Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

Abstract This thesis examines the postural effects of Alexander Technique training on a classical singer. The aim was to see how working with an Alexander Technique instructor would improve my singing. I have been taking lessons in Alexander technique on a weekly basis and practicing Alexander technique for approximately an hour each day. I have conducted an interview with singer and longtime Alexander technique practitioner, Anne Cecilie Røsjø Kvammen. I have talked to my physiotherapist, Carl Colliander, about pain linked to a tight psoas muscle. Four songs were memorized and recorded two times, once in December and once in April. The recordings were analyzed, first by me and then by Barbro Olsson, Alexander technique instructor. I found that my alignment has generally improved and, as a result, my head position has become more stable. I have become better at managing stress during performances. The enhanced awareness of alignment has helped me make more successful choices in the practice rooms. It also has made me better at interpreting my singing pedagogue’s instructions during lessons. Additionally I have less pain, especially in the neck area.

No description available.

The purpose of this study was to identify whether firms that implement and develop core competencies perform significantly better than firms that do not. A model of core competency implementation and development in restaurant firms was developed and tested in three casual dining restaurant firms. The amount of co-alignment in the core competency process was compared to financial performance. Results indicated that firms that had a greater amount of alignment performed better. The highest performance was evidenced in the firm that not only had internal alignment but that appeared to have competencies that are also critical to success in the restaurant industry. / Ph. D.

One of the keys for restaurant managers in conducting a proper assessment of their business opportunities is through understanding the level of risk these opportunities bear. This can be achieved by analyzing the causal relationships between external environmental forces and internal capabilities of the firm, and then make a strategic choice in what opportunities to invest. The purpose of this study was to investigate the concept of risk and its underlying dimensions that influence the restaurant industry's cash flows and stock returns. This study proposed a contemporary framework that enables restaurant industry executives to develop a better understanding of the risk factors (macroeconomic and industry) that influence their firms' cash flows and stock returns. The primary unit of analysis was at industry (portfolio) level. In addition, as a second step, three restaurant firms were selected to demonstrate the practical application of the model. Exploratory factor analysis indicated that the restaurant industry risk is represented by three dimensions: "Output," "PPI Meats," and "IP Restaurants." The macroeconomic risk construct was represented by the five variables of Arbitrage Pricing Theory of Chen et al. (1986). Time series-analysis regression of the portfolio of 75 restaurant firms, for the 1993-2004 period, revealed that macroeconomic variables explained a significant portion of restaurant stock returns. On the other hand, both macroeconomic and industry models explained a significant level of variation in operating cash flows. The addition of September 11 "dummy" variable improved the explained variation in stock returns for both equations (macroeconomic and industry). At a firm level, the industry model accounted for a significant variation in internal value drivers (operating cash flows, food cost, and labor cost) for all three restaurant companies. The industry risk model survived after controlling for the effect of macroeconomic variables on operating cash flows. The results indicate that the industry model provides a parsimonious solution in estimating variation in operating cash flows by capturing macroeconomic effects. / Ph. D.

The purpose of this study was to investigate the concepts of remote and task risks in relation to the structure of the casual theme restaurant industry, and to examine the performance consequences of their relationships. This study proposed a framework of analysis that will enable industry participants to develop an improved understanding of the relationships among environmental risk drivers, and of the influence of their strategic decisions on the environment-performance connection. Specifically, it was proposed that task risk factors could be identified, and that they would mediate the influence that some identifiable remote risk factors would have on the performance of the industry. It was also expected that this mediated relationship would be moderated by the influence of the structure of industry. The primary unit of analysis was at the industry sector level as the performance construct was operationalized using a portfolio of 24 casual theme restaurant firms. Exploratory factor analysis was used to identify the remote and task risk factors. The analysis suggested that three remote factors and three task factors represent the two environmental constructs: "Interest rates", "Expectations" and "Exchange rates" for the remote environment, and "Input quantities", "Input restaurant" and "Input prices" for the task environment. A number of time-series regression analyses were subsequently conducted for the 1993-2006 period to investigate the various proposed relationships. The results indicated that a number of significant direct effects of the remote and task risk factors on the cash flow returns on invested capital of the industry portfolio existed. Also, a significant mediated relationship was found: the "Input prices" mediated the influence of the "Expectations" on changes in the cash flow returns on invested capital. However, and despite numerous significant direct effects between the industry structure variables and the performance variables, no moderation could be established. The present study paved the way for future research on the relationships between the remote and task environment and the performance of firms. In particular, further research should be conducted that delves into the role of the cyclical nature of environmental risk factors. Besides, additional investigations of the influence of the structure of the industry should be conducted by attempting to compare more contrasted states of the industry. / Ph. D.

To manufacture better cameras at lower costs is of great interest to the surveillance industry. Inthe process of manufacturing cameras, the mounting of the optics and the digital image sensor, isa crucial part of producing a high quality image. For high resolution cameras, mechanical passivealignment of the optics and image sensor is insufficient for producing a picture of adequate quality.This is caused by inherit problems from manufacturing, resulting in performance issues for theparts. For the lens, these performance issues causes the light path to deviate and the focal pointto be off center. In the same way, manufacturing of the image sensor causes similar problems.These problems results in an image of subpar quality, if the interface solely relies on mechanicalpassive alignment. To compensate for these problems a computer aided machine is used to alignthe lens and the image sensor. The lens and the sensor, are placed in the machine, aligned forbest possible image quality and fixated in its place. This fixation is done with UV light curedadhesive. The process is drawn with some issues, the curing of the adhesive causes unpredictableshrinkage that affects the image quality. In addition, contaminations such as dust or dirt on theparts, are impossible to remove once the fixation is complete, causing blemishes on the images.These faults results in scrapping of expensive parts, which is costly for the manufacturer. Thisthesis aims to find alternative mounting solutions to the parts, that result in less scrapping ofexpensive components, without sacrificing image quality. The result is two concepts that can beused as inspiration for future improvement of surveillance camera manufacturing. A new adhesiveinterface, that can reduce, manufacturing cost and the unreliable shrinkage of the adhesive, as wellas a new mechanical coupling that allows reassembly after cleaning, is presented.iii

Semantically-enabled applications, such as ontology-based search and data integration, take into account the semantics of the input data in their algorithms. Such applications often use ontologies, which model the application domains in question, as well as alignments, which provide information about the relationships between the terms in the different ontologies. The quality and reliability of the results of such applications depend directly on the correctness and completeness of the ontologies and alignments they utilize. Traditionally, ontology debugging discovers defects in ontologies and alignments and provides means for improving their correctness and completeness, while ontology alignment establishes the relationships between the terms in the different ontologies, thus addressing completeness of alignments. This thesis focuses on the integration of ontology alignment and debugging for taxonomy networks which are formed by taxonomies, the most widely used kind of ontologies, connected through alignments. The contributions of this thesis include the following. To the best of our knowledge, we have developed the first approach and framework that integrate ontology alignment and debugging, and allow debugging of modelling defects both in the structure of the taxonomies as well as in their alignments. As debugging modelling defects requires domain knowledge, we have developed algorithms that employ the domain knowledge intrinsic to the network to detect and repair modelling defects. Further, a system has been implemented and several experiments with real-world ontologies have been performed in order to demonstrate the advantages of our integrated ontology alignment and debugging approach. For instance, in one of the experiments with the well-known ontologies and alignment from the Anatomy track in Ontology Alignment Evaluation Initiative 2010, 203 modelling defects (concerning incomplete and incorrect information) were discovered and repaired.

Indiana University-Purdue University Indianapolis (IUPUI) / Proteoforms are distinct protein molecule forms created by variations in genes, gene expression, and other biological processes. Many proteoforms contain multiple primary structural alterations, including amino acid substitutions, terminal truncations, and posttranslational modifications. These primary structural alterations play a crucial role in determining protein functions: proteoforms from the same protein with different alterations may exhibit different functional behaviors. Because top-down mass spectrometry directly analyzes intact proteoforms and provides complete sequence information of proteoforms, it has become the method of choice for the identification of complex proteoforms. Although instruments and experimental protocols for top-down mass spectrometry have been advancing rapidly in the past several years, many computational problems in this area remain unsolved, and the development of software tools for analyzing such data is still at its very early stage. In this dissertation, we propose several novel algorithms for challenging computational problems in proteoform identification by top-down mass spectrometry. First, we present two approximate spectrum-based protein sequence filtering algorithms that quickly find a small number of candidate proteins from a large proteome database for a query mass spectrum. Second, we describe mass graph-based alignment algorithms that efficiently identify proteoforms with variable post-translational modifications and/or terminal truncations. Third, we propose a Markov chain Monte Carlo method for estimating the statistical signi ficance of identified proteoform spectrum matches. They are the first efficient algorithms that take into account three types of alterations: variable post-translational modifications, unexpected alterations, and terminal truncations in proteoform identification. As a result, they are more sensitive and powerful than other existing methods that consider only one or two of the three types of alterations. All the proposed algorithms have been incorporated into TopMG, a complete software pipeline for complex proteoform identification. Experimental results showed that TopMG significantly increases the number of identifications than other existing methods in proteome-level top-down mass spectrometry studies. TopMG will facilitate the applications of top-down mass spectrometry in many areas, such as the identification and quantification of clinically relevant proteoforms and the discovery of new proteoform biomarkers. / 2019-06-21

Maintenance has traditionally been viewed as an unavoidable part of the manufacturing function. It is often identified as an opportunity to wantonly reduce costs, whenever the need to reduce manufacturing cost arises. Its potential to contribute to an organisation’s competitive advantage and business sustainability, has not received significant attention, and consequently formulation and execution of maintenance strategies have been poor, inconsistent or unfocused. Alignment of business strategy and maintenance strategy should help an organization to achieve or improve upon its business performance. Likewise, maintenance performance measures should be linked to an organization’s strategy, in order to provide useful information for making effective decisions. This fit or alignment, can only be achieved when maintenance is viewed as a critical business function, integrated with other business functions in support of business strategy. The impact of alignment between maintenance strategy and business strategy - on business strategy - is studied empirically in this thesis. The results confirm that alignment between maintenance and business strategy is strongly positively correlated with business performance. Copyright / Dissertation (MBA)--University of Pretoria, 2010. / Gordon Institute of Business Science (GIBS) / unrestricted