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  • Lauranto, Yrjö (Helsingin yliopisto, 2015)
    This study examines directivity and imperative clauses (henceforth i-clauses) in Finnish. It consists of 3 publications (P1, P2 and P3). While the theoretical basis of the study is systemic-functional linguistics, use is also made of other approaches. P1 concentrates on the description of the imperative, and, thus, the data consist mainly of intuited examples. Firstly, the Finnish imperative can be regarded as a paradigm consisting of the personal forms of the present. This is reflected in traditional descriptions of the Finnish verb, which treat the imperative as one of the moods. This is referred to as the synchronic-morphological perspective. Secondly, the imperative can be examined from the perspective of interaction and interactional constructions. This is called the diachronic-interactive perspective. P2 investigates the canonical i-clause in everyday conversations between friends and family members. The data consist of approx. 140 conversations or excerpts of conversation. 70 % of the data are telephone conversations. One of the characteristics of the i-clause is that it is employed as a response to what has been said before or as a response to the non-linguistic action that is going on during the conversation. Approx. 63 % of the i-clauses in the data (n = 243) can be considered strongly responsive. Another significant finding is that only 10 % of the i-clauses of the data are interpreted by the participants in the conversations as commands. P2 suggests two ways of defining the notion of a directive. From a wider perspective, directives include not only exhortations to action but also offers and permissions. From a narrow perspective, offers and permissions are excluded because they are used to provide addressees with commodities or to enable them to act in the way they themselves wish. P3 discusses two clause constructions that begin with a finite verb conjugated in the 2nd person of the conditional mood but which do not allow a pronoun functioning as the subject. The data consist of everyday interaction and electronically mediated conversations from the Internet. One of the constructions is clearly an optative structure, whereas the other tends to be used as a persuasive expression. It can thus be seen as a grammaticalization of directivity. The study sheds light on the Finnish i-clause and its use, but also on directivity in general. The results are also of relevance to the teaching of Finnish as a second language. Key words: interactional syntax, interpersonal, imperative clause, morphological imperative, everyday conversations, directives, directivity, grammatical metaphor, optative, persuasion, grammaticalization, systemic-functional linguistics
  • Varis, Jarno (2013)
    Tutkielmassa käydään läpi Dirichletin ja Bergmanin avaruuksien ominaisuuksia, ja tutkitaan niiden yhteyttä analyyttiseen Poincarén epäyhtälöön. Tämän lisäksi tutkitaan erilaisia yhdesti yhtenäisiä, rajoitettuja alueita, joissa ei päde analyyttinen Poincarén epäyhtälö. Dirichletin avaruus on niiden rajoitetussa alueessa määriteltyjen analyyttisten funktioiden joukko, joiden derivaattafunktion L2 normi kyseisen alueen yli on äärellinen, ja Bergmanin avaruus on niiden analyyttisten funktioiden joukko, joiden L2 normi vastaavan alueen yli on äärellinen. Tutkielman alussa annetaan karakterisaatio sille, milloin Dirichletin avaruus on Bergmanin avaruuden osajoukko yhdesti yhtenäisissä, rajoitetuissa alueissa. Käyttämällä suljetun kuvaajan teoreemaa, ja funktionaalianalyysin perustuloksia, todistetaan, että Dirichletin avaruuden sisältyminen Bergmanin avaruuteen rajoitetussa alueessa on ekvivalenttia sen kanssa, että kyseisessä alueessa pätee analyyttinen Poincarén epäyhtälö. Tämän tuloksen avulla todistetaan, että rajoitetuissa, tähtimäisissä alueissa pätee analyyttinen Poincarén epäyhtälö. Tästä edetään määrittelemällä paloittain tähtimäinen alue, ja todistamalla, että siinä pätee analyyttinen Poincarén epäyhtälö. Tutkielmassa etsitään myös kompleksitason origokeskisen kiekon analyyttiselle Poincarén epäyhtälölle konkreettinen vakio. Seuraavaksi esitetään kompleksitason rajoitettu, yhdesti yhtenäinen alue, jossa ei päde analyyttinen Poincarén epäyhtälö. Konstruktiossa hyödynnetään kompleksianalyysin ja analyyttisen geometrian perusideoita. Tätä aluetta muokkaamalla löydetään yhdesti yhtenäinen, rajoitettu alue, jossa pä- tee analyyttinen Poincarén (2, 2) epäyhtälö, mutta jos epäyhtälössä korvataan vasemmanpuoleisen funktion L2-normi oleellisella supremum-normilla, niin epäyhtälö ei enää päde. Tutkielman lopuksi esitetään erityisen yksinkertainen konstruktio spiraalimaisesta, rajoitetusta alueesta, jossa analyyttinen Poincarén epäyhtälö ei päde.
  • Vähäkangas, Aleksi (Helsingin yliopisto, 2008)
    The object of this dissertation is to study globally defined bounded p-harmonic functions on Cartan-Hadamard manifolds and Gromov hyperbolic metric measure spaces. Such functions are constructed by solving the so called Dirichlet problem at infinity. This problem is to find a p-harmonic function on the space that extends continuously to the boundary at inifinity and obtains given boundary values there. The dissertation consists of an overview and three published research articles. In the first article the Dirichlet problem at infinity is considered for more general A-harmonic functions on Cartan-Hadamard manifolds. In the special case of two dimensions the Dirichlet problem at infinity is solved by only assuming that the sectional curvature has a certain upper bound. A sharpness result is proved for this upper bound. In the second article the Dirichlet problem at infinity is solved for p-harmonic functions on Cartan-Hadamard manifolds under the assumption that the sectional curvature is bounded outside a compact set from above and from below by functions that depend on the distance to a fixed point. The curvature bounds allow examples of quadratic decay and examples of exponential growth. In the final article a generalization of the Dirichlet problem at infinity for p-harmonic functions is considered on Gromov hyperbolic metric measure spaces. Existence and uniqueness results are proved and Cartan-Hadamard manifolds are considered as an application.
  • Leinonen, Taina (Helsingin yliopisto, 2014)
    Socioeconomic factors are major predictors of disability retirement. Socioeconomic position and other socio-demographic factors also shape the retirement process, thereby modifying health outcomes after the transition. This study focuses on the socioeconomic differences in disability retirement and the influences of socio-demographic factors on mental health and mortality in relation to the transition. The study was based mainly on longitudinal register data on a representative sample of the Finnish population, but also included survey data on a municipal employee cohort linked to register data. Cox proportional hazard and linear regression models were used in the analyses. Low education and occupational social class were more strongly associated with disability retirement than a low level of income. Part of the effect of each of these three socioeconomic factors was explained by or mediated through the other two. Education, social class and income therefore have both independent and interdependent pathways to disability retirement. Social-class differences were particularly large in retirement due to musculoskeletal diseases. The association between social class and disability retirement was mediated largely through physical working conditions and partly also through job control. The contribution of health behaviours to the association was modest. Improvements in working conditions among those in lower social classes could reduce socioeconomic differences as well as the overall incidence of disability retirement in the population. Depressive morbidity measured via purchases of antidepressant medication decreased after disability retirement, following a pre-retirement increase. Such changes were more pronounced in retirement due to mental disorders, particularly depression. Compared to the general population, those who retired due to depression and other mental disorders had a high mortality risk, particularly from unnatural and alcohol-related causes. Socioeconomic position and family ties had only limited protective influence on mental ill-health and mortality after disability retirement. Among young adults disability retirement was particularly strongly associated with prolonged mental-health problems and a high risk of mortality, especially from unnatural causes. Particular attention should therefore be paid to younger adults in terms of mental ill health, work disability and other social problems.
  • Blackie, Daniel (Helsingin yliopisto, 2010)
    This thesis addresses the following broad research question: what did it mean to be a disabled Revolutionary War veteran in the early United States during the period from 1776 to roughly 1840? The study approaches the question from two angles: a state-centred one and an experiential one. In both cases, the theoretical framework employed comes from disability studies. Consequently, disability is regarded as a sociocultural phenomenon rather than a medical condition. The state-centred dimension of the study explores the meaning of disability and disabled veterans to the early American state through an examination of the major military pension laws of the period. An analysis of this legislation, particularly the invalid pension acts of 1793 and 1806, indicates that the early United States represents a key period in the development of the modern disability category. The experiential approach, in contrast, shifts the focus of attention away from the state towards the lived experiences of disabled veterans. It seeks to address the issue of whether or not the disabilities of disabled veterans had any significant material impact on their everyday lives. It does this through a comparison of the situation of 153 disabled veterans with that of an equivalent number of nondisabled veterans. The former group received invalid pensions while the latter did not. In comparing the material conditions of disabled and nondisabled veterans, a wide range of primary sources from military records to memoirs and letters are used. The most important sources in this regard are the pension application papers submitted by veterans in the early nineteenth century. These provide us with a unique insight into the everyday lives of veterans. Looking at the issue of experience through the window of the pension files reveals that there was not much difference in the broad contours of disabled and nondisabled veteran life. This finding has implications for the theorisation of disability that are highlighted and discussed in the thesis. The main themes covered in this study are: the wartime experiences of injured American soldiers, the military pension establishment of the early United States and the legal construction of disability, and the post-war working and family lives of disabled veterans. Keywords: disability, early America, veterans, military pensions, disabled people, Revolutionary War, United States, disability theory.
  • Müller-Klestil, Sebastian (Helsingin yliopisto, 2009)
    This thesis proposes that national or ethnic identity is an important and overlooked resource in conflict resolution. Usually ethnic identity is seen both in international relations and in social psychology as something that fuels the conflict. Using grounded theory to analyze data from interactive problem-solving workshops between Palestinians and Israelis a theory about the role of national identity in turning conflict into protracted conflict is developed. Drawing upon research from, among others, social identity theory, just world theory and prejudice it is argued that national identity is a prime candidate to provide the justification of a conflict party’s goals and the dehumanization of the other necessary to make a conflict protracted. It is not the nature of national identity itself that lets it perform this role but rather the ability to mobilize a constituency for social action (see Stürmer, Simon, Loewy, & Jörger, 2003). Reicher & Hopkins (1996) have demonstrated that national identity is constructed by political entrepreneurs to further their cause, even if this construction is not a conscious one. Data from interactive problem-solving workshops suggest that the possibility of conflict resolution is actually seen by participants as a direct threat of annihilation. Understanding the investment necessary to make conflict protracted this reaction seems plausible. The justification for ones actions provided by national identity makes the conflict an integral part of a conflict party’s identity. Conflict resolution, it is argued, is therefore a threat to the very core of the current national identity. This may explain why so many peace agreements have failed to provide the hoped for resolution of conflict. But if national identity is being used in a constructionist way to attain political goals, a political project of conflict resolution, if it is conscious of the constructionist process, needs to develop a national identity that is independent of conflict and therefore able to accommodate conflict resolution. From this understanding it becomes clear why national identity needs to change, i.e. be disarmed, if conflict resolution is to be successful. This process of disarmament is theorized to be similar to the process of creating and sustaining protracted conflict. What shape and function this change should have is explored from the understanding of the role of national identity in supporting conflict. Ideas how track-two diplomacy efforts, such as the interactive problem-solving workshop, could integrate a process by both conflict parties to disarm their respective identities are developed.
  • Hellstén, Linda (Helsingfors universitet, 2015)
    The EU securities market regulation is under a reform. The new Market Abuse Regulation (the MAR) was passed in summer 2014 and it will come into force and replace the current Market Abuse Directive (the MAD) in July 2016. The MAR has been enacted as a regulation and it thus has a direct effect, i.e. it will be directly applicable in all Member States. The MAR will tighten the ongoing disclosure regulation, which means in practice that issuers are required to disclose more information than ever before. Most importantly, the MAR extends the obligation to disclose also to uncertain information relating to future events. Consequently, such a far-reaching disclosure obligation requires correction not to jeopardise issuer interests. Correction is provided by the delayed disclosure provision, the interpretation of which will be the hot question of the EU disclosure regulation in the near future. The delayed disclosure mechanism will serve as a safe harbour to issuers. However, entry to the safe harbour is strictly regulated by three criteria (i.e. legitimate interests of the issuer, misleading the public and confidentiality of the information) which need to be met in order to grant the access to the harbour. The interpretation of the criteria is a dilemma and a solution to it needs to be found to strike an optimal balance between disclosure and delayed disclosure. In other words, there is a conflict of transparency, favoured by investors, and confidentiality, favoured by issuers, and a balance between these conflicting interests is needed. Finding the optimal balance is not only in the interest of issuers and investors but also of the market in general, as disclosure is a key to efficient and well-functioning securities markets. The answer to the dilemma lies in how broadly or narrowly the criteria for delayed disclosure are interpreted, and this thesis thus focuses on searching for the optimal balance by means of interpretation. The thesis concentrates on the following research problems: 1) what is the current status of the disclosure regulation across Europe, 2) on what grounds may an issuer delay the disclosure of inside information, and 3) how should the disclosure and delayed disclosure be balanced i.e. what should the balance be between transparency and confidentiality? Discussing the first question lays the foundation for the thesis. The implementation of MAD in chosen Member States, i.e. Germany, France, the UK, Italy, Finland, Sweden and Denmark, will be discussed in order to map the current status of the disclosure regulation and the challenges that will be faced in the era of the MAR. Discussing the second question includes a thorough analysis of the criteria for delayed disclosure, the interpretation of which is the key to finding the optimal balance for transparency and confidentiality. Again, the practices adopted across Member States will be analysed in order to get an overall picture of the functioning of the delayed disclosure mechanism. Finally, the third question leads to the core of the thesis and to the proposed solution on how the conflict of transparency and confidentiality should be solved and how the disclosure and delayed disclosure should be balanced. The thesis contributes mainly to the EU securities market law, but interfaces to other fields of law, company and criminal law in particular, have also been taken into account. A pluralistic method has been adopted in the thesis and it contains elements from legal dogmatics, law and economics as well as from comparative law. Legal dogmatics is the core, whereas law and economics and comparative law bring perspective to the thesis and diversify the analysis. Further, a market-based interpretation method has been applied, which combines the teleological interpretation method typical for EU law and economic argumentation needed in securities market law. Using the market-based method in interpreting the disclosure regulation is crucial in order to take into consideration the market environment and the purpose of the regulation and to find an optimal balance for disclosure and delayed disclosure.
  • Vähämaa, Miika (2004)
    This work is an attempt to complement social constructionist approach with the theory of discourse ethics. Therefore, the nature of this work is theoretical, though there is an empirical part backing up the theorizations. This thesis reflects a sort of scientific commentary style, and is written to resemble an academic story. The basic idea of this paper is to take a critical look at social constructionism as a theory, and to provide an account of complementary perspective of discourse ethics. Discourse ethics, introduced by the German social theorist Jürgen Habermas suggests that all linguistic activities -- including that of social science -- must rely on discourse. Thus, it is discourse itself that provides means of justified articulation and argumentation regarding any subject matter. Habermasians assert that it is possible both to settle and accept disagreements and achieve agreements in terms of ethical and acceptable discourse. According to Habermas, the method to gain an ethical discourse is acquired as an intuitive heritance through socialization. Thus, the communicative action that underlies all linguistic activies, outlines the rules and direction of rational discourse. Habermasian rational discourse, however, has limitations. These limitations can be addressed as latent social constructs that hinder the potential of discourse. The function of this type of latent constructs is examined in this thesis through an empirical case. Theoretical suggestion is that as the latent constructs become manifested, the potentional to gain common understanding through rational discourse increases. Thus, the participants of any rational discourse move closer to normativity that Habermas has described as that of an ideal speech situation. The philosophical reconstruction of an ideal speech situation theorizes the potential of communication to serve as a tool of social justification. The conclusion of this paper can be outlined as a three-step process, depicting the elements that create the grounds for rational discourse: (i) One enters the domain of communication through socialization and becomes a potential participant of rationally cultivated discourse, (ii) One has to be skeptical towards language. It is important to recognize the constructedness of every meaning structure and discuss about these structures rationally, (iii) Finally, it has to noticed that latent constructs may hinder the cultivation of rational discourse. As these latent constructs are made more visible, the potential to gain common understanding among participants of discourse increases.
  • Holli, Anne Maria (2003)
    The article dissertation analysed Finnish discourse and politics for gender equality from the late 1960s to the late 1990s. Three questions were investigated: How was the discourse on gender equality organised and how did it change over time? What were the strategies and impact of women's policy offices and women's movements? What are the possibilities for women to pursue change via gender equality, public policies and the state in more general terms? The study outlined a more post-structuralist inspired version of the feminist-discursive approach to gender equality, which analyses gender equality as part of social discourse and pays attention to its political consequences and implications. The data consisted of statements by women's policy offices and women's movements, policy documents, press materials and interviews. The study applied various text analysis methods to the data. The study described changes in the Finnish concept and discourse of gender equality from 1970s to 1990s. The masculine normativity of gender equality was in the 1980s replaced by a more radical conceptualisation, partly thanks to the activity of the Council for Gender Equality between Men and Women. The new version could be utilised by women for change without them giving up their sexual difference. Simultaneously, support of gender equality as a norm expanded in Finnish society. In the 1990s, the tide turned: the potential for change diminished as gender equality was conceptualised as an already 'present' characteristic in Finnish society, which also legitimised the idea that there was nothing left to do. The analysis also shows that, comparatively speaking, the policy success of Finnish women's movements in gendering public policies has been above average. In the context of moderately closed policy sub-systems and left-wing governmental power, women's movements tended to be successful, if they only managed to mobilise to a sufficient degree on an issue. However, in the Finnish context, the characteristics of the political environment also seem to affect the possibility of movement mobilisation. Women's policy agencies were very effective linkages between the women's movements and the state. The prominent role played by these agencies can be understood by their participation in the "strategic partnerships" typical to Finnish women's activity. However, the analysis of the actual policy change modified to some degree the results concerning women's policy success and the responsiveness of the state. Women's demands met an invisible barrier in both job training and prostitution policy. However, in job training women's substantive impact was more limited, due to the closed sub-system and the strong vested interests that excluded women. On the basis of the empirical analyses, the study also aimed at providing partial and situated answers to the questions concerning the nature of the concept of gender equality and the relation between women and the state, which have been prominent in feminist theory. The results can be condensed into the notion that feminist studies should avoid too simplistic viewpoints and start paying more attention to the multifaceted and contextualised character of both gender equality and the state.
  • Holli, Anne Maria (2003)
    Artikkeliväitöskirjassa analysoitiin suomalaisia tasa-arvodiskursseja ja -politiikkaa 1960-luvun lopulta 2000-luvun taitteeseen. Siinä tarkasteltiin kolmea kysymystä: Miten sukupuolten tasa-arvosta on puhuttu ja miten nämä tavat ovat muuttuneet? Miten tasa-arvoelimet ja naisliikkeet ovat toimineet tavoitteidensa puolesta ja millaisia vaikutuksia niillä on ollut? Millaisia mahdollisuuksia naisilla on ylipäätään toimia tasa-arvon käsitteen, julkisen politiikan ja valtion kautta? Tutkimuksessa luonnosteltiin poststrukturalis-vaikutteisempaa versiota feministis-diskursiivisesta tasa-arvoanalyysistä, jossa sukupuolten tasa-arvoa tarkastellaan osana yhteiskunnallisia puhumoita ja huomiota kiinnitetään sen poliittisiin vaikutuksiin ja seurauksiin. Aineistoina käytettiin tasa-arvoelinten ja naisliikkeiden kannanottoja, parlamentaariseen lainvalmisteluun liittyviä asiakirjoja, lehdistömateriaalia ja haastatteluja. Metodisesti työssä sovellettiin erilaisia tekstianalyysin menetelmiä. Tutkimus kuvasi suomalaisen tasa-arvokäsityksen ja -keskustelun muutoksia 1970-luvulta 1990-luvulle. 1970-luvun miehiseen normiin kiinnittynyt tasa-arvo muuntui 1980-luvulla - osin Tasa-arvoasiain neuvottelukunnan ansiosta - radikaalimmaksi käsitteeksi, jota naiset saattoivat käyttää muutoksen argumenttina sukupuolierostaan luopumatta. Samalla tasa-arvo alkoi laajeta yleisemmin hyväksytyksi yhteiskunnalliseksi normiksi. 1990-luku käänsi suunnan: käsitteen muutospotentiaali kaventui, kun tasa-arvo alettiin mieltää suomalaisen yhteiskunnan jo-läsnäolevaksi piirteeksi. Tämä legitimoi myös käsitystä, että tasa-arvon eteen ei ollut enää tarpeen tehdä mitään. Tulokset osoittivat myös, että kansainvälisesti katsoen suomalaiset naisliikkeet ovat olleet keskimääräistä menestyksekkäämpiä saamaan vaateitaan läpi politiikassa. Naisliikkeet pääsääntöisesti onnistuivat politiikan sisältöjen sukupuolittamisessa silloin, kun ne ylipäätään mobilisoituivat jonkin asian puolesta tilanteessa, jossa päätöksenteon alajärjestelmä on vain suhteellisen suljettu ja vasemmisto hallitusvallassa. Analyysi viittasi kuitenkin siihen, että Suomessa poliittisen ympäristön piirteet vaikuttivat myös naisliikkeiden kykyyn mobilisoitua. Tasa-arvoelimet osoittautuivat erittäin tehokkaiksi naisliikkeiden vaateiden välittäjiksi valtioon päin, arvion mukaan siksi, että ne olivat usein osa suomalaisten naisten toiminnalle tyypillisiä "strategisia kumppanuuksia". Analysoitaessa naisliikkeiden toiminnan tosiasiallisia vaikutuksia politiikan muuttumiseen käsitys sekä toiminnan tuloksekkuudesta että valtion responsiivisuudesta suhteellistui hieman: sekä prostituutiopolitiikassa että työllisyyskoulutuspolitiikassa naisten muutospyrkimykset törmäsivät eräänlaiseen näkymättömään muuriin. Naisliikkeiden tosiasiallinen vaikutus oli kuitenkin suurempi prostituutiopolitiikassa, kun taas työllisyyskoulutuksen suljettu päätöksenteko ja vahvat etujärjestöintressit sulkivat naiset ulos. Empiiristen analyysien avulla tutkimuksessa pyrittiin antamaan myös osittaisia, paikannettuja vastauksia feminististä tutkimusta puhuttaneisiin kysymyksiin tasa-arvon käsitteen ja naisten ja valtion suhteen luonteesta. Tulokset voi tiivistää huomioon, että tutkimuksen tulisi välttää yksioikoisia näkemyksiä ja kiinnittää enemmän huomiota sekä tasa-arvon käsitteen että valtion monimuotoiseen ja kontekstisidonnaiseen luonteeseen.
  • Gutierrez Zamora, Violeta (2014)
    Currently La Via Campesina plays an important role in the political field of food and agriculture, and as some scholars from rural and development studies have highlighted (Desmarais 2007; Patel 2006; Wittman 2009; Martínez-Torres and Rosset 2010; Borras 2010) it has increased the visibility of peasants and other agrarian workers among international actors within the international political field of food and agriculture. In addition, La Via Campesina has challenged important concepts used in international development agencies, such as food security, with the formulation of new notions like Food Sovereignty. For long time the neglected voices of peasants are gaining recognition in the international arena and thereby contributing in political debates over rural development and more recently in environmental sustainability. Nevertheless, as some activists have declared and researchers have exposed (Edelman 2003, Borras 2010; Desmarais 2007, 2008) bringing together such diverse organizations has not been an easy task and requires great efforts. Few scholars (Desmarais 2007, Borras 2008) have analyzed the relationships between organizations within this transnational social movement and there is a trend of studying La Via Campesina on a world scale and assumed as a homogenous actor. This leads to a problematic supposition that La Via Campesina is a homogenous unity rather than a field of action (Borras, 2010) where different identities, claims and contexts converge, and as such cannot be free of conflicts. The aim of this Master’s thesis is to explore the dynamics between La Via Campesina as a transnational social movement and two Mexican peasant organization members of the movement: Unión Nacional de Organizaciones Regionales Campesinas Autónomas (UNORCA) and Asociación Nacional de Empresas Comercializadoras de Productores del Campo (ANEC). The former has been one of the key founding members of La Vía Campesina and remain the main organization functioning as a representative within the Regional Coordination; the later has had a limited involvement in the recent years and has questioned the effectiveness of participation in La Via Campesina’s representation structures, particularly in the North American region. The findings of this thesis present that empty signifiers as “Peasant” and “Food sovereignty” enables that these groups achieve to develop temporary attachments in which they perceive themselves as part of this transnational movement.However, in Mexico both organizations have had persistent differences and conflicts that did not allow them to work together in the construction of common strategies. Consequently, this blocked the construction of a solid coalition with La Via Campesina North American regional coordination.
  • Hyttinen, Antti (Helsingin yliopisto, 2013)
    The causal relationships determining the behaviour of a system under study are inherently directional: by manipulating a cause we can control its effect, but an effect cannot be used to control its cause. Understanding the network of causal relationships is necessary, for example, if we want to predict the behaviour in settings where the system is subject to different manipulations. However, we are rarely able to directly observe the causal processes in action; we only see the statistical associations they induce in the collected data. This thesis considers the discovery of the fundamental causal relationships from data in several different learning settings and under various modeling assumptions. Although the research is mostly theoretical, possible application areas include biology, medicine, economics and the social sciences. Latent confounders, unobserved common causes of two or more observed parts of a system, are especially troublesome when discovering causal relations. The statistical dependence relations induced by such latent confounders often cannot be distinguished from directed causal relationships. Possible presence of feedback, that induces a cyclic causal structure, provides another complicating factor. To achieve informative learning results in this challenging setting, some restricting assumptions need to be made. One option is to constrain the functional forms of the causal relationships to be smooth and simple. In particular, we explore how linearity of the causal relations can be effectively exploited. Another common assumption under study is causal faithfulness, with which we can deduce the lack of causal relations from the lack of statistical associations. Along with these assumptions, we use data from randomized experiments, in which the system under study is observed under different interventions and manipulations. In particular, we present a full theoretical foundation of learning linear cyclic models with latent variables using second order statistics in several experimental data sets. This includes sufficient and necessary conditions on the different experimental settings needed for full model identification, a provably complete learning algorithm and characterization of the underdetermination when the data do not allow for full model identification. We also consider several ways of exploiting the faithfulness assumption for this model class. We are able to learn from overlapping data sets, in which different (but overlapping) subsets of variables are observed. In addition, we formulate a model class called Noisy-OR models with latent confounding. We prove sufficient and worst case necessary conditions for the identifiability of the full model and derive several learning algorithms. The thesis also suggests the optimal sets of experiments for the identification of the above models and others. For settings without latent confounders, we develop a Bayesian learning algorithm that is able to exploit non-Gaussianity in passively observed data.
  • Sandoval Zárate, América Andrea (2015)
    Personalised medicine involves the use of individual information to determine the best medical treatment. Such information include the historical health records of the patient. In this thesis, the records used are part of the Finnish Hospital Discharge Register. This information is utilized to identify disease trajectories for individuals for the FINRISK cohorts. The techniques usually implemented to analyse longitudinal register data use Markov chains because of their capability to capture temporal relations. In this thesis a first order Markov chain is used to feed the MCL algorithm that identifies disease trajectories. These trajectories highlight the most prevalent diseases in the Finnish population: circulatory diseases, neoplasms and musculoskeletal disorders. Also, they defined high level interactions between other diseases, some of them showing an agreement with physiological interactions widely studied. For example, circulatory diseases and their thoroughly studied association with symptoms from the metabolic syndrome.
  • Marttinen, Pekka (Helsingin yliopisto, 2008)
    Advancements in the analysis techniques have led to a rapid accumulation of biological data in databases. Such data often are in the form of sequences of observations, examples including DNA sequences and amino acid sequences of proteins. The scale and quality of the data give promises of answering various biologically relevant questions in more detail than what has been possible before. For example, one may wish to identify areas in an amino acid sequence, which are important for the function of the corresponding protein, or investigate how characteristics on the level of DNA sequence affect the adaptation of a bacterial species to its environment. Many of the interesting questions are intimately associated with the understanding of the evolutionary relationships among the items under consideration. The aim of this work is to develop novel statistical models and computational techniques to meet with the challenge of deriving meaning from the increasing amounts of data. Our main concern is on modeling the evolutionary relationships based on the observed molecular data. We operate within a Bayesian statistical framework, which allows a probabilistic quantification of the uncertainties related to a particular solution. As the basis of our modeling approach we utilize a partition model, which is used to describe the structure of data by appropriately dividing the data items into clusters of related items. Generalizations and modifications of the partition model are developed and applied to various problems. Large-scale data sets provide also a computational challenge. The models used to describe the data must be realistic enough to capture the essential features of the current modeling task but, at the same time, simple enough to make it possible to carry out the inference in practice. The partition model fulfills these two requirements. The problem-specific features can be taken into account by modifying the prior probability distributions of the model parameters. The computational efficiency stems from the ability to integrate out the parameters of the partition model analytically, which enables the use of efficient stochastic search algorithms.
  • Haiminen, Niina (Helsingin yliopisto, 2004)
  • Toivonen, Hannu (Helsingin yliopisto, 1996)
  • Faccio, Greta (Helsingin yliopisto, 2011)
    Enzymes offer many advantages in industrial processes, such as high specificity, mild treatment conditions and low energy requirements. Therefore, the industry has exploited them in many sectors including food processing. Enzymes can modify food properties by acting on small molecules or on polymers such as carbohydrates or proteins. Crosslinking enzymes such as tyrosinases and sulfhydryl oxidases catalyse the formation of novel covalent bonds between specific residues in proteins and/or peptides, thus forming or modifying the protein network of food. In this study, novel secreted fungal proteins with sequence features typical of tyrosinases and sulfhydryl oxidases were iden-tified through a genome mining study. Representatives of both of these enzyme families were selected for heterologous produc-tion in the filamentous fungus Trichoderma reesei and biochemical characterisation. Firstly, a novel family of putative tyrosinases carrying a shorter sequence than the previously characterised tyrosinases was discovered. These proteins lacked the whole linker and C-terminal domain that possibly play a role in cofactor incorporation, folding or protein activity. One of these proteins, AoCO4 from Aspergillus oryzae, was produced in T. reesei with a production level of about 1.5 g/l. The enzyme AoCO4 was correctly folded and bound the copper cofactors with a type-3 copper centre. However, the enzyme had only a low level of activity with the phenolic substrates tested. Highest activity was obtained with 4-tert-butylcatechol. Since tyrosine was not a substrate for AoCO4, the enzyme was classified as catechol oxidase. Secondly, the genome analysis for secreted proteins with sequence features typical of flavin-dependent sulfhydryl oxidases pinpointed two previously uncharacterised proteins AoSOX1 and AoSOX2 from A. oryzae. These two novel sulfhydryl oxidases were produced in T. reesei with production levels of 70 and 180 mg/l, respectively, in shake flask cultivations. AoSOX1 and AoSOX2 were FAD-dependent enzymes with a dimeric tertiary structure and they both showed activity on small sulfhydryl compounds such as glutathione and dithiothreitol, and were drastically inhibited by zinc sulphate. AoSOX2 showed good stabil-ity to thermal and chemical denaturation, being superior to AoSOX1 in this respect. Thirdly, the suitability of AoSOX1 as a possible baking improver was elucidated. The effect of AoSOX1, alone and in combi-nation with the widely used improver ascorbic acid was tested on yeasted wheat dough, both fresh and frozen, and on fresh water-flour dough. In all cases, AoSOX1 had no effect on the fermentation properties of fresh yeasted dough. AoSOX1 nega-tively affected the fermentation properties of frozen doughs and accelerated the damaging effects of the frozen storage, i.e. giving a softer dough with poorer gas retention abilities than the control. In combination with ascorbic acid, AoSOX1 gave harder doughs. In accordance, rheological studies in yeast-free dough showed that the presence of only AoSOX1 resulted in weaker and more extensible dough whereas a dough with opposite properties was obtained if ascorbic acid was also used. Doughs containing ascorbic acid and increasing amounts of AoSOX1 were harder in a dose-dependent manner. Sulfhydryl oxidase AoSOX1 had an enhancing effect on the dough hardening mechanism of ascorbic acid. This was ascribed mainly to the produc-tion of hydrogen peroxide in the SOX reaction which is able to convert the ascorbic acid to the actual improver dehydroascorbic acid. In addition, AoSOX1 could possibly oxidise the free glutathione in the dough and thus prevent the loss of dough strength caused by the spontaneous reduction of the disulfide bonds constituting the dough protein network. Sulfhydryl oxidase AoSOX1 is therefore able to enhance the action of ascorbic acid in wheat dough and could potentially be applied in wheat dough baking.