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,

Postimerkit merisotataidon dokumentteina : Britannian ja Saksan laivastojen varustelu maailmansotien välisenä aikana

Merisodassa tapahtunut muutos – erityisesti konevoiman syrjäyttäessä purjeet ja raudan korvatessa puumateriaalin 1800-luvun loppupuolella – johti nykypäivänäkin merkittäviin merisodan teoreettisiin tarkasteluihin. Teorioihin pohjautuneet merisotataidon yleisperiaatteet saivat ensimmäisen maailmansodan aikana käytännön testauksensa. Voittajat ja häviäjät analysoivat taistelut sekä maailmalla vallinneen ripeän teknisen kehityksen, minkä seurauksena laivastojen varustelu kiihtyi uudestaan valtapolitiikan tueksi. Maailmansotien välisenä aikana pyrittiin kansainvälisin sopimuksin säätelemään suurten laivastojen, kuten Britannian, Ranskan, Italian, Japanin ja Yhdysvaltojen varustelukilpailua. Versaillesin rauhansopimus rajoitti samanaikaisesti Saksan merivoimien kokoa. Tässä työssä tutkitaan Britannian ja Saksan merivoimien varustelua ja merisotataidon kehittymistä maailmansotien välisenä aikana. Merisotataidon kehittymisen tarkastelu tapahtuu postimerkkien avulla. Postimerkki syntyi Englannissa vuonna 1840 ja sen käyttö yleistyi ympäri maailman lähes samanaikaisesti konevoimaa käyttäneiden laivojen kanssa. Postimerkkien kuva-aiheet olivat aluksi valtioiden päämiehiä, heraldiikkaa, maisemia tai abstrakteja aiheita. Vasta 1900-luvun alkupuolella kuva-aiheina saattoi olla lähes mitä vain, myös sotalaivojen kuvia. Postimerkkikokoelmastani erottuu tutkimusaiheeseen 335 merkkiä. Britannian ja Saksan kansallisarkistojen alkuperäislähteiden ja tutkimuskirjallisuuden dokumenttianalyysiin perustuvaa merisotataidon moninaista kehitystä verrataan tutkimuksessani postimerkkien kuva-aiheisiin ja niiden yksityiskohtiin 3 300 kertaa. Tällä menettelyllä pyrin selvittämään voiko postimerkkejä käyttää ja pitää merisotaidon kehityksen kattavina dokumentteina. Postimerkeissä satunnaisiksi jääneet virheet tai propaganda eivät vähennä merisotataidon kehityksen kuvaamisen dokumenttiarvoa. Postimerkkien sotalaivoihin liittyvät kuvat kattavat muutamaa laivaluokkaa lukuunottamatta molempien maiden kaikki taistelualuslajit- ja luokat. Postimerkeistä voidaan nähdä vanhat sotalaivat, niiden peruskorjaukset ja uudet luokat lentotukialuksista sukellusveneisiin. Alusten kuvat voidaan liittää Britannian kansainyhteisön muuttuneisiin strategisiin ja taktisiin tavoitteisiin niin Atlantilla kuin Kaukoidässä. Saksan merivoimien nousu Versaillesin rauhanehtojen rajoituksista ja lopulta pyrkimys Britannian kauppamerenkulun tuhoajaksi välittyy myös postimerkeistä. Yleinen sotatekninen kehitys, lentoneiden tulo merisotanäyttämölle ja aikanaan kansainvälisten tonnistorajoitusten poistuminen näkyvät postimerkeissä. Kokopostimerkin historian aikana vuoteen 2012 mennessä purjeettomien, nykyaikaisten sotalaivojen kuvia on julkaistu noin 3 350 postimerkillä, jotka on koottu Maailman suurin laivasto-osasto -postimerkkikokoelmaani noin 35 vuoden aikana

Evaluation of Major E-commerce Companies Business Model

Technological advances have enabled a large spread of online retailers. E-commerce business is challenging the nature of traditional foundation of trade, therefore trade is on transition. The Internet allows consumers to compare and examine online store offerings, regardless of place and time. Digitalization has created new opportunities for creating customer value. The growing trend towards online shopping world has taken place in a very short period of time. Businesses, either use e-commerce as an additional operation, or completely rely, on the Internet business opportunities. The aim of this Master`s thesis is to define and evaluate key business model factors of two major e-commerce companies, Alibaba.com and Amazon.com. These key business model factors have a positive effect on successful e-commerce business. In addition, Alibaba.com and Amazon.com are compared with the help of these identified factors. Moreover, e-commerce business factors provide opportunities to create greater customer value regardless of the industry. Customer value is the core of business and a competitive advantage. Customer value is defined as a ratio between sacrifices and benefits. E-commerce companies should effectively evaluate customer value, so they could customize their offerings to meet better desired customer needs. Even though e-commerce business is a relatively new phenomenon, it has been widely studied

Formal modelling for digital media distribution

Human beings have always strived to preserve their memories and spread their ideas. In the beginning this was always done through human interpretations, such as telling stories and creating sculptures. Later, technological progress made it possible to create a recording of a phenomenon; first as an analogue recording onto a physical object, and later digitally, as a sequence of bits to be interpreted by a computer. By the end of the 20th century technological advances had made it feasible to distribute media content over a computer network instead of on physical objects, thus enabling the concept of digital media distribution. Many digital media distribution systems already exist, and their continued, and in many cases increasing, usage is an indicator for the high interest in their future enhancements and enriching. By looking at these digital media distribution systems, we have identified three main areas of possible improvement: network structure and coordination, transport of content over the network, and the encoding used for the content. In this thesis, our aim is to show that improvements in performance, efficiency and availability can be done in conjunction with improvements in software quality and reliability through the use of formal methods: mathematical approaches to reasoning about software so that we can prove its correctness, together with the desirable properties. We envision a complete media distribution system based on a distributed architecture, such as peer-to-peer networking, in which different parts of the system have been formally modelled and verified. Starting with the network itself, we show how it can be formally constructed and modularised in the Event-B formalism, such that we can separate the modelling of one node from the modelling of the network itself. We also show how the piece selection algorithm in the BitTorrent peer-to-peer transfer protocol can be adapted for on-demand media streaming, and how this can be modelled in Event-B. Furthermore, we show how modelling one peer in Event-B can give results similar to simulating an entire network of peers. Going further, we introduce a formal specification language for content transfer algorithms, and show that having such a language can make these algorithms easier to understand. We also show how generating Event-B code from this language can result in less complexity compared to creating the models from written specifications. We also consider the decoding part of a media distribution system by showing how video decoding can be done in parallel. This is based on formally defined dependencies between frames and blocks in a video sequence; we have shown that also this step can be performed in a way that is mathematically proven correct. Our modelling and proving in this thesis is, in its majority, tool-based. This provides a demonstration of the advance of formal methods as well as their increased reliability, and thus, advocates for their more wide-spread usage in the future.

Design thinking framework of experience innovation

Innovation remains one of the key drivers of sustainable and successful business. The variety of innovation approaches such as open models, intersectional thinking and co-creation tackles the challenge of viable novel offerings across the world. These approaches have certain similarities and their elements constitute design thinking. Recent market and society trends such as technological advances and globalization have intensify companies’ interaction with customers. Emotional engagement, pleasing communication and delight have gained equal to functionality importance. The complex of these components constitutes consumer experience. Academic research conceptualizes these changes by introducing customer-centered innovation, which replaces product-oriented approaches. However, both methods omit experience concept and provide fragmented explanation of experience innovation. Experience is an essential process of offering perception, which drives customer decisions. Therefore, an agenda of experience innovation development can systemize and explain the mechanisms of experience innovation. The purpose of this study is to create and explain the stage process framework of experience innovation by the means of design thinking approach. The research proceeds in accordance with the following sub-objectives: 1. Conceptualization of consumer experience through customer value. 2. Creation of experience innovation framework by the means of design thinking. This study is conducted by the means of conceptual research methods. The main theoretical contribution of the study is creation of the integrated framework of consumer experience innovation. The elaboration of design thinking agenda and methods applied to experience design builds the guidelines of experience innovation development. This research synthesizes the conceptual elements of the framework that resolves inconsistencies and duplications of theories. This essential clarification simplifies application of the experience innovation agenda, which can be useful for the wide range of specialists, from marketing to strategists, and from managers to entrepreneurs, willing to offer compelling experience to customers. The study highlights the crucial role of consumer experience in maintaining customer loyalty and designs the roadmap of innovating experience through the communication with customers.

Exploring the strategic impact of technological change - Studies on the role of Internet in magazine publishing

Over the past few decades, turbulent change has characterized the situation in the media industry. It has been noted that digitalization and new media are strongly influencing the industry: it is changing the existing market dynamics and requires new strategies. Prior research on the impact of digitalization and the Internet has emphasized news-focused media such as newspaper publishing and broadcasting, yet magazine publishing is very seldom the focus of the research. This study examines how the Internetimpacts magazine publishing. The work presents a multi-level analysis on the role and impact of the Internet on magazine products, companies and industry. The study is founded on strategic management, technology management and media economics literature. This study consists of two parts. The first part introduces the research topic and discusses the overall results of the study. The second part comprises five research publications. Qualitative research methods are used throughout. The results of the study indicate that the Internet has not had a disruptive effect on magazine publishing, and that its strategic implications could rather be considered complementary to the print magazine and the business as a whole. It seems that the co-specialized assets, together with market-related competencies and unchanged core competence have protected established firms from the disruptive effect of the new technology in magazine publishing. In addition, it seems that the Internet offers a valuable possibility to build and nourish customer relationships. The study contributes tomedia management and economics research by moving from product- or industry-level investigations towards a strategic-management perspective.

Technological and business challenges of smart grids

Growing recognition of the electricity grid modernization to enable new electricity generation and consumption schemes has found articulation in the vision of the Smart Grid platform. The essence of this vision is an autonomous network with two-way electricity power flows and extensive real-time information between the generation nodes, various electricity-dependent appliances and all points in-between. Three major components of the Smart Grids are distributed intelligence, communication technologies, and automated control systems. The aim of this thesis is to recognize the challenges that Smart Grids are facing, while extinguishing the main driving factors for their introduction. The scope of the thesis also covers possible place of electricity Aggregator Company in the current and future electricity markets. Basic functions of an aggregator and possible revenue sources along with demand response feasibility calculations are reviewed within this thesis.

Some advances in mathematical models for preference relations

Preference relations, and their modeling, have played a crucial role in both social sciences and applied mathematics. A special category of preference relations is represented by cardinal preference relations, which are nothing other than relations which can also take into account the degree of relation. Preference relations play a pivotal role in most of multi criteria decision making methods and in the operational research. This thesis aims at showing some recent advances in their methodology. Actually, there are a number of open issues in this field and the contributions presented in this thesis can be grouped accordingly. The first issue regards the estimation of a weight vector given a preference relation. A new and efficient algorithm for estimating the priority vector of a reciprocal relation, i.e. a special type of preference relation, is going to be presented. The same section contains the proof that twenty methods already proposed in literature lead to unsatisfactory results as they employ a conflicting constraint in their optimization model. The second area of interest concerns consistency evaluation and it is possibly the kernel of the thesis. This thesis contains the proofs that some indices are equivalent and that therefore, some seemingly different formulae, end up leading to the very same result. Moreover, some numerical simulations are presented. The section ends with some consideration of a new method for fairly evaluating consistency. The third matter regards incomplete relations and how to estimate missing comparisons. This section reports a numerical study of the methods already proposed in literature and analyzes their behavior in different situations. The fourth, and last, topic, proposes a way to deal with group decision making by means of connecting preference relations with social network analysis.

Forest Biomass Resources and Technological Prospects for the Production of Second-generation Biofuels in Finland by 2020

Introduction of second-generation biofuels is an essential factor for meeting the EU’s 2020 targets for renewable energy in the transport sector and enabling the more ambitious targets for 2030. Finland’s forest industry is strongly involved in the development and commercialising of second-generation biofuel production technologies. The goal of this paper is to provide a quantified insight into Finnish prospects for reaching the 2020 national renewable energy targets and concurrently becoming a large-scale producer of forest biomass based second-generation biofuels feeding the increasing demand in European markets. The focus of the paper is on assessing the potential for utilising forest biomass for liquid biofuels up to 2020. In addition, technological issues related to the production of second-generation biofuels were reviewed. Finland has good opportunities to realise a scenario to meet 2020 renewable energy targets and for large-scale production of wood based biofuels. In 2020, biofuel production from domestic forest biomass in Finland may reach nearly a million ton (40 PJ). With the existing biofuel production capacity (20 PJ/yr) and national biofuel consumption target (25 PJ) taken into account, the potential net export of biofuels from Finland in 2020 would be 35 PJ, corresponding to 2–3% of European demand. Commercialisation of second-generation biofuel production technologies, high utilisation of the sustainable harvesting potential of Finnish forest biomass, and allocation of a significant proportion of the pulpwood harvesting potential for energy purposes are prerequisites for this scenario. Large-scale import of raw biomass would enable remarkably greater biofuel production than is described in this paper.

Building Successful, Open Repository Software Ecosystems: Technology and Community

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

Structural dynamics in the global pulp and paper industry

The pulp and paper industry is currently facing broad structural changes due to global shifts in demand and supply. These changes have significant impacts on national economies worldwide. Planted forests (especially eucalyptus) and recovered paper have quickly increased their importance as raw material for paper and paperboard production. Although advances in information and communication technologies could reduce the demand for communication papers, and the growth of paper consumption has indeed flattened in developed economies, particularly in North America and Western Europe, the consumption is increasing on a global scale. Moreover, the focal point of production and consumption is moving from the Western world to the rapidly growing markets of Southeast Asia. This study analyzes how the so-called megatrends (globalization, technological development, and increasing environmental awareness) affect the pulp and paper industry’s external environment, and seeks reliable ways to incorporate the impact of the megatrends on the models concerning the demand, trade, and use of paper and pulp. The study expands current research in several directions and points of view, for example, by applying and incorporating several quantitative methods and different models. As a result, the thesis makes a significant contribution to better understand and measure the impacts of structural changes on the pulp and paper industry. It also provides some managerial and policy implications.