Wireless cellular networks, which serve a large area by geographically partitioning users, suffer from interference from adjacent cells transmitting in the same frequency band. This interference can theoretically be completely mitigated via transceiver cooperation in both the uplink and downlink. Optimally, base stations serving the users can utilize high-capacity backbones. to jointly transmit and receive all the data in the network across all the base stations. In reality, the backbone connecting the base stations is of finite capacity, limiting joint processing to localized clusters. Even with joint processing on a small scale, the overhead involved in sharing data between multiple base stations is large and time-sensitive. Other forms of cooperation have been shown to require less overhead while exhibiting much of the performance benefit from interference mitigation. One particular strategy, called interference alignment (IA), has been shown to exploit all the spatial degrees of freedom in the channel provided data cannot be shared among base stations. Interference alignment was developed for the multi-user interference channel to exploit independent channel observations when all of the links in the network have high signal-to-noise ratio, and assumes all the nodes utilizing the physical resources are participating in the cooperative protocol. When some or all of the links are at moderate signal-to-noise ratio, or when there are non-cooperating users, IA is suboptimal. In this dissertation, I take three approaches to addressing the drawbacks of IA. First, I develop cooperative transmission strategies that outperform IA in various operationg regimes, including at low-to-moderate SNR and in the presence of non-cooperating users. These strategies have the same complexity and overhead as IA. I then develop algorithms for network partitioning by directly considering the overhead of cooperative strategies. Partitioning balances the capacity gains of cooperation with the overhead required to achieve them. Finally, I develop the shared relaying model, which is equivalent to the interference channel but with a single multi-antenna relay mediating communications between transceivers. The shared relay requires less overhead and cooperation than interference alignment but requires added infrastructure. It is shown to outperform conventional relaying strategies in cellular networks with a fixed number of total relay antennas. / text

A capital project represents a significant investment by a firm to create future economic benefits. Since the global economic recession begun in 2008, corporate owners have paid increased attention to business-project interfaces with the aim of improving alignment between business strategy and capital project development. Despite its importance, the business-project interface has not been quantitatively measured and no empirical evidence exists about its effects on performance outcomes. This dissertation intends to identify and quantify the business-project interfaces in the development of a capital project in terms of personnel involvement and task interaction, and to investigate its effects on performance outcomes and the value of best practices. To achieve these objectives, a conceptual framework for assessing the involvement and interaction on business-project interfaces was developed. Based on the conceptual framework, a questionnaire including quantitative measures for the assessment of personnel involvement and task interaction was designed. Supplemental survey responses were received for several industrial capital projects that had initially provided capital project data to the CII Benchmarking & Metrics database. The effects of the business-project interface in terms of cost, schedule, change, and business performance were documented. Data analyses show that project groups with high involvement by business personnel and high interaction between business and project units tend to show remarkably improved project performance. Furthermore, this dissertation presents confirmation that projects with high involvement of business unit personnel and intensive implementation of best practices tend to show superior project performance. The primary contribution of this research is to provide a quantitative assessment tool to assess the business-project interface and to document the interface throughout project life cycle. Another contribution is empirical evidence of the benefits on project performance from implementing best practices that were supported by management. / text

The availability of complete plastid genomes has been playing an important role in resolving phylogenetic relationships among the major clades of land plants and in improving our understanding of the evolution of genomic organization. The increased availability of complete genome sequences has enabled researchers to build large multi-gene datasets for phylogenetic and molecular evolutionary studies. In chapter 2 of this thesis a web-based multiple sequence web viewer and alignment tool (MSWAT) is developed to handle large amount of data generated from complete genome sequences for phylogenetic and evolutionary analyses. We expect that MSWAT will be of general interest to biologists who are building large data matrices for evolutionary analyses. The third chapter presents the sequenced plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales). Data from these genomes, in combination with 32 other angiosperm plastid genomes, were used to assess phylogenetic relationships of magnoliids to other angiosperms and to examine patterns of variation of GC content. Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots. The fourth chapter presents the Trifolium subterraneum plastid genome sequence, which is unusual in genome size and organization relative to other angiosperm plastid genomes. The Trifolium plastid genome is an excellent model system to examine mechanisms of rearrangements and the evolution of repeats and unique DNA. / text

For as long as biologists have been computing alignments of sequences, the question of what values to use for scoring substitutions and gaps has persisted. In practice, substitution scores are usually chosen by convention, and gap penalties are often found by trial and error. In contrast, a rigorous way to determine parameter values that are appropriate for aligning biological sequences is by solving the problem of Inverse Parametric Sequence Alignment. Given examples of biologically correct reference alignments, this is the problem of finding parameter values that make the examples score as close as possible to optimal alignments of their sequences. The reference alignments that are currently available contain regions where the alignment is not specified, which leads to a version of the problem with partial examples.In this dissertation, we develop a new polynomial-time algorithm for Inverse Parametric Sequence Alignment that is simple to implement, fast in practice, and can learn hundreds of parameters simultaneously from hundreds of examples. Computational results with partial examples show that best possible values for all 212 parameters of the standard alignment scoring model for protein sequences can be computed from 200 examples in 4 hours of computation on a standard desktop machine. We also consider a new scoring model with a small number of additional parameters that incorporates predicted secondary structure for the protein sequences. By learning parameter values for this new secondary-structure-based model, we can improve on the alignment accuracy of the standard model by as much as 15% for sequences with less than 25% identity.

Information technology (IT) is more pervasive than ever before, constituting a significant factor for performance and survival in the business arena. It is essential that IT within organizations understands what the Business needs in order to provide the necessary support and bring value, which is also true when IT is also the main value creator. Therefore, alignment between the Business and IT within organizations is an issue of great concern and it is still open for solvency both for business and IT executives and practitioners. This work is scoped to the alignment linkage between business strategy and information systems (IS), where business strategy typically constitutes the primary exponent of the Business and IS typically encapsulates the elements of IT sustaining an organization. Current approaches are either focused on detailed aspects of IS and treat business strategy abstractly or use distinct business strategy formulations (e.g. Value Chain) but deal with IS only partially. This is problematic because the abstract use of business strategy hinders traceability of strategic intentions and initiatives towards features/aspects of IS, which are aimed to actualize and support such intentions. Because approaches using distinct business strategy formulations are not relevant to all organizations and are limited only to the IS aspects addressed. Introducing a model-driven approach for the alignment linkage is aimed at addressing the outlined shortcomings. Following a design science research paradigm, the main artifact developed is the Unified Business Strategy Meta-Model (UBSMM), which is based on conceptualizing established business strategy formulations (e.g. Value Chain) and integrating them. UBSMM supports mappings to IS models used in organizations, such as IS requirements, enterprise models and enterprise architecture, and provides unambiguous utilization of business strategy for the alignment linkage. Contributions of this thesis are grounded both on the process of building UBSMM and mapping to IS models, as well as the artifact itself. Conceptualizing and integrating business strategy formulations provides a less ambiguous and unified view of strategic concepts. This limits variations in interpretation and reinforces mappings to IS models, which are defined based on inter-schema properties across models. Therefore, UBSMM can link business strategy to IS models enhancing their communication in a traceable manner, ergo, support alignment. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 10: Submitted. Paper 11: Accepted.</p>

We present a novel method for building 3D models from a user sketch. Given a 2D sketch as input, the approach aligns and deforms a chosen 3D template model to match the sketch. This is guided by a set of user-specified correspondences and an algorithm that deforms the 3D model to match the sketched profile. Our primary contribution is related to fitting the 3D deformable geometry to the 2D user sketch. We demonstrate our technique on several examples.

Cheap electronic storage and Internet bandwidth has increased the amount of online data. Large quantities of metadata are created to manage this wealth of information. Methods to organize and structure metadata has led to the development of ontologies - data that is organized to describe the relation between elements. The creation of large ontologies has brought forth the need for ontology management strategies. Ontology alignment and merging techniques are standard operations for ontology management. Accurate ontology alignment methods are typically semi-automatic, meaning they require periodic user input. This becomes infeasible on large ontologies and the accuracy and efficiency drops significantly when these algorithms are forced to align without human interaction. Bioinformatics, for example, has seen the influx of large ontologies, such as signal pathway sets with thousands of elements or protein-protein interaction (PPI) databases with hundreds of thousands of elements. This drives the need for a reliable method of large-scale ontology alignment. Many bioinformatics ontologies contain references to domain ontologies - manually curated ontologies describing additional, general information about the terms in the ontologies. For example, more than 2/3 of proteins in PPI data sets contain at least one annotation to the domain ontology the Gene Ontology. We use the domain ontology references as features to compute similarity between elements. However, there are few efficient ways to compute similarity from structured features. We present a novel, automatic method for aligning ontologies based on such domain ontology features. Specifically, we use simulated annealing to reduce the complexity of the domain ontologys structure by finding approximate relevant clusters of elements. An intermediate step performs hierarchical clustering based on the similarity between elements of the ontology. Then the mapping between clusters across aligning ontologies is built. The final step builds an alignment between matched clusters. To evaluate our methods, we perform an alignment between Human (Homo Sapiens) and Yeast (Saccharomyces cerevisiae) signal pathways provided by the Reactome database. The results were compared against reliable homology studies of proteins. The final mapping produces alignments that are significantly more accurate than the traditional ontology alignment methods, without any human involvement.

The progression of knee osteoarthritis (OA), the most common cause of physical disability in older adults, is influenced by muscular and biomechanical factors. Reliability of muscular and biomechanical measures, including knee muscle strength and limb alignment, is critical. Furthermore, conservative interventions that slow the course of OA disease progression and prevent disability are urgently needed. The objectives of this thesis were to: 1) investigate the reliability of measures of knee muscle strength and alignment in persons with knee OA, and 2) determine the influence of an exercise intervention targeting hip muscles on knee joint loading in those with medial knee OA. In the first study reliability of knee muscle strength measures was evaluated within one testing session in 40 persons with knee OA. Isometric and isokinetic peak torque values for the quadriceps and hamstring muscles demonstrated high degrees of intra-session reliability. Reliability of lower limb alignment measures was determined following a bone landmark-based approach with use of a computer program. Excellent reliability coefficients were found which compared favorably with reliability of manual measures from schematics of limb deformities drawn with AutoCAD® software. When the computer method was applied to 100 full-limb radiographs of persons with or at risk for knee OA, alignment measures demonstrated high inter- and intra-reader reliability. Hip muscle weakness may influence loading of the medial knee compartment. Hip abductor strength was evaluated in 40 individuals with medial compartment knee OA in comparison to a control group of 40 healthy older adults. The effect of an 8-week home-based hip abductor strengthening program on the knee adduction moment was also assessed in this group with knee OA, compared with the control group which received no intervention. Following the exercise program the OA group demonstrated improvements in hip abductor strength and functional performance on a sit-to-stand task. There were no changes in the knee adduction moment. Thus, hip muscle strengthening did not influence joint loading, but may improve function in persons with knee OA. Results from this thesis provide increased understanding of knee OA, from muscular and biomechanical perspectives, in the areas of measurement reliability and exercise intervention. / Thesis (Ph.D, Rehabilitation Science) -- Queen's University, 2008-09-25 01:29:13.675

Self-assembly of nanorods (NRs) enhanced by functionalization with liquid crystals (LC) ligands has been demonstrated. First, CTAB (cetyltrimethylammonium bromide) coated gold NRs were prepared in water through a modified one-step seed growth process. The hydrophilic GNRs were then converted into hydrophobic NRs employing a surface modification process using liquid crystalline organosilanes. The functionalized GNRs were characterized by TEM (transmission electron microscopy) and SAXS (small angle X-ray scattering) to investigate the packing mode of the GNRs. The results propose models of the assembly of the GNRs depending on nature and connectivity of the attached liquid crystal molecules. Furthermore, a macroscopic orientation of the GNRs doped in LC was achieved via an alignment technique of the liquid crystal host. SAXS analysis of the doped DLC indicated modification of lattice parameters due to the insertion of the DLC-GNRs, which resulted in an enhancement of the charge carrier mobility.

The deterministic microasperities play a vital role in reducing the coefficient of friction and wear of thrust surfaces and improve the tribological properties of the surfaces. Deterministic microasperities have a specific pattern in terms of size, shape and spacing. These specified geometries are controllable and repeatable. The microasperities are micron scaled asperities and cavities on a surface that form the surface roughness. The present thesis shows the detailed process to fabricate the deterministic microasperities on thrust surfaces, i.e. stainless substrate, using micro-fabrication processes such as lapping and ultra-violet photolithography in combination with an electroplating (nickel) process. A Novel alignment technique is used to align the photomask with the substrate to get repeatable and aligned patterns on the thrust surface. Deterministic microasperities are characterized by using precision instruments such as an Optical profilometer, Scanning Electron Microscope (SEM) and Optical microscope to study the various surface parameters such as Average roughness (Ra), Root mean square value (rms) and Peak value (PV) of the thrust surface.