and formation of conductance channel.

Dermicidina (DCD) é um gene mapeado no cromossomo 12, lócus 12q13.1, e codifica uma proteína de 110 aminoácidos, que sofre um processamento proteolítico, gerando peptídeos ativos. O peptídeo C-terminal (DCD-1L) de 48 aminoácidos tem uma carga -2, e exerce função antibacteriana e antifúngica, e o peptídeo C-terminal splice variante, denominado DCD-SV de 59 aminoácidos, tem carga neutra, e suas propriedades ainda não foram estabelecidas. Neste trabalho são apresentados os resultados da expressão, purificação e sequenciamento da DCD nativa produzida em E. coli BL21 transformada com o vetor pAE-DCD. Na segunda parte são descritas as análises físico-químicas e bioquímicas da interação dos peptídeos sintéticos DCD-1L e DCD-SV com vesículas lipídicas gigantes e vesículas unilamelar grandes sintetizadas com palmitoil-oleoil-fosfatidilcolina. As preferenciais estruturais dos peptídeos foram investigadas por espectroscopia de Dicroísmo Circular. Nossos resultados sugerem que a DCD-SV tem alta propensão para adotar uma estrutura helicoidal permitindo sua inserção e oligomerização em membranas biomiméticas, e possível formação de canais de condutância molecular. / Dermicidin (DCD) is mapped a gene on chromosome 12, locus 12q1.13 whose 110 amino acids protein is proteolytically processed to N and C-terminal peptides. The 48-amino acid C-terminal peptide (DCD-1L) has -2 net charges and display antibacterial and antifungal properties and the 59-amino acid splice variant C-terminal peptide (DCD-SV) has neutral net charge; however, its structure and biological function are unknown. Here we show the results of expression, purification and amino acid sequencing of recombinant DCD protein produced in E.coli transformed with pAE-DCD vector. We also describe the results of physical-chemical and biochemical analyses showing the visible differences between the interactions of DCD-1LL and DCD-SV synthetic peptides with giant unilamellar vesicles and large unilamellar vesciles made of palmitoyl-oleoyl phosphatidylcholine, used as biomimetic membranes. The structural preferences of peptides were analyzed by circular dichroism spectroscopy. Our results suggest that DCD-SV peptide has higher propensity to adopt helicoidal structure enabling it to insert into mimetic membranes, undergo oligomerization and formation of conductance channel.

<p>Past earthquake damage assessments have shown the seismic vulnerability of older non-ductile reinforced concrete buildings. The life safety-risk these buildings pose has motivated researchers to study, develop, and improve modeling techniques to better simulate their behavior with the aim to prioritize retrofits.</p><p><br></p> <p>This study focuses on the lap splice detailing at the base of the building in columns, shorter than those recommended by modern codes which consider seismic effects. Current modeling efforts in non-ductile reinforced concrete frame structures have considered the connection at the foundation fixed. This study models the influence of the performance of short lap splices on the simulation of response of an instrumented perimeter-frame-non-ductile building located in Van Nuys, California, and to compare results with those of previous studies of the same building.</p><p><br></p> <p>The methodology consisted of evaluating the response of a non-ductile concrete building subjected to a suite of ground motions through the comparison of three base connections: fixed, pinned, and a rotational spring modeling the short lap splice. Comparison and performance evaluation are done on the basis of drift as the main performance metric. In the building response evaluation flexure and shear forces in frame elements were also compared using the different base conditions. </p><p><br></p> <p>The models consist of two-dimensional frames in orthogonal direction, including interior and exterior frames, totaling into 4 frames. The dynamic analysis was performed using SAP2000 analysis software. The proposed rotational spring at the base was defined using the Harajli & Mabsout (2002) bond stress – slip relationship and moment – curvature sectional analysis, applied to 24d_b and 36d_b lap splices. Deformation considered flexure and slip. Adequacy of shear strength was checked prior to the analysis to verify that shear failure did not occur prior to either reaching first yield of the column reinforcement or splice capacity. </p><p><br></p> In this study, the response of the frames using the proposed rotational spring model was found to be between the fixed and pinned base conditions with regard to roof displacement and interstory drift ratio, also termed as story drift ratio. The behavior of the frames changed depending on the yielding of the longitudinal reinforcement, as depicted by the interstory drift ratio and displacement. The performance of the building frames also depended on the ground motion. The N-S and E-W direction frame computational models considered three and four earthquakes, respectively, totaling to 14 computational models per base condition. Three computational models out of the 14 with the proposed rotational spring base condition simulated recorded roof displacement results with accuracy. In the frame simulations where yielding of most of the column longitudinal bars was not calculated, the maximum interstory drift occurred in the upper stories, matching column damage observations during the event. The findings of the study showed that short lap splice increases the drift and displacement compared to the fixed base supporting its effect, i.e. the behavior of a non-ductile reinforced concrete case study building to an earthquake.

No description available.

Master of Science / Department of Computing and Information Sciences / Doina Caragea / Several computational biology and bioinformatics problems involve DNA sequence classification using supervised machine learning algorithms. The performance of these algorithms is largely dependent on the availability of labeled data and the approach used to represent DNA sequences as {\it feature vectors}. For many organisms, the labeled DNA data is scarce, while the unlabeled data is easily available. However, for a small number of well-studied model organisms, large amounts of labeled data are available. This calls for {\it domain adaptation} approaches, which can transfer knowledge from a {\it source} domain, for which labeled data is available, to a {\it target} domain, for which large amounts of unlabeled data are available. Intuitively, one approach to domain adaptation can be obtained by extracting and representing the features that the source domain and the target domain sequences share. \emph{Latent Dirichlet Allocation} (LDA) is an unsupervised dimensionality reduction technique that has been successfully used to generate features for sequence data such as text. In this work, we explore the use of LDA for generating predictive DNA sequence features, that can be used in both supervised and domain adaptation frameworks. More precisely, we propose two dimensionality reduction approaches, LDA Words (LDAW) and LDA Distribution (LDAD) for DNA sequences. LDA is a probabilistic model, which is generative in nature, and is used to model collections of discrete data such as document collections. For our problem, a sequence is considered to be a ``document" and k-mers obtained from a sequence are ``document words". We use LDA to model our sequence collection. Given the LDA model, each document can be represented as a distribution over topics (where a topic can be seen as a distribution over k-mers). In the LDAW method, we use the top k-mers in each topic as our features (i.e., k-mers with the highest probability); while in the LDAD method, we use the topic distribution to represent a document as a feature vector. We study LDA-based dimensionality reduction approaches for both supervised DNA sequence classification, as well as domain adaptation approaches. We apply the proposed approaches on the splice site predication problem, which is an important DNA sequence classification problem in the context of genome annotation. In the supervised learning framework, we study the effectiveness of LDAW and LDAD methods by comparing them with a traditional dimensionality reduction technique based on the information gain criterion. In the domain adaptation framework, we study the effect of increasing the evolutionary distances between the source and target organisms, and the effect of using different weights when combining labeled data from the source domain and with labeled data from the target domain. Experimental results show that LDA-based features can be successfully used to perform dimensionality reduction and domain adaptation for DNA sequence classification problems.

Group I introns are catalytic RNAs with the ability to splice out of RNA transcripts, often without the aid of proteins. These self-splicing introns have been reengineered to create ribozymes with the ability to catalyze reactions. One such ribozyme, derived from a Pneumocystis carinii group I intron, has been engineered to sequence specifically remove a targeted segment from within an RNA substrate, which is called the trans excision-splicing reaction.The two catalytic steps of the trans excision-splicing reaction occur at positions on the substrate known as the 5' and 3' splice sites. Strict sequence requirements at these sites could potentially limit the target choices for the trans excision-splicing ribozyme, so the sixteen possible base pair combinations at the 5' splice site and the four possible nucleotides at the 3' splice site were tested for reactivity. All base pair combinations at the 5' splice site allow the first reaction step (5' hydrolysis) to occur and several combinations allow the second step to occur, resulting in trans excision-splicing product formation. Moreover, we found that non-Watson-Crick base pairs are important for 5' splice site recognition and prevent product degradation via hydrolysis at other sequence positions. The sequence requirement at the 3' splice site is absolute, as guanosine alone produced complete product.To date, the experiments with the trans excision-splicing ribozyme have been conducted in vitro. The further development of this ribozyme as a biochemical tool and as a potential therapeutic agent requires in vivo reactivity. Thus, a prokaryotic system was designed and tested to assess the catalytic potential of the trans excision-splicing ribozyme. We show that the ribozyme successfully excised a single, targeted nucleotide from a mutated green fluorescent protein transcript in Escherichia coli. On average, 12% correction was observed as measured by fluorescence and approximately 1.2% correction was confirmed through sequence analysis of isolated transcripts.We have used these studies to further characterize trans excision-splicing ribozymes in vitro and to pave the way for future development of this ribozymereaction in vivo. These results increase our understanding of this ribozyme and advance this reaction as a biochemical tool with potential therapeutic applications.

As traffic demand on bridges increases, loading cycles on critical components will increase, reducing their service life. Modular bridge expansion joints, which are imperative to allowing the bridge superstructure to move, are susceptible to fatigue damage at their field splice. These splices are used to connect segments of the total joint, during staged construction. Current splice designs are either bolted or welded connections, which allow stress concentrations to induce pre-mature fatigue failure. This thesis examines the use of a hybrid FRP/steel design under fatigue loading for use as a splice detail. The splice detail consists of steel plates bolted to steel beam webs and CFRP pultruded plates adhesively bonded to the underside of the steel beam flanges. Two different moduli of CFRP were examined: Normal Modulus and Ultra High Modulus. Two beams of each modulus were tested under static conditions and six under constant amplitude fatigue loading. A testing rig was used to simulate similar bending moments experienced in bridge joints. In the static tests, slippage of the web plates caused considerable stiffness loss and the slippage load varied drastically between CFRP moduli. For the fatigue tests, the intention was to reach two million cycles at the different constant load ranges. Stiffness degradation was noticed during the fatigue process, and was likely due to bolt pre-tension loss and/or plastic deformation of the adhesive. Specimens that reached two million cycles were monotonically loaded to failure. Once the CFRP had failed, a secondary mechanism was observed for reserve load capacity. Simple beam mechanics were used to create prediction models for the initial spliced beam stiffness and peak CFRP load. Flexural and shear deformations of the spliced system were considered for beam stiffness. For the CFRP failure load prediction, a design peak strain in the CFRP was used to account for shear lag effects in the material and variability of the splice detail. While the model was inaccurate for beam stiffness, it provided a good approximate of the peak CFRP load. Based on the presented test data, the Normal Modulus CFRP hybrid splice detail showed better fatigue performance than conventional steel connection details. / Thesis (Master, Civil Engineering) -- Queen's University, 2013-07-24 11:28:19.728

Doctor of Philosophy / Department of Computing and Information Sciences / Doina Caragea / The large volume of data generated in the recent years has created opportunities for discoveries in various fields. In biology, next generation sequencing technologies determine faster and cheaper the exact order of nucleotides present within a DNA or RNA fragment. This large volume of data requires the use of automated tools to extract information and generate knowledge. Machine learning classification algorithms provide an automated means to annotate data but require some of these data to be manually labeled by human experts, a process that is costly and time consuming. An alternative to labeling data is to use existing labeled data from a related domain, the source domain, if any such data is available, to train a classifier for the domain of interest, the target domain. However, the classification accuracy usually decreases for the domain of interest as the distance between the source and target domains increases. Another alternative is to label some data and complement it with abundant unlabeled data from the same domain, and train a semi-supervised classifier, although the unlabeled data can mislead such classifier. In this work another alternative is considered, domain adaptation, in which the goal is to train an accurate classifier for a domain with limited labeled data and abundant unlabeled data, the target domain, by leveraging labeled data from a related domain, the source domain. Several domain adaptation classifiers are proposed, derived from a supervised discriminative classifier (logistic regression) or a supervised generative classifier (naïve Bayes), and some of the factors that influence their accuracy are studied: features, data used from the source domain, how to incorporate the unlabeled data, and how to combine all available data. The proposed approaches were evaluated on two biological problems -- protein localization and ab initio splice site prediction. The former is motivated by the fact that predicting where a protein is localized provides an indication for its function, whereas the latter is an essential step in gene prediction.