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,

The Russian National Innovation System - an International Perspective

Russia inherited a large research and development (R&D) sector from the Soviet times, and has retained a substantial R&D sector today, compared with other emerging economies. However, Russia is falling behind in all indicators measuring innovative output in comparison with most developed countries. Russia’s innovation performance is disappointing, despite the available stock of human capital and overall investment in R&D. The communist legacy still influences the main actors of the innovation system. The federal state is still the most important funding source for R&D. Private companies are not investing in innovative activities, preferring to “import” innovations embedded in foreign technologies. Universities are outsiders in the innovation system, only a few universities carry out research activities. Nowadays, Russia is a resource-depended country. The economy depends on energy and metals for growth. The Russian economy faces the challenge of diversification and should embrace innovation, and shift to a knowledge economy to remain competitive in the long run. Therefore, Russia has to tackle the challenge of developing an efficient innovation system with its huge potential in science expertise and engineering know-how.

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.

Sähkönmyyntiyhtiön riskienhallinnan kehittäminen

Sähkönmyyntiyhtiön liiketoimintaan liittyy muiden yritysten toiminnan tavoin erilaisia riskejä. Riskit jaetaan operationaalisiin ja markkinariskeihin. Operationaalisia riskejä ovat esimerkiksi erilaiset henkilöstöön, tietojärjestelmiin tai operatiiviseen toimintaan liittyvät riskit. Sähkönmyyntiyhtiön liiketoimintaan kohdistuu myös erilaisia markkinariskejä, joihin tyypillisesti liittyy sekä voiton että tappion mahdollisuus. Sähkönmyyntiyhtiön liiketoimintaan liittyviä markkinariskejä ovat esimerkiksi volyymiriski, profiiliriski, hintariski ja johdannaisriski. Työssä käydään läpi myös muita markkinariskejä sekä pohditaan riskien suojautumiskeinoja. Markkinariskejä voidaan hallita useiden eri keinojen avulla. Tavallisimpia näistä ovat esimerkiksi johdannaisten ja peak- sekä profiilituotteiden hankkiminen, joiden avulla hallitaan markkinahintojen muutosten vaikutuksia liiketoiminnan tulokseen. Lisäksi yritys voi käyttää riskienhallintakeinoina monipuolista jälkilaskentaa sekä raportointia liiketoiminnan keskeisiltä osilta. Erityisesti riskienhallintakeinona käytetään erilaisia riskimittareita, joista Profit at Risk-riskimittarin katsottiin soveltuvan parhaiten sähkönmyyntiyhtiön riskienhallinnan tueksi. Riskienhallinnan kehityksen näkökulmasta yrityksen on syytä miettiä sopimusten hinnoitteluaan sekä suojausstrategiaansa.

Kustannuslaskentamallin kehittäminen yrityksessä tapahtuvan merkittävän tuotantoinvestoinnin johdosta - Case Isku Yhtymä Oy

Työn tavoitteena oli kehittää case-yrityksen kustannuslaskentamallia tilanteessa, jossa yrityksen tuotanto muuttuu merkittävästi suuren tuotantoinvestoinnin vaikutuksesta. Työ koostuu teoreettisesta kirjallisuuskatsauksesta ja sitä soveltavasta empiirisestä case-tutkimuksesta. Tarkastelun kohteena on yrityksen nykyinen kustannuslaskentamalli ja sen ongelmat. Näitä ongelmia pyritään ratkaisemaan hahmottelemalla uuden kustannuslaskentamallin perusteita. Merkittävin muutos kustannuslaskennassa tapahtui erityisesti välillisten kustannusten allokoinnin kohdalla, jossa useassa merkittävässä kustannuserässä pystyttiin löytämään tapa allokoida kustannukset jopa tuotteille asti. Empiriassa teoriapohjana käytettiin pääasiassa Robert Kaplanin vuonna 2004 luomaa toimintokohtaisen kustannuslaskennan kehittyneempää mallia (TDACB). Case-yrityksen kustannuslaskenta oli perustunut aiemmin standardikustannuslaskentaan ja huomattavien yleiskustannuskertoimien käyttöön. Kehittämällä kustannuslaskentaa, voidaan estää virheellisten päätösten tekeminen ja antaa koko organisaatiolle parempaa kustannusinformaatiota

Lean Innovation in Large Companies: a Case of Implementation in R&D

The main objective of the study is to evaluate the impact of Lean Innovation management philosophy on the creativity potential of the large multinational enterprise. A theory of Lean Innovation indicates that the modern company in any industry can successfully combine both waste-decreasing approach and innovative potential promotion through creativity cultivation or, at least, preservation. The theoretical part of the work covers the main factors, pros and cons of Lean thinking and Innovation management separately, along with generalized new product development overview. While the modern international market becomes more accessible for entrepreneural initiatives, small enterprises and start-ups, large international corporations are more subject to adopt the Lean Innovation approach in both operational and product development sectors due to extended resources and capabilities. Moreover, a multinational enterprise is a highly probable pioneer in Lean innovation implementation. The empirical part of the thesis refers to a case of large European enterprise, operating in many markets around the globe, that currently undergoes innovation management adjustments and implementations in product development while already have related themselves with operational process optimization process through Lean thinking. A goal of the work is to understand what kind of difficulties and consequences a large international firm faces when dealing with Lean Innovation to improve own performance, if they can be sealed for generalized approach.

Review of water electrolysis technologies and design of renewable hydrogen production systems

An electric system based on renewable energy faces challenges concerning the storage and utilization of energy due to the intermittent and seasonal nature of renewable energy sources. Wind and solar photovoltaic power productions are variable and difficult to predict, and thus electricity storage will be needed in the case of basic power production. Hydrogen’s energetic potential lies in its ability and versatility to store chemical energy, to serve as an energy carrier and as feedstock for various industries. Hydrogen is also used e.g. in the production of biofuels. The amount of energy produced during hydrogen combustion is higher than any other fuel’s on a mass basis with a higher-heating-value of 39.4 kWh/kg. However, even though hydrogen is the most abundant element in the universe, on Earth most hydrogen exists in molecular forms such as water. Therefore, hydrogen must be produced and there are various methods to do so. Today, the majority hydrogen comes from fossil fuels, mainly from steam methane reforming, and only about 4 % of global hydrogen comes from water electrolysis. Combination of electrolytic production of hydrogen from water and supply of renewable energy is attracting more interest due to the sustainability and the increased flexibility of the resulting energy system. The preferred option for intermittent hydrogen storage is pressurization in tanks since at ambient conditions the volumetric energy density of hydrogen is low, and pressurized tanks are efficient and affordable when the cycling rate is high. Pressurized hydrogen enables energy storage in larger capacities compared to battery technologies and additionally the energy can be stored for longer periods of time, on a time scale of months. In this thesis, the thermodynamics and electrochemistry associated with water electrolysis are described. The main water electrolysis technologies are presented with state-of-the-art specifications. Finally, a Power-to-Hydrogen infrastructure design for Lappeenranta University of Technology is presented. Laboratory setup for water electrolysis is specified and factors affecting its commissioning in Finland are presented.

The role of import intermediary companies in the Russian imports from the EU A case study of a Russian industrial company’s point of view on import intermediaries

The literature on agency suggests different implications for the use of export intermediaries. However, only few studies provide a view on import intermediaries. This thesis tries for its part to fill this research gap by studying the import intermediaries in the EU–Russia trade from a Russian industrial company’s point of view. The aim is to describe import intermediation and explain the need for import intermediary companies in the EU–Russia trade. The theoretical framework of this thesis originates from an article by Peng and York (2001), in which they study the performance of export intermediaries. This thesis applies resource-based theory, transaction cost theory and agency cost theory, following the idea of Peng and York. The resource-based theory approach is utilised for describing an ideal import intermediary company, and transaction cost theory provides a basis for understanding the benefits of using the services of import intermediary companies, while agency cost theory is applied in order to understand the risks the Russian industrial company faces when it decides to use the services of import intermediaries. The study is performed in the form of a case interview with a representative of a major Russian metallurgy company. The results of the study suggest that an ideal intermediary has the skills required specifically for the imports process, in order to save time and money of the principal company. The intermediary company helps reducing the amount of time the managers and the staff of the principal company use to make imports possible, thus reducing the salary costs and providing the possibility to concentrate on the company’s core competencies. The benefits of using the services of import intermediary companies are the reduced transaction costs, especially salary costs that are minimised because of the effectiveness and specialisation of import intermediaries. Intermediaries are specialised in the imports process and thus need less time and resources to organise the imports. They also help to reduce the fixed salary costs, because their services can be used only when needed. The risks of being misled by intermediaries are minimised by the competition on the import intermediary market. In case an intermediary attempts fraud, it gets replaced by its rival.

Underwater Remote Welding Technology for Offshore Structures

The construction of offshore structures, equipment and devices requires a high level of mechanical reliability in terms of strength, toughness and ductility. One major site for mechanical failure, the weld joint region, needs particularly careful examination, and weld joint quality has become a major focus of research in recent times. Underwater welding carried out offshore faces specific challenges affecting the mechanical reliability of constructions completed underwater. The focus of this thesis is on improvement of weld quality of underwater welding using control theory. This research work identifies ways of optimizing the welding process parameters of flux cored arc welding (FCAW) during underwater welding so as to achieve desired weld bead geometry when welding in a water environment. The weld bead geometry has no known linear relationship with the welding process parameters, which makes it difficult to determine a satisfactory weld quality. However, good weld bead geometry is achievable by controlling the welding process parameters. The doctoral dissertation comprises two sections. The first part introduces the topic of the research, discusses the mechanisms of underwater welding and examines the effect of the water environment on the weld quality of wet welding. The second part comprises four research papers examining different aspects of underwater wet welding and its control and optimization. Issues considered include the effects of welding process parameters on weld bead geometry, optimization of FCAW process parameters, and design of a control system for the purpose of achieving a desired bead geometry that can ensure a high level of mechanical reliability in welded joints of offshore structures. Artificial neural network systems and a fuzzy logic controller, which are incorporated in the control system design, and a hybrid of fuzzy and PID controllers are the major control dynamics used. This study contributes to knowledge of possible solutions for achieving similar high weld quality in underwater wet welding as found with welding in air. The study shows that carefully selected steels with very low carbon equivalent and proper control of the welding process parameters are essential in achieving good weld quality. The study provides a platform for further research in underwater welding. It promotes increased awareness of the need to improve the quality of underwater welding for offshore industries and thus minimize the risk of structural defects resulting from poor weld quality.

Prospects of Bitcoin diffusion

Currency is something people deal with every day in their lives. The contemporary society is very much revolving around currencies. Even though technological development has been rapid, the principle of currency has stayed relatively unchanged for a long time. Bitcoin is a digital currency that introduced an alternative to other digital currencies, and to the traditional physical currencies. Bitcoin is peer-to-peer, open source, and it erases the need of a third party in transactions. Bitcoin has since inception gained certain fame, but it has not established itself as a common currency in the world. The purpose of this study was to analyse what kind of potential does Bitcoin have to become a widely accepted currency in day-to-day transactions. The main research question was divided into three sub questions: • What kind of a process is the diffusion of new innovations? • What kinds of factors speak for the wider adoption of Bitcoin? • What kinds of factors speak against the wider adoption of Bitcoin? The purpose of the study was approached by having diffusion of innovations as the theoretical framework. The four elements in diffusion of innovations are, innovation, communication, time, and social system. The theoretical framework is applied to Bitcoin, and the research questions answered by analysing Bitcoin’s potential diffusion prospects. The body of research data consisted of media texts and statistics. In this study, content analysis was the research method. The main findings of the study are that Bitcoin has clear strengths, but it faces a large amount of uncertainty. Bitcoin’s strong areas are the transactions. They are fast, easy, and cheap. From the innovation diffusion perspective Bitcoin is still relatively unknown, and the general public’s attitudes towards it are sceptical. The research findings purport that Bitcoin has potential demand especially when the financial system of a region is dysfunctional, or when there is a financial crisis. Bitcoin is not very trusted, and the majority of people do not see a reason to start using Bitcoin in the future. A large number of people associate it with illegal activities. In general people are largely unaware of what Bitcoin is or what are the strengths and weaknesses. Bitcoin is an innovative alternative currency. However, unless people see a major need for Bitcoin due to a financial crisis, or dysfunctionality in the financial system, Bitcoin will not become much more widespread as it is today. Bitcoin’s underlying technology can be harnessed to multiple uses. Developments in that field in the future are something that future researchers could look into.

The role of import intermediary companies in the Russian imports from the EU A case study of a Russian industrial company’s point of view on import intermediaries

The literature on agency suggests different implications for the use of export intermediaries. However, only few studies provide a view on import intermediaries. This thesis tries for its part to fill this research gap by studying the import intermediaries in the EU–Russia trade from a Russian industrial company’s point of view. The aim is to describe import intermediation and explain the need for import intermediary companies in the EU–Russia trade. The theoretical framework of this thesis originates from an article by Peng and York (2001), in which they study the performance of export intermediaries. This thesis applies resource-based theory, transaction cost theory and agency cost theory, following the idea of Peng and York. The resource-based theory approach is utilised for describing an ideal import intermediary company, and transaction cost theory provides a basis for understanding the benefits of using the services of import intermediary companies, while agency cost theory is applied in order to understand the risks the Russian industrial company faces when it decides to use the services of import intermediaries. The study is performed in the form of a case interview with a representative of a major Russian metallurgy company. The results of the study suggest that an ideal intermediary has the skills required specifically for the imports process, in order to save time and money of the principal company. The intermediary company helps reducing the amount of time the managers and the staff of the principal company use to make imports possible, thus reducing the salary costs and providing the possibility to concentrate on the company’s core competencies. The benefits of using the services of import intermediary companies are the reduced transaction costs, especially salary costs that are minimised because of the effectiveness and specialisation of import intermediaries. Intermediaries are specialised in the imports process and thus need less time and resources to organise the imports. They also help to reduce the fixed salary costs, because their services can be used only when needed. The risks of being misled by intermediaries are minimised by the competition on the import intermediary market. In case an intermediary attempts fraud, it gets replaced by its rival.

A human-centric service approach for architecting and reengineering global system

Production of a new system in any range is expanding dramatically and new ideas are there upon introduced, the logic stands behind the matter is the growth of application of the internet and granting web-based systems. Before producing a system and distribute to the customer, various aspects should be studied which multiple the profit of the system. The process of productizing a new system from being unprocessed idea until delivers to the final user has been unambiguous. In this thesis, the systematize service in a way that benefits both the customer and provider, along with an effort to establish trust and diminish customer’s risk and increase service productivity are in detail presented. Characteristics of Servitization and Productization as two faces of one coin have been interpreted. Apart from the abovementioned issues state of art, service-oriented architecture (SOA) and New Service Development (NSD) has been included in this report for solving the problem of gradually decline in value of companies.

Kaupallisen sekajätteen mekaaniset käsittelyprosessit ja laitos investoinnin kannattavuus

Työn tavoitteena oli tutkia mekaanisia käsittelylaitteita ja -prosesseja kaupalliselle sekajätteelle ja selvittää mahdollisen laitoshankkeen kannattavuutta case-yritykselle. Jätehuollon yritykset ovat jatkuvan muutoksen alla kasvavien keräys- ja käsittelykustannusten takia, joka vaatii säästöjen etsimistä. Sekajäte sisältää arvokkaita kierrätysraaka-aineita ja näiden erottelu voisi luoda lisäarvoa alentuneina hävityskustannuksina ja lisääntyneinä myyntituottoina. Työssä selvitettiin kaupallisen sekajätteen koostumusta lajittelukokeen ja muiden sekajätetutkimusten avulla. Mekaanisia käsittelylaitteita tutkittiin kirjallisuuden ja case-esimerkkien kautta. Laitoshakkeen kannattavuutta arvioitiin taulukkolaskentamallin avulla. Laitosvaihtoehtoja tarkasteltiin 10-30 tuhannen tonnin kapasiteetin välillä. Laskelmien ja kirjallisuustutkimuksen pohjalta kannattavimpana vaihtoehtona nähtiin SRF kierrätyspolttoainetta valmistava laitos. Kirjallisuustutkimuksen ja case-laitosten pohjalta luotiin kaksi investointiskenaariota, joille laskettiin taulukkolaskentamallin avulla yksikkökustannukset, nettonykyarvot ja sisäiset korot. Kustannusaineisto oli peräisin case-yritykseltä ja muista laitostutkimuksista. Kannattavuuslaskelmien mukaan skenaario 2, jossa SRF-tuotannon lisäksi eroteltaisiin sekalaisia muoveja, on kannattavampi. Skenaarioiden 1 ja 2 kriittiset pisteet olivat noin 15,3 ja 13,6 tuhatta tonnia vuodessa. Kumpikaan skenaarioista ei kuitenkaan ole kannattava case-yrityksen omilla vuotuisilla kuormilla (10 000 tonnia). Lisää käsiteltävää jätettä tulisi hankkia ulkopuolisilta yrityksiltä taloudellisesti edullisen vaakamaksun avulla. Skenaarion 2 ongelmaksi kuitenkin muodostuu sekalaisten muovien poistuminen SRF:n komponenttina, mikä vaikuttaa SRF:n markkinoitavuuteen tehollisen lämpöarvon alenemisen takia.

Secular Possession: Cinematic Iconography of Addiction

Addiction, and the experience of being addicted, is notoriously difficult to describe verbally and explain rationally. Would multifaceted and multisensory cinematic images work better in making addiction understandable? This study enquires how cinematic expression can render visible the experience of being addicted which is invisible as such. The basic data consists of circa 50 mainly North American and European fiction films from the early 1900s to the early 2000s that deal with addictive disorders as defined in the psychiatric DSM-V classification (substance dependence- and gambling disorders). The study develops an approach for analyzing and interpreting a large volume of digital film data: digital cinematic iconography is a framework to study the multifaceted cinematic images by processing and viewing them in the “digital image-laboratory” of the computer. Images are cut and classified by editing software and algorithmic sorting. The approach draws on early 1900s German art historian Aby Waburg’s image research and media archaeology, that are connected to film studies inspired by the phenomenology of the body and Gilles Deleuze’s film-philosophy. The first main chapter, “Montage”, analyses montage, gestural and postural images, and colors in addiction films. The second main chapter, “Thingness”, focuses on the close-ups of material objects and faces, and their relation to the theme of spirituality in cinema and art history, The study argues that the cinema engages the spectator to "feel" what addiction is through everyday experience and art historical imagery. There is a particular, historically transmitted cinematic iconography of addiction that is profane, material, thing-centered, abject, and repetitive. The experience of being addicted is visualized through montages of images characterized by dark and earthy colors, horizontal compositions and downward- directed movements. This is very profane and secular imagery that, however, circulates image-historical traces of Christian iconography, such as that of being in the grip of an unknown power.