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).

Professional development among educators pursuing a B.Ed. program in special education in Tanzania : a study of motives and perceived outcomes

Implementation of different policies and plans aiming at providing education for all is a challenge in Tanzania. The need for educators and professionals with relevant knowledge and qualifications in special education is substantial. Teacher education does not equip educators with sufficient knowledge and skills in special education and professional development programs in special education are few in number. Up to 2005 no degree programs in special education at university level were available in Tanzania. The B.Ed. Special Education program offered by the Open University of Tanzania in collaboration with Åbo Akademi University in Finland was one of the efforts aimed at addressing the big national need for teachers and other professionals with degree qualifications in special education. This pilot program offered unique possibilities to study professional development in Tanzania. The research group in this study consisted of the group of students who participated in the degree program 2005-2007. The study is guided by three theoretical perspectives: individual, social and societal. The individual perspective emphasizes psychological factors as motives, motivation, achievement, self-directed behavior and personal growth. Within social perspective, professional development is viewed as situated within the social and cultural context. The third perspective, the societal, focuses on change, reforms, innovations and transformation of school systems and societies. Accordingly, professional development is viewed as an individual, social and societal phenomenon. The overall aim of the study is to explore the participants’ motives for participating in a B.Ed. Special Education program and the perceived outcomes of the program in terms of professional development. In order to achieve the objectives of the study, a case study approach was adopted. Questionnaires and semi-structured interviews were administered in three waves between January 2007 and February 2009 to the 35 educators participating in the B.Ed. Special Education program. The findings of the study reveal that the participants expressed motives which were related to job performance, knowledge, skills, academic degree and career. Also altruistic motives were expressed by the participants in terms of helping and supporting students with special needs and their communities. The perceived outcomes of the program were in line with the expressed motives. However, the results indicate that the participants also learned new skills, as interaction skills and guidance and counseling skills. Increased self-confidence was also mentioned as an outcome. The participants also got deepened understanding of disability issues. In addition, they learned strategies for creating awareness of persons with disability in the communities. Thus the findings of the study indicate positive outcomes of the program in terms of professional development. The conclusion of the study is that individual, social and societal factors interact when it comes to explaining why Tanzanian educators in special education choose to pursue a degree program in special education. The individual motives, as increased knowledge and better prospects of career development interact with the social and societal motives to help and support vulnerable student groups. The study contributes to increased understanding of the complexity of professional development and of the realities educators meet when educational reforms are implemented in a developing country.

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