Reconstructing the evolutionary history of a set of species is a fundamental problem in biology. This thesis concerns computational problems that arise in different settings and stages of phylogenetic tree reconstruction, but also in other contexts. The contributions include: • A new distance-based tree reconstruction method with optimal reconstruction radius and optimal runtime complexity. Included in the result is a greatly simplified proof that the NJ algorithm also has optimal reconstruction radius. (co-author Jens Lagergren) • NP-hardness results for the most common variations of Multiple Alignment. In particular, it is shown that SP-score, Star Alignment, and Tree Alignment, are NP hard for all metric symbol distances over all binary or larger alphabets. • A 1.375-approximation algorithm for Sorting By Transpositions (SBT). SBT is the problem of sorting a permutation using as few block-transpositions as possible. The complexity of this problem is still open and it was a ten-year-old open problem to improve the best known 1.5-approximation ratio. The 1.375-approximation algorithm is based on a new upper bound on the diameter of 3-permutations. Moreover, a new lower bound on the transposition diameter of the symmetric group is presented and the exact transposition diameter of simple permutations is determined. (co-author Tzvika Hartman) • Approximation, fixed-parameter tractable, and fast heuristic algorithms for two variants of the Ancestral Maximum Likelihood (AML) problem: when the phylogenetic tree is known and when it is unknown. AML is the problem of reconstructing the most likely genetic sequences of extinct ancestors along with the most likely mutation probabilities on the edges, given the phylogenetic tree and sequences at the leafs. (co-author Tamir Tuller) • An algorithm for computing the number of mutational events between aligned DNA sequences which is several hundred times faster than the famous Phylip packages. Since pairwise distance estimation is a bottleneck in distance-based phylogeny reconstruction, the new algorithm improves the overall running time of many distancebased methods by a factor of several hundred. (co-author Jens Lagergren) / QC 20110121

In this paper, I have examined if and how Saul Bass adapts his title sequences to the respective film in the matter of genre, plot, milieu, feeling and appearance. Saul Bass was really a graphic artist who has made himself a long career in film production, foremost as a creator of title sequences. Of all the films Bass has created title sequences to, I’ve chosen six films, whose title sequences I analyse more thoroughly. I do this to point out the differences between them and thus also show how Bass adapt them to the individual work. To do this I’ve used an auteuristic perspective. The analysis I’ve made of the six films points to that Bass adapts his title sequences to the respective films. I have for instance found that certain title sequences is an integrated part of the film itself, others work as a prologue to the plot of the movie, and others present the genre, the plot or a specific theme. Most of the title sequences also introduce a fundamental feeling, that follows the viewer throughout the whole film. However, it has also come forth certain likenesses in his work, certain images and themes. Despite this, I believe that Saul Bass designs his title sequences according to the specific work and not according to his personal style. / I denna uppsats har jag undersökt om och hur Saul Bass anpassar sina förtexter till respektive film ifråga om genre, handling, miljö, känsla eller utseende. Saul Bass var i grunden en grafisk designer som har gjort sig en lång karriär inom filmproduktionen, och då främst som skapare av förtexter. Av alla filmer som Bass har gjort förtexter till har jag valt ut sex filmer, vars förtexter jag analyserar mer ingående. Detta gör jag för att belysa olikheterna dem emellan och därmed också hur Bass anpassar dem efter det individuella verket. Till detta använder jag mig av ett auteuristiskt perspektiv. De analyser jag har gjort av de sex filmerna pekar på att Bass verkligen anpassar sina förtexter till respektive film. Jag har till exempel funnit att vissa förtexter är en integrerad del av själva filmen, vissa fungerar som prologer till filmens handling och vissa presenterar genren, handlingen eller ett specifikt tema. De allra flesta av förtexterna introducerar även en grundläggande känsla, som sedan följer med åskådaren genom hela filmen. Dock har det även dykt upp vissa likheter i hans arbeten, vissa bilder och teman. Detta till trots anser jag att Saul Bass utformar sina förtexter med tanke på det specifika verket och inte med tanke på hans personliga stil.

In recent years, uranium pollution in the environment has been recognized as a serious threat, and novel in situ microbial bioremediation strategies have been incorporated into field-scale contaminated sites. The Oak Ridge Integrated Field-scale Subsurface Research Challenge (IFC) site is one of the largest uranium contaminated areas in the United States, and a literature review has revealed the potential of uranium reduction by dominant Anaeromyxobacter dehalogenans species that respire during bioremediation. A genome-scale model of A. dehalogenans, a unique microbe with diverse metabolic capabilities that thrives in the natural environment, has been developed, and applied to an in silico field-scale computational setting for evaluation of the biotic uranium reduction in the Oak Ridge IFC site. The metabolic model of A. dehalogenans was integrated into an expanded microbial community framework for the prediction of chemical profiles, and subsequent scenario evaluation of in situ measured data.

Botryococcus braunii (Chlorophyta, Botryococcaceae) is a colony-forming green microalga that produces large amounts of liquid hydrocarbons, which can be converted into transportation fuels. While B. braunii has been well studied for the chemistry of the hydrocarbon production, very little is known about the molecular biology of B. braunii. As such, this study developed both apparatus and techniques to culture B. braunii for use in the genetic and biochemical characterization. During genetic studies, the genome size was determined of a representative strain of each of the three races of B. braunii, A, B, and L, that are distinguished based on the type of hydrocarbon each produces. Flow cytometry analysis indicates that the A race, Yamanaka strain, of B. braunii has a genome size of 166.0 +/- 0.4 Mb, which is similar to the B race, Berkeley strain, with a genome size of 166 +/- 2.2 Mb, while the L race, Songkla Nakarin strain, has a substantially larger genome size at 211.3 +/- 1.7 Mb. Phylogenetic analysis with the nuclear small subunit (18S) rRNA and actin genes were used to classify multiple strains of A, B, and L races. These analyses suggest that the evolutionary relationship between B. braunii races is correlated with the type of liquid hydrocarbon they produce. Biochemical studies of B. braunii primarily focused on the B race, because it uniquely produces large amounts of botryococcenes that can be used as a fuel for internal combustion engines. C30 botryococcene is metabolized by methylation to generate intermediates of C31, C32, C33, and C34. Raman spectroscopy was used to characterize the structure of botryococcenes. The spectral region from 1600?1700 cm^-1 showed v(C=C) stretching bands specific for botryococcenes. Distinct botryococcene Raman bands at 1640 and 1647 cm^-1 were assigned to the stretching of the C=C bond in the botryococcene branch and the exomethylene C=C bonds produced by the methylations, respectively. A Raman band at 1670 cm^-1 was assigned to the backbone C=C bond stretching. Finally, confocal Raman microspectroscopy was used to map the presence and location of methylated botryococcenes within a living colony of B. braunii cells.

This thesis focuses on the analysis of the cardiac electrical and kinematic function for heart failure patients. An expected outcome is a set of computational tools that may help a clinician in understanding, diagnosing and treating patients suffering from cardiac motion asynchrony, a specific aspect of heart failure. Understanding the inverse electro-kinematic coupling relationship is the main task of this study. With this knowledge, the widely available cardiac image sequences acquired non-invasively at clinics could be used to estimate the cardiac electrophysiology (EP) without having to perform the invasive cardiac EP mapping procedures. To this end, we use real clinical cardiac sequence and a cardiac electromechanical model to create controlled synthetic sequence so as to produce a training set in an attempt to learn the cardiac electro-kinematic relationship. Creating patient-specific database of synthetic sequences allows us to study this relationship using a machine learning approach. A first contribution of this work is a non-linear registration method applied and evaluated on cardiac sequences to estimate the cardiac motion. Second, a new approach in the generation of the synthetic but virtually realistic cardiac sequence which combines a biophysical model and clinical images is developed. Finally, we present the cardiac electrophysiological activation time estimation from medical images using a patient-specific database of synthetic image sequences.

In data-dependent superimposed training (DDST) system, the data sequence subtracts a data-dependent sequence before transmission. The receiver cannot correctly find the unknown term which causes an error floor at high SNR. In this thesis, we list some helpful conditions to enhance the performance for precoding design in DDST system, and analyze the major cause of data misidentification by singular value decomposition (SVD) method. Finally, we propose a precoding matrix based on [C.-P. Li and W.-C. Huang, ¡§A constructive representation for the Fourier dual of the Zadoff¡VChu sequences,¡¨ IEEE Trans. Inf. Theory, vol. 53, no. 11, pp. 4221¡Ð4224, Nov. 2007]. The precoding matrix is constructed by an inverse discrete Fourier transform (IDFT) matrix and a diagonal matrix with the elements consist of an arbitrary perfect sequence. The proposed method satisfies these conditions and simulation results show that the data identification problem is solved.

Reinforcement learning is the problem faced by an agent that must learn behavior through trial-and-error interactions with a dynamic environment. Generally, the problem to be solved contains subtasks that repeat at different regions of the state space. Without any guidance an agent has to learn the solutions of all subtask instances independently, which degrades the learning performance. In this thesis, we propose two approaches to build connections between different regions of the search space leading to better utilization of gained experience and accelerate learning is proposed. In the first approach, we first extend existing work of McGovern and propose the formalization of stochastic conditionally terminating sequences with higher representational power. Then, we describe how to efficiently discover and employ useful abstractions during learning based on such sequences. The method constructs a tree structure to keep track of frequently used action sequences together with visited states. This tree is then used to select actions to be executed at each step. In the second approach, we propose a novel method to identify states with similar sub-policies, and show how they can be integrated into reinforcement learning framework to improve the learning performance. The method uses an efficient data structure to find common action sequences started from observed states and defines a similarity function between states based on the number of such sequences. Using this similarity function, updates on the action-value function of a state are reflected to all similar states. This, consequently, allows experience acquired during learning be applied to a broader context. Effectiveness of both approaches is demonstrated empirically by conducting extensive experiments on various domains.

Abstract MtDNA D-loop sequences and cranial morphometrics were used to analyze the phylogenetic relationships of bharal (Pseudois nayaur szechuanensis) populations. The habitat preferences of bharal were also investigated in Helanshan, Ningxia. The results from the analysis of mtDNA D-loop sequences and cranial morphometrics were in accordance. Among all populations analyzed, the phylogenetic relationships between populations in Lixian, Sichuan and Helanshan, Ningxia were most distantly related, while populations in Dulan, Qinghai and Subei, Gansu were close to one another. No matter in summer or winter, bharal generally prefer to stay in meadows, but they would appear in forests and shrubs as well.

<p>Reconstructing the evolutionary history of a set of species is a fundamental problem in biology. This thesis concerns computational problems that arise in different settings and stages of phylogenetic tree reconstruction, but also in other contexts. The contributions include:</p><p>• A new distance-based tree reconstruction method with optimal reconstruction radius and optimal runtime complexity. Included in the result is a greatly simplified proof that the NJ algorithm also has optimal reconstruction radius. (co-author Jens Lagergren)</p><p>• NP-hardness results for the most common variations of Multiple Alignment. In particular, it is shown that SP-score, Star Alignment, and Tree Alignment, are NP hard for all metric symbol distances over all binary or larger alphabets.</p><p>• A 1.375-approximation algorithm for Sorting By Transpositions (SBT). SBT is the problem of sorting a permutation using as few block-transpositions as possible. The complexity of this problem is still open and it was a ten-year-old open problem to improve the best known 1.5-approximation ratio. The 1.375-approximation algorithm is based on a new upper bound on the diameter of 3-permutations. Moreover, a new lower bound on the transposition diameter of the symmetric group is presented and the exact transposition diameter of simple permutations is determined. (co-author Tzvika Hartman)</p><p>• Approximation, fixed-parameter tractable, and fast heuristic algorithms for two variants of the Ancestral Maximum Likelihood (AML) problem: when the phylogenetic tree is known and when it is unknown. AML is the problem of reconstructing the most likely genetic sequences of extinct ancestors along with the most likely mutation probabilities on the edges, given the phylogenetic tree and sequences at the leafs. (co-author Tamir Tuller)</p><p>• An algorithm for computing the number of mutational events between aligned DNA sequences which is several hundred times faster than the famous Phylip packages. Since pairwise distance estimation is a bottleneck in distance-based phylogeny reconstruction, the new algorithm improves the overall running time of many distancebased methods by a factor of several hundred. (co-author Jens Lagergren)</p>

Thesis (doctoral)--Faculté des lettres de Stockholm, 1962. / Thesis t.p. inserted. Includes bibliographical references (p. [260]-267) and index.