<p>The architecture, distribution and facies of sandstone bodies in the Gog Group of the southern Rocky Mountains of western Canada record the dynamics of sand movement on the broad continental shelf of West Laurentia during the Early Cambrian phase of worldwide transgression. This study focuses on the stratigraphy, sedimentology and ichnology in the Bow Valley region, specifically the sector from Mount Assiniboine northwest to the North Saskatchewan River. The objectives of this project were several-fold: (1) revise the existing stratigraphic nomenclature; (2) document the sedimentary facies; (3) identify facies assemblages and interpret them in terms of sedimentary processes and environments; (4) characterize sandstone body geometries; (5) develop a sequence-stratigraphic framework; (6) document trace-fossil occurrences; and (7) characterize different trace-fossil assemblages in terms of colonization trends and prevailing paleoenvironmental conditions.</p> <p>The Gog Group in this area has historically comprised four units, the Fort Mountain, Lake Louise, St. Piran and Peyto formations. North of Bow Pass an additional unit, the Jasper Formation, occurs below the Fort Mountain Formation and is related to accommodation created by active rift-faulting during the latest Neoproterozoic. In the Lake Louise and Lake O'Hara area, four new formal subdivisions within the St. Piran Formation are proposed: Lake O'Hara, Lake Oesa, Lake Moraine and Wiwaxy Peaks members.</p> <p>The sequence stratigraphy of tide-dominated setting has yet not been fully explored. The stratal architecture of the Lake O'Hara and Lake Oesa members reveals a new mechanism for the formation of the regressive surface of marine erosion landward of the lever point of balance between sedimentation and erosion in the subtidal environment. As the shoreline is forced to regress with falling sea level, the laterally continuous tidal flats advance and the preexisting shallow-subtidal compound dunes are scoured by strong tidal currents that carve gradually a new equilibrium profile. We argue that the accretion of intertidal flats on top of subtidal sands is an overlooked yet predictable component of falling-stage systems tracts in tide-dominated settings.</p> <p>The Gog Group also offers an opportunity to explore animal-sediment relationships in a high-energy setting, during the early phase of Phanerozoic diversification. The presence of constrasting ichnofabrics within a single Early Cambrian sand-sheet complex illuminates how the colonisation trends of suspension and detritus feeders were controlled by factors specific to the various subenvironments.<p> <p>The variety of sandbody types in the Gog Group reflects varying sediment supply and location on the inner continental shelf. Five types of compound cross-stratified sandstone are distinguished based on foreset geometry, sedimentary structures and internal heterogeneity. These represent five broad categories of subtidal sandbodies: (1) compound-dune fields; (2) sand sheets; (3) sand ridges; and (4) patchy dunes. Trace-fossil distribution in these tide-dominated sand bodies and adjacent sediments is mostly controlled by an interplay of substrate mobility, grain size, turbidity, water-column productivity, and sediment organic matter. Salinity is a critical factor in marginal-marine locations but played no role in this region of the shelf.</p>

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.

The wild origin, early breeding history, and diversity of the China Rose group, including R. chinensis and its varieties, cultivars, and hybrids, are largely unknown. The aims of this study were to investigate the genetic diversity and relationships of the China Roses with related species and hybrids, including information in support of, or refuting, the hypothesis that these roses are the hybrid result of the wild R. chinensis var. spontanea and R. odorata var. gigantea. Ninety Rosa accessions, including China Roses, a Miscellaneous Old Garden Rose, Noisettes, early Polyanthas, Bourbons, Teas, and species from Sections Indicae and Synstylae were surveyed using 23 microsatellite primer pairs. The trnH-psbA chloroplast intergenic spacer was also sequenced for the China Roses, Misc. Old Garden Rose, and the species to look specifically at maternal relationships. A total of 291 alleles were scored for the 23 microsatellites, with alleles per locus ranging from 6-22 and averaging 12.65. A dendrogram based on Dice similarity and a three-dimensional Principle Coordinate Analysis (PCoorA) graph were plotted with the data. In the cluster analysis, the similarity coefficients ranged from ~0.15-0.99, with the cultivated roses forming well-defined groups at about 0.45 similarity. These groups generally reflected the American Rose Society horticultural classifications. A large number of sports and synonyms in the China Rose group were identified through this analysis as well. The PCoorA gave a better graphical representation of the relationships of the species and cultivars, and with the inclusion of the chloroplast sequence haplotypes, some maternal relationships could also be identified. This study shows that the cultivated China Roses are a closely related group and identified which accessions were likely Hybrid China Roses. The results also suggest that the China Roses were maternally derived from R. chinensis var. spontanea. Based on the microsatellites and chloroplast sequence haplotypes, the identity of the R. odorata var. gigantea accessions in this study are suspect, but the China Roses may also have this species in their background as the result of natural or artificial hybridization.

Modeling software with object-oriented technique and Unified Modeling Language (UML) has become the new paradigm of modern information systems analysis and design. Selonen et al. (2003) proposed a framework for transformation within UML. However, they do not precisely define the operations and the rules they use. This research presents a systematic method which enhances Selonen et al.¡¦s work to transform the sequence diagram into the class diagram. The transformation process consists of three phases: (1) mapping the given sequence diagram to a notation-independent and semantically equivalent minimal model, (2) transforming the minimal model of the sequence diagram into the minimal model of a class diagram, and (3) mapping the minimal model to a class diagram. A real-world case is used to illustrate the concepts, application, and the advantages of using the proposed method. With this approach, the system developer can transform sequence diagram into class diagram automatically and thereby enhance the efficiency of system development.

The progress of studies on genes concerning the development and differentiation of early swine embryos have been delayed by limited paucity material. In order to identify the porcine ESTs associates with promoting its breeding efficiency, a cDNA library and ESTs database from oocytes of high reproductive swine is established. Oocytes were obtained from Duroc pig by superovulation which was performed by Taiwan Livestock Research Institute, Council of Agriculture. Total RNA was isolated from 50 mature oocytes, reverse transcription is then performed, followed by PCR based amplification of the cDNA. The amplified cDNA size ranges from 0.4 to 5 kb. The derived cDNA were ligated to a pCR2.1 vector, and the library has complexities of about 5.26¡Ñ104 independent clones. A total of 320 clones was picked and sequenced. By BLASTx analysis, among the 123 sequences, more than 43.07%¡]53/123¡^ mitochondrial proteins are found, 56.91¢H¡]70/123¡^ of the sequence were homologous to known transcripts from human, mouse, Drosophila. In nucleotide level analysis, 82.11¢H¡]101/123¡^ matched with the mitochondrial, ribosome genes and 17.89¢H¡]22/123¡^matched with other homologous genes by BLASTn. PCR analysis of the oocyte library for specific genes revealed transcripts for genes including homologous genes¡]2 pairs highly abundance and 2 pairs low abundance genes¡^, housekeeping genes¡]ACT£] and G3PDH¡^ and developmental genes¡]NEK2 and ZP1¡^. However, novel genes of swine are supposed to be the candidates for high productive phenotypes of swine. The library is a valuable resource for the isolation of clones representing genes active at the early stage. The ability to construct cDNA expression library from a few cells will allow gene expression analysis from oocyte biopsies and derived by nuclear transfer procedures.

Today, modeling the software with unified modeling language (UML) and computer-aided software engineering (CASE) tool becomes the main stream for the objected-oriented systems analysis and design. To enhance the degree of ransformation automation and reuse in the system development process, prior research suggested that most parts of the class diagram can be transformed from the sequence diagram directly. However, the explicit guideline for the transformation is lacking. This study presents a methodology, extended from Selonen et al (2003), to transform the sequence diagram into the class diagram. A real-world case using the integrated techniques is presented to illustrate the concepts, application, and the advantages of using the proposed approach. With this approach, the system developer can transform most parts of the sequence diagram into its associated class diagram automatically and thereby enhance the efficiency of system development.

A complex array for constructing perfect sequences is presented in this paper. The row sequences and their discrete Fourier transform form two sets of perfect sequences. The column sequences are orthogonal to each other for any cyclic shift. In addition, any combination of the column sequences with complex weighting coefficients of equal amplitude is also a perfect sequence. In addition, a superimposed training scheme is also proposed for channel estimation in OFDM systems. The perfect sequence is adopted since it has a constant magnitude in both the time domain and the frequency domain. Although the derived channel estimator has a slightly worse performance since the unknown data contributes extra noise, the effective data throughput is substantially increased. In addition, the proposed scheme is shown to have a much better peak-to-average power ratio (PAPR) because the added perfect sequence has a constant magnitude in the time domain.

We synthesize polyamide compounds containing bithiophene functional group and lexitropsin analogs and study their biological activity.

The multiple sequence alignment (MSA) is a fundamental technique of molecular biology. Biological sequences are aligned with each other vertically in order to show the similarities and differences among them. Due to its importance, many algorithms have been proposed. With dynamic programming, finding the optimal alignment for a pair of sequences can be done in O(n2) time, where n is the length of the two strings. Unfortunately, for the general optimization problem of aligning k sequences of length n , O(nk) time is required. In this thesis, we shall first propose an efficient group alignment method to perform the alignment between two groups of sequences. Then we shall propose a clustering method to build the tree topology for merging. The clustering method is based on the concept that the two sequences having the longest distance should be split into two clusters. By our experiments, both the alignment quality and required time of our algorithm are better than those of NJ (neighbor joining) algorithm and Clustal W algorithm.

The compositions of a series of poly (ethylene/trimethylene terephthalate) copolyesters were identified by 1H-NMR and 13C-NMR. The ethylene terephthalate (ET) units are 8.9, 33.7, 37.9, 50.1, 72.5, 77.8, and 90.8% in the copolyesters with sample codes of C2, C3, C4, C5, C6, C7, and C8, respectively. The triad sequence probabilities were determined from the normalized areas of aromatic quaternary carbons. The calculated average-number sequence lengths of ethylene- and trimethylene- terephthalate units range from 1.0 to 10.2 that depends on the relative ratio of both units in the copolymer. The values of randomness parameter for all of these copolyesters are between 0.96 and 1.1. Both values of sequence length and randomness parameter indicate that these copolyesters are random copolymers. Differential scanning calorimeter (DSC) was used to study the isothermal crystallization kinetics and the melting behaviors at heating rates of 10 and 50¢XC/min. The average enthalpy of isothermal crystallization (DH) decreased from 47 to 28 J/g when the ET units in the copolymer increased from 8.9% (C2) to 72.5% (C6), and then the enthalpy increased up to 42 J/g for the C8 copolymer with 90.8% of ET units. The results of Avrami analysis yielded one (n1) or two exponents. The n1 values of all of these copolymers were between 2.03 and 2.98. It suggests that the primary crystallization followed a heterogeneous nucleation with two-three dimensional form of growth. While investigating the isothermal crystallization, DSC specimens were crystallized for 9-14 times of the peak time to ensure the completion of crystallization. Both heating curves at 10 and 50¢XC/min showed multiple endothermic peaks. Triple-melting peaks were detected at lower crystallization temperature (Tc), then the medium and the highest temperature peaks merged gradually to form double-melting peaks with increase in Tc, finally, all three peaks merged together to become a single peak at higher Tc. The low temperature melting peak was associated with the last step of secondary crystallization. The middle temperature melting peak was considered to be characteristic of the melting of the crystals formed in the primary crystallization. The highest temperature melting peak may be due to the melting of crystallite formed by melting and recrystallization during the DSC heating scans. From the results of multiple melting behaviors at a heating rate of 50¢XC/min, the melting peak temperatures of primary crystals were plotted versus the crystallization temperature, Tc. The Hoffman-Weeks plot gave an equilibrium melting temperature, . Using the half-time of crystallization (t1/2) for analysis, regime II¡÷III transition was found for each copolyester. The pairs of ( , ) in unit of ¢XC are (237.1, 193.6), (198.9, 147.3), (187.9, 140.4), (226.6, 164.8), (230.1, 172.0), and (261.1, 208.4) for C2, C3, C4, C6, C7, and C8, respectively. Finally, the overall crystallization rates (1/ t1/2) were compared at equivalent supercooling, DT ( - Tc). The C2 copolyester crystallized the fastest and at lower supercooling. C3 and C4 copolyesters had very similar rates. The C6 copolyester crystallized the slowest and at higher supercooling. At DT = 50~60¢XC, the rates of C7 were close to those of C3 and C4 copolyesters, then the C7 copolyester crystallized faster at higher supercooling. The average value of DH or crystallinity decreased from ¡V47 to ¡V32 J/g when the minor component, ET unit, increasesd from 8.9% (C2) to 37.9% (C4), and then the crystallinity increased from ¡V28 to ¡V42 J/g as the ET unit increases from 72.5% (C6) to 90.8% (C8). It indicated that the number and the distribution of minor component in the main chain should affect the nucleation rate, the growth rate and the final crystallinity of the copolyesters.