DNA-binding proteins play an important role in various essential biological processes such as DNA replication, recombination, repair, gene transcription, and expression. The identification of DNA-binding proteins and the residues involved in the contacts is important for understanding the DNA-binding mechanism in proteins. Moreover, it has been reported in the literature that the mutations of some DNA-binding residues on proteins are associated with some diseases. The identification of these proteins and their binding mechanism generally require experimental techniques, which makes large scale study extremely difficult. Thus, the prediction of DNA-binding proteins and their binding sites from sequences alone is one of the most challenging problems in the field of genome annotation. Since the start of the human genome project, many attempts have been made to solve the problem with different approaches, but the accuracy of these methods is still not suitable to do large scale annotation of proteins. Rather than relying solely on the existing machine learning techniques, I sought to combine those using novel “stacking technique” and used the problem-specific architectures to solve the problem with better accuracy than the existing methods. This thesis presents a possible solution to the DNA-binding proteins prediction problem which performs better than the state-of-the-art approaches.

Identification and annotation of RNA Binding Proteins (RBPs) and RNA Binding residues from sequence information alone is one of the most challenging problems in computational biology. RBPs play crucial roles in several fundamental biological functions including transcriptional regulation of RNAs and RNA metabolism splicing. Existing experimental techniques are time-consuming and costly. Thus, efficient computational identification of RBPs directly from the sequence can be useful to annotate RBP and assist the experimental design. Here, we introduce AIRBP, a computational sequence-based method, which utilizes features extracted from evolutionary information, physiochemical properties, and disordered properties to train a machine learning method designed using stacking, an advanced machine learning technique, for effective prediction of RBPs. Furthermore, it makes use of efficient machine learning algorithms like Support Vector Machine, Logistic Regression, K-Nearest Neighbor and XGBoost (Extreme Gradient Boosting Algorithm). In this research work, we also propose another predictor for efficient annotation of RBP residues. This RBP residue predictor also uses stacking and evolutionary algorithms for efficient annotation of RBPs and RNA Binding residue. The RNA-binding residue predictor also utilizes various evolutionary, physicochemical and disordered properties to train a robust model. This thesis presents a possible solution to the RBP and RNA binding residue prediction problem through two independent predictors, both of which outperform existing state-of-the-art approaches.

A k-majority tournament is a directed graph that models a k-majority voting scenario, which is realized by 2k - 1 rankings, called linear orderings, of the vertices in the tournament. Every k-majority voting scenario can be modeled by a tournament, but not every tournament is a model for a k-majority voting scenario. In this thesis we show that all acyclic tournaments can be realized as 2-majority tournaments. Further, we develop methods to realize certain quadratic residue tournaments as k-majority tournaments. Thus, each tournament within these classes of tournaments is a model for a k-majority voting scenario. We also explore important structures specifically pertaining to 2- and 3-majority tournaments and introduce the idea of pseudo-3-majority tournaments and inherited 2-majority tournaments.

The use of mortar and pestles has long been associated with acorn processing in California. Based on ethnographic and archaeological evidence, groundstone was used to process a multitude of resources, including small mammals. Twenty groundstone artifacts recovered from the Rock Camp Site in the San Bernardino Mountains were analyzed for protein residues using the crossover immunological electrophoresis (CIEP) method. Using previously obtained data from the Summit Valley, a comparative analysis was done to determine if processing small mammals on groundstone was a common occurrence throughout the San Bernardino Mountain region.

This thesis is a pilot study, designed to test and develop methods suitable for the study of Scandinavian flint spearhead functionality. The functionality of projectile and lithic point armament has not been studied for almost 30 years in Scandinavia. Meanwhile, methods used to analyse lithic projectiles have developed considerably. However, few of these methods are precise enough to be used in conjunction with Scandinavian stone technological analyses that emphasize the societal aspect of lithic points. Consequently, two methods were chosen that could provide data for Scandinavian research issues: 3D-scanning/continuum mechanical simulations and organic residue analysis. The methods were tested on 6 experimental spearheads. The continuum mechanical simulation generated both visual and numerical data that could be used to create precise functional-morphological descriptions. The data could also potentially be used for projectile point classification. The organic residue analysis revealed promising results for the use of an artefact and activity specific analysis, with a sequential extraction protocol. In unison, the results from both analyses could be used to reveal how spearheads were functionally designed and used in Stone Age Scandinavia, even though there are methodological and technological issues that need solving.

[pt] Nesta dissertação apresenta-se o estudo de viabilidade de incorporação de lodo proveniente de processos de clarificação de estações de tratamento de água, na produção de cerâmica vermelha; resíduo que atualmente é disposto indiscriminadamente em um manancial de captação, contribuindo para a alteração da qualidade das águas. Entende-se que a busca de uma solução viável para a destinação adequada deste resíduo, traga ganhos ambientais com baixos custos operacionais; sendo este o objetivo principal deste estudo. A relevância do assunto está na implantação de um sistema de gestão que proporcione a destinação adequada do resíduo e sua viabilização como insumo para a produção de cerâmica vermelha. Para tal, optou-se por fazer ensaios de caracterização da argila, do resíduo gerado em estações de tratamento de água e, por fim, estudou-se a incorporação a 40%, 50% e 60% do referido resíduo à argila, resultando em um produto cerâmico do qual foram estudadas as características físico-químicas e mecânicas. Os resultados alcançados indicaram a possibilidade de aproveitamento do resíduo, sendo necessário, para a adoção desta técnica, que sejam estabelecidos parâmetros de controle no processo produtivo de cerâmica vermelha. / [en] The Msc thesis, presents a viability study of incorporation the mud generated in the clarification step treatment plants (WTP), for the production of red ceramic. This residue that currently is disposed indiscriminately in the rivers, contributes to degradation of the quality of waters. In view of that, the search of a viable solution for the appropriate destination of this residue should bring environmental benefits with low operational costs, being this the main objective of this study. The relevance of the subject is in the implantation of a management system that provides the appropriate destination of the residue in subject and your viability as raw-material for industrial production. In order to pursue that, physical-chemical and mechanical characterization of the clay used for the manufacturing of red ceramic, as well as of the WTP mud and 40%, 50% and 60% mixtures of the mud into the clay - which resulted in ceramic test samples, were carried out. The results obtained indicated the possibility of incorporating of the residue into the clay, provided specific conditions for red ceramic production are implemented.

The desire of the minerals industry to be more sustainable has led towards the increasing development of by-products. One such industry is the production of Alumina. The Alumina industry in Australia is the major producer of alumina in the western world with over 25 million tonnes of Bauxite Residue per annum. Alcoa World Alumina (Alcoa) has three refineries in Western Australia producing approximately 20,000 tonnes of Mud and a similar level of Red Sand each day. These as yet unutilised potential resources are being stockpiled, occupying a significant footprint. It is widely recognised within industry that there would be economic, environment and social benefits if a sustainable use for these materials were found. One such potential by-product is the production of coarse bauxite residue (Red Sand), neutralised and washed low in salt. The main purpose of this research was to establish a potential market for this material, through scientific evaluation of Red Sand as a replacement of natural fine aggregate (Natural Yellow Sand) in concrete mixes. For this research, the mixed stream of Bauxite Residue (fine and coarse) obtained in the Bayer process was neutralized by a process of carbonation then washed using cyclones and counter current wash towers to a value added byproduct. The coarse particles (Washed and Carbonated Sand-WCS) of the stream were separated by Wet High Intensity Magnetic Separation technique (WHIMS) so that different segments such as High Iron Sand (HIS) and Low Iron Sand (LIS) were formed. Physical, chemical and mineralogical properties of these materials have been tested and compared with that of natural sand. Several mixes of concrete were then designed using Red Sand as a fine aggregate in order to verify their effects on strength and durability indicators of concrete. / The comparative analysis between normal mix proportions and the mix proportions utilizing Red Sand was also achieved. In addition, the impact of marine environment on concrete mix design and properties of manufactured concrete were evaluated with a series of standard laboratory tests. The findings were promising in terms of both mechanical properties and durability and suggested that Red Sand, in particular Low Iron Sand is likely to be effective in place of fine aggregates and can be used within marine grade concrete with no major differences when compared to normal concrete. From the results obtained, it can be deduced that this material can be used in a wide range of concrete applications in Civil Engineering and Construction.

Bibliography: leaves 105-129.

<p>ABSTRACT</p><p>Anaerobic digestion is one way of handling biowaste and generating energy in the form of methane, biogas.</p><p>This study shows that spore forming bacterias survive the process of pasteurisation and anaerobic digestion in biogas plants. It has also been established that both the nonpasteurised-and digestion- waste contains pathogen spore forming bacterias. Two Swedish full-scale</p><p>commercial biogas plants were sampled before pasteurisation, after pasteurisation and after digestion on 10 occasions with one week intervals. The samples were analysed quantitatively</p><p>and qualitatively, with biochemical methods, for Clostridium spp and Bacillus spp.</p><p>Polymerase Chain Reaction, a biomolecular method, was used for</p><p>C. chauvei analysis, with C. chauvei specific primers. For this analyse the biogas plants were sampled at 11 occasions.</p><p>Survival of pathogenic spore forming bacteria in digestion residue may be a health risk for both humans and animals. The digested residue may be used as fertiliser on arable land and the risk of contamination by pathogenic Clostridium spp and Bacillus spp is hard to assess, but can not be neglected.</p>

Pannexins are vertebrate proteins with limited sequence homology to the invertebrate gap junction proteins, the innexins. However, in contrast to innexins and the vertebrate connexins, pannexins do not form gap junction channels. Instead they appear to solely function as unpaired membrane channels allowing the flux of molecules, including ATP, across the plasma membrane. We provided additional evidence for their ATP release function by demonstrating that the connexin mimetic peptides, which were thought to inhibit ATP release through connexin channels, do not inhibit their host connexin channels but instead inhibit pannexin1 channels by a mechanism of steric block. Therefore, the inhibitory effects of mimetic peptides on ATP release may represent supporting evidence for a role of pannexin1 in ATP release. We also analyzed the pore structure of pannexin1 channels with the Substituted Cysteine Accessibility Method. The thiol reagents MBB and MTSET reacted with several positions in the external portion of the first transmembrane segment and the first extracellular loop. In addition, MTSET reactivity was found in the internal portion of TM3. These data suggest that portions of TM1, E1 and TM3 line the pore of pannexin1 channels. Thus, the pore structure of pannexin1 is similar to that of connexin channels.