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,

Developing purchase invoice processing through workflow automation

The aim of this master’s thesis is to research and analyze how purchase invoice processing can be automated and streamlined in a system renewal project. The impacts of workflow automation on invoice handling are studied by means of time, cost and quality aspects. Purchase invoice processing has a lot of potential for automation because of its labor-intensive and repetitive nature. As a case study combining both qualitative and quantitative methods, the topic is approached from a business process management point of view. The current process was first explored through interviews and workshop meetings to create a holistic understanding of the process at hand. Requirements for process streamlining were then researched focusing on specified vendors and their purchase invoices, which helped to identify the critical factors for successful invoice automation. To optimize the flow from invoice receipt to approval for payment, the invoice receiving process was outsourced and the automation functionalities of the new system utilized in invoice handling. The quality of invoice data and the need of simple structured purchase order (PO) invoices were emphasized in the system testing phase. Hence, consolidated invoices containing references to multiple PO or blanket release numbers should be simplified in order to use automated PO matching. With non-PO invoices, it is important to receive the buyer reference details in an applicable invoice data field so that automation rules could be created to route invoices to a review and approval flow. In the beginning of the project, invoice processing was seen ineffective both time- and cost-wise, and it required a lot of manual labor to carry out all tasks. In accordance with testing results, it was estimated that over half of the invoices could be automated within a year after system implementation. Processing times could be reduced remarkably, which would then result savings up to 40 % in annual processing costs. Due to several advancements in the purchase invoice process, business process quality could also be perceived as improved.

Improving productivity by developing knowledge management practices for a consulting company

The objective of the research was to identify knowledge conversion states in consultancy sales and delivery processes for the company’s one business unit, to know where to store certain types of information and knowledge, and to create best practices for the company’s knowledge management activities in the selected business processes. The used research methodology was action research. The current business processes were analyzed by interviewing people involved in them. The results were documented and catego- rized, and based on them the target states of the processes were developed. Knowledge man- agement activities were integrated to the business processes. The main findings of the research were that roles and responsibilities in the processes were not clear to people, information systems did not fully support individuals and time was wasted searching for information and knowledge. There were also many variations of how the processes actually realized, which affected the overall quality of the process. The conclusions of the research were that knowledge management activities should be high- lighted in businesses where knowledge workers are the main assets of the company. Knowledge management practices can be supported by company culture, leadership and in- formation systems. However, one main factor is each individual’s willingness to share knowledge. By integrating knowledge management activities to business processes and hav- ing information systems supporting knowledge management, individual productivity can be improved.

Developing asset management in district heating and cooling business in a large energy company

The purpose of this Master´s Thesis is to develop asset management and its practices in case company. District heating and cooling systems operated by case company around Finland, Sweden, Poland and the Baltics form an enormous-sized asset base where some parts are starting to reach their end of life-cycles. Large-sized asset renewal actions are under discussion and maintenance spending is increasing. Financially justified decisions in changing business environment are needed. Asset management is one of the most important concepts for production organization which operates with capital-intensive production assets. Organizations profitability is highly dependent on assets´ performance. Such assets, like district heating and cooling systems, should be utilized as efficiently as possible within their life-cycles but also maintained and renewed optimally. In this qualitative thesis, empirical interview study was conducted to describe the current situation on how the assets are managed in the case company and to examine the readiness to implement a new, risk-based solution. Asset management revealed to be a very well-known concept. From proposed risk-based asset management point of view, several key observations were made. It was seen as a suitable solution, but further development will be needed. Based on the need and findings, several key processes and frameworks were created and also tested with a case study. Assets` condition monitoring should be improved, which would have a positive impact on event probability assessment. Risk acceptance is also a thing to be discussed further. When the evaluation becomes fluent in single investment cases, portfolio-level expansion should be considered and started. As a result, thesis proposes a solution how risk-based asset management could be performed practically in a capital-intensive case company in order to optimize the maintenance spending in a long run. Created practical framework is made universal: similar principles can be applied into multiple cases in case company but also in other energy companies. Risk-based asset management`s benefits could be utilized best in portfolio-level optimization where the capital would be invested to the most important objects from total risk point of view. Eventually, such approach would allow case company to optimize capital spending in a situation where funds are not adequate to cover all the mandatory needs and prioritization between the investment alternatives will truly be needed.

In search of good relationships to music : understanding aspiration and challenge in developing music school teacher practices

This study focuses on teacher practices in publicly funded music schools in Finland. As views on the aims of music education change and broaden, music schools across Europe share the challenge of developing their activities in response. In public and scholarly debate, there have been calls for increased diversity of contents and concepts of teaching. In Finland, the official national curriculum for state-funded music schools builds on the ideal that teaching and learning should create conditions which promote ‘a good relationship to music’. The meaning of this concept has been deliberately left open in order to leave room for dialogue, flexibility, and teacher autonomy. Since what is meant by ‘good’ is not defined in advance, the notion of ‘improving’ practices is also open to discussion. The purpose of the study is to examine these issues from teachers’ point of view by asking what music school teachers aim to accomplish as they develop their practices. Methodologically, the study introduces a suggestion for building empirical research on Alperson’s ‘robust’ praxial approach to music education, a philosophical theory which is strongly committed to practitioner perspectives and musical diversity. A systematic method for analysing music education practices, interpretive practice analysis, is elaborated with support from interpretive research methods originally used in policy analysis. In addition, the research design shows how reflecting conversations (a collaborative approach well-known in Nordic social work) can be fruitfully applied in interpretive research and combined with teacher inquiry. Data have been generated in a collaborative project involving five experienced music school teachers and the researcher. The empirical material includes transcripts from group conversations, data from teacher inquiry conducted within the project, and transcripts from follow-up interviews. The teachers’ aspirations can be understood as strivings to reinforce the connection between musical practices and various forms of human flourishing such that music and flourishing can sustain each other. Examples from their practices show how the word ‘good’ receives its meaning in context. Central among the teachers’ concerns is their hope that students develop a free and sustainable interest in music, often described as inspiration. I propose that ‘good relationships to music’ and ‘inspiration’ can be understood as philosophical mediators which support the transition from an indeterminate ‘interest in music’ towards specific ways in which music can become a (co-)constitutive part of living well in each person’s particular circumstances. Different musical practices emphasise different aspects of what is considered important in music and in human life. Music school teachers consciously balance between a variety of such values. They also make efforts to resist pressure which might threaten the goods they think are most important. Such goods include joy, participation, perseverance, solid musical skills related to specific practices, and a strong sense of vitality. The insights from this study suggest that when teachers are able to create inspiration, they seem to do so by performing complex work which combines musical and educational aims and makes general positive contributions to their students’ lives. Ensuring that teaching and learning in music schools remain as constructive and meaningful as possible for both students and teachers is a demanding task. The study indicates that collaborative, reflective and interdisciplinary work may be helpful as support for development processes on both individual and collective levels of music school teacher practices.

Developing Supply Chain Process Management and Measurement in Global Manufacturing Company

The objective of this research is to create a current state analysis of pulp supply chain processes from production planning to deliveries to customers. A cross-functional flowchart is being used to model these processes. These models help finding key performance indicators (KPIs) which enable examinations of the supply chain efficiency. Supply chain measures in different processes reveal the changes need processes that affect the whole supply chain and its efficiency and competitiveness. Structure of pulp supply chain differs from most of the other supply chains. The fact that there are big volumes of bulk products, small product variations and supply forecasts are made for the year ahead make the difference. This factor brings different benefits but also challenges when developing supply chain. This thesis divides pulp supply chain in three different main categories: production planning, warehousing and transportation. It provides tools for estimating the functionality of supply chain as well as developing the efficiency for different functions of supply chain. By having a better understanding of supply chain processes and measurement the whole supply chain structure can be developed significantly.

Data and Inventory Management in Spare Part Business: Developing Operations in the Case Company

After sales business is an effective way to create profit and increase customer satisfaction in manufacturing companies. Despite this, some special business characteristics that are linked to these functions, make it exceptionally challenging in its own way. This Master’s Thesis examines the current situation of the data and inventory management in the case company regarding possibilities and challenges related to the consolidation of current business operations. The research examines process steps, procedures, data requirements, data mining practices and data storage management of spare part sales process, whereas the part focusing on inventory management is reviewing the current stock value and examining current practices and operational principles. There are two global after sales units which supply spare parts and issues reviewed in this study are examined from both units’ perspective. The analysis is focused on the operations of that unit where functions would be centralized by default, if change decisions are carried out. It was discovered that both data and inventory management include clear shortcomings, which result from lack of internal instructions and established processes as well as lack of cooperation with other stakeholders related to product’s lifecycle. The main product of data management was a guideline for consolidating the functions, tailored for the company’s needs. Additionally, potentially scrapped spare part were listed and a proposal of inventory management instructions was drafted. If the suggested spare part materials will be scrapped, stock value will decrease 46 percent. A guideline which was reviewed and commented in this thesis was chosen as the basis of the inventory management instructions.

Developing and nurturing professional learning communities: principles used by elementary administrators /

This study examined the strategies used by elementary school principals to facilitate and nurture the development of professional learning communities (PLC) within their school settings. Using a reputational sample of administrators whose schools were demonstrating observable characteristics of PLCs, this study documented and described the strategies and actions taken by the principals to move their schools forward. Data collection included the use of open-ended interviews as well as observations capturing the means by which the principals addressed the areas of culture, processes, and structures within their school setting. A grounded theory approach to data analysis uncovered 4 guiding principles used by the principals to facilitate the development of the PLCs within their school: (a) protecting the purpose; (b) attending to relationships; (c) sharing the responsibility; and (d) valuing the journey. The guiding principles were used by each administrator to anchor the decisions they made and develop responsive, contextspecific strategies to support the PLC at their school. The results highlighted the complex role of the principal and the supports required to tackle the difficult work of facilitating PLCs.

Computationally Efficient Bootstrap Prediction Intervals for Returns and Volatilities in ARCH and GARCH Processes

We propose a novel, simple, efficient and distribution-free re-sampling technique for developing prediction intervals for returns and volatilities following ARCH/GARCH models. In particular, our key idea is to employ a Box–Jenkins linear representation of an ARCH/GARCH equation and then to adapt a sieve bootstrap procedure to the nonlinear GARCH framework. Our simulation studies indicate that the new re-sampling method provides sharp and well calibrated prediction intervals for both returns and volatilities while reducing computational costs by up to 100 times, compared to other available re-sampling techniques for ARCH/GARCH models. The proposed procedure is illustrated by an application to Yen/U.S. dollar daily exchange rate data.

Aprender investigando. Una experiencia formativa en el ámbito de la enfermería = Research teaching processes used as a methodological strategy in the education of healthcare professionals

Este trabajo tiene como propósito presentar y valorar, desde la perspectiva del alumnado participante, un proyecto de investigación-formación puesto en marcha durante el curso 2003-2004 en la elaboración del trabajo de tesina, fin de carrera, en la Escuela de Enfermería de Vitoria, dentro del programa de Licenciatura Europea de Enfermería. Constituye el punto de partida de un proyecto a largo plazo, iniciado con la intención de desarrollar principios teóricos y procedimientos prácticos que nos permitan sistematizar procesos formativos que, centrados en la investigación, articulen la teoría y la práctica e integren una perspectiva comunicativa y cooperativa

Developing a desertification indicator system for a small Mediterranean catchment: a case study from the Serra de Rodes, Alt Empordà, Catalunya, NE Spain

La desertificació és un problema de degradació de sòls de gran importància en regions àrides, semi-àrides i sub-humides, amb serioses conseqüències ambientals, socials i econòmiques com a resultat de l'impacte d'activitats humanes en combinació amb condicions físiques i medi ambientals desfavorables (UNEP, 1994). L'objectiu principal d'aquesta tesi va ser el desenvolupament d'una metodologia simple per tal de poder avaluar de forma precisa l'estat i l'evolució de la desertificació a escala local, a través de la creació d'un model anomenat sistema d'indicators de desertificació (DIS). En aquest mateix context, un dels dos objectius específics d'aquesta recerca es va centrar en l'estudi dels factors més importants de degradació de sòls a escala de parcel.la, comportant un extens treball de camp, analisi de laboratori i la corresponent interpretació i discussió dels resultats obtinguts. El segon objectiu específic es va basar en el desenvolupament i aplicació del DIS. L'àrea d'estudi seleccionada va ser la conca de la Serra de Rodes, un ambient típic Mediterràni inclòs en el Parc Natural del Cap de Creus, NE Espanya, el qual ha estat progressivament abandonat pels agricultors durant el segle passat. Actualment, els incendis forestals així com el canvi d'ús del sòl i especialment l'abandonament de terres són considerats els problemes ambientals més importants a l'àrea d'estudi (Dunjó et al., 2003). En primer lloc, es va realitzar l'estudi dels processos i causes de la degradació dels sòls a l'àrea d'interés. En base a aquest coneixement, es va dur a terme la identificació i selecció dels indicadors de desertificació més rellevants. Finalment, els indicadors de desertificació seleccionats a escala de conca, incloent l'erosió del sòl i l'escolament superficial, es van integrar en un model espaial de procés. Ja que el sòl és considerat el principal indicador dels processos d'erosió, segons la FAO/UNEP/UNESCO (1979), tant el paisatge original així com els dos escenaris d'ús del sòl desenvolupats, un centrat en el cas hipotétic del pas d'un incendi forestal, i l'altre un paisatge completament cultivat, poden ser ambients classificats sota baixa o moderada degradació. En comparació amb l'escenari original, els dos escenaris creats van revelar uns valors més elevats d'erosió i escolament superficial, i en particular l'escenari cultivat. Per tant, aquests dos hipotètic escenaris no semblen ser una alternativa sostenible vàlida als processos de degradació que es donen a l'àrea d'estudi. No obstant, un ampli ventall d'escenaris alternatius poden ser desenvolupats amb el DIS, tinguent en compte les polítiques d'especial interés per la regió de manera que puguin contribuir a determinar les conseqüències potencials de desertificació derivades d'aquestes polítiques aplicades en aquest escenari tan complexe espaialment. En conclusió, el model desenvolupat sembla ser un sistema força acurat per la identificació de riscs presents i futurs, així com per programar efectivament mesures per combatre la desertificació a escala de conca. No obstant, aquesta primera versió del model presenta varies limitacions i la necessitat de realitzar més recerca en cas de voler desenvolupar una versió futura i millor del DIS.

Developing the next-generation climate system models: challenges and achievements

Although climate models have been improving in accuracy and efficiency over the past few decades, it now seems that these incremental improvements may be slowing. As tera/petascale computing becomes massively parallel, our legacy codes are less suitable, and even with the increased resolution that we are now beginning to use, these models cannot represent the multiscale nature of the climate system. This paper argues that it may be time to reconsider the use of adaptive mesh refinement for weather and climate forecasting in order to achieve good scaling and representation of the wide range of spatial scales in the atmosphere and ocean. Furthermore, the challenge of introducing living organisms and human responses into climate system models is only just beginning to be tackled. We do not yet have a clear framework in which to approach the problem, but it is likely to cover such a huge number of different scales and processes that radically different methods may have to be considered. The challenges of multiscale modelling and petascale computing provide an opportunity to consider a fresh approach to numerical modelling of the climate (or Earth) system, which takes advantage of the computational fluid dynamics developments in other fields and brings new perspectives on how to incorporate Earth system processes. This paper reviews some of the current issues in climate (and, by implication, Earth) system modelling, and asks the question whether a new generation of models is needed to tackle these problems.

Surface wave processes in air-sea interaction

We review briefly recent progress on understanding the role of surface waves on the marine atmospheric boundary layer and the ocean mixed layer and give a global perspective on these processes by analysing ERA-40 data. Ocean surface waves interact with the marine atmospheric boundary layer in two broad regimes: (i) the conventional wind-driven wave regime, when fast winds blow over slower moving waves, and (ii) a wave-driven wind regime when long wavelength swell propagates under low winds, and generates a wave-driven jet in the lower part of the marine boundary layer. Analysis of ERA-40 data indicates that the wave-driven wind regime is as prevalent as the conventional wind-driven regime. Ocean surface waves also change profoundly mixing in the ocean mixed layer through generation of Langmuir circulation. Results from large-eddy simulation are used here to develop a scaling for the resulting Langmuir turbulence, which is a necessary step in developing a parametrization of the process. ERA-40 data is then used to show that the Langmuir regime is the predominant regime over much of the global ocean, providing a compelling motivation for parameterising this process in ocean general circulation models.

Increased apoptosis in first trimester extravillous trophoblasts from pregnancies at higher risk of developing preeclampsia

Preeclampsia complicates 5 to 10% of pregnancies and is a leading cause of maternal and fetal mortality and morbidity. Although the cause is unknown, inadequate invasion and remodeling of maternal uterine arteries by extravillous trophoblasts (EVTs) in the first trimester is a common feature. Uterine spiral artery resistance as detected by Doppler ultrasound is commonly used in the second trimester to identify pregnancies destined to develop preeclampsia. Correlation between high uterine resistance and the failure of trophoblast invasion has been reported as early as 12 weeks. However, the reason for this failure has not been established. Understanding the processes involved would significantly improve our diagnostic potential. In this study, we correlated increased first trimester uterine artery resistance with a biological abnormality in trophoblast function. EVTs derived from high-resistance pregnancies were more sensitive to apoptotic stimuli than those from normal-resistance pregnancies. Survival of EVTs from high-resistance pregnancies could be increased by nitric oxide, whereas inhibition of nitric oxide in cells from normal-resistance pregnancies increased apoptotic sensitivity. This predates the onset of symptoms by several weeks and provides evidence for a mechanism responsible for the incomplete uterine vessel remodeling and the differences in artery resistance between preeclamptic and normal pregnancies.

Student-teachers' perspectives on positive and negative social processes in schools

In recent years, the Standards for Qualified Teacher Status in England have placed new emphasis on student-teachers' ability to become integrated into the 'corporate life of the school' and to work with other professionals. Little research, however, has been carried out into how student-teachers perceive the social processes and interactions that are central to such integration during their initial teacher education school placements. This study aims to shed light on these perceptions. The data, gathered from 23 student-teachers through interviews and reflective writing, illustrate the extent to which the participants perceived such social processes as supporting or obstructing their development as teachers. Signals of inclusion, the degree of match or mismatch in students' and school colleagues' role expectations, and the social awareness of both school and student-teacher emerged as crucial factors in this respect. The student-teachers' accounts show their social interactions with school staff to be meaningful in developing their 'teacher self' and to be profoundly emotionally charged. The implications for mentor and student-teacher role preparation are discussed in this article.