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  • Pihanurmi, Seila (2014)
    Goals. The purpose of this study was to examine, whether the dynamicity of pitch has an effect on duration perception in synthetic auditory stimuli and if the effect, if observed, is dependent on first language. Furthermore, it was of interest to see, if mother tongue has an effect to the way static auditory stimuli are perceived. The effect of dynamic pitch on duration perception is a topic little researched and the results obtained are contradictory which is why this thesis is relevant. The duration discrimination abilities of Finnish and Chinese people have not been compared to each other before, so this thesis has some new information to offer about the perception of duration. Method. The research consisted of different kinds of behavioral tests, which measured the ability to discriminate the differences between two auditory stimuli. Two alternative forced choice method was used in all the experiments. In the first experiment the discrimination ability was measured in stimuli which only differed in duration. In the second experiment the stimuli were dynamic and in the third experiment the stimuli only differed in pitch. There were altogether 30 subjects, 15 of which Finnish and 15 Mandarin Chinese speakers. The answers of the subjects were analyzed with logistic linear regression models fit for multiple variables. Results and conclusions. According to the results mother tongue does have an effect to the answers given and the dynamicity of pitch does lengthen the perceived duration. The effect of language background was also apparent in static stimuli although the significance was marginal. It is nevertheless possible to conclude from the results that the perception of duration between Finnish and Mandarin Chinese speakers does differ from each other. The research on the effect of dynamic pitch on duration perception needs to be continued. Further research is especially needed over the conventions of perceiving natural auditory stimuli and the perception of pitch when tied to a linguistic context.
  • Kostiainen, Nikke (2017)
    Peliäänet ovat pelaajalle tarkoitettuja ääniä, joita peliohjelmisto toistaa suorituksen aikana. Työssä tarkastellaan ja arvioidaan erilaisten peliäänien kehityksen piirteitä ja vertaillaan mahdollisia ratkaisumenetelmiä keskenään. Työssä hyödynnettiin kirjallisia lähteitä ja työn osana toteutettiin yksinkertainen peliäänimoottori. Moottorin käytön helppoutta eri skenaarioissa arvioitiin sanallisesti. Vertailu toteutusmentelmien välillä suoritettiin käyttäen lähteistä löytyvää tietoa, sekä kokemuspohjaa olemassa olevien ratkaisujen käytöstä ja peliäänimoottorin toteutuksesta. Vertailussa todettiin eri ratkaisumenetelmien sopivan tiettyyn pelinkehitystilanteisiin paremmin ja toisiin huonommin. Itse kehitettävät pelimoottoriratkaisut sopivat hyvin tilanteisiin, joissa kehitettävä alusta on suorituskyvyltään rajattu tai peliäänimoottorin vaatimukset edellyttävät toimintoja, joita olemassa olevissa ratkaisuissa ei ole. Vastaavasti olemassaolevat ratkaisut sopivat hyvin suurempiin projekteihin, joissa peliäänien avulla tavoitellaan realistisuutta
  • Isomäki, Riina (2023)
    Maatalouden rakennemuutos ja liiketoimintaympäristön muuttuminen edellyttävät nykypäivän maatiloilta uudenlaisia kyvykkyyksiä. Miksi toiset tilat selviävät muutoksessa paremmin kuin toiset tilat? Strategiatutkimus lähestyy kysymystä käyttäen selittäjänä dynaamisten kyvykkyyksien teoriaa. Kyvykkyyksien avulla selvitetään, miten maatilayrittäjä aistii muutoksen liiketoimintaympäristössään ja miten hän tarttuu havaittuun muutokseen miettien tilansa jatkuvaa uudistamista. Tutkimuksessa haastateltiin seitsemää yrittäjää, joiden päätuotantosuuntana oli emolehmät. Yrittäjät olivat päätoimisia yrittäjiä tai emolehmätuotanto oli eriytetty tilan muista toiminnoista, joten tuotannon kannattavuuden arvioiminen oli konkreettisempaa. Teemahaastatteluna toteutetut haastattelut tehtiin kyselylomakkeen pohjalta, joka oli muotoiltu Teecen (2007b) ajatusten perustalle dynaamisista kyvykkyyksistä. Miten tunnistetaan, tartutaan sekä otetaan muutos käytäntöön suomalaisilla emolehmätiloilla. Yrittäjän päätöksiin tutkimuksessa vaikuttivat tilan resurssit, strategia sekä yrittäjän oma arvomaailma tilan historiaan kytkettynä. Yrittäjät olivat kyllä avoimia uudelle, keräsivät tietoa toimintaympäristöstään sisä- ja ulkopuolelta mutta käytännön toteutuksen suhteen monella tilalla oli parannettavaa. Pitkän- ja lyhyen aikavälin suunnitelmia olisi hyvä tehdä myös paperille asti. Tavoitteena tutkielmassa ei ole tehdä yleistettäviä päätelmiä emolehmätuotannon johtamistavoista. Tulosten avulla voidaan havainnoida vain, miten pieni määrä emolehmätiloja tekee päätöksiä tuotantonsa suhteen. Tulevaisuuden tutkimuksissa tulisikin perehtyä laajemmin dynaamisten kyvykkyyksien vaikutuksiin yleensä maatilojen johtamisessa.
  • Dajie, Wang (2017)
    This thesis summarises the adaptive bitrate streaming technology called Dynamic Adaptive Streaming over HTTP, also named as MPEG-DASH, as it is developed by the Moving Picture Experts Group. The thesis introduces and summarises MPEG-DASH standard, including the content of the standard, Profiles from MPEG and DASH Industry Forum, and an evaluation of the standard. The thesis then analyses the MPEG-DASH system and provides related research papers. It is organized into three different parts based on the workflow of the whole system, including the hosted Media Presentation Description file and video Segments in server, network infrastructures and DASH clients. In the end, the thesis discusses about the adoptions of the MPEG-DASH system in different industries, including Broadband, Broadcast, Mobile and 3D.
  • Kangas, Pinja (2022)
    Sulfuric acid has a central role in atmospheric chemistry, as it is considered to have a significant contribution in cloud formation and acid rain. In the gas phase, hydrolysis of SO3 catalysed by a single water molecule is contemplated to be the primary pathway to form sulfuric acid in the atmosphere. However, in previous studies it has been calculated that when the hydrolysis reaction is catalysed by a formic acid (FA) molecule, the potential energy barrier is significantly lower than for the water molecule catalysed reaction. In this work, the role of dynamic and steric effects for both reactions were studied through ab initio molecular dynamics (AIMD) collision simulations. The simulations were done by either colliding FA or a water molecule with SO3-H2O complex or a water dimer with the SO3-molecule. Altogether 230 trajectories were calculated at PBE/6-311+G(2pd,2df) level of theory, 70 for the collision of a water dimer and SO3, and 80 for both the collision of a water molecule or FA with SO3-H2O. The collision of FA with SO3-H2O led to the formation of sulfuric acid in 5 % of the simulations, whereas for the collision of a water molecule with SO3-H2O the reaction does not occur within the simulation time. Additionally, the SO3-H2O-FA pre-reactive complex formed in the simulations is shown to be more stable, most likely due to a less constrained ring structure. The collision of a water dimer with SO3 most commonly leads to the formation of SO3-H2O, and either sticking or evading of the second water molecule of the dimer. Based on the simulation results, strictly in terms of dynamic and steric effects, the FA-catalysed mechanism seems to be favored over the H2O-catalysed one
  • Joensuu, Juhana (2022)
    Currency risk is an important yet neglected consideration for investors holding internationally diversified investment portfolios. The foreign exchange market is an extremely liquid and efficient market, with daily transaction volumes exceeding the equivalent of several trillion euros. International investors have to decide upon the level of exposure on various currency risks typically by hedging some or all of the underlying currency exposure with currency derivative contracts. The currency overlay refers to an approach where the aggregate currency exposure from the investment portfolio is managed with a separate derivatives strategy, aimed at improving the overall portfolio’s risk adjusted returns. In this thesis, we develop a novel systematic, data-driven approach to manage the currency risk of investors holding diversified bond-equity portfolios, accounting for both risk minimization and expected returns maximization objectives on the portfolio level. The model is based upon modern portfolio theory, leveraging findings from prior literature in covariance modelling and expected currency returns. The focus of this thesis is in ensuring efficient risk diversification through the use of accurate covariance estimates fed by high-frequency data on exchange rates, bonds and equity indexes. As to the expected returns estimate, we identify purchasing power parity (PPP) and carry signals as credible alternatives to improve the expected risk-adjusted returns of the strategy. A block bootstrap simulation methodology is used to conduct empirical tests on different specifications of the developed dynamic overlay model. We find that dynamic risk-minimizing strategies significantly decrease portfolio risk relative to either unhedged or fully hedged portfolios. Using high-freqency data based returns covariance estimates is likely to improve portfolio diversification relative to a simple daily data-based estimator. The empirical results are much less clear in terms of risk adjusted returns. We find tentative evidence that the tested dynamic strategies improve risk adjusted returns. Due to the limited data sample used in this study, the findings regarding expected returns are highly uncertain. Nevertheless, considering evidence from prior research covering much longer time-horizons, we expect that both the risk-minimizing and returns maximizing components of the developed model are likely to improve portfolio-level risk adjusted returns. We recommend using the developed model as an input to support the currency risk management decision for investors with globally diversified investment portfolios, along with other relevant considerations such as solvency or discretionary market views.
  • Fornaro, Paolo (2011)
    In recent years, thanks to developments in information technology, large-dimensional datasets have been increasingly available. Researchers now have access to thousands of economic series and the information contained in them can be used to create accurate forecasts and to test economic theories. To exploit this large amount of information, researchers and policymakers need an appropriate econometric model.Usual time series models, vector autoregression for example, cannot incorporate more than a few variables. There are two ways to solve this problem: use variable selection procedures or gather the information contained in the series to create an index model. This thesis focuses on one of the most widespread index model, the dynamic factor model (the theory behind this model, based on previous literature, is the core of the first part of this study), and its use in forecasting Finnish macroeconomic indicators (which is the focus of the second part of the thesis). In particular, I forecast economic activity indicators (e.g. GDP) and price indicators (e.g. consumer price index), from 3 large Finnish datasets. The first dataset contains a large series of aggregated data obtained from the Statistics Finland database. The second dataset is composed by economic indicators from Bank of Finland. The last dataset is formed by disaggregated data from Statistic Finland, which I call micro dataset. The forecasts are computed following a two steps procedure: in the first step I estimate a set of common factors from the original dataset. The second step consists in formulating forecasting equations including the factors extracted previously. The predictions are evaluated using relative mean squared forecast error, where the benchmark model is a univariate autoregressive model. The results are dataset-dependent. The forecasts based on factor models are very accurate for the first dataset (the Statistics Finland one), while they are considerably worse for the Bank of Finland dataset. The forecasts derived from the micro dataset are still good, but less accurate than the ones obtained in the first case. This work leads to multiple research developments. The results here obtained can be replicated for longer datasets. The non-aggregated data can be represented in an even more disaggregated form (firm level). Finally, the use of the micro data, one of the major contributions of this thesis, can be useful in the imputation of missing values and the creation of flash estimates of macroeconomic indicator (nowcasting).
  • Nyman, Thomas (2014)
    Operating System-level Virtualization is virtualization technology based on running multiple isolated userspace instances, commonly referred to as containers, on top of a single operating system kernel. The fundamental difference compared to traditional virtualization is that the targets of virtualization in OS-level virtualization are kernel resources, not hardware. OS-level virtualization is used to implement Bring Your Own Device (BYOD) policies on contemporary mobile platforms. Current commercial BYOD solutions, however, don't allow for applications to be containerized dynamically upon user request. The ability to do so would greatly improve the flexibility and usability of such schemes. In this work we study if existing OS-level virtualization features in the Linux kernel can meet the needs of use cases reliant on such dynamic isolation. We present the design and implementation of a prototype which allows applications in dynamic isolated domains to be migrated from one device to another. Our design fits together with security features in the Linux kernel, allowing the security policy influenced by user decisions to be migrated along with the application. The deployability of the design is improved by basing the solution on functionality already available in the mainline Linux kernel. Our evaluation shows that the OS-level virtualization features in the Linux kernel indeed allow applications to be isolated in a dynamic fashion, although known gaps in the compartmentalization of kernel resources require trade-offs between the security and interoperability to be made in the design of such containers.
  • Bankowski, Victor (2021)
    WebAssembly (WASM) is a binary instruction format for a stack-based virtual machine originally designed for the Web but also capable of being run on outside of the browser contexts. The WASM binary format is designed to be fast to transfer, load and execute. WASM programs are designed to be safe to execute by running them in a memory safe sandboxed environment. Combining dynamic linking with WebAssembly could allow the creation of adaptive modular applications that are cross-platform and sandboxed but still fast to execute and load. This thesis explores implementing dynamic linking in WebAssembly. Two artifacts are presented: a dynamic linking runtime prototype which exposes a POSIX-like host function interface for modules and an Android GUI interfacing prototype built on top of the runtime. In addition the results of measurements which were performed on both artefacts are presented. Dynamic linking does improve the memory usage and the startup time of applications when only some modules are needed. However if all modules are needed immediately then dynamic linked applications. perform worse than statically linked applications. Based on the results, dynamically linking WebAssembly modules could be a viable technology for PC and Android. The poor performance of A Raspberry Pi in the measurements indicates that dynamic linking might not be viable for resource contrained system especially if applications are performance critical.
  • Roininen, Kiia (2024)
    Wood construction has been increasing globally and engineered wood products (EWPs), such as Cross Laminated Timber (CLT), have had a major part in it. Increasing wood construction could help decrease the carbon footprint of the construction sector, since wood can be sustainably sourced and wood products store carbon. To use wood in construction in a more extensive way, its properties and behaviour as a construction material must be known. Wood has many properties of which moisture has a great impact on other properties, such as strength. Too high moisture can also cause problems, such as fungal growth, on its own. Therefore, it is important to monitor the moisture levels and understand the factors affecting them. In this study, the wood moisture content (MC) of CLT wall elements was monitored with resistance-based moisture meters from the manufacturing plant, through transportation and construction of a building at the Hyytiälä forestry station in Finland. There were sensors in five locations around the building and they all measured MC in three different depths inside the wall. The objective was to see how, where and when did the MC change within the CLT elements. The data was analysed with statistical tests and presented through various types of graphs. The results showed that variation within the data was large, approximately from 8% to 16%. On average the MC was at its highest near the surface of the CLT elements, after the protective canopy was removed. Two measuring locations on the opposite sides of the building had consistently higher MC than in the other measuring locations. The MC stayed below FSP (Fibre saturation point) throughout the monitoring period and, therefore, the risk for moisture induced damage is very low.
  • Antipina, Dina (2013)
    The subject of our research is the behavior of the economy in response to monetary and technology shocks. To understand these issues we use a Dynamic Money-in-the-Utility-Function framework. We implement a non-separable property of the utility function that implies non-neutrality of real money balances. We construct a toy theoretic model with two representative agents who maximize their functions subject to constraints. We analytically solve the model using a method of log-linearization around the steady state and obtain the system of linear equations. We analyze the response of economic equilibrium with respect to implemented shocks using a method of undetermined coefficients and solve a system of linear difference expectation equations. In addition to analytical solution we also present Impulse Response Functions of the model. We compute the impacts of monetary and technology shocks on the model and find that in case of a positive monetary shock expected inflation effect dominates the liquidity effect, while in case of a positive productivity shock income effect dominates substitution effect. The findings regarding the impact of a technology shock contradict the theory of real business cycles that predicts the domination of substitution effect over the income effect
  • Tolonen, Topias (2020)
    We consider a so-called principal-agent problem, where our aim is to construct an optimal contract that maximises utilities for the contractor, the principal, and for the effort-exerting party, the agent. In our setting, the time-horizon of the contract is infinite, and the agent receives a continuously paid compensation for exerting effort. Our main goal is to establish a problem introduced in Sannikov (2008) and characterise an optimal contract by restricting the menu of feasible contracts, an approach inspired by Cvitanic et. al. (2018) We begin with an extensive literature review, where we review the continuous-time principal-agent problems and further motivate the scope of this thesis. We start from the notable article Holmström et. al. (1987), and we progress towards the works Williams (2008), Sannikov (2008) and Cvitanic et. al. (2018) Following the review, we construct the problem and lay the mathematical foundations for it. We focus on a new benchmark setting, adapted from Sannikov (2008) and Cvitanic et. al. (2018). We first define the so-called controlled state equation, and construct the canonical probability space. Then, we introduce then impose few assumptions regarding the core concepts, and identify the problems of the agent and the principal and characterise their objective functions. After characterising the problem, we characterise the optimal contract and show that the optimal contract maximises the principal's profit. We characterise the difference function of Sannikov (2008) to the agent's optimisation problem, and then follow Cvitanic et. al. (2018) on the reduction of the problem. The reduction is done by restricting the possible menu of contracts and thus reduce the non-standard problem to a dynamic programming problem. We introduce the corresponding Hamiltonian functionals, together with the value functions to the both principal and the agent. Furthermore, we introduce a family restricted processes, which we show to characterise the optimal contract. We finish with showing that the optimal contract exists even with the notion of retirement. Having completed the main technical contribution, that is, having solved for the optimal contract, we briefly discuss the results and their implications against previous literature. Additionally, we discuss the possible extensions to our research.
  • Mielikäinen, Lasse (2016)
    Dynamic scoring is an approach, which strives to take into account the effects that public policy changes and changes in the law have on the macroeconomic variables. Scoring is an estimate of the effects the policy change is expected to bring. Compared to the traditional approach, dynamic scoring offers more information of the effects, but does this with increased uncertainty. In their paper “Dynamic scoring: A back-of-the-envelope guide” (2006) N. Gregory Mankiw and Matthew Weinzierl use neoclassical growth model, or Ramsey growth model, to examine how large a part of capital and labor income tax cuts pay for themselves by inducing higher economic growth, i.e. the size of the dynamic feedback effect. Their focus is on the changes of tax revenue. They use first a basic model with Cobb-Douglas production and inelastic labor supply, then relax those assumptions for a more general Ramsey model and then in turn include parameters allowing for finite horizon households, imperfect competition, and externalities to capital investment. Depending on the model used, the dynamic feedback effect varies from model to model, for a capital tax cut from 50 to 74 percent and for a labor income tax cut from zero (with inelastic labor supply) to 21 percent. This thesis extends the Mankiw–Weinzierl model by including a tax on consumption to examine how this affects the dynamic feedback effect. In all the models, there is an increase in the dynamic feedback effect: depending on the model used, it varies for a capital tax cut from 60 to 87 percent and for a labor income tax cut from zero (with inelastic labor supply) to 25 percent. The values of some of the key parameters, namely the constant-consumption elasticity of labor supply and the elasticity of substitution between capital and labor, and the tax rates are revised as well. This further increases the dynamic feedback effect all along the line, in some cases even suggesting a capital tax cut to more than compensate the static revenue loss. Including a tax on consumption into the models increases the dynamic feedback effect, working into the same direction as rising the initial rates of capital and labor income taxes. Using alternative tax rates and values of the key parameters also has a significant impact on the size of the dynamic feedback effect.
  • Nestaite, Ernesta (2023)
    Intestinal epithelium is capable of rapid regeneration, which is associated with transient changes in cellular identity. Some of these changes involve an enrichment of fetal-like gene expression and simultaneous suppression of adult stem cell signature. Interestingly, the upregulation of fetal-like marker Stem cell antigen 1 (Sca1) is modulated by extracellular matrix (ECM) which is known to guide epithelial cells during regeneration. Our recently published decellularized small intestinal ECM (iECM) system retains the composition and topology of natural ECM. This makes it an attractive system for ex vivo studies addressing regeneration. This thesis aimed to gain insight into the fetal-like identity and its dynamics using an ex vivo iECM system. Intriguingly, Sca1 expressing cells on iECM displayed migratory features, such as a leading edge and changes in nuclear morphology. Curiously, these features are typical for epithelial cells during development. Furthermore, based on marker gene expression during iECM re-epithelization, fetal-like state was upregulated while adult stem cell state was downregulated, revealing a gradually emerging inverse correlation. Additionally, data suggests that circadian rhythms may have a role in modulating the fetal-like state. iECM from an active-state mice indicated a reduced capability to induce fetal-like identity and overall re-epithelization compared to the rest-state iECM. The results of this thesis suggest further potential of iECM system in studying emergence of fetal-like state during re-epithelization and circadian rhythm impact on it.
  • Nikinmaa, Laura (2017)
    The physiological effects of drought on trees has been studied excessively but many of them remain unclear. In this thesis I studied tree sugar dynamics under drying-wetting cycle as well as the role of soil hydraulic conductivity on how trees experience drought. I experimented with five Norway spruce seedlings in October and November 2016. The seedlings were in water after which they were put in to PEG solution of -0.5 MPa for 24 h and then transferred back to water. Sugar samples were taken from liquids, needles and roots once for every phase. Osmolality samples were taken from current year needles and water potential samples were taken from current year needles and roots every half an hour during day time. Continuous gas exchange measurements were done with Walz GFS-3000. There was no change in osmolality and no significant change in photosynthesis or transpiration rate. For sugar concentrations there was significant increase of non-structural carbohydrates in needles and significant decrease in roots. There was no change in sugar concentration in liquid. Overall impression was that trees did not suffer much from the PEG treatment. The results supported my hypothesis that changes in soil hydraulic conductivity are more important to effects of drought than changes in soil water potential.
  • Nurminen, Niilo Waltteri (2021)
    Phase transitions in the early Universe and in condensed matter physics are active fields of research. During these transitions, objects such as topological solitons and defects are produced by the breaking of symmetry. Studying such objects more thoroughly could shed light on some of the modern problems in cosmology such as baryogenesis and explain many aspects in materials research. One example of such topological solitons are the (1+1) dimensional kinks and their respective higher dimensional domain walls. The dynamics of kink collisions are complicated and very sensitive to initial conditions. Making accurate predictions within such a system has proven to be difficult, and research has been conducted since the 70s. Especially difficult is predicting the location of resonance windows and giving a proper theoretical explanation for such a structure. Deeper understanding of these objects is interesting in its own right but can also bring insight in predicting their possibly generated cosmological signatures. In this thesis we have summarized the common field theoretic tools and methods for the analytic treatment of kinks. Homotopy theory and its applications are also covered in the context of classifying topological solitons and defects. We present our numerical simulation scheme and results on kink-antikink and kink-impurity collisions in the $\phi^4$ model. Kink-antikink pair production from a wobbling kink is also studied, in which case we found that the separation velocity of the produced kink-antikink pair is directly correlated with the excitation amplitude of the wobbling kink. Direct annihilation of the produced pair was also observed. We modify the $\phi^4$ model by adding a small linear term $\delta \phi^3$, which modifies the kinks into accelerating bubble walls. The collision dynamics and pair production of these objects are explored with the same simulation methods. We observe multiple new effects in kink-antikink collisions, such as potentially perpetual bouncing and faster bion formation in comparison to the $\phi^4$ model. We also showed that the $\delta$ term defines the preferred vacuum by inevitably annihilating any kink-antikink pair. During pair production we noticed a momentum transfer between the produced bion and the original kink and that direct annihilation seems unlikely in such processes. For wobbling kink - impurity collisions we found an asymmetric spectral wall. Future research prospects and potential expansions for our analysis are also discussed.
  • Milosavljevic, Silvija (2021)
    Post-transcriptional modifications (PTMs) in RNA are present in all known RNA species and conserved in all kingdoms of life. Transfer RNA (tRNA) has been shown to have numerous conserved modifications, which exemplifies the importance of modifications having impact on the structure of the tRNA and its function as carrier of the amino acids. Ribosomal RNAs (rRNA) are universally modified as well, and modifications are situated at functionally important spots of the ribosome. Given the fact that types and sites of modifications are conserved, it is likely that these modifications have been selected for and that they optimize the ribosomal structure and functions. Stress, such as temperature or infection by a pathogen, is known to change the presence or abundance of modifications in RNA molecules and thereby affect translation efficacy. In line with that, this master’s thesis project sought to gain insight into the dynamics of PTMs in tRNA and rRNA upon oxidative stress, with the goal of utilizing recently optimized UPLC/MS method for identifying modified ribonucleosides. As the specific aim of the thesis was to estimate the change in PTMs in tRNA and rRNA in response to oxidative stress with 0.5 mM and 2 mM hydrogen peroxide H2O2, 3 immediate goals were: (i) to isolate total tRNA from yeast grown in stress conditions, (ii) to isolate rRNA from yeast 80S ribosomes, and (iii) to identify present modifications using mass spectrometry. Yeast was cultured in presence of H2O2 as a stressor in mentioned concentrations, and both treatments considered showed a difference in survival when compared to the control. Rough cell concentration estimates (OD600) did not show the effect of the stressor on cell survival clearly, but when number of viable cells per mL was estimated, it was clear that growth of the stressed yeast cultures was hindered 2 hours after exposure to H2O2 but recovered during the 24 hours. Firstly, using UPLC/MS analysis, 29 modifications were identified in tRNA from control and H2O2 treated yeast. Most identified modifications showed no change in abundance in treatments, which is to be verified with additional replicates. However, distinct dynamics of stress-related change was found for several modifications, revealing additional modifications that may play a role in stress related modificome reprogramming to the previously known signature modifications of oxidative stress. It was expected that recovery of culture growth after 24 hours may be accompanied with modification level recovery. However, that was not demonstrated here as downregulation at 2 hours followed by upregulation at 24 hours was seen for 2-methylthio-N6-methyladenosine, N4-acetylcytidine and 5-methoxycarbonylmethyl-2-thiouridine, and the reverse was shown for N4-methylcytidine. Upregulation in both time points was also shown here for some modifications. Taken together, these results confirm a complex and dynamic control of tRNA modifications in cellular survival responses. Modifications found to be affected by oxidative stress are most frequently located on the wobble position 34 and anticodon loop position 37, so it is expected that changes in their modification levels could directly affect the tRNA function in translation, making them a specific target for future research. Secondly, modifications in rRNA from control yeast cultures were identified, such as expected methylations of all 4 canonical nucleosides. However, further analysis will be needed to confirm the other identified modifications, due to the potential mRNA and tRNA contamination. Optimizing the method for rRNA modifications identifications by acquiring more modified nucleosides specific for the rRNA to use as standards in the analysis, analyzing rRNA types separately and using tandem mass spectrometry would enable getting a deeper understanding of which modifications are present and where they are positioned. Finally, it would enable reliable identification of the signals of novel modifications present in rRNA, such as the tRNA modification 5-carbamoylmethyluridine signal found here. In conclusion, this thesis work lays the foundation to study the evolutionary conserved function of PTM changes during stress as modulators of translation, using the methodological approaches discussed in-depth within the thesis, primarily to confirm the intriguing results found here.
  • Kähönen, Simo (2020)
    Context. Software Product Line (SPL) is a set of software system products that have common features and product-specific features. Dynamic Software Product Line (DSPL) is an SPL that features runtime variability. Objective. The main objective of this study is to evaluate the latest research related to SPL dynamic variability in general. The second objective of this study is to investigate dynamic variability modeling methods and tools that are utilized and introduced for SPLs by the scholars. The third objective of this study is to investigate testing methods and tools that are utilized and introduced for DSPLs by the scholars. Method. The scientific research method of this study is Systematic Literature Review (SLR). Papers included are published between years 2015 and 2017. Four scientific digital libraries were used as data sources for the papers. Results. The main result of this study is that between years 2015 and 2017, there has been an active research community studying SPL dynamic variability. For all 25 papers included in this study, on a scale of 0 to 10, the arithmetic mean of the quality scores is 7.14 (median is 7.5). One industrial practice DSPL implementation case study was presented by the scholars. Three other case studies seemed to be more or less simplified exemplar of industry practice DSPL implementations. Two studies were focusing in testing aspects of DSPLs. The second result of this study is that scholars have utilized 19 existing dynamic variability modeling methods for SPLs, and introduced 17 new dynamic variability modeling methods for SPLs. Scholars have utilized seven existing dynamic variability modeling tools for SPLs, and introduced four new dynamic variability modeling tools for SPLs. The third result of this study is that scholars have introduced four new testing methods for DSPLs, and utilized two existing testing tools for DSPLs. Conclusions. The general conclusion of this study is that albeit SPL dynamic variability has been actively studied between years 2015 and 2017, there are still open research areas, especially in the field of industry practice use and testing of DSPLs. 2012 ACM Computing Classification System (CCS): Software and its engineering -> Software creation and management -> Software development techniques -> Reusability -> Software product lines Software and its engineering -> Software creation and management -> Designing software -> Software design engineering
  • Kainulainen, Henna (2015)
    In this thesis we consider dynamic X-ray computed tomography (CT) for a two dimensional case. In X-ray CT we take X-ray projection images from many different directions and compute a reconstruction from those measurements. Sometimes the change over time in the imaged object needs to be taken into account, for example in cardiac imaging or in angiography. This is why we're looking at the dynamic (something changing in time, while taking the measurements) case. At the beginning of the thesis in chapter 2 we present some necessary theory on the subject. We first go through some general theory about inverse problems and the concentrate on X-ray CT. We talk about ill-posedness of inverse problems, regularization and the measurement proses in CT. Different measurement settings and the discretization of the continuous case are introduced. In chapter 3 we introduce a solution method for the problem: total variation regularization with Barzilai-Borwein minimization method. The Barzilai-Borwein minimization method is an iterative method and well suited for large scale problems. We also explain two different methods, the multi-resolution parameter choice method and the S-curve method, for choosing the regularization parameter needed in the minimization process. The 4th chapter shows the materials used in the thesis. We have both simulated and real measured data. The simulated data was created using a rendering software and for the real data we took X-ray projection images of a Lego robot. The results of the tests done on the data are shown in chapter 5. We did tests on both the simulated and the measured data with two di erent measurement settings. First assuming we have 9 xed source-detector pairs and then that we only one source-detector pair. For the case where we have only one pair, we tested the implemented regularization method we begin by considering the change in the imaged object to be periodic. Then we assume can only use some number of consecutive moments, based on the rate the object is chancing, to collect the data. Here we only get one X-ray projection image at each moment and we combine measurements from multiple di erent moments. In the last chapter, chapter 6, we discuss the results. We noticed that the regularization method is quite slow, at least partly because of the functions used in the implementation. The results obtained were quite good, especially for the simulated data. The simulated data had less details than the measured data, so it makes sense that we got better results with less data. Already with only four angles, we cold some details with the simulated data, and for the measured data with 8 angles and with 16 angles details were also visible in the case of measured data.
  • Levänen, Tuuli (2015)
    Introduction. Previous studies suggest that dyslexic pupils have inordinate difficulties learning foreign languages at school. The present study examined the mismatch negativity (MMN) brain responses elicited by foreign language words and nonwords in dyslexic children compared to typically reading controls. MMN reflects early processing stages in auditory cortex. The aim of this study was to determine whether dyslexic pupils have impaired MMNs for foreign language words or speech stimuli in general, and whether word familiarity has a different effect on the two groups. In addition, the correlations between MMN differences and reading and cognitive skills were analysed. Methods. Participant groups consisted of 14 dyslexic school children, and 14 typically reading controls. Before brain recordings, literacy skills and cognitive functioning were tested. Brain responses to English words (she, shy) and nonwords (shoy), and Finnish words (sai, soi) and nonwords (sii) were measured with electroencephalography (EEG). Results and conclusions. The results suggested that compared to controls, dyslexic children's MMN responses to foreign language were impaired for a familiar word she, but only. However, the groups did not differ in processing speech-sounds in general. In addition, weak MMN responses to the foreign word were associated with poorer reading skills and slower rapid naming in mother language. The results of this study suggest that the establishment, access and activation of memory representations for foreign words is impaired in dyslexia. In addition, the finding that poor performance in native language reading is correlated with the strength of brain responses to foreign language suggests that there are common factors underlying literacy skills and foreign language learning.