Analysis of association studies and inference of haplotypic phase using hidden Markov models

In this thesis I focus on the development and application of hidden Markov model (HMM) to solve problems in statistical genetics. Our method, based on a HMM, models the joint haplotype structure in the samples, where the parameters in the model are estimated by the Baum-Welch EM algorithm. Also, the model does not require pre-defined blocks or a sliding window scheme to define haplotype boundaries. Thus our method is computationally efficient and applicable for either the whole genome sequence or the candidate gene sequence. The first application of this model is for disease association testing using inferred ancestral haplotypes. We employed a HMM to cluster haplotypes into groups of predicted common ancestral haplotypes from diploid genotypes. The results from simulation studies show that our method greatly outperforms single-SNP analyses and has greater power than a haplotype-based method, CLADHC, in most simulation scenarios. The second application is for inferring haplotypic phase and to predict missing genotypes in polyploid organisms. Using a simulation study we demonstrate that the method provides accurate estimates of haplotypic phase and missing genotypes for diploids, triploids and tetraploids. The third application is for joint CNV/SNP haplotype and missing data inference. The results are very encouraging for this application. With the increasing availability of genotype data in both diploid and polyploid organisms, we believe that our programs can facilitate the investigation of genetic variations in genome-wide scale studies

Analysis on the Value of Inner Music Hearing for Cultivation of Piano Learning

Piano performance, which is an auditory art, delivers fantastic melody into one’s brain through his ears. Then, the music appreciators can resonate emotionally and achieve a mutual correspondence with their aesthetic ideas. Therefore, one not only needs to absorb music with their external hearing but also needs to cultivate their inner music perception during piano learning. This paper gives a comprehensive elaboration and some suggestions on how to cultivate the inner music hearing during piano learning

Moving Towards the Science-based Fisheries Management (SBFM) in China

Sustainable fisheries management requires decisions to be made based on sound science. To help ensure this, a Science-Based Fisheries Management (SBFM) system should be established to produce the best available science (BAS) and to ensure that the BAS forms the basis of decision-making. The goal of this dissertation is to look at how China, the world’s largest marine fisheries country, might build an effective SBFM system to enable its marine fisheries to attain sustainability. Studies were conducted to answer the following guiding questions: 1) what is SBFM? 2) why is it necessary for China to deploy SBFM? 3) what are China’s challenges, roadblocks, and opportunities in implementing SBFM?, and 4) how to overcome the obstacles by reforming China’s fisheries system. This dissertation is structured into four chapters. An extensive literature review was conducted in Chapter 1 to determine the concept and enablers of SBFM in the world. A framework that included a thorough set of criteria and a basic operational structure for SBFM was given. The evolution of China’s marine fisheries management practices from 1949 to 2019 was examined in Chapter 2 based on a comprehensive literature review and the researcher’s observations in meetings and conversations with Chinese fisheries experts. This Chapter provides materials to help people better understand the features and trends of China’s marine fisheries policies, as well as the characteristics of its marine capture fisheries. The study indicated that China’s sustainable marine fisheries management faces numerous challenges and hurdles, the majority of which are associated with SBFM - inefficient science-policy interactions and data shortages. The checklist of SBFM criteria defined in Chapter 1 was used in Chapter 3 to analyze China’s marine fisheries management system from a system engineering perspective. The benefits and drawbacks of the system for implementing SBFM were examined. Finally, in Chapter 4, the advantages and disadvantages of China’s marine fisheries management system were summarized, and recommendations for China’s marine fisheries reform with the goal of constructing a more successful SBFM were provided. This dissertation concluded that 1) China’s sustainable marine fisheries management cannot succeed without institutional reforms to support stronger science and its integration into fisheries policymaking; 2) reforming the fisheries management system from the perspective of system engineering can be an effective way to promote the production of better BAS and its use in policies; and, 3) use of the SBFM framework developed in this study can help China evaluate and reform its marine fisheries legal and institutional framework, and at the same time leverage the localized TAC pilot programs to develop and test a structured approach for SBFM. With the expansion of TAC pilots, the approach can be revised accordingly and finally inform the development and implementation of SBFM at large

Ab initio molecular orbital investigations of molecular structures for lithiated hydrocarbons

Organolithium compounds are important reagents of widespread use in synthetic organic chemistry. Structures of organolithium hydrocarbons do not follow classical rules; replacement of a hydrogen by lithium in their molecules almost always results in a major change in geometry, electronic state, or both. The structures of many of these compounds still remain unknown and a subject of controversy. This study investigated the geometries and electronic states of the ground states of dilithioacetylene and dilithiomethane molecules by using ab initio molecular orbital calculations. The geometries of both the molecules have been fully optimized at both the single determinant Hartree-Fock self consistent field (HF SCF) and the multiconfiguration self consistent field (MC SCF) levels with a variety of basis sets. Linear and planar bridged forms for dilithioacetylene and tetradedral-like, cis planar, and trans planar forms for dilithiomethane were studied. The electronic states examined were the singlet state for both molecules and the triplet state for dilithiomethane. It has been found that the equilibrium geometries, a linear and a planar bridged structures for dilithioacetylene molecule, and a cis planar and a tetrahedral-like forms for the singlet and triplet states of dilithiomethane molecule, are rather sensitive to the choice of the basis set at the Hartree-Fock level of theory. Calculations at the MC-SCF level of theory behave the same way but in smaller active multi configuration spaces, and do not seem to depend on the basis set in larger active spaces. Both the molecules have a relatively flat potential energy surface and do not exhibit strong preferences for the optimized structures. This lack of preference for the optimized structures is especially true for the MCSCF calculations on the multiplicity of the ground state structures for dilithiomethane molecule

Conformal isoparametric spacelike hypersurfaces in conformal spaces Q⁴₁ and Q⁵₁

We study the conformal geometry of conformal spacelike hypersurfaces in the conformal spaces Q⁴₁ and Q⁵₁. We obtain a complete classification of conformal isoparametric spacelike hypersurfaces in Q⁴₁ and Q⁵₁.Вивчено конформну геометрiю конформних простороподiбних гiперповерхонь у конформних просторах Q⁴₁ and Q⁵₁. Отримано повну класифiкацiю конформних iзопараметричних простороподiбних гiперповерхонь у Q⁴₁ та Q⁵₁