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.

Visual Customer Segmentation and Data Exploration with the Self-Organizing Map

Advancements in information technology have made it possible for organizations to gather and store vast amounts of data of their customers. Information stored in databases can be highly valuable for organizations. However, analyzing large databases has proven to be difficult in practice. For companies in the retail industry, customer intelligence can be used to identify profitable customers, their characteristics, and behavior. By clustering customers into homogeneous groups, companies can more effectively manage their customer base and target profitable customer segments. This thesis will study the use of the self-organizing map (SOM) as a method for analyzing large customer datasets, clustering customers, and discovering information about customer behavior. Aim of the thesis is to find out whether the SOM could be a practical tool for retail companies to analyze their customer data.

Expressing the self in postmodern travel consumption: a case study of students

The study approaches student travel from the perspective of postmodern consumption. The background is in the observation that the student travel market has a vast potential, but it is not necessarily capitalized upon to the extent it could. This might partly have to do with the peculiarities of postmodernity: consumption is characterized by unpredictability and abstract motives. The research questions are built around what constitutes student travel consumption and how can students be categorized according to motivation, behaviour and values. Also identity and expressiveness are present and it is evaluated, if travel services facilitate these background is the observation that the student travel market has a vast potential, but it is not necessarily capitalized upon to the extent it could be. This might partly have to do with the peculiarities of postmodernity: consumption is characterized by unpredictability and abstract motives. The research questions are built around what constitutes student travel consumption and how can students be categorized according to motivation, behaviour and values. Also identity and expressiveness are present and it is evaluated whether travel services facilitate these constructs. The topic is approached by discovering the key concepts such as self-identity. This was done in order to create survey questions that reflect the underlying theories. The survey was sent to chosen student groups of Turku School of Economics. The data was analyzed using statistical methods, mainly principal component analysis, in order to categorize students’ motives and behaviour into distinct profiles. The findings indicate that students have a high level of awareness in their travel consumption choices. Travel services seem to facilitate identity and lifestyle expressiveness, one central dimension of postmodernity. Psychographics such as motivation seem to work well as a segmentation criteria when it comes to the student traveler market. Travel offers students an opportunity for relaxation, escape, enjoyment and gaining new experiences and social contacts. Furthermore, the enjoyment of the travel experience extends to the pre- and post-trip time.

The ramp-up of new products in the outbound logistics

Tässä diplomityössä on perehdytty kaaoksen ja oppivan organisaation mekaniikkaan ja olemukseen. Niitä on sovellettu uuden tuotteen saattamiseen logistiikan toimitusketjuun Nokia Oyj:n Networks toimialaryhmässä. Samalla on pyritty löytämään ratkaisuja toiminnan parantamiseksi. Kaaosjohtaminen tarjoaa prosessijohtamista täydentävän tavan mallintaa muutosta ja selittää sen aikaansaamia ilmiöitä. Näiden kahden viitekehyksen avulla on pyritty pureutumaan laajaan ja moniulotteiseen ongelmakenttään. Muotoaan hakevassa organisaatiossa kaaoksen elementit ovat voimakkaasti läsnä. Kaaoksen hallintaan liittyy saumattomasti itseorganisoituminen ja oppiminen. Oppinen ei ole organisaatiolle yhtä luontainen kyky kuin se on yksilölle. Se vaatii organisaation jäseniltä oman roolinsa tiedostamista ja tiedon jakamista. Organisaation tavoitteet saattavat yksilön näkökulmasta tuntua joskus epäkonkreettisilta ja samalla muutokset hallitsemattomilta. Markkinoiden ja teknologian muuttuminen on ollut erityisen nopeaa telekommunikaatioalalla. Näissä olosuhteissa on tärkeää pyrkiä oppivaan organisaatioon, joka tukee organisaation toimintaa läpi muutoksen.

The Strengths and Difficulties Questionnaire (SDQ-Fin) among Finnish children and adolescents

Objective: The psychometric properties of The Strengths and Difficulties Questionnaire (SDQ-Fin), a Finnish version of a brief screening instrument were studied. Emotional and behavioural problems of 7- to 15-year-olds measured by the SDQ were reported, as well as the occurrence of self-reported eating disturbance symptoms and alcohol use among adolescents. Methods and samples: The cross-sectional school survey included 25 items of the SDQ-Fin, items about eating disturbance, alchol use and child psychiatric help-seeking. The study consists of three community samples: 1. The SDQ-Fin parent (n = 703) and teacher (n = 376) versions of 7 – 12 –year-olds, and self-report versions (n = 528) of 11 – 16 years-olds were obtained, and 2. the parent (n = 81) and self-report versions of 15-16 –year olds (n = 129) were obtained in Laitila and Pyhäranta. 3. The self-report versions of 13 – 16 – year-olds (n = 1458) in Salo and Rovaniemi were obtained. Results: The psychometric properties of the SDQ-Fin were for the most part comparable with the other European SDQ research results. The internal consistency (Cronbach’s alpha = 0.71 in all informants’ reports) and inter-rater reliability (between the pairs of reports r = 0.38 - 0.44) were adequate. The concurrent validity (r = 0.75 between the SDQ and the CBCL total scores; r = 0.71 between the SDQ and the YSR total scores) was sufficient. Factor analysis of the SDQ self-report generally confirmed the postulated structure for girls and boys, except for the conduct problems scale of boys, which was fused with emotional symptoms and with hyperactivity. The response rates, means and cut-off points of the SDQ self-report scores were similar to those found, e.g. in Norway and in Britain. A high level of psychological problems, especially emotional and conduct problems and hyperactivity-inattention, were associated with high level of eating disturbance symptoms and alcohol use. Conclusion: The results showed that the psychometric properties of the SDQ-Fin are adequate and provide additional confirmation of the usefulness of the SDQ-Fin for, e.g. screening, epidemiological research and clinical purposes.

Reducing Manufacturing Costs of the Screen Dryer’s Hot Section by Design

In this thesis, the purpose was to find the cost distribution of the screen dryer and the largest cost factors. The hot section of the screen dryer was revealed as the biggest cost factor, so composing new cost efficient solutions were directed to it. DFMA (Design for Manufacture and Assembly) was chosen to help the design process. DFMA is a product design strategy developed for taking manufacturing and assembly costs into account at the early stages of the design process. In the theory part of the thesis, other methods of economical design and tools needed for estimating manufacturing costs are introduced. In the empirical part, the hot section of the screen dryer was divided into sub-assemblies and their manufacturing costs were estimated. The design propositions were directed to the self-manufactured assemblies and parts. The new manufacturing costs were calculated for the developed propositions. Lastly, the most cost efficient solutions were summarized. The savings on the self-manufactured assemblies were about 40 %, which was about 13 % of the combined total costs of the hot section.

The Role of Cytochrome P450 3A Inducers and Inhibitors in the Metabolism and the Effects of Oxycodone

Oxycodone is an opioid used in the treatment of moderate or severe pain. It is principally metabolized in the liver by cytochrome P450 3A (CYP3A) enzymes whereas approximately 10% is metabolized by CYP2D6. Little is known about the interactions between oxycodone and other drugs, herbals and nutritional substances. In this work the effects of CYP3A inducers rifampicin and St. John’s wort and CYP3A inhibitors voriconazole, grapefruit juice, ritonavir and lopinavir/ritonavir were investigated on the pharmacokinetics and pharmacodynamics of oxycodone. All studies were randomized, balanced, placebo-controlled crossover clinical studies in healthy volunteers. The plasma concentrations of oxycodone and its metabolites were determined for 48 hours and pharmacodynamic parameters were recorded for 12 hours in each study. Pharmacokinetic parameters were calculated by noncompartmental methods. Rifampicin decreased the plasma concentrations, analgesic effects, and oral bioavailability of oral oxycodone. St. John’s wort reduced the concentrations of oxycodone and diminished the self-reported drug effect. Voriconazole increased the exposure to oral oxycodone by 3.6-fold whereas grapefruit juice, which inhibits predominantly the intestinal CYP3A, elevated the mean concentrations of oxycodone by 1.7-fold. Ritonavir and lopinavir/ritonavir increased the mean AUC of oxycodone by 3.0- and 2.6-fold, respectively, and prolonged its elimination half-life. In spite of increased oxycodone plasma concentrations during concomitant administration of CYP3A inhibitors, the analgesic effects were not increased. These studies show that the induction or inhibition of CYP3A alters the pharmacokinetics and pharmacologic effects of oxycodone. The exposure to oxycodone decreased after induction and increased after inhibition of CYP3A. As a conclusion, the clinicians should avoid concomitant administration of CYP3A inducers or inhibitors and oral oxycodone. If this is not possible, they should be prepared to interactions leading to impaired analgesia after CYP3A inducers or increased adverse effects after CYP3A inhibitors and oral oxycodone.

Vaccination Competence - The Concept and Evaluation

The purpose of this two-phase study was to define the concept of vaccination competence and assess the vaccination competence of graduating public health nurse students (PHN students) and public health nurses (PHNs) in Finland, with the goal of promoting and maintaining vaccination competence and developing vaccination education. The first phase of the study included semi-structured interviews with vaccination professionals, graduating PHN students and clients (a total of n=40), asking them to describe vaccination competence as well as the factors strengthening and weakening it. The data were analyzed through content analysis. In the second phase of the study, structured instruments were developed, and vaccination competence of PHN students (n=129) in Finland and PHNs (n=405) was assessed using a self-assessment scale (VAS) and taking a knowledge test. PHNs were used as a reference group, enabling us to determine whether a satisfactory level of vaccination competence was achieved by the end of studies, or whether it was gained through work experience vaccinating clients. The data were collected from five polytechnic institutions and seven health centers located in various parts of the country. The data were collected using instruments developed for this study, and were analyzed statistically. In the first phase, based on the results of the interviews, vaccination competence was defined as a large multi-faceted entity, including the concepts of competent vaccinator, competent implementation of the vaccination, and the outcome of the implementation. Semi-structured interviews revealed that factors strengthening and weakening vaccination competence were connected to the vaccinator, the client being vaccinated, the vaccination environment and vaccinator education. On the whole, factors strengthening and weakening vaccination were the opposite of each other. In the second phase, on the self-assessment of vaccination competence, students rated themselves as significantly lower than working professionals. On the knowledge test, the percentage of correct answers was lower for students than PHNs. When all background variables were taken into account in multivariate analysis, there was no longer a significant difference between the students and PHNs on the self-assessment. However, in multivariate analysis, the PHNs still performed better than students on the knowledge test. For this study, a satisfactory level of vaccination competence was defined as a mean of 8.0 on the self-assessment and 80% correct answers on the knowledge test. Based on these criteria, students almost reached the level of satisfactory in their overall self-assessment, and PHNs did. Both groups, however, did rank themselves as satisfactory in some sum variables. On the knowledge test the students did not achieve a level of satisfactory (80%) in their total score, though PHNs did. As before, both groups did achieve a level of satisfactory in several sum variables. Further research and development should focus on vaccination education, the testing of vaccination competence and vaccination practices in clinical practice, as well as on developing the measurement tools.

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.

The bifurcational behaviour of the spatially distributed Rayleigh equation

At the present work the bifurcational behaviour of the solutions of Rayleigh equation and corresponding spatially distributed system is being analysed. The conditions of oscillatory and monotonic loss of stability are obtained. In the case of oscillatory loss of stability, the analysis of linear spectral problem is being performed. For nonlinear problem, recurrent formulas for the general term of the asymptotic approximation of the self-oscillations are found, the stability of the periodic mode is analysed. Lyapunov-Schmidt method is being used for asymptotic approximation. The correlation between periodic solutions of ODE and PDE is being investigated. The influence of the diffusion on the frequency of self-oscillations is being analysed. Several numerical experiments are being performed in order to support theoretical findings.

Conceptualizing and measuring human anxiety on the Internet

Since the 1990’s, the Internet has played a central role in our daily lives. The Internet is an integral part of our personal, business, family, research, entertainment, academic and social life. However, there are social implications in using the Internet that are dependent on categories such as gender, age, ethnicity and cultural attributes. This social aspect can play a detrimental role in the expression of human anxiety on the Internet. An anxiety is a complex phenomenon that requires further elaboration. Thus, the aim of this thesis is to investigate human anxiety, or specifically, whether Internet anxiety can be conceptualized and measured. This thesis utilizes literature, qualitative and quantitative research methodologies, and a triangulation validation approach to conceptualize and measure the Internet anxiety phenomenon. In particular, the aim is to explore anxiety levels of Internet participants to develop and validate an Internet anxiety scale based on earlier research on Internet anxiety. The results of the dissertation present a two phase study. In Phase I, a smaller set of studies were conducted with a limited sample size. In Phase II, the research topic was investigated using 385 participants. Based on a number of studies or experiments, the state-of-the-art discovered in this thesis is creation, design, and validation of two scales, the Self-Assessment Scale (SAS) and a Modified Internet Anxiety Scale (MIAS) for measuring users’ anxieties on the Internet. The result of this dissertation is a conceptualization and measurement of various types of Internet anxiety and measurement of affective feelings of users on the Internet. As a proof-of-concept of measuring Internet anxiety, this thesis describes the author’s implementation of three sets of tools: MyAnxiety, introducing Internet anxieties types; Intelligentia, for collecting Internet anxieties types; and MyIAControl tool, implemented as a browser plug-in, for measuring affective feelings of users on the Internet. Conclusions drawn from the results show that these empirically validated scales and tools might be useful for researchers and practitioners in understanding and measuring the Internet anxiety phenomenon further.

Online peer to peer lending: clustering borrowers using self-organizing maps

The purpose of this thesis is to find out whether all the peer to peer lenders are unworthy of credit and also if there are single qualities or combinations of qualities that determine the probability of default of a person or group of people. Distinguishing qualities are searched with self-organizing maps (SOM). Qualities and groups of people found by the self-organizing map are then compared to the average. The comparison is carried out by looking how big proportion of borrowers meeting the criteria is two months or more behind with their payments. Research data used is collected by an Estonian peer to peer lending company during the years of 2011-2014. Data consists of peer to peer borrowers and information gathered from them.

Measuring Effectiveness of Marketing Message: The Role of Verbal, Visual and Brand Elements

The aim of this paper is to study the role of verbal, visual and brand elements while meas-uring effectiveness of marketing message. The thesis is written in the context of mobile gaming industry. The object of the study is marketing message. To achieve the aim, the main research question was formulated: How do the elements of marketing message, such as verbal, visual and brand, affect the consumer’s attitude toward the ad, emotional response and attention capture? The theory development chapter lays on three corner stones – analysis of previous litera-ture on marketing message and its elements, namely verbal, visual and brand; overview of literature on attitude formation and particularly attitude toward the ad. In addition, investiga-tion of key points of emotional response and attention capture literature finalizes the chap-ter. The empirical part consists of experiment, conducted with 27 participants. Experiment includes the self-report semantically anchored scale, measuring the attitude toward the ad, as well as autonomic measures – eye tracking (attention capture) and facial expressions (emotional response). The results of the experiment showed that the size of the brand element – the logo – has an effect on the attention capture and the overall attitude toward the ad. The bigger the logo, the more time people spend viewing it, and they realise the message is more educa-tional and factual. The measure related to the visual element – the visual complexity – in-creases the intensity of participant’s facial expression. While the measure of verbal ele-ment – the contrast between text and background colours – leads to a better attitude to-ward the ad. The higher the contrast between text and background, the more known the message appears to the viewer.