Lattice density-functional theory on graphene

A density-functional approach on the hexagonal graphene lattice is developed using an exact numerical solution to the Hubbard model as the reference system. Both nearest-neighbour and up to third nearest-neighbour hoppings are considered and exchange-correlation potentials within the local density approximation are parameterized for both variants. The method is used to calculate the ground-state energy and density of graphene flakes and infinite graphene sheet. The results are found to agree with exact diagonalization for small systems, also if local impurities are present. In addition, correct ground-state spin is found in the case of large triangular and bowtie flakes out of the scope of exact diagonalization methods.

Efficient search for statistically significant dependency rules in binary data

Analyzing statistical dependencies is a fundamental problem in all empirical science. Dependencies help us understand causes and effects, create new scientific theories, and invent cures to problems. Nowadays, large amounts of data is available, but efficient computational tools for analyzing the data are missing. In this research, we develop efficient algorithms for a commonly occurring search problem - searching for the statistically most significant dependency rules in binary data. We consider dependency rules of the form X->A or X->not A, where X is a set of positive-valued attributes and A is a single attribute. Such rules describe which factors either increase or decrease the probability of the consequent A. A classical example are genetic and environmental factors, which can either cause or prevent a disease. The emphasis in this research is that the discovered dependencies should be genuine - i.e. they should also hold in future data. This is an important distinction from the traditional association rules, which - in spite of their name and a similar appearance to dependency rules - do not necessarily represent statistical dependencies at all or represent only spurious connections, which occur by chance. Therefore, the principal objective is to search for the rules with statistical significance measures. Another important objective is to search for only non-redundant rules, which express the real causes of dependence, without any occasional extra factors. The extra factors do not add any new information on the dependence, but can only blur it and make it less accurate in future data. The problem is computationally very demanding, because the number of all possible rules increases exponentially with the number of attributes. In addition, neither the statistical dependency nor the statistical significance are monotonic properties, which means that the traditional pruning techniques do not work. As a solution, we first derive the mathematical basis for pruning the search space with any well-behaving statistical significance measures. The mathematical theory is complemented by a new algorithmic invention, which enables an efficient search without any heuristic restrictions. The resulting algorithm can be used to search for both positive and negative dependencies with any commonly used statistical measures, like Fisher's exact test, the chi-squared measure, mutual information, and z scores. According to our experiments, the algorithm is well-scalable, especially with Fisher's exact test. It can easily handle even the densest data sets with 10000-20000 attributes. Still, the results are globally optimal, which is a remarkable improvement over the existing solutions. In practice, this means that the user does not have to worry whether the dependencies hold in future data or if the data still contains better, but undiscovered dependencies.

Improving GPS time series for geodynamic studies

Accurate and stable time series of geodetic parameters can be used to help in understanding the dynamic Earth and its response to global change. The Global Positioning System, GPS, has proven to be invaluable in modern geodynamic studies. In Fennoscandia the first GPS networks were set up in 1993. These networks form the basis of the national reference frames in the area, but they also provide long and important time series for crustal deformation studies. These time series can be used, for example, to better constrain the ice history of the last ice age and the Earth s structure, via existing glacial isostatic adjustment models. To improve the accuracy and stability of the GPS time series, the possible nuisance parameters and error sources need to be minimized. We have analysed GPS time series to study two phenomena. First, we study the refraction in the neutral atmosphere of the GPS signal, and, second, we study the surface loading of the crust by environmental factors, namely the non-tidal Baltic Sea, atmospheric load and varying continental water reservoirs. We studied the atmospheric effects on the GPS time series by comparing the standard method to slant delays derived from a regional numerical weather model. We have presented a method for correcting the atmospheric delays at the observational level. The results show that both standard atmosphere modelling and the atmospheric delays derived from a numerical weather model by ray-tracing provide a stable solution. The advantage of the latter is that the number of unknowns used in the computation decreases and thus, the computation may become faster and more robust. The computation can also be done with any processing software that allows the atmospheric correction to be turned off. The crustal deformation due to loading was computed by convolving Green s functions with surface load data, that is to say, global hydrology models, global numerical weather models and a local model for the Baltic Sea. The result was that the loading factors can be seen in the GPS coordinate time series. Reducing the computed deformation from the vertical time series of GPS coordinates reduces the scatter of the time series; however, the long term trends are not influenced. We show that global hydrology models and the local sea surface can explain up to 30% of the GPS time series variation. On the other hand atmospheric loading admittance in the GPS time series is low, and different hydrological surface load models could not be validated in the present study. In order to be used for GPS corrections in the future, both atmospheric loading and hydrological models need further analysis and improvements.

Multiscale study on hydrogen mobility in metallic fusion divertor material

For achieving efficient fusion energy production, the plasma-facing wall materials of the fusion reactor should ensure long time operation. In the next step fusion device, ITER, the first wall region facing the highest heat and particle load, i.e. the divertor area, will mainly consist of tiles based on tungsten. During the reactor operation, the tungsten material is slowly but inevitably saturated with tritium. Tritium is the relatively short-lived hydrogen isotope used in the fusion reaction. The amount of tritium retained in the wall materials should be minimized and its recycling back to the plasma must be unrestrained, otherwise it cannot be used for fueling the plasma. A very expensive and thus economically not viable solution is to replace the first walls quite often. A better solution is to heat the walls to temperatures where tritium is released. Unfortunately, the exact mechanisms of hydrogen release in tungsten are not known. In this thesis both experimental and computational methods have been used for studying the release and retention of hydrogen in tungsten. The experimental work consists of hydrogen implantations into pure polycrystalline tungsten, the determination of the hydrogen concentrations using ion beam analyses (IBA) and monitoring the out-diffused hydrogen gas with thermodesorption spectrometry (TDS) as the tungsten samples are heated at elevated temperatures. Combining IBA methods with TDS, the retained amount of hydrogen is obtained as well as the temperatures needed for the hydrogen release. With computational methods the hydrogen-defect interactions and implantation-induced irradiation damage can be examined at the atomic level. The method of multiscale modelling combines the results obtained from computational methodologies applicable at different length and time scales. Electron density functional theory calculations were used for determining the energetics of the elementary processes of hydrogen in tungsten, such as diffusivity and trapping to vacancies and surfaces. Results from the energetics of pure tungsten defects were used in the development of an classical bond-order potential for describing the tungsten defects to be used in molecular dynamics simulations. The developed potential was utilized in determination of the defect clustering and annihilation properties. These results were further employed in binary collision and rate theory calculations to determine the evolution of large defect clusters that trap hydrogen in the course of implantation. The computational results for the defect and trapped hydrogen concentrations were successfully compared with the experimental results. With the aforedescribed multiscale analysis the experimental results within this thesis and found in the literature were explained both quantitatively and qualitatively.

Japanese Video Game Localization : A Case Study of Sony's Sairen Series

This thesis is a comparative case study in Japanese video game localization for the video games Sairen, Sairen 2 and Sairen Nyûtoransurêshon, and English-language localized versions of the same games as published in Scandinavia and Australia/New Zealand. All games are developed by Sony Computer Entertainment Inc. and published exclusively for Playstation2 and Playstation3 consoles. The fictional world of the Sairen games draws much influence from Japanese history, as well as from popular and contemporary culture, and in doing so caters mainly to a Japanese audience. For localization, i.e. the adaptation of a product to make it accessible to users outside the original market it was intended for in the first place, this is a challenging issue. Video games are media of entertainment, and therefore localization practice must preserve the games’ effects on the players’ emotions. Further, video games are digital products that are comprised of a multitude of distinct elements, some of which are part of the game world, while others regulate the connection between the player as part of the real world and the game as digital medium. As a result, video game localization is also a practice that has to cope with the technical restrictions that are inherent to the medium. The main theory used throughout the thesis is Anthony Pym’s framework for localization studies that considers the user of the localized product as a defining part of the localization process. This concept presupposes that localization is an adaptation that is performed to make a product better suited for use during a specific reception situation. Pym also addresses the factor that certain products may resist distribution into certain reception situations because of their content, and that certain aspects of localization aim to reduce this resistance through significant alterations of the original product. While Pym developed his ideas with mainly regular software in mind, they can also be adapted well to study video games from a localization angle. Since modern video games are highly complex entities that often switch between interactive and non-interactive modes, Pym’s ideas are adapted throughout the thesis to suit the particular elements being studied. Instances analyzed in this thesis include menu screens, video clips, in-game action and websites. The main research questions focus on how the games’ rules influence localization, and how the games’ fictional domain influences localization. Because there are so many peculiarities inherent to the medium of the video game, other theories are introduced as well to complement the research at hand. These include Lawrence Venuti’s discussions of foreiginizing and domesticating translation methods for literary translation, and Jesper Juul’s definition of games. Additionally, knowledge gathered from interviews with video game localization professionals in Japan during September and October 2009 is also utilized for this study. Apart from answering the aforementioned research questions, one of this thesis’ aims is to enrich the still rather small field of game localization studies, and the study of Japanese video games in particular, one of Japan’s most successful cultural exports.

Methodological and Empirical Advances in the Quantitative Analysis of Spontaneous Responses in Psychophysiological Time Series

The aim of the present study was to advance the methodology and use of time series analysis to quantify dynamic structures in psychophysiological processes and thereby to produce information on spontaneously coupled physiological responses and their behavioral and experiential correlates. Series of analyses using both simulated and empirical cardiac (IBI), electrodermal (EDA), and facial electromyographic (EMG) data indicated that, despite potential autocorrelated structures, smoothing increased the reliability of detecting response coupling from an interindividual distribution of intraindividual measures and that especially the measures of covariance produced accurate information on the extent of coupled responses. This methodology was applied to analyze spontaneously coupled IBI, EDA, and facial EMG responses and vagal activity in their relation to emotional experience and personality characteristics in a group of middle-aged men (n = 37) during the administration of the Rorschach testing protocol. The results revealed new characteristics in the relationship between phasic end-organ synchronization and vagal activity, on the one hand, and individual differences in emotional adjustment to novel situations on the other. Specifically, it appeared that the vagal system is intimately related to emotional and social responsivity. It was also found that the lack of spontaneously synchronized responses is related to decreased energetic arousal (e.g., depression, mood). These findings indicate that the present process analysis approach has many advantages for use in both experimental and applied research, and that it is a useful new paradigm in psychophysiological research. Keywords: Autonomic Nervous System; Emotion; Facial Electromyography; Individual Differences; Spontaneous Responses; Time Series Analysis; Vagal System

Teacher Education, School Effectiveness and Improvement : A Study of Academic and Professional Qualification on Teachers' Job Effectiveness in Nigerian Secondary Schools

This academic work begins with a compact presentation of the general background to the study, which also includes an autobiography for the interest in this research. The presentation provides readers who know little of the topic of this research and of the structure of the educational system as well as of the value given to education in Nigeria. It further concentrates on the dynamic interplay of the effect of academic and professional qualification and teachers' job effectiveness in secondary schools in Nigeria in particular, and in Africa in general. The aim of this study is to produce a systematic analysis and rich theoretical and empirical description of teachers' teaching competencies. The theoretical part comprises a comprehensive literature review that focuses on research conducted in the areas of academic and professional qualification and teachers' job effectiveness, teaching competencies, and the role of teacher education with particular emphasis on school effectiveness and improvement. This research benefits greatly from the functionalist conception of education, which is built upon two emphases: the application of the scientific method to the objective social world, and the use of an analogy between the individual 'organism' and 'society'. To this end, it offers us an opportunity to define terms systematically and to view problems as always being interrelated with other components of society. The empirical part involves describing and interpreting what educational objectives can be achieved with the help of teachers' teaching competencies in close connection to educational planning, teacher training and development, and achieving them without waste. The data used in this study were collected between 2002 and 2003 from teachers, principals, supervisors of education from the Ministry of Education and Post Primary Schools Board in the Rivers State of Nigeria (N=300). The data were collected from interviews, documents, observation, and questionnaires and were analyzed using both qualitative and quantitative methods to strengthen the validity of the findings. The data collected were analyzed to answer the specific research questions and hypotheses posited in this study. The data analysis involved the use of multiple statistical procedures: Percentages Mean Point Value, T-test of Significance, One-Way Analysis of Variance (ANOVA), and Cross Tabulation. The results obtained from the data analysis show that teachers require professional knowledge and professional teaching skills, as well as a broad base of general knowledge (e.g., morality, service, cultural capital, institutional survey). Above all, in order to carry out instructional processes effectively, teachers should be both academically and professionally trained. This study revealed that teachers are not however expected to have an extraordinary memory, but rather looked upon as persons capable of thinking in the right direction. This study may provide a solution to the problem of teacher education and school effectiveness in Nigeria. For this reason, I offer this treatise to anyone seriously committed in improving schools in developing countries in general and in Nigeria in particular to improve the lives of all its citizens. In particular, I write this to encourage educational planners, education policy makers, curriculum developers, principals, teachers, and students of education interested in empirical information and methods to conceptualize the issue this study has raised and to provide them with useful suggestions to help them improve secondary schooling in Nigeria. Though, multiple audiences exist for any text. For this reason, I trust that the academic community will find this piece of work a useful addition to the existing literature on school effectiveness and school improvement. Through integrating concepts from a number of disciplines, I aim to describe as holistic a representation as space could allow of the components of school effectiveness and quality improvement. A new perspective on teachers' professional competencies, which not only take into consideration the unique characteristics of the variables used in this study, but also recommend their environmental and cultural derivation. In addition, researchers should focus their attention on the ways in which both professional and non-professional teachers construct and apply their methodological competencies, such as their grouping procedures and behaviors to the schooling of students. Keywords: Professional Training, Academic Training, Professionally Qualified, Academically Qualified, Professional Qualification, Academic Qualification, Job Effectiveness, Job Efficiency, Educational Planning, Teacher Training and Development, Nigeria.

Molecular and Cellular Mechanisms Behind Juvenile Neuronal Ceroid Lipofuscinosis (JNCL, Batten disease)

Neurodegenerative disorders are chronic, progressive, and often fatal disorders of the nervous system caused by dysfunction, and ultimately, death of neuronal cells. The underlying mechanisms of neurodegeneration are poorly understood, and monogenic disorders can be utilised as disease models to elucidate the pathogenesis. Juvenile neuronal ceroid-lipofuscinosis (JNCL, Batten disease) is a recessively inherited lysosomal storage disorder with progressive neurodegeneration and accumulation of autofluorescent storage material in most tissues. It is caused by mutations in the CLN3 gene; however, the exact function of the corresponding CLN3 protein, as well as the molecular mechanisms of JNCL pathogenesis have remained elusive. JNCL disease exclusively affects the central nervous system leaving other organs unaffected, and therefore it is of a particular importance to conduct studies in brain tissue and neuronal cells. The aim of this thesis project was to elucidate the molecular and cell biological mechanisms underlying JNCL. This was the first study to describe the endogenous Cln3 protein, and it was shown that Cln3 localised to neuronal cells in the mouse brain. At a subcellular level, endogenous Cln3 was localised to the presynaptic terminals and to the synaptosome compartment, but not to the synaptic vesicles. Studies with the CLN3-deficient cells demonstrated an impaired endocytic membrane trafficking, and established an interconnection between CLN3, microtubulus-binding Hook1 and Rab proteins. This novel data was not only important in characterising the roles of CLN3 in cells, but also provided significant information delineating the versatile role of the Rab proteins. To identify affected cellular pathways in JNCL, global gene expression profiling of the knock-out mouse Cln3-/- neurons was performed and systematically analysed; this revealed a slight dysfunction of the mitochondria, cytoskeletal abnormality in the microtubule plus-end, and an impaired recovery from depolarizing stimulus when specific N-type Ca2+ channels were inhibited, thus leading to a prolonged time of higher intracellular calcium. All these defective pathways are interrelated, and may together be sufficient to initiate the neurodegenerative process. Results of this thesis also suggest that in neuronal cells, CLN3 most likely functions at endocytic vesicles at the presynaptic terminal, potentially involved in the regulation of the calcium-mediated synaptic transmission.

Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.

A Decentralized Session Management Framework for Heterogeneous Ad-Hoc and Fixed Networks

Wireless technologies are continuously evolving. Second generation cellular networks have gained worldwide acceptance. Wireless LANs are commonly deployed in corporations or university campuses, and their diffusion in public hotspots is growing. Third generation cellular systems are yet to affirm everywhere; still, there is an impressive amount of research ongoing for deploying beyond 3G systems. These new wireless technologies combine the characteristics of WLAN based and cellular networks to provide increased bandwidth. The common direction where all the efforts in wireless technologies are headed is towards an IP-based communication. Telephony services have been the killer application for cellular systems; their evolution to packet-switched networks is a natural path. Effective IP telephony signaling protocols, such as the Session Initiation Protocol (SIP) and the H 323 protocol are needed to establish IP-based telephony sessions. However, IP telephony is just one service example of IP-based communication. IP-based multimedia sessions are expected to become popular and offer a wider range of communication capabilities than pure telephony. In order to conjoin the advances of the future wireless technologies with the potential of IP-based multimedia communication, the next step would be to obtain ubiquitous communication capabilities. According to this vision, people must be able to communicate also when no support from an infrastructured network is available, needed or desired. In order to achieve ubiquitous communication, end devices must integrate all the capabilities necessary for IP-based distributed and decentralized communication. Such capabilities are currently missing. For example, it is not possible to utilize native IP telephony signaling protocols in a totally decentralized way. This dissertation presents a solution for deploying the SIP protocol in a decentralized fashion without support of infrastructure servers. The proposed solution is mainly designed to fit the needs of decentralized mobile environments, and can be applied to small scale ad-hoc networks or also bigger networks with hundreds of nodes. A framework allowing discovery of SIP users in ad-hoc networks and the establishment of SIP sessions among them, in a fully distributed and secure way, is described and evaluated. Security support allows ad-hoc users to authenticate the sender of a message, and to verify the integrity of a received message. The distributed session management framework has been extended in order to achieve interoperability with the Internet, and the native Internet applications. With limited extensions to the SIP protocol, we have designed and experimentally validated a SIP gateway allowing SIP signaling between ad-hoc networks with private addressing space and native SIP applications in the Internet. The design is completed by an application level relay that permits instant messaging sessions to be established in heterogeneous environments. The resulting framework constitutes a flexible and effective approach for the pervasive deployment of real time applications.

Barrett's Esophagus and Associated Adenocarcinoma : studies on pathogenesis, clinical staging and cost-utility of cancer treatment

Esophageal and gastroesophageal junction (GEJ) adenocarcinoma is rapidly increasing disease with a pathophysiology connected to oxidative stress. Exact pre-treatment clinical staging is essential for optimal care of this lethal malignancy. The cost-effectiviness of treatment is increasingly important. We measured oxidative metabolism in the distal and proximal esophagus by myeloperoxidase activity (MPA), glutathione content (GSH), and superoxide dismutase (SOD) in 20 patients operated on with Nissen fundoplication and 9 controls during a 4-year follow-up. Further, we assessed the oxidative damage of DNA by 8-hydroxydeoxyguanosine (8-OHdG) in esophageal samples of subjects (13 Barrett s metaplasia, 6 Barrett s esophagus with high-grade dysplasia, 18 adenocarcinoma of the distal esophagus/GEJ, and 14 normal controls). We estimated the accuracy (42 patients) and preoperative prognostic value (55 patients) of PET compared with computed tomography (CT) and endoscopic ultrasound (EUS) in patients with adenocarcinoma of the esophagus/GEJ. Finally, we clarified the specialty-related costs and the utility of either radical (30 patients) or palliative (23 patients) treatment of esophageal/GEJ carcinoma by the 15 D health-related quality-of-life (HRQoL) questionnaire and the survival rate. The cost-utility of radical treatment of esophageal/GEJ carcinoma was investigated using a decision tree analysis model comparing radical, palliative, and hypothetical new treatment. We found elevated oxidative stress ( measured by MPA) and decreased antioxidant defense (measured by GSH) after antireflux surgery. This indicates that antireflux surgery is not a perfect solution for oxidative stress of the esophageal mucosa. Elevated oxidative stress in turn may partly explain why adenocarcinoma of the distal esophagus is found even after successful fundoplication. In GERD patients, proximal esophageal mucosal anti-oxidative defense seems to be defective before and even years after successful antireflux surgery. In addition, antireflux surgery apparently does not change the level of oxidative stress in the proximal esophagus, suggesting that defective mucosal anti-oxidative capacity plays a role in development of oxidative damage to the esophageal mucosa in GERD. In the malignant transformation of Barrett s esophagus an important component appears to be oxidative stress. DNA damage may be mediated by 8-OHdG, which we found to be increased in Barrett s epithelium and in high-grade dysplasia as well as in adenocarcinoma of the esophagus/GEJ compared with controls. The entire esophagus of Barrett s patients suffers from increased oxidative stress ( measured by 8-OhdG). PET is a useful tool in the staging and prognostication of adenocarcinoma of the esophagus/GEJ detecting organ metastases better than CT, although its accuracy in staging of paratumoral and distant lymph nodes is limited. Radical surgery for esophageal/GEJ carcinoma provides the greatest benefit in terms of survival, and its cost-utility appears to be the best of currently available treatments.