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.

Development of porous glass-fiber reinforced composite for bone implants. Evaluation of antimicrobial effect and implant fixation

Cranial bone reconstructions are necessary for correcting large skull bone defects due to trauma, tumors, infections and craniotomies. Traditional synthetic implant materials include solid or mesh titanium, various plastics and ceramics. Recently, biostable glass-fiber reinforced composites (FRC), which are based on bifunctional methacrylate resin, were introduced as novel implant solution. FRCs were originally developed and clinically used in dental applications. As a result of further in vitro and in vivo testing, these composites were also approved for clinical use in cranial surgery. To date, reconstructions of large bone defects were performed in 35 patients. This thesis is dedicated to the development of a novel FRC-based implant for cranial reconstructions. The proposed multi-component implant consists of three main parts: (i) porous FRC structure; (ii) bioactive glass granules embedded between FRC layers and (iii) a silver-polysaccharide nanocomposite coating. The porosity of the FRC structure should allow bone ingrowth. Bioactive glass as an osteopromotive material is expected to stimulate the formation of new bone. The polysaccharide coating is expected to prevent bacterial colonization of the implant. The FRC implants developed in this study are based on the porous network of randomly-oriented E-glass fibers bound together by non-resorbable photopolymerizable methacrylate resin. These structures had a total porosity of 10–70 volume %, of which > 70% were open pores. The pore sizes > 100 μm were in the biologically-relevant range (50-400 μm), which is essential for vascularization and bone ingrowth. Bone ingrowth into these structures was simulated by imbedding of porous FRC specimens in gypsum. Results of push-out tests indicated the increase in the shear strength and fracture toughness of the interface with the increase in the total porosity of FRC specimens. The osteopromotive effect of bioactive glass is based on its dissolution in the physiological environment. Here, calcium and phosphate ions, released from the glass, precipitated on the glass surface and its proximity (the FRC) and formed bone-like apatite. The biomineralization of the FRC structure, due to the bioactive glass reactions, was studied in Simulated Body Fluid (SBF) in static and dynamic conditions. An antimicrobial, non-cytotoxic polysaccharide coating, containing silver nanoparticles, was obtained through strong electrostatic interactions with the surface of FRC. In in vitro conditions the lactose-modified chitosan (chitlac) coating showed no signs of degradation within seven days of exposure to lysozyme or one day to hydrogen peroxide (H2O2). The antimicrobial efficacy of the coating was tested against Staphylococcus aureus and Pseudomonas aeruginosa. The contact-active coating had an excellent short time antimicrobial effect. The coating neither affected the initial adhesion of microorganisms to the implant surface nor the biofilm formation after 24 h and 72 h of incubation. Silver ions released to the aqueous environment led to a reduction of bacterial growth in the culture medium.

Yhteiskunnallisen sisältöpalvelun sosioteknologinen tarkastelu Kohosen itseorganisoituvien karttojen avulla - Case deittipalvelu

Työn tavoitteena on tutkia deittipalvelun käyttäjien anonyymiaineistoa neuroverkko-opetuksessa segmentoituneiden piirrekarttojen (SOM, Self-Organizing Map) avulla. Näiden piirrekarttojen avulla on tarkoitus selvittää, löytyykö mahdollisesti selkeitä SMS- ja e-mail - käyttäjäryhmiä. Tutkimusta lähestytään perehtymällä ensin yrityksen tekniseen palvelualusta-arkkitehtuuriin ja myös varsinaiseen deittipalveluun käyttäjän kannalta.Tutkimus aloitettiin koodaamalla tietoaineisto SOM Toolbox-ohjelmalle käytettäväksi. Varsinaisia tutkimustuloksia analysoitiin valitsemalla otoksia neuroverkko-opetuksessa segmentoituneista piirrekartoista. Saadut tulokset osoittavat, ettäSOM-teknologia soveltuu hyvin sisältöpalveluiden sosioteknologiseen tutkimukseen ja sitä on myös mahdollista käyttää asiakkuudenhallinnassa erilaisten käyttäjäryhmien profilointiin.

Surface Studies of Thiolate Adsorbates on Some Metals

The results and discussions in this thesis are based on my studies about selfassembled thiol layers on gold, platinum, silver and copper surfaces. These kinds of layers are two-dimensional, one molecule thick and covalently organized at the surface. They are an easy way to modify surface properties. Self-assembly is today an intensive research field because of the promise it holds for producing new technology at nanoscale, the scale of atoms and molecules. These kinds of films have applications for example, in the fields of physics, biology, engineering, chemistry and computer science. Compared to the extensive literature concerning self-assembled monolayers (SAMs) on gold, little is known about the structure and properties of thiolbased SAMs on other metals. In this thesis I have focused on thiol layers on gold, platinum, silver and copper substrates. These studies can be regarded as a basic study of SAMs. Nevertheless, an understanding of the physical and chemical nature of SAMs allows the correlation between atomic structure and macroscopic properties. The results can be used as a starting point for many practical applications. X-ray photoelectron spectroscopy (XPS) and synchrotron radiation excited high resolution photoelectron spectroscopy (HR-XPS) together with time-offlight secondary ion mass spectrometry (ToF-SIMS) were applied to investigate thin organic films formed by the spontaneous adsorption of molecules on metal surfaces. Photoelectron spectroscopy was the main method used in these studies. In photoelectron spectroscopy, the sample is irradiated with photons and emitted photoelectrons are energy-analyzed. The obtained spectra give information about the atomic composition of the surface and about the chemical state of the detected elements. It is widely used in the study of thin layers and is a very powerful tool for this purpose. Some XPS results were complemented with ToF-SIMS measurements. It provides information on the chemical composition and molecular structure of the samples. Thiol (1-Dodecanethiol, CH3(CH2)11SH) solution was used to create SAMs on metal substrates. Uniform layers were formed on most of the studied metal surfaces. On platinum, surface aligned molecules were also detected in investigations by XPS and ToF-SIMS. The influence of radiation on the layer structure was studied, leading to the conclusion that parts of the hydrocarbon chains break off due to radiation and the rest of the layer is deformed. The results obtained showed differences depending on the substrate material. The influence of oxygen on layer formation was also studied. Thiol molecules were found to replace some of the oxygen from the metal surfaces.

Synthesis and characterization of nanoperforated metal oxide thin films

For advanced devices in the application fields of data storage, solar cell and biosensing, one of the major challenges to achieve high efficiency is the fabrication of nanopatterned metal oxide surfaces. Such surfaces often require both precise structure at the nanometer scale and controllable patterned structure at the macro scale. Nowadays, the dominating candidates to fabricate nanopatterned surfaces are the lithographic technique and block-copolymer masks, most of which are unfortunately costly and inefficient. An alternative bottom-up approach, which involves organic/inorganic self-assembly and dip-coating deposition, has been studied intensively in recent years and has proven to be an effective technique for the fabrication of nanoperforated metal oxide thin films. The overall objective of this work was to optimize the synthesis conditions of nanoperforated TiO2 (NP-TiO2) thin films, especially to be compatible with mixed metal oxide systems. Another goal was to develop fabrication and processing of NP-TiO2 thin films towards largescale production and seek new applications for solar cells and biosensing. Besides the traditional dip-coating and drop-casting methods, inkjet printing was used to prepare thin films of metal oxides, with the advantage of depositing the ink onto target areas, further enabling cost-effective fabrication of micro-patterned nanoperforated metal oxide thin films. The films were characterized by water contact angle determination, Atomic Force Microscopy, Scanning Electron Microscopy, X-ray Photoelectron Spectroscopy and Grazing Incidence XRay Diffraction. In this study, well-ordered zinc titanate nanoperforated thin films with different Zn/Ti ratios were produced successfully with zinc precursor content up to 50 mol%, and the dominating phase was Zn2Ti3O8. NP-TiO2 structures were also obtained by a cost-efficient means, namely inkjet printing, at both ambient temperature and 60 °C. To further explore new biosensing applications of nanoperforated oxide thin films, inkjet printing was used for the fabrication of both continuous and patterned polymeric films onto NP-TiO2 and perfluorinated phosphate functionalized NP-TiO2 substrates, respectively. The NP-TiO2 films can be also functionalized with a fluoroalkylsilane, resulting in hydrophobic surfaces on both titania and silica. The surface energy contrast in the nanoperforations can be tuned by irradiating the films with UV light, which provides ideal model systems for wettability studies.

Hydrothermal carbonization in the synthesis of sustainable porous carbon materials

Carbon materials are found versatile and applicable in wide range of applications. During the recent years research of carbon materials has focussed on the search of environmentally friendly, sustainable, renewable and low-cost starting material sources as well as simple cost-efficient synthesis techniques. As an alternative synthesis technique in the production of carbon materials hydrothermal carbonization (HTC) has shown a great potential. Depending on the application HTC can be performed as such or as a pretreatment technique. This technique allows synthesis of carbon materials i.e. hydrochars in closed vessel in the presence of water and self-generated pressure at relatively low temperatures (180-250 ˚C). As in many applications well developed porosity and heteroatom distribution are in a key role. Therefore in this study different techniques e.g. varying feedstock, templating and post-treatment in order to introduce these properties to the hydrochars structure were performed. Simple monosaccharides i.e. fructose or glucose and more complex compounds such as cellulose and sludge were performed as starting materials. Addition of secondary precursor e.g. thiophenecarboxaldehyde and ovalbumin was successfully exploited in order to alter heteroatom content. It was shown that well-developed porosity (SBET 550 m2/g) can be achieved via one-pot approach (i.e. exploitation of salt mixture) without conventionally used post-carbonization step. Nitrogen-enriched hydrochars indicated significant Pb(II) and Cr(VI) removal efficiency of 240 mg/g and 68 mg/g respectively. Sulphur addition into carbon network was not found to have enhancing effect on the adsorption of methylene blue or change acidity of the carbon material. However, these hydrochars were found to remove 99.9 % methylene blue and adsorption efficiency of these hydrochars remained over 90 % even after regeneration. In addition to water treatment application N-rich high temperature treated carbon materials were proven applicable as electrocatalyst and electrocatalyst support. Hydrothermal carbonization was shown to be workable technique for the production of carbon materials with variable physico-chemical properties and therefore hydrochars could be applied in several different applications e.g. as alternative low-cost adsorbent for pollutant removal from water.

Liikevaihdon ja materiaalivirtojen kasvun vaatimukset logistiikkakeskukselle

Incap Furniture Oy on koottavien mäntyhuonekalujen sopimusvalmistaja. Yrityksen tavoitteena on saavuttaa 70 miljoonan euron liikevaihto Kärsämäen tehtaalla vuonna 2008. Suurin osa komponenttituotannosta ostetaan alihankintaverkostosta ja valmiit tuotteet pakataan logistiikkakeskuksessa. Diplomityön tavoitteena oli selvittää miten kasvavat materiaalivirrat saadaan tulevaisuudessa käsiteltyä Kärsämäen tehtaan logistiikkakeskuksessa Työn teoriaosassa on ensin käsitelty mahdollisuuksia vähentää kokoonpanon puutetilanteita ostotoimintaa kehittämällä. Teoriaosassa esitellään lisäksi varastonohjausmenetelmiä, sekä yleisesti varastoinnin tehtäväkenttää. Empiirisessä osassa analysoitiin annettujen tietojen avulla vuoden 2008 tavoitetilaa, sekä simuloitiin tavoitetilan materiaalivirtoja suhteessa logistiikkakeskuksen kapasiteettiin. Kasvavat materiaalivirrat pakottavat kehittämään logistiikkakeskuksen toimintaa. Eräluonteisen toiminnan vuoksi kaikkien komponenttien kohdalla on pyrittävä MRP ohjaukseen. Komponenttientilauseriä on pyrittävä pienentämään vastaamaan todellista tarvetta. Kriittisille A- ja B- komponenteille tarvitaan lisäksi puskurivarastot tasaamaan toimitusajan vaihtelua ulkomaantoimituksissa. Pakkauseristä yli jäävät C nimikkeet tulee varastoida jatkossa erillään logistiikkakeskuksesta ja korkeavarastosta. D- ja E-nimikkeitä ei kannata tuoda ulkomailta, eikä niitä ole kannattavaa varastoida lainkaan. Pakkaamon täytyy toimia tulevaisuudessa kolmessa vuorossa ja korkeavaraston työjonoa on lyhennettävä kolmesta vuorokaudesta 4-6 työvuoroon. Edellä mainituilla toimenpiteillä ja toimitusten aktiivisella seurannalla saavutetaan toimintaympäristö, jolloin logistiikkakeskuksen kapasiteetti riittää materiaalivirtojen kasvaessa.

Transparent Network Interfaces to Mobile Peer-to-Peer Environment

The fact that most of new Personal Data Assistant (PDA) devices and smartphones have the ability to communicate via different wireless technologies has made several new applications possible. While traditional network model is based on the idea of static hosts, mobile devices can create decentralized, self-organizing ad-hoc networks and act as peers in the network. This kind of adapting network is suitable for mobile devices which can freely join and leave the networks. Because several different wireless communication technologies are involved, flexible changing of the networking technology must be handled in order to enable seamless communication between these networks. This thesis presents a transparent network interface to mobile Peer-to-Peer environment which is named as Virtual PeerHood. Different wireless technologies and aspects of providing a seamless connectivity between these technologies are explored. The result is a middleware platform for mobile Peer-to-Peer environment, capable of handling several networking technologies.

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.

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.

Understanding Online Game Players' Post-adoption Behavior: an Investigation of Social Network Games in China

Retaining players and re-attracting switching players has long been a central topic for SNG providers with regard to the post-adoption stage of playing an online game. However, there has not been much research which has explored players’ post-adoption behavior by incorporating the continuance intention and the switching intention. In addition, traditional IS continuance theories were mainly developed to investigate users’ continued use of utilitarian IS, and thus they may fall short when trying to explain the continued use of hedonic IS. Furthermore, compared to the richer literature on IS continuance, far too little attention has been paid to IS switching, leading to a dearth of knowledge on the subject, despite the increased incidence of the switching phenomenon in the IS field. By addressing the limitations of prior literature, this study seeks to examine the determinants of SNG players’ two different post-adoption behaviors, including the continuance intention and the switching intention. This study takes a positivist approach and uses survey research method to test five proposed research models based on Unified Theory of Acceptance and Use of Technology 2; Use and Gratification Theory; Push-Pull-Mooring model; Cognitive Dissonance Theory; and a self-developed model respectively with empirical data collected from the SNG players of one of the biggest SNG providers in China. A total of 3919 valid responses and 541 valid responses were used to examine the continuance intention and the switching intention, respectively. SEM is utilized as the data analysis method. The proposed research models are supported by the empirical data. The continuance intention is determined by enjoyment, fantasy, escapism, social interaction, social presence, social influence, achievement and habit. The switching intention is determined by enjoyment, satisfaction, subjective norms, descriptive norms, alternative attractiveness, the need for variety, change experience, and adaptation cost. This study contributes to IS theories in three important ways. Firstly, it shows IS switching should be included in IS post-adoption research together with IS continuance. Secondly, a modern IS is usually multi-functional and SNG players have multiple reasons for using a SNG, thus a player’s beliefs about the hedonic, social and utilitarian perceptions of their continued use of the SNG exert significant effects on the continuance intention. Thirdly, the determinants of the switch ing intention mainly exert push, pull, and mooring effects. Players’ beliefs about their current SNG and the available alternatives, as well as their individual characteristics are all significant determinants of the switching intention. SNG players combine these effects in order to formulate the switching intention. Finally, this study presents limitations and suggestions for future research.