M.Ing. / In recent years, many research and development projects have focused on the study of fibre Bragg gratings. Fibre Bragg gratings have been used in the field of sensors, lasers and communications systems. Commercial products that use fibre Bragg gratings are available. On the other hand, in the field of software development, object-oriented programming techniques are also becoming very popular and powerful. The focus of this work is on solving fibre Bragg grating problems by a simulation program with object-oriented programming techniques. For fibre Bragg grating problems, widely used theories and numerical methods such as the coupled-mode theory and the transfer matrix method will be applied in the analysis, modelling and simulation. The coupled-mode theory is a suitable tool for analysis and for obtaining quantitative information about the spectrum of a fibre Bragg grating. The transfer matrix can be used to solve non-uniform fibre Bragg gratings. Two coupled-mode equations can be obtained and simplified by using the weak waveguide approximation. The spectrum characteristics can be obtained by solving these coupled-mode equations. The optical numerical libraries of fibre Bragg gratings have been built by using object-oriented techniques. The code was realized by C++ and Object Pascal language in the Delphi4, C++ Builder4 and Visual C++6 environment. The compiled binary files and the code of the simulation program are available for both the end user and program developer. This simulation program can be used to analyze the performance of sensors and communication systems that use fibre Bragg gratings. Uniform, chirped, apodized, discrete phase shifted and sampled Bragg gratings have already been simulated by using the direct numerical integration method and the transfer matrix method. The reflected and transmitted spectra, time delay and dispersion of fibre Bragg gratings can be obtained by using this simulation program. At the same time, the maximum reflectivity, 3dB-bandwidth and centre wavelength can also be obtained. This thesis consists of three parts. The first part introduces a suitable theory and modelling that have been used to analyze the characteristics of fibre Bragg gratings. Secondly, the codes of the modelling are realized by the suitable programming languages in different development environments. Finally, this simulation program is utilized to analyse real physical problems with fibre Bragg grating applications.

Ph.D. (Mathematics) / Please refer to full text to view abstract

The objective of the thesis was to construct a deterministic single year, farm planning model that would enable vegetable producers to select an optimal farm plan from among alternative crops and crop production methods so as to maximize farm income consistent with technological and resource constraints and other goals. The model was to be readily adaptable to a wide range of commercial vegetable farmers in Canada but sufficiently flexible to be adaptable to the particular situation of a specific farm. A multiperiod linear programming model was built and validated through its application to a large commercial vegetable farm. The relevant theory of the firm was reviewed with special attention made to the theory's application to vegetable farms. The structure of a linear programming problem was discussed and related to the theory of the firm and vegetable farms. Special emphasis was placed on the problem of modeling the machinery used in vegetable production. The work of agricultural engineers was examined to determine the technological relationships involved in machine operation. Other crop budgeting models which involved the construction of similar planning models for a different sector of the agricultural community, especially the Purdue Crop Budgeting Models were reviewed. The model constructed was able to deal with machinery constraints by building a number of machine operating activities and tractor transfers so that the time constraint for a particular job would consist of any subset of the predefined set of time periods. Standard coefficients were prepared based on engineering formulae for fuel consumption and repair and maintenance costs for tractors. All inputs in the model except repair and maintenance costs were in physical units. This made it necessary to build several different types of purchasing or renting activities but facilitates the interpretation of data and the use of the model in a large number of different situations. The model was validated through its application to a large commercial vegetable farm in British Columbia. The model was run in simulation mode by forcing the model to follow the farm's 1974 crop plan and altering yields and prices to yields and prices that actually occured in that year. In this manner the reliability of the cost coefficients of the input data and the relationships between resources could be evaluated and compared with the results recorded in the farm's CANFARM records. The model was run in optimization mode with expected 1976 prices and yields to demonstrate the use of the model in selecting an optimal farm plan. A total of six plans were prepared based on alternate market and risk constraints and yields. These were compared with the plan selected by the farmer without the aid of the model. A detailed report on one of the farm plans v/as also prepared. / Land and Food Systems, Faculty of / Graduate

This thesis provides a methodology for examining forest harvesting operations through simulation. The model is capable of simulating multiple landing, single dump logging configurations. Facility locations, equipment types and numbers, parameters, and functional relationships may be varied so that a wide range of west coast British Columbia logging operations can be represented. The model was written in General Purpose Simulation System V (GPSSV) language. A substantial saving in development cost is realized over a FORTRAN-based simulation. The model allows independent users to make modifications within the program in order to adapt to the particular operating rules and policies of their operations. Model formulation for this thesis is based on an actual west coast logging division. Verification of the model involves a three-stage approach. First, a set of hypotheses and postulates are constructed for the subsystems of the harvesting operation and, secondly, these are empirically tested. Historical data is compared to simulation results in order to confirm that particular subsystems adequately model the real system. Tactical considerations and experimental design regarding model execution are presented. It is shown that antithetic variates can be effectively used to reduce the variance of the mean of a response. An improved truck dispatching routine is developed with the objective of maximizing productivity, subject to the availability of yarding and trucking resources. This policy balances the objectives of minimizing truck travel time, truck delays at landings, and yarding stoppages due to timber "saturated" landings. In comparison with other dispatching policies, productivity can be increased from two to over ten percent. The dispatching algorithm has been programmed for a Hewlett-Packard 9830A desktop computing system. The dispatcher, utilizing radio communications with all of the landings and trucks, can theoretically be supplied with the optimum landing to which a truck should be dispatched. Some other practical applications of the timber harvesting simulation model are discussed. Flexibility in the model, in parameter initialization and the substitution of new relationships, allows the investigation of many features of forest resource planning and machine allocation and scheduling. The determination of equipment requirements for various configurations, the evaluation of new equipment and the comparison of different operating policies can be undertaken with the model. Another benefit derived from the development of the model is an increased understanding of the timber harvesting system which allows the design of better operating policies and greater control within the system. / Forestry, Faculty of / Graduate

This project was designed to study the patterns of variability in fish populations. My hypothesis is that specific population patterns should be related to evolutionary concepts (phylogenetic patterns} , zoogeographic considerations (faunal patterns), and their vertical distributions. These patterns should be detected by comparing certain population parameters [growth parameters (K, LINF), the natural mortality coefficient (M) size at first maturity (LM), age at first maturity (TM), size at age 1 (L1) , the weight-length exponential coefficient (b) , and life span (T95)] which are intrinsic biological features of the population. Comparative methods were used to analyze data from published fish population studies by comparing fish population parameters, individually, in pairs (ratio or linear regression), or grouped together (discriminant analysis or Cooley and Lohnes' classification method), in order to find the similarities or differences among different categories, and then to group these into patterns. Published data provided 682 parameter records from 43 families (171 species) of fishes. My findings suggested that more satisfactory results would be obtained from a greater volume of data. Therefore, all the analyses were based mainly on 15 families with large sample sizes (Bothidae, Clupeidae, Cyprinidae, Engraulidae, Gadidae, Hiodontidae, Osmeridae, Percidae, Pleuronectidae, Salmonidae, Sciaenidae, Scombridae, Scorpaenidae, Sparidae, and Sgualidae). Sample sizes, mean values, standard errors, and coefficients of variation for population parameters and relative characters of the 15 families of fishes are listed in the summary table. These data would enable the extrapolation of results based on many areas for management of other fish stocks where data are lacking. In the majority of families significant linear regression relationships were found between 1/K--LINF, between LM--LINF, and between M--K. This means that fish having a greater asymptotic length (LINF) also have a larger size at first maturity (LM), a lower natural mortality coefficient (M), and a lower rate (K) at which the asymptotic length is reached. Using the F-test and the appropriate t-test as a basis for comparison of variances and means of individual parameters, it is evident that in most cases there are significant differences between families. This confirms one of my hypothesis; namely that differences between families, as shown by population parameters, exist from phylogenetic considerations. By comparing the four characters (K, LINF, LM, and LH/LINF) the fish families can be divided into the following groups: A) Shoaling pelagic fishes - Engraulidae, Clupeidae, and Osmeridae. These families have the highest K values (1.6 for Engraulidae, over 0.4 for the others), the smallest LINF, LM, and a very high LM/LINF ratio (over 0.7). B) Large pelagic fishes - Scombridae. This family has a moderately high K value (around 0.35) and the largest LINF. C) Demersal fishes - Gadidae, Pleuronectidae, Scorpaenidae, Sparidae etc. These families have low K values (less than 0.25), intermediate LINF size, and lower LM/LINF ratios (less than 0.6). D) Freshwater fish - Cyprinidae. This family has K and LINF values which are similar to those of the demersal fishes, but has a smaller LM length and, especially, the lowest LK/LINF (0.4) and TH/T95 (0.2) ratios. Stepwise discriminant analysis based on 7 variables in the 15 families showed that over 90% of the 620 cases considered independently could be correctly classified into the right families. Cooley and Lohnes' classification method was also utilized among species within 5 major families (Clupeidae, Cyprinidae, Gadidae, Pleuronectidae, and Scombridae). Correct classification ranged from 5 8.6% (Pleuronectidae) to 87.6% (Cyprinidae). These results further confirmed the existence of population patterns by examination of population parameters. Cluster analysis based on 7 population parameters displayed the closeness among the 15 families. Dendrograph relationships brought out the ecological, rather than the systematic, affinities between families. / Science, Faculty of / Zoology, Department of / Graduate

Thousands of risk variants underlying complex phenotypes (quantitative traits and diseases) have been identified in genome-wide association studies (GWAS). However, there are still several challenges towards deepening our understanding of the genetic architectures of complex phenotypes. First, the majority of GWAS hits are in non-coding region and their biological interpretation is still unclear. Second, most complex traits are suggested to be highly polygenic, i.e., they are affected by a vast number of risk variants with individually small or moderate effects, whereas a large proportion of risk variants with small effects remain unknown. Third, accumulating evidence from GWAS suggests the pervasiveness of pleiotropy, a phenomenon that some genetic variants can be associated with multiple traits, but there is a lack of unified framework which is scalable to reveal relationship among a large number of traits and prioritize genetic variants simultaneously with functional annotations integrated. In this thesis, we propose two statistical methods to address these challenges using integrative analysis of summary statistics from GWASs and functional annotations. In the first part, we propose a latent sparse mixed model (LSMM) to integrate functional annotations with GWAS data. Not only does it increase the statistical power of identifying risk variants, but also offers more biological insights by detecting relevant functional annotations. To allow LSMM scalable to millions of variants and hundreds of functional annotations, we developed an efficient variational expectation-maximization (EM) algorithm for model parameter estimation and statistical inference. We first conducted comprehensive simulation studies to evaluate the performance of LSMM. Then we applied it to analyze 30 GWASs of complex phenotypes integrated with nine genic category annotations and 127 cell-type specific functional annotations from the Roadmap project. The results demonstrate that our method possesses more statistical power than conventional methods, and can help researchers achieve deeper understanding of genetic architecture of these complex phenotypes. In the second part, we propose a latent probit model (LPM) which combines summary statistics from multiple GWASs and functional annotations, to characterize relationship and increase statistical power to identify risk variants. LPM can also perform hypothesis testing for pleiotropy and annotations enrichment. To enable the scalability of LPM as the number of GWASs increases, we developed an efficient parameter-expanded EM (PX-EM) algorithm which can execute parallelly. We first validated the performance of LPM through comprehensive simulations, then applied it to analyze 44 GWASs with nine genic category annotations. The results demonstrate the benefits of LPM and can offer new insights of disease etiology.

Marine sponges are economically and environmentally valuable, but restoration, commercial, and biomedical demands exceed what wild populations and aquaculture can provide. In vitro culture of sponge cells is a promising alternative, but has remained elusive until recent breakthroughs involving improved nutrient medium M1 in two-dimensional culture. The advantages of three-dimensional over two-dimensional cell culture have been increasingly recognized. Here we report the successful 21-day culture of cells from the marine sponge Geodia neptuni using multiple three-dimensional cell culture methods: FibraCel© disks, thin hydrogel layers, gel micro droplets, and spheroid cell culture. These methods performed comparably to two-dimensional control cultures, and each method offers advantages for restoration or in vitro applications using sponge cells. Further optimization of these methods may lead to the ability to culture fully functioning sponges from dissociated, cryopreserved cells, which will reduce the need for wild harvest of sponge tissues for commercial, restoration, and biomedical purposes. / Includes bibliography. / Thesis (MS)--Florida Atlantic University, 2021. / FAU Electronic Theses and Dissertations Collection

Time-series data draw extensive attention from many research domains, such as financial and biomedical engineering. Researchers often face the difficultly of visualizing multiple time-series data simultaneously. The predominant techniques suffer from visual clutter either due to over-plotting or an overwhelming number of small graphs that carries a high cognitive load. This research study proposes a Colored slope, a combination of Tufte's slope graph and time-series heatmap, to visualize multiple time-series data at once, balancing scalability and accuracy. Colored slope inherits the complementary advantages from each method, regarding visualizing temporal changes within a period and identifying precise values. The efficacy, effectiveness, and graphical perception of the Colored slope on visualizing multiple time-series data with publicly accessible stock data were evaluated and compared it to popular time-series visualizations, including line graphs, time-series heatmap, and small multiple spark area graphs. Analyzing the experimental data, this study concludes that Colored slope contributes to (1) allowing users to identify the extreme values (maximum and minimum), co-variability, the general trend of the data, and rate of change effectively for an optimally large number of visual marks(time-series data); (2) capable of display more instances of time-series data with a less visual clutter problem. Finally, several possible applications and limitations with the Colored slope are demonstrated.

This thesis describes a series of investigations into the problems that hamper the progress of myocardial preservation for transplantation in man. Six positive aspects of cardiac preservation have emerged from this study: - (1) A clear fluid hyperosmolar solution was formulated that adequately preserved viability of pig and baboon hearts. (2) A pneumatically powered portable preservation unit was designed which successfully preserved pig and baboon hearts when assessed by either functional testing or orthotopic transplantation. (3) A method of in vitro testing of hearts was developed that correlated with results from orthotopic transplantation. (4) A technique of cardiac autotransplantation in baboons was perfected. (5) The high release of lysosomal acid phosphatase during the period of hypothermic preservation was shown to be non-pathological and was reversible after a period of warm blood perfusion. (6) Successful preservation of human hearts for periods longer than 4 hours, not previously achieved, was obtained. The preservation solution and the portable preservation unit that emerged from this experimental study were thoroughly investigated before clinical application. During the development of this perfusate the author had numerous consultations and discussions with colleagues and senior members of neighbouring departments.

Generalized aeroelastic methods are here defined as methodsthat allow aeroelastic analysis of problems in many engineeringdisciplines. Aeroelastic/fluid-elastic phenomena are ofsignificant importance in many industrial applications, but fewtools exist for efficient analysis of these systems. In theaeronautical world, methods that neglect wing thickness andassume slender body for non lift generating bodies areutilized. These methods also use zero incidence flow conditionsas equilibrium condition. Except for acoustic problemsbasically only nonlinear methods that have emerged during thepast few years exists for general applications. These nonlinearmethods are generally very inefficient for the study ofproblems involving high frequencies. In the framework of the project reported here, a method/toolhas been developed to perform efficient aeroelastic analysis ingeneral applications. The selected approach makes it possibleto simulate systems that cannot be approximated by neglectingthickness of the structure. The numerical boundary elementmethod has been used to discretize the steady and unsteadyvelocity potential equation that is used as mathematical modelof the fluid dynamics. The use of the boundary element methodenables unstructured meshes to be used on the fluid-structureinterfaces. Applications ranging from Micro Electro-MechanicalSystems to large scale systems can be analyzed. The method, asa subset of the aeroelastic capabilities also, enablesefficient analysis of flow fields, acoustics and acoustics inflow fields. By combining the developed linear method withnonlinear tools and/or measurements it is possible to create anunderstanding of the behaviour of very complex problems. A summary of the method is presented in the introduction ofthis thesis. Additionally the influence of wing thickness onthe aeroelastic characteristics of the bending-torsion mode forthe so called BAH-wing has been studied. / <p>NR 20140805</p>