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.

Orthogonal function method in modelling paper web quality variation

This work is devoted to the analysis of signal variation of the Cross-Direction and Machine-Direction measurements from paper web. The data that we possess comes from the real paper machine. Goal of the work is to reconstruct the basis weight structure of the paper and to predict its behaviour to the future. The resulting synthetic data is needed for simulation of paper web. The main idea that we used for describing the basis weight variation in the Cross-Direction is Empirical Orthogonal Functions (EOF) algorithm, which is closely related to Principal Component Analysis (PCA) method. Signal forecasting in time is based on Time-Series analysis. Two principal mathematical procedures that we used in the work are Autoregressive-Moving Average (ARMA) modelling and Ornstein–Uhlenbeck (OU) process.

Social capital, coping and information behaviour of long-term unemployed people in Finland

Avhandlingen studerar hur långtidsarbetslösa klarar av sin situation, hurdant socialt kapital och informationsbeteende de har, samt granskar hur de ovannämnda faktorerna är relaterade till varandra. Därtill undersöks om det finns skillnader mellan finsk- och svenskspråkiga långtidsarbetslösa på de här tre livsområdena. I undersökningen består socialt kapital av sociala relationer, deltagande i organisatoriska aktiviteter samt känslan av tillhörighet med olika grupper och samfund. Gällande informationsbeteende är fokus på vardaglig informationssökning, vilka källor som används, och hurdana problem man stöter på när man söker information. Som mest påfrestande upplevdes arbetslösheten av män, som var i början eller mitten av sin arbetskarriär. De äldre (över 55 år) verkade på många sätt klara av arbetslöshetssituationen bättre än de yngre, som drabbades hårdare av ekonomiska problem och stress. Kvinnor kunde bättre än män bibehålla en positiv inställning, de hade t.ex. starkare sociala nätverk som stöd, medan mäns sociala relationer i högre grad verkade vila på en arbetsgemenskap, som blev allt svagare i och med utdragen arbetslöshet. Yngre män upplevde också ofta att deras hälsa hade försämrats, när den för kvinnor och äldre arbetslösa i genomsnitt blev bättre. När arbetslösas bemästring av arbetslöshetssituationen, sociala relationer och informationssökning granskades, framgick att människor som var aktiva på ett livsområde också var aktiva på andra livsområden. I de flesta fall framkom inte några större skillnader mellan finsk- och svenskspråkiga arbetslösa. Beträffande informationssökning var de upplevda problemen ändå av diametralt motsatt karaktär – för svenskspråkiga åsamkade för lite tillgänglig information ofta problem, medan problemet för de finskspråkiga var att hitta det väsentliga i informationsflödet. Finskspråkiga kände sig också mera fast anknutna till sin boendemiljö och det finska samhället i stort, svenskspråkiga hade däremot i genomsnitt bredare och tätare sociala nätverk.

Corrosion behaviour of boiler tube materials during combustion of fuels containing Zn and Pb

Många förbränningsanläggningar som bränner utmanande bränslen såsom restfraktioner och avfall råkar ut för problem med ökad korrosion på överhettare och/eller vattenväggar pga. komponenter i bränslena som är korrosiva. För att minimera problemen i avfallseldade pannor hålls ångparametrarna på en relativt låg nivå, vilket drastiskt minskar energiproduktionen. Beläggningarna i avfallseldade pannor består till största delen av element som är förknippade med högtemperaturkorrosion: Cl, S, alkalimetaller, främst K och Na, och tungmetaller som Pb och Zn, och det finns också indikationer av Br-förekomst. Det låga ångtrycket i avfallseldade pannor påverkar också stålrörens temperatur i pannväggarna i eldstaden. I dagens läge hålls temperaturen normalt vid 300-400 °C. Alkalikloridorsakad (KCl, NaCl) högtemperaturkorrosion har inte rapporterats vara relevant vid såpass låga temperaturer, men närvaro av Zn- och Pb-komponenter i beläggningarna har påvisats förorsaka ökad korrosion redan vid 300-400 °C. Vid förbränning kan Zn och Pb reagera med S och Cl och bilda klorider och sulfater i rökgaserna. Dessa tungmetallföreningar är speciellt problematiska pga. de bildar lågsmältande saltblandningar. Dessa lågsmältande gasformiga eller fasta föreningar följer rökgasen och kan sedan fastna eller kondensera på kallare ytor på pannväggar eller överhettare för att sedan bilda aggressiva beläggningar. Tungmetallrika (Pb, Zn) klorider och sulfater ökar risken för korrosion, och effekten förstärks ytterligare vid närvaro av smälta. Motivet med den här studien var att få en bättre insikt i högtemperaturkorrosion förorsakad av Zn och Pb, samt att undersöka och prediktera beteendet och motståndskraften hos några stålkvaliteter som används i överhettare och pannväggar i tungmetallrika förhållanden och höga materialtemperaturer. Omfattande laboratorie-, småskale- och fullskaletest utfördes. Resultaten kan direkt utnyttjas i praktiska applikationer, t.ex. vid materialval, eller vid utveckling av korrosionsmotverkande verktyg för att hitta initierande faktorer och förstå deras effekt på högtemperaturkorrosion.

Simulation methods in the modelling of bioaffinity assays

Computational model-based simulation methods were developed for the modelling of bioaffinity assays. Bioaffinity-based methods are widely used to quantify a biological substance in biological research, development and in routine clinical in vitro diagnostics. Bioaffinity assays are based on the high affinity and structural specificity between the binding biomolecules. The simulation methods developed are based on the mechanistic assay model, which relies on the chemical reaction kinetics and describes the forming of a bound component as a function of time from the initial binding interaction. The simulation methods were focused on studying the behaviour and the reliability of bioaffinity assay and the possibilities the modelling methods of binding reaction kinetics provide, such as predicting assay results even before the binding reaction has reached equilibrium. For example, a rapid quantitative result from a clinical bioaffinity assay sample can be very significant, e.g. even the smallest elevation of a heart muscle marker reveals a cardiac injury. The simulation methods were used to identify critical error factors in rapid bioaffinity assays. A new kinetic calibration method was developed to calibrate a measurement system by kinetic measurement data utilizing only one standard concentration. A nodebased method was developed to model multi-component binding reactions, which have been a challenge to traditional numerical methods. The node-method was also used to model protein adsorption as an example of nonspecific binding of biomolecules. These methods have been compared with the experimental data from practice and can be utilized in in vitro diagnostics, drug discovery and in medical imaging.

Element speciation and behaviour in metal-rich Boreal river and estuarine systems using ultrafiltration and chemical modelling

The bioavailability of metals and their potential for environmental pollution depends not simply on total concentrations, but is to a great extent determined by their chemical form. Consequently, knowledge of aqueous metal species is essential in investigating potential metal toxicity and mobility. The overall aim of this thesis is, thus, to determine the species of major and trace elements and the size distribution among the different forms (e.g. ions, molecules and mineral particles) in selected metal-enriched Boreal river and estuarine systems by utilising filtration techniques and geochemical modelling. On the basis of the spatial physicochemical patterns found, the fractionation and complexation processes of elements (mainly related to input of humic matter and pH-change) were examined. Dissolved (<1 kDa), colloidal (1 kDa-0.45 μm) and particulate (>0.45 μm) size fractions of sulfate, organic carbon (OC) and 44 metals/metalloids were investigated in the extremely acidic Vörå River system and its estuary in W Finland, and in four river systems in SW Finland (Sirppujoki, Laajoki, Mynäjoki and Paimionjoki), largely affected by soil erosion and acid sulfate (AS) soils. In addition, geochemical modelling was used to predict the formation of free ions and complexes in these investigated waters. One of the most important findings of this study is that the very large amounts of metals known to be released from AS soils (including Al, Ca, Cd, Co, Cu, Mg, Mn, Na, Ni, Si, U and the lanthanoids) occur and can prevail mainly in toxic forms throughout acidic river systems; as free ions and/or sulfate-complexes. This has serious effects on the biota and especially dissolved Al is expected to have acute effects on fish and other organisms, but also other potentially toxic dissolved elements (e.g. Cd, Cu, Mn and Ni) can have fatal effects on the biota in these environments. In upstream areas that are generally relatively forested (higher pH and contents of OC) fewer bioavailable elements (including Al, Cu, Ni and U) may be found due to complexation with the more abundantly occurring colloidal OC. In the rivers in SW Finland total metal concentrations were relatively high, but most of the elements occurred largely in a colloidal or particulate form and even elements expected to be very soluble (Ca, K, Mg, Na and Sr) occurred to a large extent in colloidal form. According to geochemical modelling, these patterns may only to a limited extent be explained by in-stream metal complexation/adsorption. Instead there were strong indications that the high metal concentrations and dominant solid fractions were largely caused by erosion of metal bearing phyllosilicates. A strong influence of AS soils, known to exist in the catchment, could be clearly distinguished in the Sirppujoki River as it had very high concentrations of a metal sequence typical of AS soils in a dissolved form (Ba, Br, Ca, Cd, Co, K, Mg, Mn, Na, Ni, Rb and Sr). In the Paimionjoki River, metal concentrations (including Ba, Cs, Fe, Hf, Pb, Rb, Si, Th, Ti, Tl and V; not typical of AS soils in the area) were high, but it was found that the main cause of this was erosion of metal bearing phyllosilicates and thus these metals occurred dominantly in less toxic colloidal and particulate fractions. In the two nearby rivers (Laajoki and Mynäjoki) there was influence of AS soils, but it was largely masked by eroded phyllosilicates. Consequently, rivers draining clay plains sensitive to erosion, like those in SW Finland, have generally high background metal concentrations due to erosion. Thus, relying on only semi-dissolved (<0.45 μm) concentrations obtained in routine monitoring, or geochemical modelling based on such data, can lead to a great overestimation of the water toxicity in this environment. The potentially toxic elements that are of concern in AS soil areas will ultimately be precipitated in the recipient estuary or sea, where the acidic metalrich river water will gradually be diluted/neutralised with brackish seawater. Along such a rising pH gradient Al, Cu and U will precipitate first together with organic matter closest to the river mouth. Manganese is relatively persistent in solution and, thus, precipitates further down the estuary as Mn oxides together with elements such as Ba, Cd, Co, Cu and Ni. Iron oxides, on the contrary, are not important scavengers of metals in the estuary, they are predicted to be associated only with As and PO4.

Formal development and quantitative verification of dependable systems

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Collaborative information behaviour : a case study of two research groups

The aim of the licentiate thesis is to examine researchers' information practices in research groups. The researchers were involved with study communication and media related issues within Social Sciences and Humanities Faculties. The theoretical framework of the study comprises the new holistic models of information seeking (for example: Meho and Tibbo, 2003; Seldén, 1999) and the collective aspects of information behaviour (Prekop, 2002 ; Talja, 2002; Talja and Hansen, 2006). The research questions are: 1. How do scholars seek information in research groups? 2 What kind of collaborative information behaviour occurs in the research groups? The research data was gathered by interviews and observations. Three meetings of a research group at the University of Tampere were observed during the autumn of 2004. The group members and the group leader of the research group were interviewed in the spring of 2005. The research group members and the group leader of a research group at the University of Jyväskylä were interviewed in the autumn of 2005. Altogether, two research group leaders and eight researchers were interviewed. The significance of the research group for information seeking is more important in closeknit research groups than in rather loose research groups. The significance of the research group for information seeking can be at least threefold. First, research group members can inform the group about relevant information resources and potential library or other information services. Second, the research group can to some extent compensate for the information seeking systems of libraries by distributing material and information resources. Third, information seeking can be carried out in collaboration in research groups. The significance of the research group was found to be most important in informing about new information services and marketing library systems. Recommendations from colleagues were often needed to mobilize researchers into using new library services. The significance of colleagues in informing about library services is in line with earlier studies. The present study showed that sometimes information from colleagues was regarded as more important than information distributed directly by the local library. A culture of information sharing, including mutual trust, seemed mainly to be reflected in collaboration and collaborative information seeking in the research groups studied. The timing of the onset of individual research seemed to be related to the information sharing culture and social networks in research groups. The simultaneous onset of the research work by group members seemed to promote the growth of unbiased collaboration, also in information seeking.

Kirja-arvostelu : The behaviour and welfare of the horse

Kirjallisuusarvostelu

Myyjien organisaatioon sitoutuminen ja esimiehen vaikutus sitoutumiseen. Case: Alko Oy

Tämän tutkielman tavoitteena on kuvata ja ymmärtää myyjien organisaatioon sitoutumista Alko Oy:ssä, sitä kuinka myyjät ovat sitoutuneita organisaatioon ja sitoutumiseen vaikuttavia tekijöitä. Tarkoituksena on selvittää ja ymmärtää esimiehen vaikutusta sitoutumiseen sekä sitä kuinka esimies voi edistää myyjien sitoutumista. Lisäksi tavoitteena on kartoittaa ja ymmärtää sitoutumisen seurauksia. Tutkimuksen teoreettinen viitekehys muodostuu organisaatioon sitoutumisen tutkimuksesta ja johtajuuden tutkimuksesta, erityisesti transformationaalisesta johtajuudesta ja sen vaikutuksesta sitoutumiseen. Tutkimus on luonteeltaan laadullinen ja pääasiallisena tutkimusmetodina on käytetty teemahaastattelua. Tutkimusaineisto kerättiin haastattelemalla 22 myyjää ja seitsemää esimiestä. Haastattelut nauhoitettiin ja litteroitiin. Haastattelujen lisäksi myyjille tehtiin kysely. Aineistoa analysoitiin teemoittain ja empiirisen aineiston analyysin tulkinta perustuu tutkimuksen teoreettiseen viitekehykseen. Tutkimustulosten mukaan myyjien sitoutuminen kohdeorganisaatiossa on hyvällä tai vähintään kohtuullisella tasolla ja se pohjautuu voimakkaimmin affektiiviseen ulottuvuuteen. Lisäksi sitoutuminen perustuu osittain jatkuvuuteen perustuvaan komponenttiin sekä pieneltä osin myös normatiiviseen. Affektiiviseen sitoutumiseen vaikuttavat merkittävimmin työn monipuolisuus, haastavuus ja mielekkyys, onnistumisen ja merkityksellisyyden tunteet sekä ilmapiiri. Jatkuvuuteen perustuvaan sitoutumiseen vaikuttavat eniten palkitseminen ja siihen liittyen osa-aikaisuus, joka jakoi myyjiä kahtia. Lisäksi työn monipuolisuudella, varmuudella sekä työllistymisvaihtoehdoilla ja perhesyillä on vaikutusta jatkuvuusperusteiseen sitoutumiseen. Normatiiviseen sitoutumiseen vaikuttavat voimakkaimmin positiivinen vapaaehtoinen vastavuoroisuus organisaatiota kohtaan sen toimintaan ja tekemiin investointeihin liittyen. Lisäksi normatiiviseen sitoutumiseen vaikuttavat sosialisaatio kasvatuksen myötä ja psykologinen sopimus odotuksineen. Esimiehen vaikutus sitoutumiseen korostuu tuloksissa ja esimiehen toiminnalla on merkittävin vaikutus affektiiviseen sitoutumiseen. Keskeisimpiä esimiehen vaikutuskeinoja myyjien sitoutumiseen ovat vastuun antaminen ja osallistaminen, palaute, avoin vuorovaikutus ja tiedonkulku sekä tasapuolisuus ja oikeudenmukaisuus toiminnassa. Myös esimiehen kannustavuus ja myyjien yksilöllinen huomiointi, osaamisen kehittämisen tukeminen sekä esimerkillinen toiminta ovat keskeisiä. Sitoutumisen seurauksista merkittävimpiä ovat vähäinen vaihtuvuus sekä työsuorituksen ja asiakaspalvelun laatu. Lisäksi organisaatiokansalaisuuskäyttäytymiseen liittyvät seikat, kuten parhaansa tekeminen, joustavuus ja itseohjautuvuus ovat keskeisiä sitoutumisen seurauksia.

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.

The genetics of behaviour and other adaptive traits in nine-spined sticklebacks (Pungitius pungitius)

One of the main goals in current evolutionary biology research is to identify genes behind adaptive phenotypic variations. The advances in genomic technologies have made it possible to identify genetic loci behind these variations, also concerning non-model species. This thesis investigates the genetics of the behaviour and other adaptive traits of the nine-spined stickleback (Pungitius pungitius) through the application of different genetic approaches. Fennoscandian nine-spined stickleback populations express large phenotypical differences especially in behaviour, life –history traits and morphology. However the underlying genetic bases for these phenotypical differences have not been studied in detail. The results of the project will lay the foundation for further genetics studies and provide valuable information for our understanding of the genetics of the adaptive divergence of the nine-spined stickleback. A candidate gene approach was used to develop microsatellite markers situating close to candidate genes for behaviour in the nine-spined stickleback. Altogether 13 markers were developed and these markers were used in the subsequent studies with the anonymous random markers and physiologically important gene markers which are already currently available for nine-spined sticklebacks. It was shown that heterozygosity correlated with behaviour in one of the marine nine-spined stickleback populations but with contrasting effects: correlations with behaviour were negative when using physiological gene markers and positive with random markers. No correlation was found between behavioural markers and behaviour. From the physiological gene markers, a strong correlation was found between osmoregulation-related gene markers and behaviour. These results indicate that both local (physiological) and general (random) effects are important in the shaping of behaviour and that heterozygosity– behaviour correlations are population dependent. In this thesis a second linkage map for nine-spined sticklebacks was constructed. Compared to the earlier nine-spined stickleback linkage map, genomic rearrangements were observed between autosomal (LG7) and sex-determing (LG12) linkage groups. This newly constructed map was used in QTL mapping studies in order to locate genomic regions associated with pelvic structures, behaviour and body size/growth. One major QTL was found for pelvic structures and Pitx1 gene was related to these traits as was predicted from three-spined stickleback studies, but this was in contrast to earlier nine-spined stickleback study. The QTL studies also revealed that behaviour and body size/growth were genetically more complex by having more QTL than pelvic traits. However, in many cases, pelvic structure, body size/growth and behaviour were linked to similar map locations indicating possible pleiotropic effects of genes locating in these QTL regions. Many of the gene related markers resided in the QTL area. In the future, studying these possible candidate genes in depth might reveal the underlying mechanism behind the measured traits.

Chaotic Behaviour of Active Magnetic Bearing System by Time Series Analysis

Chaotic behaviour is one of the hardest problems that can happen in nonlinear dynamical systems with severe nonlinearities. It makes the system's responses unpredictable. It makes the system's responses to behave similar to noise. In some applications it should be avoided. One of the approaches to detect the chaotic behaviour is nding the Lyapunov exponent through examining the dynamical equation of the system. It needs a model of the system. The goal of this study is the diagnosis of chaotic behaviour by just exploring the data (signal) without using any dynamical model of the system. In this work two methods are tested on the time series data collected from AMB (Active Magnetic Bearing) system sensors. The rst method is used to nd the largest Lyapunov exponent by Rosenstein method. The second method is a 0-1 test for identifying chaotic behaviour. These two methods are used to detect if the data is chaotic. By using Rosenstein method it is needed to nd the minimum embedding dimension. To nd the minimum embedding dimension Cao method is used. Cao method does not give just the minimum embedding dimension, it also gives the order of the nonlinear dynamical equation of the system and also it shows how the system's signals are corrupted with noise. At the end of this research a test called runs test is introduced to show that the data is not excessively noisy.