Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Forcing Usage Rules in PublicWireless LANs

Langattomien lähiverkkojen yleistyessä nopeasti suurten verkkojen teknologiana käyttösääntöjen valvonta tulee tarpeelliseksi. Tässä työssä kuvataan, kuinka käyttäjät voidaan pakottaa noudattamaan käyttösääntöjä julkisissa WLAN-verkoissa. Työssä käsiteltävät ongelmat koskevat menetelmiä epäluotettavien DHCP-palvelinten paljastamiseksi sekä omia IP-osoitteita käyttävien käyttäjien paljastamiseksi tilanteissa, jolloin IP-osoite ei ole virallisen DHCP-palvelimen myöntämä. Jokaisen menetelmän kohdalla pohditaan, kuinka tällaisia käyttäjiä voidaan estää rikkomasta käyttösääntöjä. Lisäksi pohditaan keskitetyn tietojen keruun hyödyntämistä kuvattujen tehtävien suorittamiseksi. Esitetyt ratkaisut on erityisesti suunniteltu testiverkkoa varten, mutta yleiset ideat ovat toimivia missä tahansa langattomassa verkossa.

Assembly Methods of Permanent Magnets for Synchronous Generators

This thesis examines and explains the procedure used to redesign the attachment of permanent magnets to the surface of the rotor of a synchronous generator. The methodology followed to go from the actual assembly to converge to the final purposed innovation was based on the systematic approach design. This meant that first a series of steps had to be predefined as a frame of reference later to be used to compare and select proposals, and finally to obtain the innovation that was sought. Firstly, a series of patents was used as the background for the upcoming ideas. To this end, several different patented assemblies had been found and categorized according the main element onto which this thesis if focused, meaning the attachment element or method. After establishing the technological frame of reference, a brainstorm was performed to obtain as many ideas as possible. Then these ideas were classified, regardless of their degree of complexity or usability, since at this time the quantity of the ideas was the important issue. Subsequently, they were compared and evaluated from different points of view. The comparison and evaluation in this case was based on the use of a requirement list, which established the main needs that the design had to fulfill. Then the selection could be done by grading each idea in accordance with these requirements. In this way, one was able to obtain the idea or ideas that best fulfilled these requirements. Once all of the ideas were compared and evaluated, the best or most suitable idea or ideas were separated. Finally, the selected idea or ideas was/were analyzed in extension and a number of improvements were made. Consequently, a final idea was refined and made more suitable at its performance, manufacture, and life cycle assessment. Therefore, in the end, the design process gave a solution to the problem pointed out at the beginning.

Novel Robot Solutions for Carrying out Field Joint Welding and Machining in the Assembly of the Vacuum Vessel of ITER

It is necessary to use highly specialized robots in ITER (International Thermonuclear Experimental Reactor) both in the manufacturing and maintenance of the reactor due to a demanding environment. The sectors of the ITER vacuum vessel (VV) require more stringent tolerances than normally expected for the size of the structure involved. VV consists of nine sectors that are to be welded together. The vacuum vessel has a toroidal chamber structure. The task of the designed robot is to carry the welding apparatus along a path with a stringent tolerance during the assembly operation. In addition to the initial vacuum vessel assembly, after a limited running period, sectors need to be replaced for repair. Mechanisms with closed-loop kinematic chains are used in the design of robots in this work. One version is a purely parallel manipulator and another is a hybrid manipulator where the parallel and serial structures are combined. Traditional industrial robots that generally have the links actuated in series are inherently not very rigid and have poor dynamic performance in high speed and high dynamic loading conditions. Compared with open chain manipulators, parallel manipulators have high stiffness, high accuracy and a high force/torque capacity in a reduced workspace. Parallel manipulators have a mechanical architecture where all of the links are connected to the base and to the end-effector of the robot. The purpose of this thesis is to develop special parallel robots for the assembly, machining and repairing of the VV of the ITER. The process of the assembly and machining of the vacuum vessel needs a special robot. By studying the structure of the vacuum vessel, two novel parallel robots were designed and built; they have six and ten degrees of freedom driven by hydraulic cylinders and electrical servo motors. Kinematic models for the proposed robots were defined and two prototypes built. Experiments for machine cutting and laser welding with the 6-DOF robot were carried out. It was demonstrated that the parallel robots are capable of holding all necessary machining tools and welding end-effectors in all positions accurately and stably inside the vacuum vessel sector. The kinematic models appeared to be complex especially in the case of the 10-DOF robot because of its redundant structure. Multibody dynamics simulations were carried out, ensuring sufficient stiffness during the robot motion. The entire design and testing processes of the robots appeared to be complex tasks due to the high specialization of the manufacturing technology needed in the ITER reactor, while the results demonstrate the applicability of the proposed solutions quite well. The results offer not only devices but also a methodology for the assembly and repair of ITER by means of parallel robots.

Functional characterization of proteins required for mitotic progression and the spindle assembly checkpoint

During mitotic cell division, the genetic material packed into chromosomes is divided equally between two daughter cells. Before the separation of the two copies of a chromosome (sister chromatids), each chromosome has to be properly connected with microtubules of the mitotic spindle apparatus and aligned to the centre of the cell. The spindle assembly checkpoint (SAC) monitors connections between microtubules and chromosomes as well as tension applied across the centromere. Microtubules connect to a chromosome via kinetochores, which are proteinaceous organelles assembled onto the centromeric region of the sister chromatids. Improper kinetochore-microtubule attachments activate the SAC and block chromosome segregation until errors are corrected and all chromosomes are connected to the mitotic spindle in a bipolar manner. The purpose of this surveillance mechanism is to prevent loss or gain of chromosomes in daughter cells that according to current understanding contributes to cancer formation. Numerous proteins participate in the regulation of mitotic progression. In this thesis, the mitotic tasks of three kinetochore proteins, Shugoshin 1 (Sgo1), INCENP, and p38 MAP kinase (p38 MAPK), were investigated. Sgo1 is a protector of centromeric cohesion. It is also described in the tension-sensing mechanism of the SAC and in the regulation of kinetochore-microtubule connections. Our results revealed a central role for Sgo1 in a novel branch of kinetochore assembly. INCENP constitutes part of the chromosomal passenger complex (CPC). The other members of the core complex are the Aurora B kinase, Survivin and Borealin. CPC is an important regulatory element of cell division having several roles at various stages of mitosis. Our results indicated that INCENP and Aurora B are highly dynamic proteins at the mitotic centromeres and suggested a new role for CPC in regulation of chromosome movements and spindle structure during late mitosis. The p38 MAPK has been implicated in G1 and G2 checkpoints during the cell cycle. However, its role in mitotic progression and control of SAC signaling has been controversial. In this thesis, we discovered a novel function for p38γ MAPK in chromosome orientation and spindle structure as well as in promotion of viability of mitotic cells.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

The Finnish Paper Workers' Union at a crossroads: Labor union representativeness in a changing environment, 1980-2008

This thesis consists of four articles and an introductory section. The main research questions in all the articles refer to the changes in the representativeness of the Finnish Paper Workers' Union. Representativeness stands for the entire entity of external, internal, legal and reputational factors that enable the labor union to represent its members and achieve its goals. This concept is based on an extensive reading of quantitative and qualitative industrial relations literature, which includes works based on Marxist labor-capital relations (such as Hyman's industrial relations studies), and more recent union density studies as well as gender- and ethnic diversity-based 'union revitalization' studies. Müller-Jentsch's German studies of industrial relations have been of particular importance as well as Streeck's industrial unionism and technology studies. The concept of representativeness is an attempt to combine the insights of these diverse strands of literature and bring the scientific discussion of labor unions back to the core of a union's function: representing its members. As such, it can be seen as a theoretical innovation. The concept helps to acknowledge both the heterogeneity of the membership and the totality of a labor union organization. The concept of representativeness aims to move beyond notions of 'power'. External representativeness can be expressed through the position of the labor union in the industrial relations system and the economy. Internal representativeness focuses on the aspects of labor unions that relate to the function of the union as an association with members, such as internal democracy. Legal representativeness lies in the formal legal position of the union – its rights and instruments. This includes collective bargaining legislation, co-decision rules and industrial conflict legislation. Reputational representativeness is related to how the union is seen by other actors and the general public, and can be approximated using data on strike activity. All these aspects of representativeness are path-dependent, and show the results of previous struggles over issues. The concept of representativeness goes beyond notions of labor union power and symbolizes an attempt to bring back the focus of industrial relations studies to the union's basic function of representing its members. The first article shows in detail the industrial conflict of the Finnish paper industry in 2005. The intended focus was the issue of gender in the negotiations over a new collective agreement, but the focal point of the industrial conflict was the issue of outsourcing and how this should be organized. Also, the issue of continuous shifts as an issue of working time was very important. The drawn-out conflict can be seen as a struggle over principles, and under pressure the labor union had to concede ground on the aforementioned issues. The article concludes that in this specific conflict, the union represented its' female members to a lesser extent, because the other issues took such priority. Furthermore, because of the substantive concessions. the union lost some of its internal representativeness, and the stubbornness of the union may have even harmed the reputation of the union. This article also includes an early version of the representativeness framework, through which this conflict is analyzed. The second article discusses wage developments, union density and collective bargaining within the context of representativeness. It is shown that the union has been able to secure substantial benefits for its members, regardless of declining employment. Collective agreements have often been based on centralized incomes policies, but the paper sector has not always joined these. Attention is furthermore paid to the changing competition of the General Assembly, with a surprisingly strong position of the Left Alliance still. In an attempt to replicate analysis of union density measures, an analysis of sectoral union density shows that similar factors as in aggregate data influence this measure, though – due to methodological issues – the results may not be robust. On this issue, it can be said that the method of analysis for aggregate union density is not suitable for sectoral union density analysis. The increasingly conflict-ridden industrial relations predicted have not actually materialized. The article concludes by asking whether the aim of ever-increasing wages is a sustainable one in the light of the pressures of globalization, though wage costs are a relatively small part of total costs. The third article discusses the history and use of outsourcing in the Finnish paper industry. It is shown using Hyman's framework of constituencies that over time, the perspective of the union changed from 'members of the Paper Workers' Union' to a more specific view of who is a core member of the union. Within the context of the industrial unionism that the union claims to practice, this is an important change. The article shows that the union more and more caters for a core group, while auxiliary personnel is less important to the union's identity and constituencies, which means that the union's internal representativeness has decreased. Maintenance workers are an exception; the union and employers have developed a rotating system that increases the efficient allocation of these employees. The core reason of the exceptional status of maintenance personnel is their high level of non-transferable skills. In the end it is debatable whether the compromise on outsourcing solves the challenges facing the industry. The fourth article shows diverging discourses within the union with regard to union-employer partnership for competitiveness improvements and instruments of local union representatives. In the collective agreement of 2008, the provision regulating wage effects of significant changes in the organization or content of work was thoroughly changed, though this mainly reflected decisions by the Labor Court on the pre-2008 version of the provision. This change laid bare the deep rift between the Social Democratic and Left Alliance (ex-Communist) factions of the union. The article argues that through the changed legal meaning of the provision, the union was able to transform concession bargaining into a basis for partnership. The internal discontent about this issue is nonetheless substantial and a threat to the unity of the union, both locally and at the union level. On the basis of the results of the articles, other factors influencing representativeness, such as technology and EU law and an overview of the main changes in the Finnish paper industry, it is concluded that, especially in recent years, the Finnish Paper Workers' Union has lost some of its representativeness. In particular, the loss of the efficiency of strikes is noted, the compromise on outsourcing which may have alienated a substantial part of the union's membership, and the change in the collective agreement of 2008 have caused this decline. In the latter case, the internal disunion on that issue shows the constraints of the union's internal democracy. Furthermore, the failure of the union to join the TEAM industrial union (by democratic means), the internal conflicts and a narrow focus on its own sector may also hurt the union in the future, as the paper industry in Finland is going through a structural change. None of these changes in representativeness would have been so drastic without the considerable pressure of globalization - in particular changing markets, changing technology and a loss of domestic investments to foreign investments, which in the end have benefited the corporations more than the Finnish employees of these corporations. Taken together, the union risks becoming socially irrelevant in time, though it will remain formally very strong on the basis of its institutional setting and financial situation.

The spindle assembly checkpoint as a drug target - Novel small-molecule inhibitors of Aurora kinases

Cell division (mitosis) is a fundamental process in the life cycle of a cell. Equal distribution of chromosomes between the daughter cells is essential for the viability and well-being of an organism: loss of fidelity of cell division is a contributing factor in human cancer and also gives rise to miscarriages and genetic birth defects. For maintaining the proper chromosome number, a cell must carefully monitor cell division in order to detect and correct mistakes before they are translated into chromosomal imbalance. For this purpose an evolutionarily conserved mechanism termed the spindle assembly checkpoint (SAC) has evolved. The SAC comprises a complex network of proteins that relay and amplify mitosis-regulating signals created by assemblages called kinetochores (KTs). Importantly, minor defects in SAC signaling can cause loss or gain of individual chromosomes (aneuploidy) which promotes tumorigenesis while complete failure of SAC results in cell death. The latter event has raised interest in discovery of low molecular weight (LMW) compounds targeting the SAC that could be developed into new anti-cancer therapeutics. In this study, we performed a cell-based, phenotypic high-throughput screen (HTS) to identify novel LMW compounds that inhibit SAC function and result in loss of cancer cell viability. Altogether, we screened 65 000 compounds and identified eight that forced the cells prematurely out of mitosis. The flavonoids fisetin and eupatorin, as well as the synthetic compounds termed SACi2 and SACi4, were characterized in more detail utilizing versatile cell-based and biochemical assays. To identify the molecular targets of these SAC-suppressing compounds, we investigated the conditions in which SAC activity became abrogated. Eupatorin, SACi2 and SACi4 preferentially abolished the tensionsensitive arm of the SAC, whereas fisetin lowered also the SAC activity evoked by lack of attachments between microtubules (MTs) and KTs. Consistent with the abrogation of SAC in response to low tension, our data indicate that all four compounds inhibited the activity of Aurora B kinase. This essential mitotic protein is required for correction of erratic MT-KT attachments, normal SAC signaling and execution of cytokinesis. Furthermore, eupatorin, SACi2 and SACi4 also inhibited Aurora A kinase that controls the centrosome maturation and separation and formation of the mitotic spindle apparatus. In line with the established profound mitotic roles of Aurora kinases, these small compounds perturbed SAC function, caused spindle abnormalities, such as multi- and monopolarity and fragmentation of centrosomes, and resulted in polyploidy due to defects in cytokinesis. Moreover, the compounds dramatically reduced viability of cancer cells. Taken together, using a cell-based HTS we were able to identify new LMW compounds targeting the SAC. We demonstrated for the first time a novel function for flavonoids as cellular inhibitors of Aurora kinases. Collectively, our data support the concept that loss of mitotic fidelity due to a non-functional SAC can reduce the viability of cancer cells, a phenomenon that may possess therapeutic value and fuel development of new anti-cancer drugs.

Performance characteristic of moving average trading rules in the Finnish stock market

The thesis examines the profitability of DMAC trading rules in the Finnish stock market over the 1996-2012 period. It contributes to the existing technical analysis literature by comparing for the first time the performance of DMAC strategies based on individual stock trading portfolios to the performance of index trading strategies based on the trading on the index (OMX Helsinki 25) that consists of the same stocks. Besides, the market frictions including transaction costs and taxes are taken into account, and the results are reported from both institutional and individual investor’s perspective. Performance characteristic of DMAC rules are evaluated by simulating 19,900 different trading strategies in total for two non- overlapping 8-year sub-periods, and decomposing the full-sample-period performance of DMAC trading strategies into distinct bullish- and bearish-period performances. The results show that the best DMAC rules have predictive power on future price trends, and these rules are able to outperform buy-and-hold strategy. Although the performance of the DMAC strategies is highly dependent on the combination of moving average lengths, the best DMAC rules of the first sub-period have also performed well during the latter sub-period in the case of individual stock trading strategies. According to the results, the outperformance of DMAC trading rules over buy-and-hold strategy is mostly attributed to their superiority during the bearish periods, and particularly, during stock market crashes.

Laserhitsattavan tuotteen suunnittelu

Tässä työssä tarkastellaan laserhitsattavan tuotteen suunnittelua ja sen tuotekehitykseen liittyviä tekijöitä. Tuotteen suunnittelua käsitellään valmistuksellisesta näkökulmasta, eli siitä, kuinka tuotteen suunnittelussa voidaan ottaa huomioon tuotteen valmistus- ja kokoonpanoystävällisyys. Laserhitsattavan tuotteen suunnittelua käsitellään myös tuotteen ominaisuuksien kannalta, eli kuinka lopullisesta tuotteesta saadaan mahdollisimman laadukas ja kilpailukykyinen. Suomen kaarihitsausosaaminen on kansainvälisesti korkealuokkaista, mutta laserhitsaus eroaa perinteisistä kaarihitsausprosesseista paljon. Kun laserilla hitsattavaa tuotetta suunnitellaan, ovat menetelmäkohtaiset suunnittelusäännöt erilaiset kuin kaarihitsauksessa. Laserhitsaus vaatii teknisesti pajalta enemmän, mutta se myös avaa uusia ovia tuotesuunnittelulle ja mahdollistaa tuotteita, jotka olisivat perinteisillä menetelmillä hankalia tai mahdottomia valmistaa. Oikein käyttöönotettuna laserhitsauksella voidaan päästä matalampiin valmistuskustannuksiin. Kustannustehokkaaseen tuotantoon päästäkseen täytyy kuitenkin ymmärtää tuotteen kustannusrakenne. Työn lopussa tarkastellaan ja vertaillaan perinteisen ja laserhitsatun tuotteen kustannuksia ja kustannusrakennetta.

Rules of The National Library of Finland

Confirmed by the director of the National Library of Finland on 25 Nov 2013