Molecular Mechanisms and Interactions in Regulation of Photosynthetic Reactions

In photosynthesis, light energy is converted to chemical energy, which is consumed for carbon assimilation in the Calvin-Benson-Bassham (CBB) cycle. Intensive research has significantly advanced the understanding of how photosynthesis can survive in the ever-changing light conditions. However, precise details concerning the dynamic regulation of photosynthetic processes have remained elusive. The aim of my thesis was to specify some molecular mechanisms and interactions behind the regulation of photosynthetic reactions under environmental fluctuations. A genetic approach was employed, whereby Arabidopsis thaliana mutants deficient in specific photosynthetic protein components were subjected to adverse light conditions and assessed for functional deficiencies in the photosynthetic machinery. I examined three interconnected mechanisms: (i) auxiliary functions of PsbO1 and PsbO2 isoforms in the oxygen evolving complex of photosystem II (PSII), (ii) the regulatory function of PGR5 in photosynthetic electron transfer and (iii) the involvement of the Calcium Sensing Receptor CaS in photosynthetic performance. Analysis of photosynthetic properties in psbo1 and psbo2 mutants demonstrated that PSII is sensitive to light induced damage when PsbO2, rather than PsbO1, is present in the oxygen evolving complex. PsbO1 stabilizes PSII more efficiently compared to PsbO2 under light stress. However, PsbO2 shows a higher GTPase activity compared to PsbO1, and plants may partially compensate the lack of PsbO1 by increasing the rate of the PSII repair cycle. PGR5 proved vital in the protection of photosystem I (PSI) under fluctuating light conditions. Biophysical characterization of photosynthetic electron transfer reactions revealed that PGR5 regulates linear electron transfer by controlling proton motive force, which is crucial for the induction of the photoprotective non-photochemical quenching and the control of electron flow from PSII to PSI. I conclude that PGR5 controls linear electron transfer to protect PSI against light induced oxidative damage. I also found that PGR5 physically interacts with CaS, which is not needed for photoprotection of PSII or PSI in higher plants. Rather, transcript profiling and quantitative proteomic analysis suggested that CaS is functionally connected with the CBB cycle. This conclusion was supported by lowered amounts of specific calciumregulated CBB enzymes in cas mutant chloroplasts and by slow electron flow to PSI electron acceptors when leaves were reilluminated after an extended dark period. I propose that CaS is required for calcium regulation of the CBB cycle during periods of darkness. Moreover, CaS may also have a regulatory role in the activation of chloroplast ATPase. Through their diverse interactions, components of the photosynthetic machinery ensure optimization of light-driven electron transport and efficient basic production, while minimizing the harm caused by light induced photodamage.

Minimizing Circulating Current in Parallel-Connected Photovoltaic Inverters

Parallel-connected photovoltaic inverters are required in large solar plants where it is not economically or technically reasonable to use a single inverter. Currently, parallel inverters require individual isolating transformers to cut the path for the circulating current. In this doctoral dissertation, the problem is approached by attempting to minimize the generated circulating current. The circulating current is a function of the generated common-mode voltages of the parallel inverters and can be minimized by synchronizing the inverters. The synchronization has previously been achieved by a communication link. However, in photovoltaic systems the inverters may be located far apart from each other. Thus, a control free of communication is desired. It is shown in this doctoral dissertation that the circulating current can also be obtained by a common-mode voltage measurement. A control method based on a short-time switching frequency transition is developed and tested with an actual photovoltaic environment of two parallel inverters connected to two 5 kW solar arrays. Controls based on the measurement of the circulating current and the common-mode voltage are generated and tested. A communication-free method of controlling the circulating current between parallelconnected inverters is developed and verified.

A systematic mapping study of web services discovery mechanisms

Context: Web services have been gaining popularity due to the success of service oriented architecture and cloud computing. Web services offer tremendous opportunity for service developers to publish their services and applications over the boundaries of the organization or company. However, to fully exploit these opportunities it is necessary to find efficient discovery mechanism thus, Web services discovering mechanism has attracted a considerable attention in Semantic Web research, however, there have been no literature surveys that systematically map the present research result thus overall impact of these research efforts and level of maturity of their results are still unclear. This thesis aims at providing an overview of the current state of research into Web services discovering mechanism using systematic mapping. The work is based on the papers published 2004 to 2013, and attempts to elaborate various aspects of the analyzed literature including classifying them in terms of the architecture, frameworks and methods used for web services discovery mechanism. Objective: The objective if this work is to summarize the current knowledge that is available as regards to Web service discovery mechanisms as well as to systematically identify and analyze the current published research works in order to identify different approaches presented. Method: A systematic mapping study has been employed to assess the various Web Services discovery approaches presented in the literature. Systematic mapping studies are useful for categorizing and summarizing the level of maturity research area. Results: The result indicates that there are numerous approaches that are consistently being researched and published in this field. In terms of where these researches are published, conferences are major contributing publishing arena as 48% of the selected papers were conference published papers illustrating the level of maturity of the research topic. Additionally selected 52 papers are categorized into two broad segments namely functional and non-functional based approaches taking into consideration architectural aspects and information retrieval approaches, semantic matching, syntactic matching, behavior based matching as well as QOS and other constraints.

The Impact of Electrical Capacity Market Mechanisms on Capacity Mobility and End Use Customer Pricing

Potential impacts of electrical capacity market design on capacity mobility and end use customer pricing are analyzed. Market rules and historical evolution are summarized to provide a background for the analysis. The summarized rules are then examined for impacts on capacity mobility. A summary of the aspects of successful capacity markets is provided. Two United States market regions are chosen for analysis based upon their market history and proximity to each other. The MISO region is chosen due to recent developments in capacity market mechanisms. The PJM region neighbors the MISO region and is similar in size and makeup. The PJM region has had a capacity market mechanism for over a decade and allows for a controlled comparison of the MISO region’s developments. Capacity rules are found to have an impact on the mobility of capacity between regions. Regulatory restrictions and financial penalties for the movement of capacity between regions are found which effectively hinder such mobility. Capacity market evolution timelines are formed from the historical evolution previously summarized and compared to historical pricing to inspect for a correlation. No direct and immediate impact on end use customer pricing was found due to capacity market design. The components of end use customer pricing are briefly examined.

Value of Information Logistics Integration in Digital Business Ecosystem

Digital business ecosystems (DBE) are becoming an increasingly popular concept for modelling and building distributed systems in heterogeneous, decentralized and open environments. Information- and communication technology (ICT) enabled business solutions have created an opportunity for automated business relations and transactions. The deployment of ICT in business-to-business (B2B) integration seeks to improve competitiveness by establishing real-time information and offering better information visibility to business ecosystem actors. The products, components and raw material flows in supply chains are traditionally studied in logistics research. In this study, we expand the research to cover the processes parallel to the service and information flows as information logistics integration. In this thesis, we show how better integration and automation of information flows enhance the speed of processes and, thus, provide cost savings and other benefits for organizations. Investments in DBE are intended to add value through business automation and are key decisions in building up information logistics integration. Business solutions that build on automation are important sources of value in networks that promote and support business relations and transactions. Value is created through improved productivity and effectiveness when new, more efficient collaboration methods are discovered and integrated into DBE. Organizations, business networks and collaborations, even with competitors, form DBE in which information logistics integration has a significant role as a value driver. However, traditional economic and computing theories do not focus on digital business ecosystems as a separate form of organization, and they do not provide conceptual frameworks that can be used to explore digital business ecosystems as value drivers—combined internal management and external coordination mechanisms for information logistics integration are not the current practice of a company’s strategic process. In this thesis, we have developed and tested a framework to explore the digital business ecosystems developed and a coordination model for digital business ecosystem integration; moreover, we have analysed the value of information logistics integration. The research is based on a case study and on mixed methods, in which we use the Delphi method and Internetbased tools for idea generation and development. We conducted many interviews with key experts, which we recoded, transcribed and coded to find success factors. Qualitative analyses were based on a Monte Carlo simulation, which sought cost savings, and Real Option Valuation, which sought an optimal investment program for the ecosystem level. This study provides valuable knowledge regarding information logistics integration by utilizing a suitable business process information model for collaboration. An information model is based on the business process scenarios and on detailed transactions for the mapping and automation of product, service and information flows. The research results illustrate the current cap of understanding information logistics integration in a digital business ecosystem. Based on success factors, we were able to illustrate how specific coordination mechanisms related to network management and orchestration could be designed. We also pointed out the potential of information logistics integration in value creation. With the help of global standardization experts, we utilized the design of the core information model for B2B integration. We built this quantitative analysis by using the Monte Carlo-based simulation model and the Real Option Value model. This research covers relevant new research disciplines, such as information logistics integration and digital business ecosystems, in which the current literature needs to be improved. This research was executed by high-level experts and managers responsible for global business network B2B integration. However, the research was dominated by one industry domain, and therefore a more comprehensive exploration should be undertaken to cover a larger population of business sectors. Based on this research, the new quantitative survey could provide new possibilities to examine information logistics integration in digital business ecosystems. The value activities indicate that further studies should continue, especially with regard to the collaboration issues on integration, focusing on a user-centric approach. We should better understand how real-time information supports customer value creation by imbedding the information into the lifetime value of products and services. The aim of this research was to build competitive advantage through B2B integration to support a real-time economy. For practitioners, this research created several tools and concepts to improve value activities, information logistics integration design and management and orchestration models. Based on the results, the companies were able to better understand the formulation of the digital business ecosystem and the importance of joint efforts in collaboration. However, the challenge of incorporating this new knowledge into strategic processes in a multi-stakeholder environment remains. This challenge has been noted, and new projects have been established in pursuit of a real-time economy.

The Arctic Ocean between Greenland and Nova Zemla and between the 60th and 82d parallel of latitude from Swedish, Danish, British, Russian and German surveys and explorations up to 1871

Kartta kuuluu A. E. Nordenskiöldin kokoelmaan

Virtual Runtime Application Partitions for Resource Management in Massively Parallel Architectures

This thesis presents a novel design paradigm, called Virtual Runtime Application Partitions (VRAP), to judiciously utilize the on-chip resources. As the dark silicon era approaches, where the power considerations will allow only a fraction chip to be powered on, judicious resource management will become a key consideration in future designs. Most of the works on resource management treat only the physical components (i.e. computation, communication, and memory blocks) as resources and manipulate the component to application mapping to optimize various parameters (e.g. energy efficiency). To further enhance the optimization potential, in addition to the physical resources we propose to manipulate abstract resources (i.e. voltage/frequency operating point, the fault-tolerance strength, the degree of parallelism, and the configuration architecture). The proposed framework (i.e. VRAP) encapsulates methods, algorithms, and hardware blocks to provide each application with the abstract resources tailored to its needs. To test the efficacy of this concept, we have developed three distinct self adaptive environments: (i) Private Operating Environment (POE), (ii) Private Reliability Environment (PRE), and (iii) Private Configuration Environment (PCE) that collectively ensure that each application meets its deadlines using minimal platform resources. In this work several novel architectural enhancements, algorithms and policies are presented to realize the virtual runtime application partitions efficiently. Considering the future design trends, we have chosen Coarse Grained Reconfigurable Architectures (CGRAs) and Network on Chips (NoCs) to test the feasibility of our approach. Specifically, we have chosen Dynamically Reconfigurable Resource Array (DRRA) and McNoC as the representative CGRA and NoC platforms. The proposed techniques are compared and evaluated using a variety of quantitative experiments. Synthesis and simulation results demonstrate VRAP significantly enhances the energy and power efficiency compared to state of the art.

Phenomena and mechanisms in purification of animal fat

Työn tarkoitus oli tutkia eläinrasvan puhdistusta biodieselin valmistusta varten. Eläinrasvaa syntyy elintarviketeollisuuden sivutuotteena ja sitä saadaan myös myymättä jääneistä elintarvikkeista. Rasva sisältää epäpuhtauksia, jotka on poistettava ennen biodieselprosessia. Tässä työssä tutkittavat epäpuhtaudet ovat typpi, fosfori, rauta, natrium, kalsium ja magnesium. Puhdistusmenetelminä käytettiin saostamista sitruunahapolla sekä adsorbointia kahdella eri adsorbentilla. Tavoitteena oli selvittää riittävä määrä happoa ja adsorbenttia sekä tutkia puhdistuksen mekanismia. Lisäksi tarkasteltiin lämpötilan vaikutusta adsorption aikana.

Molecular Mechanisms of Sexual Dimorphism in Threespine Stickleback

Sexual dimorphism is commonly understood as differences in external features, such as morphological features or coloration. However, it can more broadly encompass behavior and physiology and at the core of these differences is the genetic mechanism – mRNA and protein expression. How, and which, molecular mechanisms influence sexually dimorphic features is not well understood thus far. DNA, RNA and proteins are the template required to create the phenotype of an individual, and they are connected to each other via processes of transcription and translation. As the genome of males and females are almost identical with the exception of the few genes on the sex chromosome or the sex-determining alleles (in the case of organisms without sex chromosomes), it is likely that many of the downstream processes resulting in sexual dimorphism are produced by changes in gene regulation and result from a regulatory cascade and not from a vastly different gene composition. Thus, in this thesis a systems biology approach is used to understand sexual dimorphism at all molecular levels and how different genomic features, e.g. sex chromosome evolution, can affect the interplay of these molecules. The threespine stickleback, Gasterosteus aculeatus, is used as the model to investigate molecular mechanisms of sexual dimorphism. It has well-characterized ecology and behavior, especially in the breeding season when sexual dimorphism is high. Moreover, threespine stickleback has a recently evolved Y chromosome in the early stages of sex chromosome evolution, characterized by a lack of recombination leading to degeneration (i.e. gene loss). The aim of my thesis is to investigate how the genotype links to the molecular phenotype and relates to differences in molecular expression between males and females. Based on previous research on sex differences in mRNA expression, I investigated sex-biased protein expression in adult fish outside the breeding season to see if differences persisted after translation. As sex-biased expression also prevailed in the proteome and previous transcription expression seemed to be related to the sex chromosomes, I investigated the genome level with a particular focus on the sex-chromosomes. I characterized the status of Y chromosome degeneration in the threespine stickleback and its effects on gene function. Furthermore, since the degeneration process leaves genes in a single copy in males, I examined whether the resulting dosage difference of messenger RNA for hemizygous genes is compensated as it is in other organisms. In addition, threespine sticklebacks have wellcharacterized behavioral differences related to the male’s social status during the breeding season. To understand the connection between the genotype and behavior, I examined gene expression patterns related to breeding behavior using dominant and subordinate males as well as female

Agent-based management systems for many-core platforms : rigorous design and efficient implementation

Due to various advantages such as flexibility, scalability and updatability, software intensive systems are increasingly embedded in everyday life. The constantly growing number of functions executed by these systems requires a high level of performance from the underlying platform. The main approach to incrementing performance has been the increase of operating frequency of a chip. However, this has led to the problem of power dissipation, which has shifted the focus of research to parallel and distributed computing. Parallel many-core platforms can provide the required level of computational power along with low power consumption. On the one hand, this enables parallel execution of highly intensive applications. With their computational power, these platforms are likely to be used in various application domains: from home use electronics (e.g., video processing) to complex critical control systems. On the other hand, the utilization of the resources has to be efficient in terms of performance and power consumption. However, the high level of on-chip integration results in the increase of the probability of various faults and creation of hotspots leading to thermal problems. Additionally, radiation, which is frequent in space but becomes an issue also at the ground level, can cause transient faults. This can eventually induce a faulty execution of applications. Therefore, it is crucial to develop methods that enable efficient as well as resilient execution of applications. The main objective of the thesis is to propose an approach to design agentbased systems for many-core platforms in a rigorous manner. When designing such a system, we explore and integrate various dynamic reconfiguration mechanisms into agents functionality. The use of these mechanisms enhances resilience of the underlying platform whilst maintaining performance at an acceptable level. The design of the system proceeds according to a formal refinement approach which allows us to ensure correct behaviour of the system with respect to postulated properties. To enable analysis of the proposed system in terms of area overhead as well as performance, we explore an approach, where the developed rigorous models are transformed into a high-level implementation language. Specifically, we investigate methods for deriving fault-free implementations from these models into, e.g., a hardware description language, namely VHDL.

Implementing Green IT approach for transferring Big Data over Parallel Data Link

The whole research of the current Master Thesis project is related to Big Data transfer over Parallel Data Link and my main objective is to assist the Saint-Petersburg National Research University ITMO research team to accomplish this project and apply Green IT methods for the data transfer system. The goal of the team is to transfer Big Data by using parallel data links with SDN Openflow approach. My task as a team member was to compare existing data transfer applications in case to verify which results the highest data transfer speed in which occasions and explain the reasons. In the context of this thesis work a comparison between 5 different utilities was done, which including Fast Data Transfer (FDT), BBCP, BBFTP, GridFTP, and FTS3. A number of scripts where developed which consist of creating random binary data to be incompressible to have fair comparison between utilities, execute the Utilities with specified parameters, create log files, results, system parameters, and plot graphs to compare the results. Transferring such an enormous variety of data can take a long time, and hence, the necessity appears to reduce the energy consumption to make them greener. In the context of Green IT approach, our team used Cloud Computing infrastructure called OpenStack. It’s more efficient to allocated specific amount of hardware resources to test different scenarios rather than using the whole resources from our testbed. Testing our implementation with OpenStack infrastructure results that the virtual channel does not consist of any traffic and we can achieve the highest possible throughput. After receiving the final results we are in place to identify which utilities produce faster data transfer in different scenarios with specific TCP parameters and we can use them in real network data links.

Impacts of capacity remunerative mechanisms on cross-border trade

The European ambitious targets to increase the share of renewable generation pose a challenge to the generation adequacy. Many European member states are concerned that energy-only markets alone might not be able to deliver sufficient capacity required to meet the future electricity demand and back up shortfalls of energy from renewable energy sources (RES) during periods of low wind and sun. Many EU members consider to re-design their energy-only markets and establish different forms of capacity remunerative mechanisms (CRMs) to maintain the security of supply. There is a certain concern that market design changes at the level of EU member countries might conflict with the European goal of a single market. As soon as many European markets are highly interconnected, uncoordinated CRMs might create negative crossborder effects and hinder the achievement of the Internal Electricity Market in Europe. The pros and cons of capacity markets are well examined at the national level. However, the cross-border effects of capacity markets within the European market aiming at higher integration have received less attention. This doctoral dissertation examines the cross-border effects of unilateral implementation of CRMs applying both theoretical and case study analyses. The results show that capacity remunerative mechanisms (CRMs) may cause negative cross-border effects, especially if they are implemented unilaterally.

Natural born weight gainers: The mechanisms of obesity in transgenic mice overexpressing neuropeptide Y

Neuropeptide Y (NPY) is a neurotransmitter promoting energy storage by activating Y-receptors and thus affecting food intake, thermogenesis and adipose tissue metabolism. NPY is expressed both in the central and sympathetic nervous system. Hypothalamic NPY is known to stimulate feeding, but the effects of noradrenergic neuron NPY are more ambiguous. Chronic stress stimulates fat accumulation via NPY release from noradrenergic neurons. Furthermore, polymorphism in the human Npy gene has been associated with metabolic disturbances and increased NPY secretion after sympathetic stimulation. The main objective of this study was to clarify the mechanisms of noradrenergic neuron NPY in the development of obesity. The metabolic phenotype of a homozygous mouse overexpressing NPY in the brain noradrenergic neurons and sympathetic nervous system (OE-NPYDβH mouse) was characterized. OE-NPYDβH mice had an increased fat mass and body weight, which caused impairments of glucose metabolism and hyperinsulinaemia with age. There were no differences in energy intake or expenditure, but the sympathetic tone was down-regulated and the endocannabinoid system activated. Furthermore, peripheral Y2-receptors in energy-rich conditions played an important role in mediating the fat-accumulating effect of NPY. These results indicate that noradrenergic neuron NPY promotes obesity via direct effects in the periphery and by modulating the sympatho-adrenal and endocannabinoid systems. Additionally, NPY in the central noradrenergic neurons is believed to possess many important roles. The phenotype of the OE-NPYDβH mouse resembles the situations of chronic stress and Npy gene polymorphism and thus these mice may be exploited in testing novel drug candidates for the treatment of obesity.