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.

Construction Plan Image Service for Mobile Devices

The forthcoming media revolution of exchanging paper documents to digital media in construction engineering requires new tools to be developed. The basis of this bachelor’s thesis was to explore the preliminary possibilities of exporting imagery from a Building Information Modelling –software to a mobile phone on a construction yard. This was done by producing a Web Service which uses the design software’s Application Programming Interface to interact with a structures model in order to produce the requested imagery. While mobile phones were found lacking as client devices, because of limited processing power and small displays, the implementation showed that the Tekla Structures API can be used to automatically produce various types of imagery. Web Services can be used to transfer this data to the client. Before further development the needs of the contractor, benefits for the building master and inspector and the full potential of the BIM-software need to be mapped out with surveys.

Making Sense of Shared Leadership. A case study of leadership processes and practices without formal leadership structure in the team context

Leadership is essential for the effectiveness of the teams and organizations they are part of. The challenges facing organizations today require an exhaustive review of the strategic role of leadership. In this context, it is necessary to explore new types of leadership capable of providing an effective response to new needs. The presentday situations, characterized by complexity and ambiguity, make it difficult for an external leader to perform all leadership functions successfully. Likewise, knowledge-based work requires providing professional groups with sufficient autonomy to perform leadership functions. This study focuses on shared leadership in the team context. Shared leadership is seen as an emergent team property resulting from the distribution of leadership influence across multiple team members. Shared leadership entails sharing power and influence broadly among the team members rather than centralizing it in the hands of a single individual who acts in the clear role of a leader. By identifying the team itself as a key source of influence, this study points to the relational nature of leadership as a social construct where leadership is seen as social process of relating processes that are co-constructed by several team members. Based on recent theoretical developments concerned with relational, practice-based and constructionist approaches to the study of leadership processes, this thesis proposes the study of leadership interactions, working processes and practices to focus on the construction of direction, alignment and commitment. During the research process, critical events, activities, working processes and practices of a case team have been examined and analyzed with the grounded theory –approach in the terms of shared leadership. There are a variety of components to this complex process and a multitude of factors that may influence the development of shared leadership. The study suggests that the development process of shared leadership is a common sense -making process and consists of four overlapping dimensions (individual, social, structural, and developmental) to work with as a team. For shared leadership to emerge, the members of the team must offer leadership services, and the team as a whole must be willing to rely on leadership by multiple team members. For these individual and collective behaviors to occur, the team members must believe that offering influence to and accepting it from fellow team members are welcome and constructive actions. Leadership emerges when people with differing world views use dialogue and collaborative learning to create spaces where a shared common purpose can be achieved while a diversity of perspectives is preserved and valued. This study also suggests that this process can be supported by different kinds of meaning-making and process tools. Leadership, then, does not reside in a person or in a role, but in the social system. The built framework integrates the different dimensions of shared leadership and describes their relationships. This way, the findings of this study can be seen as a contribution to the understanding of what constitutes essential aspects of shared leadership in the team context that can be of theoretical value in terms of advancing the adoption and development process of shared leadership. In the real world, teams and organizations can create conditions to foster and facilitate the process. We should encourage leaders and team members to approach leadership as a collective effort that the team can be prepared for, so that the response is rapid and efficient.

Sitouttamisretoriikka yritysviestinnässä

This study focuses on work commitment creation on rhetorical level, that is to say, the rhetorical and linguistic means that are used to construct or elicit worker commitment. The commitment of the worker is one of the most important objectives of all business communication. There is a strong demand for commitment, identification, or adherence to work in various walks of life, although the actual circumstances are often somewhat insecure and shortsighted. The analysis demonstrates that the actual object of commitment may vary from work itself or work organization to one’s career or professional development. The ideal pattern for commitment appears as comprehensive: it contains affective and rational as well as ideological dimensions. This thesis is a rhetorical discourse analysis, or rhetorical analysis with discourse-analytic influences. Primarily it is a rhetorical analysis in which discourses are observed mainly as tools of a rhetorician. The study also draws on various findings of sociology of work and organizational studies. Research material consists of magazines from three and web pages from six different companies. This study explores repeated discourses in commitment rhetoric, mainly through pointing core concepts and recurrent patterns of argumentation. In this analysis section, a semantic and concept-analytic approach is also employed. Companies talk about ideas, values, feelings and attitudes thus constructing a united and unanimous group and an ideal model of commitment. Probably the most important domain of commitment rhetoric is the construction of group and community. Collective identity is constructed through shared meanings, values and goals, and these rhetorical group constructs that can be used and modified in various ways. Every now and then business communication also focuses on the individual, employing different speakers, positions and discourses associated to them. Constructing and using these positions also paints the picture of an ideal worker and ideal work orientation. For example, the so called entrepreneurship model is frequently used here. Commitment talk and the rhetorical situation it constructs are full of tensions and contradictions; the presence of seemingly contradictory values, goals or identities is constant. This study demonstrates tensions like self-fulfilment and individuality versus conformity, and constant change and development versus dependable establishment, and analyses how they are used, processed and dealt with. An important dimension in commitment rhetoric is the way companies define themselves in respect of current social issues, and how they define themselves as responsible social actors, and how they, in this sense, seek to appear as attractive workplaces. This point of view gives rise to problematic questions as companies process the tensions between, for example, rhetoric and action, ethical ideals and business conditions and so on. For its part, the commitment talk also defines the meaning of waged work in human life. Changing society, changing working life, and changing business environments set new claims and standards for workers and contents of work. In this point of view this research contributes to the study of working life and takes part in current public discussion concerning the meaning, role and future of waged work.

Animal Lovers, Bridge-Builders, and Supervising Watchdogs: Framing and Civil Society Construction by Japanese Pro-Animal Organizations in the Kansai and Tokyo Areas

Unlike their counterparts in Europe and America, the citizen organizations acting for the well-being of animals in Japan have not received scholarly attention. In this research, I explore the activities of twelve Japanese pro-animal organizations in Tokyo and Kansai area from the perspective of social movement and civil society studies. The concept of a ‘pro-animal organization’ is used to refer generally to the collectives promoting animal well-being. By using the collective action frame analysis and the three core framing tasks – diagnostic, prognostic, and motivational – as the primarily analytical tools, I explore the grievances, tactics, motivational means, constructions of agency and identity as well as framing of civil society articulated in the newsletters and the interviews of the twelve organizations I interviewed in Japan in 2010. As the frame construction is always done in relation to the social and political context, I study how the organizations construct their roles as civil society actors in relation to other actors, such as the state, and the idea of citizen activism. The deficiencies in the animal welfare law and lack of knowledge among the public are identified as the main grievances. The primary tactic to overcome these problems was to educate and inform the citizens and authorities, because most organizations lack the channels to influence politically. The audiences were mostly portrayed as either ignorant bystanders or potential adherents. In order to motivate people to join their cause and to enforce the motivation within the organization, the organizations emphasized their uniqueness, proved their efficiency, claimed credit and celebrated even small improvements. The organizations tended to create three different roles for citizen pro-organizations in civil society: reactive, apolitical and emphatic animal lovers concentrating on saving individual animals, proactive, educative bridge-builders seeking to establish equal collaborative relations with authorities, and corrective, supervising watchdogs demanding change in delinquencies offending animal rights. Based on the results of this research, I suggest that by studying how and why the different relations between civil society and the governing actors of the state are constructed, a more versatile approach to citizens’ activism in its context can be achieved.

Nollapersoonalause suomessa ja virossa. Tutkimus kirjoitetun kielen aineistosta

The present study focuses on the zero person constructions both in Finnish and Estonian. In the zero person construction, there is no overt subject and the verb is in the 3rd person singular form: Fin. Tammikuussa voi hiihtää Etelä-Suomessakin. Est. Jaanuaris saab suusatada ka Lõuna-Soomes ‘In January one can ski even in South-Finland’. The meaning of the zero construction is usually considered generic and open. However, the zero may be interpreted as indexically open so that the reference can be construed from the context. This study demonstrates how the zero may be interpreted as referring to the speaker, the addressee, or anybody. The zero person construction in Finnish has been contrasted to the generic pronoun constructions in Indo-European languages. For example, the zero person is translated in English as you or one; in Swedish and German as man. The grammar and semantics of the Finnish zero person construction have been studied earlier to some extent. However, the differences and similarities between Finnish and Estonian, two closely related languages, have not been thoroughly studied before. The present doctoral thesis sheds light on the zero person construction, its use, functions, and interpretation both in Finnish and Estonian. The approach taken is contrastive. The data comes from magazine articles published in Finnish and translated into Estonian. The data consists of Finnish sentences with the zero person and their Estonian translations. In addition, the data includes literary fiction, and non-translated Estonian corpora texts as well. Estonian and Finnish are closely related and in principle the personal system of the two languages is almost identical, nevertheless, there are interesting differences. The present study shows that the zero person construction is not as common in Estonian as it is in Finnish. In my data, a typical sentence with the zero person in both languages is a generic statement which tells us what can or cannot be done. When making generic statements the two languages are relatively similar, especially when the zero person is used together with a modal verb. The modal verbs (eg. Fin. voida ‘can’, saada ‘may’, täytyä ‘must’; Est. võima ‘may’, saama ‘can’, tulema ’must’) are the most common verbs in both Finnish and Estonian zero person constructions. Significant differences appear when a non-modal verb is used. Overall, non-modal verbs are used less frequently in both languages. Verbs with relatively low agentivity or intentionality, such as perception verb nähdä in Finnish and nägema in Estonian, are used in the zero person clauses in both languages to certain extent. Verbs with more agentive and intentional properties are not used in the Estonian zero person clauses; in Finnish their use is restricted to specific context. The if–then-frame provides a suitable context for the zero person in Finnish, and the Finnish zero person may occur together with any kind of verb in conditional if-clause. Estonian if-clauses are not suitable contexts for zero person. There is usually a da-infinitive, a generic 2nd person singular or a passive form instead of the zero person in Estonian counterparts for Finnish if-clauses with zero person. The aim of this study was to analyze motivations for choosing the zero person in certain contexts. In Estonian, the use of the zero person constructions is more limited than in Finnish, and some of the constraints are grammatical. On the other hand, some of the constraints are motivated by the differences in actual language use. Contrasting the two languages reveals interesting differences and similarities between these two languages and shows how these languages may use similar means differently.

Segregation of powder mixtures in silos with particular reference to dry mineral-based construction materials

Segregering eller segregation är ett fenomen som kan förekomma inom olika områden av samhället. Inom samhällsvetenskaperna kan segregering definieras som det rumsliga åtskiljandet av befolkningsgrupper på urval av ras eller etniskt ursprung, kön, social härkomst, religion, ålder, yrke, osv. Segregering av befolkningsgrupper sker ofta mer eller mindre frivilligt och är motsatsen till integration. Inom partikelteknologi definieras segregering oftast som det rumsliga åtskiljandet av beståndsdelarna i en blandning av olika partiklar. Segregering sker då på urval av bl.a. partiklarnas storlek, densitet, form, elektrostatiska eller mekaniska egenskaper, och kan beskrivas som motsatsen till blandning. Segregeringsmekanismer används för att förklara hur och varför en partikelblandning segregerar samt vad slutresultatet i form av den rumsliga fördelningen av partiklarna blir till följd av att blandningen utsetts för en viss behandling. I denna avhandling har segregering av partikelblandningar och speciellt torra mineralbaserade byggmaterial (t.ex. murbruk) till följd av lagring i siloer studerats. Vid industriell produktion av mineralbaserade byggmaterial används siloer för korttidslagring av slutprodukterna precis innan förpackning. Segregering leder till kraftiga variationer i sammansättningen för partikelströmmen ut ur silon, vilket gör att slutprodukterna inte uppfyller kvalitetskraven och kan därmed inte säljas till kunder. Detta leder till arbetsam och dyr bearbetning (återcirkulation) av produkterna med påföljder för produktionsekonomin samt hållbara utvecklingen. I avhandlingen identifierades de väsentligaste segregeringsmekanismerna för torra mineralbaserade byggmaterial i siloer. Dessutom klargjordes effekterna av materialegenskaper, processbetingelser och siloparametrar. Slutligen behandlas möjliga åtgärder för minskning av partikelsegregering i siloer samt tillämpning av matematiska metoder för simulering av partikelflöden med hjälp av datorer.

Pragmatic competence of Finnish learners of English: Meaning in interaction in secondary and upper secondary schools

Tutkin pro gradu -tutkielmassani englannin kielen oppijoiden pragmaattista kompetenssia. Tarkoitukseni oli selvittää, miten suomalaiset yläkoululaiset ja lukiolaiset osaavat käyttää englannin kieltä erilaisissa kommunikaatiotilanteissa. Tutkielmani voidaan sijoittaa välikielen pragmatiikan tutkimukseen. Halusin selvittää, millä tasolla suomalaisten oppijoiden pragmaattinen kompetenssi on ja kehittyykö se yläkoulun ja lukion välillä. Lisäksi tutkin, vaikuttavatko oppimisympäristö ja oppimismahdollisuudet oppijoiden kykyyn käyttää englannin kieltä. Toisin sanoen vertasin englantipainotteisilla luokilla olevia oppilaita formaalin opetuksen oppijoihin sekä tutkin, vaikuttavatko englanninkieliset vapaa-ajan aktiviteetit ja oppijoiden mahdolliset oleskelut englanninkielisissä maissa heidän pragmaattiseen kompetenssiinsa. Tutkimukseni kohderyhmä koostui yläkoulun kahdeksasluokkalaisista ja lukion toisen vuosikurssin opiskelijoista. Testasin neljä eri ryhmää, joissa oli sekä formaalissa opetuksessa olevia oppijoita (yksi ryhmä kahdeksasluokkalaisia ja yksi ryhmä toisen vuosikurssin opiskelijoita) että kielipainotteisten luokkien oppijoita (yksi ryhmä kahdeksasluokkalaisia ja yksi ryhmä toisen vuosikurssin opiskelijoita). Arvioin kohderyhmäni pragmaattista kompetenssia monivalintatestillä, jossa testattiin oppijoiden kykyä käyttää ja ymmärtää implikaatioita, tilannekohtaisia rutiineja sekä puheakteja. Taustakysymysten avulla selvitin, kuinka usein oppijat käyttivät englantia vapaa-aikanaan ja olivatko he vierailleet englanninkielisissä maissa. Tutkimustulokseni osoittavat, että suomalaisten yläkoululaisten ja lukiolaisten pragmaattinen kompetenssi oli korkea. Pragmaattinen kompetenssi kehittyi kahdeksasluokkalaisten ja lukion toisen vuosikurssin välillä. Kehitys oli suurempaa formaalissa opetuksessa kuin kielipainotteisilla luokilla. Englantipainotteisilla luokilla olevat oppilaat suoriutuivat testistä paremmin kuin formaalin opetuksen oppilaat. Tosin erot olivat tilastollisesti merkitseviä vain yläkoulussa. Tutkimuksessani siis päättelin, että vieraskielinen opetus vaikutti enemmän nuorempiin oppijoihin. Eri oppimismahdollisuudet osoittautuivat haastaviksi analysoida. Tulokset osoittivat, että vain englanninkielisessä maassa oleskelulla oli vaikutusta oppijoiden pragmaattiseen kompetenssiin. Kysyttäessä vapaa-ajan aktiviteettien merkitystä oppijat kuitenkin kertoivat, että ne auttoivat heitä testiin vastaamisessa enemmän kuin englanninopetuksessa käydyt asiat. Kouluissa tulisikin jatkossa painottaa yhä enemmän vuorovaikutteista kieltenopetusta.

The Dark Side of International Business? Stakeholder Approach to Human Trafficking in Finnish Construction and Service Sectors

Human trafficking is not a new phenomenon. It has existed in various forms for ages around the world. Some researchers have even compared it to slavery, calling it the modern form of slavery in the 21st century. This study is particularly interested in the role of work-related human trafficking in Finnish business. In order for something to be called work-related human trafficking, the concepts of forced labour and human trafficking have to overlap. From the economic point of view, human trafficking is governed by the laws of supply and demand. In many countries the global pressure on cutting costs has created two trends: the increased supply of migrant workers and the deregulation of labour markets. These competitive pressures can have an adverse impact on the conditions of employment and, in the worst cases, can lead to forced labour and trafficking. In fact, trafficking has become one of the most profitable illicit industries worldwide, generating tremendous profits due to its low costs and huge profits. Therefore, it is important to investigate the phenomenon from the business point of view. This study is a qualitative research conducted by using theme interviews as a research approach. Altogether 13 interviews have been conducted and some secondary data has been used in order to find out what the role of human trafficking is in Finnish business. The special sectors investigated are the Finnish construction and service sectors. The theory framework used in this study follows the stakeholder approach. The relevant stakeholder groups for this study are: ‘institutions and authorities’, ‘law enforcement’, ‘management’ and ‘employees – potential victims’ of trafficking. With the help of these stakeholder groups, a holistic picture of the phenomenon is formed. It can be concluded that the role of human trafficking is complicated but it does exist in Finnish business. It appears in low-cost business sectors where the demand for cheap labour is high. Thus, often the victims are foreigners who do not know the culture or the Finnish conditions of employment. Especially smaller Finnish companies are at risk of getting involved in human trafficking or related exploitation cases since monitoring is much more scarce in these firms than in larger companies. The risk of human trafficking and exploitation is also higher at the bottom of the complicated subcontracting chains or when using foreign recruitment agencies. Thus, the study believes that active and intensive collaboration between the company’s different stakeholder groups is needed in order to prevent work-related human trafficking from flourishing in Finland.

Future trends of Finnish cement based construction

The construction material sector, as a capital intensive industry, is highly vulnerable to rapid fluctuations in the economic cycles. In Finland this was witnessed especially during the late 2000s, as in 2007 and 2008 the demand for several construction materials exceeded their supply and right after this, in 2009 the demand collapsed fast as a result of an international recession. These factors brought about the need to study the future trends of the market place of the commissioning company, Finnsementti Oy. As reliable short term market forecasts for the sector are difficult to compose, the study concentrates primarily in examining and identifying the trends that are likely to affect the Finnish cement industry, and as an extension, the concrete industry in a frame of 10 to 15 years. The study’s scope comprehends also the examination of the domestic construction sector, as it represents the end user industry of both cement and concrete. These motives for the study produce the research problem, which is to conduct a trend analysis for cement based building in the Finnish market area in the 2020s. The theoretical frame for composing a trend analysis in the case of this study is twofold. This is due to the fact that both, the macro and micro environments of the examined industries are studied. The main methods used are the PESTE-model (macro) and Porter’s five forces model (micro). The study applies a qualitative approach and the data is gathered by interviewing a group of experts from the cement, concrete and construction industries. The result of the paper is an overall trend analysis for the Finnish cement based building sector, which is based on ‘sub trend analyses’ concerning four identified sub-sectors of the Finnish construction industry. The results are a combination of findings from these sub-sectors and the analyzed data that deals with the studied sector’s macro and micro environment. The conclusions provide an overall picture of the examined sectors’ potential future as a whole and by defined sub-sectors of the construction industry. The recognition of future trends in different areas of the construction industry can be applied as a means for an industry actor’s decision making and in estimating the types of construction that are likely to grow or decline. Finally, based on the analyzed data and conclusions, the commissioning company is provided with a brief SWOT analysis, that provides additional tools for decision making and planning processes regarding the future.