Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

Harjoitustyön kehittäminen ohjelmoinnin perusteet kurssille

Työn tarkoituksena on luoda uusi harjoitustyö Ohjelmoinnin perusteet –kurssille. Harjoitustyön tavoitteena oli olla nykyistä työtä mielekkäämpi, sekä sidottu käytäntöön. Näiden avulla tavoiteltiin kurssin harjoitustyön suorittavien opiskelijoiden osuuden kasvattamista. Lopputuloksena on kolmeosainen harjoitustyö, jossa opiskelija suorittaa kuvamanipulointia sekä hyödyntää avoimia rajapintoja. Tulevaisuuteen jää haasteeksi harjoitustyön tarkastaminen ja siihen liittyvät ongelmat, sekä työn jatkokehitys.

“Between publication culture and funder mandates - What is the future for disciplinary repositories?”

Workshop at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

DSpace Metadata Panel

Panel at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Images of the future of privacy: A privacy dynamics framework and a causal layered

The future of privacy in the information age is a highly debated topic. In particular, new and emerging technologies such as ICTs and cognitive technologies are seen as threats to privacy. This thesis explores images of the future of privacy among non-experts within the time frame from the present until the year 2050. The aims of the study are to conceptualise privacy as a social and dynamic phenomenon, to understand how privacy is conceptualised among citizens and to analyse ideal-typical images of the future of privacy using the causal layered analysis method. The theoretical background of the thesis combines critical futures studies and critical realism, and the empirical material is drawn from three focus group sessions held in spring 2012 as part of the PRACTIS project. From a critical realist perspective, privacy is conceptualised as a social institution which creates and maintains boundaries between normative circles and preserves the social freedom of individuals. Privacy changes when actors with particular interests engage in technology-enabled practices which challenge current privacy norms. The thesis adopts a position of technological realism as opposed to determinism or neutralism. In the empirical part, the focus group participants are divided into four clusters based on differences in privacy conceptions and perceived threats and solutions. The clusters are fundamentalists, pragmatists, individualists and collectivists. Correspondingly, four ideal-typical images of the future are composed: ‘drift to low privacy’, ‘continuity and benign evolution’, ‘privatised privacy and an uncertain future’, and ‘responsible future or moral decline’. The images are analysed using the four layers of causal layered analysis: litany, system, worldview and myth. Each image has its strengths and weaknesses. The individualistic images tend to be fatalistic in character while the collectivistic images are somewhat utopian. In addition, the images have two common weaknesses: lack of recognition of ongoing developments and simplistic conceptions of privacy based on a dichotomy between the individual and society. The thesis argues for a dialectical understanding of futures as present images of the future and as outcomes of real processes and mechanisms. The first steps in promoting desirable futures are the awareness of privacy as a social institution, the awareness of current images of the future, including their assumptions and weaknesses, and an attitude of responsibility where futures are seen as the consequences of present choices.

Commodity Future Price Premiums – Case EU ETS

The purpose of this thesis was to study commodity future price premiums and their nature on emission allowance markets. The EUA spot and future contracts traded on the secondary market during EU ETS Phase 2 and Phase 3 were selected for empirical testing. The cointegration of spot and future prices was examined with Johansen cointegration methodology. Daily interest rates with a similar tenor to the future contract maturity were used in the cost-of-carry model to calculate the theoretical future prices and to estimate the deviation from the fair value of future contracts, assumed to be explained by the convenience yield. The time-varying dependence of the convenience yield was studied by regression testing the correlation between convenience yield and the time to maturity of the future contract. The results indicated cointegration between spot and future prices, albeit depending on assumptions on linear trend and intercept in cointegration vector Dec-14 and Dec-15 contracts. The convenience yield correlates positively with the time-to-maturity of the future contract during Phase 2, but negatively during Phase 3. The convenience yield featured positive correlation with spot price volatility and negative correlation with future price volatility during both Phases 2 and 3.

Language of the Future, Language of the PRC –Representations of Putonghua in South China Morning Post

As the national language of the PRC, the world's growing economic power and the sovereign of Hong Kong, Putonghua is a language with multiple facets of relevance for the current Special Administrative Region. This paper seeks to explore and explain different representations of Putonghua in Hong Kong's leading English-language newspaper South China Morning Post in articles published between January 2012 and February 2013. The representations are studied in the context of the different discourses in which they appear, some of which feature language(s) as a central theme and some more marginally. An overview is first presented of the scholarly research on the most important developments in Hong Kong's complex language scene from the beginnings of the colony until present day, with the aim of detecting developments and attitudes with potential relevance or parallels to the context of Putonghua today. The paper then reflects on the media and its role in producing and perpetuating discourses in the society, before turning to more practical considerations on Hong Kong's English and Chinese language media and the role of South China Morning Post in it. The methods used in analysing the discourses are those of discourse analysis, with textual analysis as its starting point, in which close attention is paid to linguistic forms as the concrete representations of meanings in a text. Particularly the immediate contexts of the appearances of the word “Putonghua” in the articles were studied carefully to detect vocabulary, grammar and semantical choices as signs of different discourses, potentially also revealing fundamental underlying assumptions and other “hidden meanings” in the text. Some of the most distinctive discourses in which different representations of Putonghua appeared were the Instrumental value for the individual (in which Putonghua was represented as a form of social capital); Othering of the mainlanders (in which Putonghua served as a concrete marker of distinction); Belonging to China (Putonghua as a symbol of unity); and Cultural distinctiveness of Hong Kong (Putonghua as a threat to Hong Kong's history and culture, as embodied in Cantonese). Some of these discourses were more prominent than others, and for example the discourse of Belonging to China was relatively rarely enacted in Hongkongers' voices. In general, the findings were not surprising in the light of the history, but showed a fair degree of consistency with what has been written earlier about the languages and attitudes towards them in Hong Kong. It has often been noted that Putonghua and its relation with Cantonese is a matter linked with the social identity of the colony and its citizens. While it appeared that there were no strict taboos in the representations of Putonghua in the societal context, the possibility of self-censorship cannot be ruled out as a factor toning down political discourses in the representations.

Value-based Reference Marketing in a Small Process Industry Software and Service Company

This master’s thesis was done for a small company, Vipetec Oy, which offers specialized technological services for companies mainly in forest industry. The study was initiated partly because the company wants to expand its customer base to a new industry. There were two goals connected to each other. First was to find out how much and what kind of value current customers have realized from ATA Process Event Library, one of the products that the company offers. Second was to determine the best way to present this value and its implications for future value potential to both current and potential customers. ATA helps to make grade and product changes, starting after machine downtime, and recovery from production break faster for customers. All three events sometimes occur in production line. The faster operation results to savings in time and material. In addition to ATA Vipetec also offers other services related to development of automation and optimization of controls. Theoretical part concentrates on the concept of value, how it can be delivered to customers, and what kind of risk customer faces in industrial purchasing. Also the function of reference marketing towards customers is discussed. In the empirical part the realized value for existing customers is evaluated based on both numerical data and interviews. There’s also a brief case study about one customer. After that the value-based reference marketing for a target industry is examined through interviews of these potential customers. Finally answers to the research questions are stated and compared also to the theoretical knowledge about the subject. Results show that those customers’ machines which use the full service concept of ATA usually are able to save more time and material than the machines which use only some features of the product. Interviews indicated that sales arguments which focus on improved competitive status are not as effective as current arguments which focus on numerical improvements. In the case of potential customers in the new industry, current sales arguments likely work best for those whose irregular production situations are caused mainly by fault situations. When the actions of Vipetec were compared to ten key elements of creating customer references, it was seen that many of them the company has either already included in its strategy or has good chances to include them with the help of the results of this study.

Susteinable steelmaking by process integration

Environmental issues, including global warming, have been serious challenges realized worldwide, and they have become particularly important for the iron and steel manufacturers during the last decades. Many sites has been shut down in developed countries due to environmental regulation and pollution prevention while a large number of production plants have been established in developing countries which has changed the economy of this business. Sustainable development is a concept, which today affects economic growth, environmental protection, and social progress in setting up the basis for future ecosystem. A sustainable headway may attempt to preserve natural resources, recycle and reuse materials, prevent pollution, enhance yield and increase profitability. To achieve these objectives numerous alternatives should be examined in the sustainable process design. Conventional engineering work cannot address all of these substitutes effectively and efficiently to find an optimal route of processing. A systematic framework is needed as a tool to guide designers to make decisions based on overall concepts of the system, identifying the key bottlenecks and opportunities, which lead to an optimal design and operation of the systems. Since the 1980s, researchers have made big efforts to develop tools for what today is referred to as Process Integration. Advanced mathematics has been used in simulation models to evaluate various available alternatives considering physical, economic and environmental constraints. Improvements on feed material and operation, competitive energy market, environmental restrictions and the role of Nordic steelworks as energy supplier (electricity and district heat) make a great motivation behind integration among industries toward more sustainable operation, which could increase the overall energy efficiency and decrease environmental impacts. In this study, through different steps a model is developed for primary steelmaking, with the Finnish steel sector as a reference, to evaluate future operation concepts of a steelmaking site regarding sustainability. The research started by potential study on increasing energy efficiency and carbon dioxide reduction due to integration of steelworks with chemical plants for possible utilization of available off-gases in the system as chemical products. These off-gases from blast furnace, basic oxygen furnace and coke oven furnace are mainly contained of carbon monoxide, carbon dioxide, hydrogen, nitrogen and partially methane (in coke oven gas) and have proportionally low heating value but are currently used as fuel within these industries. Nonlinear optimization technique is used to assess integration with methanol plant under novel blast furnace technologies and (partially) substitution of coal with other reducing agents and fuels such as heavy oil, natural gas and biomass in the system. Technical aspect of integration and its effect on blast furnace operation regardless of capital expenditure of new operational units are studied to evaluate feasibility of the idea behind the research. Later on the concept of polygeneration system added and a superstructure generated with alternative routes for off-gases pretreatment and further utilization on a polygeneration system producing electricity, district heat and methanol. (Vacuum) pressure swing adsorption, membrane technology and chemical absorption for gas separation; partial oxidation, carbon dioxide and steam methane reforming for methane gasification; gas and liquid phase methanol synthesis are the main alternative process units considered in the superstructure. Due to high degree of integration in process synthesis, and optimization techniques, equation oriented modeling is chosen as an alternative and effective strategy to previous sequential modelling for process analysis to investigate suggested superstructure. A mixed integer nonlinear programming is developed to study behavior of the integrated system under different economic and environmental scenarios. Net present value and specific carbon dioxide emission is taken to compare economic and environmental aspects of integrated system respectively for different fuel systems, alternative blast furnace reductants, implementation of new blast furnace technologies, and carbon dioxide emission penalties. Sensitivity analysis, carbon distribution and the effect of external seasonal energy demand is investigated with different optimization techniques. This tool can provide useful information concerning techno-environmental and economic aspects for decision-making and estimate optimal operational condition of current and future primary steelmaking under alternative scenarios. The results of the work have demonstrated that it is possible in the future to develop steelmaking towards more sustainable operation.

The future of branded sportswear store formats in Germany 2030: Four images of the future

A fast changing dynamic business environment is becoming a norm today in different areas, including retailing. The aims of this study are to explore existing store formats of branded sportswear retailing and their characteristics, and to identify the trends which might shape their future. The ultimate goal, however, is to create and analyze images of the future of branded sportswear retailing in Germany 2030 by applying the methods of futures studies. As theoretical background, the cyclical theories of retail evolution have been used. Empirical material is obtained by conducting a Disaggregative Policy Delphi method based study, the aim of which is to obtain well–argued qualitative and quantitative information from experts about store format development in order to create future images based on cluster analysis. Flagship stores, Concept stores, Factory Outlets, Pop-up stores, E-commerce and M-commerce represent the diversity of store formats existing in Germany today. They have different aims, roles, and advantages which retailers try to leverage. However such trends as multichannel integration, technological enhancements, growing popularity of online channels, switching customer behaviors, customization and personalization, and economic turbulence might shape the future of sportswear retailing. Four future images constructed: “Multichannel Integration”, “Smart and Personal”, “Consumer Diversification”, and “Always Online” – describe alternative futures of German branded sportswear store formats in 2030 based on different trends, assumptions, hopes and fears. They also point out uncertainties in retailing such as cannibalization of channels, the growing power and expectations of consumers, the complexity of multichannel synergies, and the switching customer behavior. Constructed future images, thus, provide readers with an opportunity to imagine and explore alternative states of the future of branded sportswear store formats in Germany 2030. They could serve well as a tool to communicate the results to decision–makers, compare them, and to analyze to inspire and direct actions for a better future tomorrow.

Future at risk: A study on the Club of Rome

Sustainability, in its modern meaning, has been discussed for more than forty years. However, many experts believe that humanity is still far from being sustainable. Some experts have argued that humanity should seek survivable development because it is too late for sustainable one, since 1990s. Obviously, some problems prevented humanity from becoming sustainable. This thesis focuses on the agenda of sustainability discussions and seeks for the essential topics missing from it. For this purpose, the research is conducted on 21 out of 33 books endorsed by the Club of Rome. All of these books are titled ‘a report to the Club of Rome’. The Club of Rome is an organization that has been constantly working on the problems of humankind for the past 40 years. This thesis has three main components: first, the messages of the reports to the Club of Rome, second, academics perceptions of the Club, and third, the Club member perceptions of its evolution, messages and missing topics. This thesis investigates the evolution of four aspects in the reports. The first one is the agenda of the reports. The second one is the basic approaches of the Club (i.e., global, long-term and holistic). The third one is the ways that the reports treat free market and growth ideology. The fourth one is the approach of the reports toward components of the global complex system (i.e., society, economy and politics). The outline of the thesis is as follows. First, the original reports are briefly summarized. After this, the academic perceptions are discussed and structured around three concepts (i.e., futures studies, sustainability and degrowth). In the final step, the perceptions of the experts are collected and analysed, using a variation of Delphi method, called ‘in-depth interviews’, and ‘quality content analysis’ method. This thesis is useful for those interested in sustainability, global problems, and the Club of Rome. This thesis concludes that the reports from 1972 up to 1980 were cohesive in discussing topics related to the problems of humankind. The topics of the reports are fragmented after this period. The basic approaches of CoR are visible in all the reports. However, after 1980, those approaches and especially holistic thinking are only visible in the background. Regarding the free market and growth ideology, although all the reports are against them, the early reports were more explicitly expressing their disagreement. A milestone is noticeable around 1980 when such objections went completely to the background. However, recent reports are more similar to those of 1970s both in adopting a holistic approach and in explicitly criticizing free market and growth ideology. Finally, concerning the components of global complex system, the society is excluded and the focus of the reports is on politics, economy and their relation. Concerning the topics missing from the debate, this thesis concludes that no major research has been conducted on the fundamental and underlying reasons of the problems (e.g. beliefs, values and culture). Studying the problems without considering their underlying reasons, obviously, leads to superficial and ineffective solutions. This might be one of the reasons that sustainability discussions have as yet led to no concrete result.

Potential and Challenges of Analog Reconfigurable Computation in Modern and Future CMOS

In this work, the feasibility of the floating-gate technology in analog computing platforms in a scaled down general-purpose CMOS technology is considered. When the technology is scaled down the performance of analog circuits tends to get worse because the process parameters are optimized for digital transistors and the scaling involves the reduction of supply voltages. Generally, the challenge in analog circuit design is that all salient design metrics such as power, area, bandwidth and accuracy are interrelated. Furthermore, poor flexibility, i.e. lack of reconfigurability, the reuse of IP etc., can be considered the most severe weakness of analog hardware. On this account, digital calibration schemes are often required for improved performance or yield enhancement, whereas high flexibility/reconfigurability can not be easily achieved. Here, it is discussed whether it is possible to work around these obstacles by using floating-gate transistors (FGTs), and analyze problems associated with the practical implementation. FGT technology is attractive because it is electrically programmable and also features a charge-based built-in non-volatile memory. Apart from being ideal for canceling the circuit non-idealities due to process variations, the FGTs can also be used as computational or adaptive elements in analog circuits. The nominal gate oxide thickness in the deep sub-micron (DSM) processes is too thin to support robust charge retention and consequently the FGT becomes leaky. In principle, non-leaky FGTs can be implemented in a scaled down process without any special masks by using “double”-oxide transistors intended for providing devices that operate with higher supply voltages than general purpose devices. However, in practice the technology scaling poses several challenges which are addressed in this thesis. To provide a sufficiently wide-ranging survey, six prototype chips with varying complexity were implemented in four different DSM process nodes and investigated from this perspective. The focus is on non-leaky FGTs, but the presented autozeroing floating-gate amplifier (AFGA) demonstrates that leaky FGTs may also find a use. The simplest test structures contain only a few transistors, whereas the most complex experimental chip is an implementation of a spiking neural network (SNN) which comprises thousands of active and passive devices. More precisely, it is a fully connected (256 FGT synapses) two-layer spiking neural network (SNN), where the adaptive properties of FGT are taken advantage of. A compact realization of Spike Timing Dependent Plasticity (STDP) within the SNN is one of the key contributions of this thesis. Finally, the considerations in this thesis extend beyond CMOS to emerging nanodevices. To this end, one promising emerging nanoscale circuit element - memristor - is reviewed and its applicability for analog processing is considered. Furthermore, it is discussed how the FGT technology can be used to prototype computation paradigms compatible with these emerging two-terminal nanoscale devices in a mature and widely available CMOS technology.