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.

Ambivalent self-understanding? : change, language and boundaries in the Shetland Islands (1970–present)

Avhandlingen berör språkets roll på Shetlandsöarna från år 1970 till idag och shetländarnas självbild som shetländare och skottar. Öarna, som ligger i Storbritanniens nordligaste del, beskrivs ofta som kulturellt annorlunda och unika. Även om shetländarna uppfattar sig själva som annorlunda, har utomstående betraktare tidvis tonat ner, tidvis betonat öarnas kulturella särdrag. Shetlandsöarna utgör ett intressant undersökningsobjekt, eftersom shetländarnas uppfattningar om sig själva som en särskild grupp har genomgått en förändring under de fyra senaste årtiondena. Den ekonomiska högkonjunktur som var en konsekvens av oljefynden i Nordsjön och 1990-talets politiska förändringar på öarna och i Skottland har båda påverkat de sätt på vilka Shetland beskrivs och förstås. I den förändrade samhällssituationen tvingades shetländarna omvärdera sin relation till det skotska fastlandet. Man var också tvungen att hitta nya svar på frågan vilka shetländarna är och på vilka sätt man borde värna om den verkliga eller föreställda kulturella autonomin. Avhandlingens syfte var att undersöka och analysera de sätt på vilka de samhälleliga förändringarna har påverkat shetländarnas självförståelse, särskilt de uppfattningar som är kopplade till språket. Undersökningen visar att många av dagens uppfattningar om en kulturell särart kan spåras till slutet av 1800-talet och tiden efter andra världskriget. Som avhandlingen visar har språkhistorien spelat en viktig roll i den process i vilken shetländarna har särskilt sig som en separat grupp. Språkets betydelse kan förstås korrekt endast om man i stället för att betrakta shetländarna som en etnisk grupp betraktar Shetlandsöarna som en relativt sett autonom beslutför region. I detta fall fungerar dialekten som en symbol för regional samhörighet.

Health-related quality of life in school children: validation of instrument, child self assessment, parent-proxy assessment and school nursing documentation of health check-ups

The aims of this study were to validate an international Health-Related Quality of Life (HRQL) instrument, to describe child self and parent-proxy assessed HRQL at child age 10 to 12 and to compare child self assessments with parent-proxy assessments and school nursing documentation. The study is part of the Schools on the Move –research project. In phase one, a cross-cultural translation and validation process was performed to develop a Finnish version of Pediatric Quality of Life Inventory™ 4.0 (PedsQL™ 4.0). The process included a two-way translation, cognitive interviews (children n=7, parents n=5) and a survey (children n=1097, parents n=999). In phase two, baseline and follow-up surveys (children n=986, parents n=710) were conducted to describe and compare the child self and parent-proxy assessed HRQL in school children between the ages 10 and 12. Phase three included two separate data, school nurse documented patient records (children n=270) and a survey (children n=986). The relation between child self assessed HRQL and school nursing documentation was evaluated. Validity and reliability of the Finnish version of PedsQL™ 4.0 was good (Child Self Report α=0.91, Parent-Proxy Report α=0.88). Children reported lower HRQL scores at the emotional (mean 76/80) than the physical (mean 85/89) health domains and significantly lower scores at the age of 10 than 12 (dMean=4, p=<0.001). Agreement between child self and parent-proxy assessment was fragile (r=0,4, p=<0.001) but increased as the child grew from age 10 to 12 years. At health check-ups, school nurses documented frequently children’s physical health, such as growth (97%) and posture (98/99%) but seldom emotional issues, such as mood (2/7%). The PedsQLTM 4.0 is a valid instrument to assess HRQL in Finnish school children although future research is recommended. Children’s emotional wellbeing needs future attention. HRQL scores increase during ages between childhood and adolescence. Concordance between child self and parent-proxy assessed HRQL is low. School nursing documentation, related to child health check-ups, is not in line with child self assessed HRQL and emotional issues need more attention.

Self-Assessement Report for International Accreditation - Bachelor's and Master's degree programmes in Energy Technology

Self-Assessment Report was made for the accreditation of degree programmes in Energy Technology. The report includes the following items: the content,concept and implementation of of the degree programmes, the resources, the quality management and further development of the degree programmes.

Self-Assessment Report for International Accreditation – Bachelor’s and Master’s degree programmes in Industrial Management

Self-assessment report for accreditation of the Bachelor's and Master's degree programs in Industrial Management.

Self assessment report for international accreditation - Bachelor's and Master's degree programmes in Mechanical Engineering

Itsearviointiraportissa kuvataan Lappeenrannan teknillisen yliopiston konetekniikan kandidaatin ja diplomi-insinöörin tutkinto-ohjelmat opetussuunnitelman 2011-2012 mukaisesti. Itsearviointiraportti on tuotettu saksalaisen ASIIN-akkreditointiorganisaation raportointimallin mukaisesti.

Self-Assessment Report for International Accreditation - Bachelor’s and Master’s degree programmes in Environmental Technology

Ympäristötekniikan kandidaatin ja diplomi-insinöörin tutkinto-ohjelmien itsearviointiraportissa käsitellään tutkinto-ohjelmien osaamistavoitteita ja niiden saavuttamista. Raportissa käydään läpi myös käytössä olevat resurssit sekä tutkinto-ohjelmiin liittyviä tunnuslukuja. Itsearviointi on toteutettu kansainvälisen akkreditointijärjestön kriteerien mukaisesti (ASIIN ja EUR-ACE).

Improving alumni administration by self-built information system : building IMMIT connected' to enhance alumni connection

Alumni are considered as precious resource of the institutions, thus improving alumni adminis-tration is critical. In information era, alumni administration is assisted by widespread information technology, such as social network sites. This paper aims to discover if a self-built information sys-tem would enhance alumni connection in the IMMIT context, and what kind of attributes would be helpful applying to the special context. The current online alumni services at other universities and at the IMMIT host university are analyzed, and then social media is introduced. After illustrating the social capital existing in IM-MIT, the type of the self-built information system is suggested, following an interpretation of the prototype. Two research models are utilized in this article: TAM and intentional social action model. The second model is adjusted with proposed parameters. Afterwards, a survey and an interview protocol are designed under the guidance of the models. The results are analyzed in several groups, and the proposed parameters are tested. A conclusion is drawn to indicate how to improve alumni‟s intention to use and how to achieve a better-accepted design.

Self-Assessment Report for International Accreditation - Chemical Engineering

Kemiantekniikan kandidaatin ja diplomi-insinöörin tutkinto-ohjelmien itsearviointiraportissa käsitellään tutkinto-ohjelmien osaamistavoitteita ja niiden saavuttamista. Raportissa käydään läpi myös käytössä olevat resurssit sekä tutkinto-ohjelmiin liittyviä tunnuslukuja. Itsearviointi on toteutettu kansainvälisen akkreditointijärjestön kriteerien mukaisesti (ASIIN ja EUR-ACE).

Poster presentation as a report of a self-designed laboratory experiment : a case study

Julkaisumaa: 203 CZ CZE Tšekki

Sivistyksestä sivilisaatioon. Kulttuurikäsitys J. V. Snellmanin historiallisessa ajattelussa

From Bildung to Civilisation. Conception of Culture in J. V. Snellman’s Historical Thinking The research explores Johan Vilhelm Snellman’s (1806–1881) conception of culture in the context of his historical thinking. Snellman was a Finnish, Swedish-speaking journalist, teacher and thinker, who held a central position in the Finnish national discourse during the nineteenth century. He has been considered as one of the leading theorists of a Finnish nation, writing widely about the themes such as the advancement of the national education, Finnish language and culture. Snellman is already a widely studied person in Finnish intellectual history, often characterised as a follower of G. W. F. Hegel’s philosophical system. My own research introduces a new kind of approach on Snellman’s texts, emphasising the conceptual level of his thought. With this approach, my aim is to broaden the Finnish research tradition on conceptual history. I consider my study as a cultural history of concepts, belonging also to the field of intellectual history. My focus is on one hand on the close reading of Snellman’s texts and on the other hand on contextualising his texts to the European intellectual tradition of the time. A key concept of Snellman’s theoretical thinking is his concept of bildning, which can be considered as a Swedish counterpart of the German concept of Bildung. The Swedish word incorporated all the main elements of the German concept. It could mean education or the so-called high culture, but most fundamentally it was about the self-formation of the individual. This is also the context in which Snellman’s concept of bildning has often been interpreted. In the study, I use the concept of bildning as a starting point of my research but I broaden my focus on the cognate concepts such as culture (kultur), spirit (anda) and civilisation. The purpose of my study is thus to illustrate how Snellman used and modified these concepts and from these observations to draw a conclusion about the nature of his conception of culture. Snellman was an early Finnish philosopher of history but also interested in the practice of the writing of history. He did not write any historical presentations himself but followed the publications in the field of history and introduced European historical writing to the Finnish, Swedish-speaking reading audience in his newspapers. The primary source material consists of different types of Snellman’s texts, including philosophical writings, lecture material, newspaper articles and private letters. I’m reading Snellman’s texts in the context of other texts produced both by his Finnish predecessors and contemporaries and by Swedish, German and French writers. Snellman’s principal philosophical works, Versuch einer spekulativen Entwicklung der Idee der Persönlichkeit (1841) and Läran om staten (1842), were both written abroad. Both of the works were contributions to contemporary debates on the international level, especially in Germany and Sweden. During the 1840s and 1850s Snellman had two newspapers of his own, Saima and Litteraturblad, which were directed towards the Swedish-speaking educated class. Both of the newspapers were very popular and their circulations were among the largest of their day in Finland. The topics of his articles and reviews covered literature, poetry, philosophy and education as well as issues concerning the economic, industrial and technical development in Finland. In his newspapers Snellman not only brought forth his own ideas but also spread the knowledge of European events and ideas to his readers. He followed very carefully the cultural and political situation in Western Europe. He also followed European magazines and newspapers and was well acquainted with German, French and also English literature – and of course Swedish literature to with which he had the closest ties. In his newspapers Snellman wrote countless number of literary reviews and critics, introducing his readers to European literature. The study consists of three main chapters in which I explore my research question in three different, yet overlapping contexts. In the first of these chapters, I analyse Snellman’n theoretical thinking and his concepts of bildning, kultur, anda and civilisation in the context of earlier cultural discourse in Finland as well as the tradition of German idealistic philosophy and neo-humanism. With the Finnish cultural discourse I refer to the early cultural discussion in Finland, which emerged after the year 1809, when Finland became an autonomous entity of its own as a Grand Duchy of Russia. Scholars of the Academy of Turku opened a discussion on the themes such as the state of national consciousness, the need for national education and the development of the Finnish language as a national language of Finland. Many of these academics were also Snellman’s teachers in the early years of his academic career and Snellman clearly formulated his own ideas in the footsteps of these Finnish predecessors. In his theoretical thinking Snellman was a collectivist; according to him an individual should always be understood in connection with the society, its values and manners, as well as to the traditions of a culture where an individual belongs to. In his philosophy of the human spirit Snellman was in many ways a Hegelian but his notion of education or ‘bildning’ includes also elements that connect him with the wider tradition of German intellectual history, namely the neo-humanist tradition and, at least to some extent, to the terminology of J. G. Herder or J. G. Fichte, for example. In this chapter, I also explore Snellman’s theory of history. In his historical thinking Snellman was an idealist, believing in the historical development of the human spirit (Geist in German language). One can characterise his theory of history by stating that it is a mixture of a Hegelian triumph of the spirit and Herderian emphasis on humanity (Humanität) and the relative nature of ‘Bildung’. For Snellman, the process of ‘bildning’ or ‘Bildung’ is being realised in historical development through the actions of human beings. Snellman believed in the historical development of the human civilization. Still Snellman himself considered that he had abandoned Hegel’s idea about the process of world history. Snellman – rightly or wrongly – criticised Hegel of emphasising the universal end of history (the realisation of the freedom of spirit) at the expense of the historical plurality and the freedom of each historical era. Snellman accused Hegel of neglecting the value and independency of different historical cultures and periods by imposing the abstract norm, the fulfilment of the freedom of spirit, as the ultimate goal of history. The historicist in Snellman believed in the individuality of each historical period; each historical era or culture had values, traditions and modes of thought of its own. This historicist in Snellman could not accept the talk about one measure or the end of history. On the other hand Snellman was also a universalist. He believed that mankind had a common task and that task was the development of ‘Bildung’, freedom or humanity. The second main chapter consists of two parts. In the first part, I explore the Finnish nationalistic discourse from the cultural point of view by analysing the notions such as a nation, national spirit or national language and showing how Snellman formulated his own ideas in a dialogic situation, participating in the Finnish discourse but also reacting to international discussions on the themes of the nation and nationality. For Snellman nationality was to a great extent the collective knowledge and customs or practices of the nation. Snellman stated that nationality is to be considered as a form of ‘bildning’. This could be seen not simply as affection for the fatherland but also for the mental identity of the nation, its ways of thinking, its practices, national language, customs and laws, the history of the nation. The simplest definition of nationality that Snellman gives is that nationality is the social life of the people. In the second part of the chapter I exam Snellman’s historical thinking and his understanding about historical development, interaction between different nations and cultures in the course of history, as well as the question of historical change; how do cultures or civilisations develop and who are the creators of culture? Snellman did not believe in one dominating culture but understood the course of history as a dialogue between different cultures. On the other hand, his views are very Eurocentric – here he follows the ideas of Hegel or for example the French historian François Guizot – for Snellman Europe represented the virtue of pluralism; in Europe one could see the diversity of cultures which, on the other hand, were fundamentally based on a common Christian tradition. In the third main chapter, my focus is on the writing of history, more precisely on Snellman’s ideas on the nature of history as a science and on the proper way of writing historical presentations. Snellman wrote critics on the works of history and introduced his readers to the writing of history especially in France, Sweden and German-speaking area – in some extend also in Britain. Snellman’s collectivistic view becomes evident also in his reviews on historical writing. For Snellman history was not about the actions of the states and their heads, nor about the records of ruling families and battles fought. He repeatedly stressed that history is a discipline that seeks to provide a total view of a phenomenon. A historian should not only collect information on historical events, since this information touches only the surface of a certain epoch or civilisation; he has to understand an epoch as totality. This required an understanding about the major contours in history, connections between civilisations and an awareness of significant turning points in historical development. In addition, it required a holistic understanding about a certain culture or historical era, including also the so-called inner life of a specific nation, a common people and their ways of life. Snellman wrote explicitly about ‘cultural history’ in his texts, referring to this kind of broad understanding of a society. In historical writing Snellman found this kind of broader view from the works of the French historians such as François Guizot and Jules Michelet. In all of these chapters, I elaborate the conceptual dimension of Snellman’s historical thinking. In my study I argue that Snellman not only adopted the German concepts of Bildung or Kultur in his own thinking but also developed the Swedish concepts in a way that include personal and innovative aspects. Snellman’s concept of bildning is not only a translation from ‘Bildung’ but he uses the Swedish concept in a versatile way that includes both the moral aspect of human development and social dimension of a human life. Along with ‘bildning’ Snellman used also the terms ‘kultur’ and ‘civilisation’ when referring to the totality of a certain nation or historical era, including both the so-called high culture (arts, science, religion) and the modes of thought as well as ways of life of the people as a whole. Unlike many of his Finnish contemporaries, Snellman did not use civilisation as a negative concept, lacking the moral essence of German term ‘Bildung’ or ‘Kultur’. Instead, for Snellman civilisation was a neutral term and here he comes close to the French tradition of using the term. In the study I argue that Snellman’s conception of culture in fact includes a synthesis of the German tradition of ‘Bildung’ and the French tradition of ‘civilisation’.