“Development work thesis” as a tool for continuing professional education

Julkaisumaa: 158 TW TWN Taiwan

Diffusion Tensor Imaging as a Diagnostic and Research Tool: A Study on Preterm Infants

Diffusion tensor imaging (DTI) is an advanced magnetic resonance imaging (MRI) technique. DTI is based on free thermal motion (diffusion) of water molecules. The properties of diffusion can be represented using parameters such as fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity, which are calculated from DTI data. These parameters can be used to study the microstructure in fibrous structure such as brain white matter. The aim of this study was to investigate the reproducibility of region-of-interest (ROI) analysis and determine associations between white matter integrity and antenatal and early postnatal growth at term age using DTI. Antenatal growth was studied using both the ROI and tract-based spatial statistics (TBSS) method and postnatal growth using only the TBSS method. The infants included to this study were born below 32 gestational weeks or birth weight less than 1,501 g and imaged with a 1.5 T MRI system at term age. Total number of 132 infants met the inclusion criteria between June 2004 and December 2006. Due to exclusion criteria, a total of 76 preterm infants (ROI) and 36 preterm infants (TBSS) were accepted to this study. The ROI analysis was quite reproducible at term age. Reproducibility varied between white matter structures and diffusion parameters. Normal antenatal growth was positively associated with white matter maturation at term age. The ROI analysis showed associations only in the corpus callosum. Whereas, TBSS revealed associations in several brain white matter areas. Infants with normal antenatal growth showed more mature white matter compared to small for gestational age infants. The gestational age at birth had no significant association with white matter maturation at term age. It was observed that good early postnatal growth associated negatively with white matter maturation at term age. Growth-restricted infants seemed to have delayed brain maturation that was not fully compensated at term, despite catchup growth.

Adsorptiojäähdyttimen käytön kannattavuus kaukolämpöjärjestelmässä

Vantaa Energy has decided to find out the district cooling business opportunities in Vantaa. One reason for starting up the cooling business is Vantaa Energy's waste-to-energy power plant which is under construction. In the future, especially in the summer time there is an oversupply of district heating because of the new power plant. The cooling using the district heat could be one way to increase the consumption of district heat in the summer. This thesis examines the use of adsorption cooling profitability. Adsorption refrigerator is a machine which uses heat as the driving energy. At Vantaa Energy's case, district heat produced at cogeneration plants would be used. The literature section of this thesis includes descriptions of district cooling, building cooling demand, as well as different ways to produce cooling energy. A tool for profitability calculations was made. It shows the payback period, internal rate of return and net present value of different projects. Based on the calculations adsorption refrigeration is not profitable. This is primarily due to the high price of the adsorption refrigerator. Payback periods become long even when the used heat energy is free. In addition, the lack of availability of the refrigerators and operating experience could become a partial barrier to the use of technology even if the investment would become profitable.

Perspectives for using light quality knowledge as an advanced ecophysiological weed management tool

The current knowledge of light quality effects on plant morphogenesis and development represents a new era of understanding on how plant communities perceive and adjust to available resources. The most important consequences of light quality cues, often mediated by decreasing in red far-red ratios with respect to the spectral composition of incident sunlight radiation, affecting weed-crop interaction are the increased plant height and shoot to root ratio in anticipation of competition by light quantity, water or nutrients. Although the concepts related to light quality have been extensively studied and several basic process of this phenomenon are well known, little applications of photomorphogenic signaling currently are related to agricultural problems or weed management. The objectives of this review are to describe how light quality change can be a triggering factor of interspecific interference responses, to analyze how this phenomenon can be used to predict weed interference, to reevaluate the critical periods of interference concept, and to discuss its potential contribution towards developing more weed competitive crop varieties. Knowledge on light quality responses involved in plant sensing of interspecific competition could be used to identify red/far-red threshold values, indicating when weed control should be started. Light quality alterations by weeds can affect grain crop development mainly in high yielding fields. Unlike the traditional concept or the critical period of competition, light quality mediated interference implies that the critical period for weed control could start before the effects of direct resource (water, nutrients and available light) limitation actually occur. The variability in light quality responses among crop genotypes and the identification of mutants insensitive to light quality effects indicate that this characteristic can be selected or modified to develop cultivars with enhanced interspecific interference ability. Knowledge on light quality-elicited responses represents a new possibility to understand the underlying biology of interspecific interference, and could be used in the development of new weed management technologies.

Reflectance indices as a diagnostic tool for weed control performed by multipurpose equipment in precision agriculture

Several tools of precision agriculture have been developed for specific uses. However, this specificity may hinder the implementation of precision agriculture due to an increasing in costs and operational complexity. The use of vegetation index sensors which are traditionally developed for crop fertilization, for site-specific weed management can provide multiple utilizations of these sensors and result in the optimization of precision agriculture. The aim of this study was to evaluate the relationship between reflectance indices of weeds obtained by the GreenSeekerTM sensor and conventional parameters used for weed interference quantification. Two experiments were conducted with soybean and corn by establishing a gradient of weed interference through the use of pre- and post-emergence herbicides. The weed quantification was evaluated by the normalized difference vegetation index (NDVI) and the ratio of red to near infrared (Red/NIR) obtained using the GreenSeekerTM sensor, the visual weed control, the weed dry matter, and digital photographs, which supplied information about the leaf area coverage proportions of weed and straw. The weed leaf coverage obtained using digital photography was highly associated with the NDVI (r = 0.78) and the Red/NIR (r = -0.74). The weed dry matter also positively correlated with the NDVI obtained in 1 m linear (r = 0.66). The results indicated that the GreenSeekerTM sensor originally used for crop fertilization could also be used to obtain reflectance indices in the area between rows of crops to support decision-making programs for weed control.

Pintamagneettikoneen magneetin asennustavan ja -työkalun kehittäminen

Työn tavoitteena oli kehitellä uusia ratkaisuita pintamagneettikoneen magneetin asennustapaan ja -työkaluun generaattoreita valmistavalle The Switch Drive Systems:lle. Asiaa lähdettiin lähestymään tekemällä alussa töitä magneetin asennustehtävissä. Tämän jälkeen aloitettiin suunnitteluprosessi, jossa sovellettiin järjestelmällistä koneensuunnittelua sekä konseptisuunnittelua. Työn tulokseksi saatiin useita eri periaatteilla toimivia magneetinasennustyökaluideoita, joiden avulla voidaan tulevaisuudessa siirtyä jatkosuunnitteluun ja työkalun valmistukseen.

OCR Correction Tool for Linguistic Corpora

We introduce a new tool for correcting OCR errors of materials in a repository of cultural materials. The poster is aimed to all who are interested in digital humanities and who might find our tool useful. The poster will focus on the OCR correction tool and on the background processes. We have started a project on materials published in Finno-Ugric languages in the Soviet Union in the 1920s and 1930s. The materials are digitised in Russia. As they arrive, we publish them in DSpace (fennougrica.kansalliskirjasto.fi). For research purposes, the results of the OCR must be corrected manually. For this we have built a new tool. Although similar tools exist, we found in-house development necessary in order to serve the researchers' needs. The tool enables exporting the corrected text as required by the researchers. It makes it possible to distribute the correction tasks and their supervision. After a supervisor has approved a text as finalised, the new version of the work will replace the old one in DSpace. The project has - benefitted the small language communities, - opened channels for cooperation in Russia. - increased our capabilities in digital humanities. The OCR correction tool will be available to others.

Design and validation of stateful composite RESTful web services

A web service is a software system that provides a machine-processable interface to the other machines over the network using different Internet protocols. They are being increasingly used in the industry in order to automate different tasks and offer services to a wider audience. The REST architectural style aims at producing scalable and extensible web services using technologies that play well with the existing tools and infrastructure of the web. It provides a uniform set of operation that can be used to invoke a CRUD interface (create, retrieve, update and delete) of a web service. The stateless behavior of the service interface requires that every request to a resource is independent of the previous ones facilitating scalability. Automated systems, e.g., hotel reservation systems, provide advanced scenarios for stateful services that require a certain sequence of requests that must be followed in order to fulfill the service goals. Designing and developing such services for advanced scenarios with REST constraints require rigorous approaches that are capable of creating web services that can be trusted for their behavior. Systems that can be trusted for their behavior can be termed as dependable systems. This thesis presents an integrated design, analysis and validation approach that facilitates the service developer to create dependable and stateful REST web services. The main contribution of this thesis is that we provide a novel model-driven methodology to design behavioral REST web service interfaces and their compositions. The behavioral interfaces provide information on what methods can be invoked on a service and the pre- and post-conditions of these methods. The methodology uses Unified Modeling Language (UML), as the modeling language, which has a wide user base and has mature tools that are continuously evolving. We have used UML class diagram and UML state machine diagram with additional design constraints to provide resource and behavioral models, respectively, for designing REST web service interfaces. These service design models serve as a specification document and the information presented in them have manifold applications. The service design models also contain information about the time and domain requirements of the service that can help in requirement traceability which is an important part of our approach. Requirement traceability helps in capturing faults in the design models and other elements of software development environment by tracing back and forth the unfulfilled requirements of the service. The information about service actors is also included in the design models which is required for authenticating the service requests by authorized actors since not all types of users have access to all the resources. In addition, following our design approach, the service developer can ensure that the designed web service interfaces will be REST compliant. The second contribution of this thesis is consistency analysis of the behavioral REST interfaces. To overcome the inconsistency problem and design errors in our service models, we have used semantic technologies. The REST interfaces are represented in web ontology language, OWL2, that can be part of the semantic web. These interfaces are used with OWL 2 reasoners to check unsatisfiable concepts which result in implementations that fail. This work is fully automated thanks to the implemented translation tool and the existing OWL 2 reasoners. The third contribution of this thesis is the verification and validation of REST web services. We have used model checking techniques with UPPAAL model checker for this purpose. The timed automata of UML based service design models are generated with our transformation tool that are verified for their basic characteristics like deadlock freedom, liveness, reachability and safety. The implementation of a web service is tested using a black-box testing approach. Test cases are generated from the UPPAAL timed automata and using the online testing tool, UPPAAL TRON, the service implementation is validated at runtime against its specifications. Requirement traceability is also addressed in our validation approach with which we can see what service goals are met and trace back the unfulfilled service goals to detect the faults in the design models. A final contribution of the thesis is an implementation of behavioral REST interfaces and service monitors from the service design models. The partial code generation tool creates code skeletons of REST web services with method pre and post-conditions. The preconditions of methods constrain the user to invoke the stateful REST service under the right conditions and the post condition constraint the service developer to implement the right functionality. The details of the methods can be manually inserted by the developer as required. We do not target complete automation because we focus only on the interface aspects of the web service. The applicability of the approach is demonstrated with a pedagogical example of a hotel room booking service and a relatively complex worked example of holiday booking service taken from the industrial context. The former example presents a simple explanation of the approach and the later worked example shows how stateful and timed web services offering complex scenarios and involving other web services can be constructed using our approach.

Glyphosate as a tool to produce shikimic acid in plants

Oseltamivir phosphate is a potent viral inhibitor produced from shikimic acid extracted from seeds of Ilicium verum, the most important natural source. With the site of action 5-enolpyruvylshikimate-3-phosphate synthase (EPSP), glyphosate is the only compound capable of inhibiting its activity with the consequent accumulation of shikimic acid in plants. Corn and soybean plants were sprayed with reduced rates of glyphosate (0.0 to 230.4 g a.i. ha¹) and shikimic acid content in the dry mass was determined by HPLC 3, 7 and 10 days after application. Results showed shikimic acid accumulation in dry mass with increases of up to 969% in corn and 33,000% on soybeans, with peak concentrations 3 days after treatment (DAT). Industrial feasibility for shikimic acid production, combined with favorable climatic conditions for growing corn and soybean in virtually all over Brazil, favor the use of reduced rates of glyphosate in shikimic acid biosynthesis, with potential for use as an inducer in exploration of alternative sources for production of oseltamivir phosphate with low environmental impact.

Making the impact on research and society : a case study: crowdsourcing solutions developed for the linguistic research and citizen science

Can crowdsourcing solutions serve many masters? Can they be beneficial for both, for the layman or native speakers of minority languages on the one hand and serious linguistic research on the other? How did an infrastructure that was designed to support linguistics turn out to be a solution for raising awareness of native languages? Since 2012 the National Library of Finland has been developing the Digitisation Project for Kindred Languages, in which the key objective is to support a culture of openness and interaction in linguistic research, but also to promote crowdsourcing as a tool for participation of the language community in research. In the course of the project, over 1,200 monographs and nearly 111,000 pages of newspapers in Finno-Ugric languages will be digitised and made available in the Fenno-Ugrica digital collection. This material was published in the Soviet Union in the 1920s and 1930s, and users have had only sporadic access to the material. The publication of open-access and searchable materials from this period is a goldmine for researchers. Historians, social scientists and laymen with an interest in specific local publications can now find text materials pertinent to their studies. The linguistically-oriented population can also find writings to delight them: (1) lexical items specific to a given publication, and (2) orthographically-documented specifics of phonetics. In addition to the open access collection, we developed an open source code OCR editor that enables the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary since these rare and peripheral prints often include already archaic characters, which are neglected by modern OCR software developers but belong to the historical context of kindred languages, and are thus an essential part of the linguistic heritage. When modelling the OCR editor, it was essential to consider both the needs of researchers and the capabilities of lay citizens, and to have them participate in the planning and execution of the project from the very beginning. By implementing the feedback iteratively from both groups, it was possible to transform the requested changes as tools for research that not only supported the work of linguistics but also encouraged the citizen scientists to face the challenge and work with the crowdsourcing tools for the benefit of research. This presentation will not only deal with the technical aspects, developments and achievements of the infrastructure but will highlight the way in which user groups, researchers and lay citizens were engaged in a process as an active and communicative group of users and how their contributions were made to mutual benefit.

Interoperability specifications and an automatic validation tool as a key factor for the support of a repository ecosystem

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

OCR Correction Tool for Linguistic Corpora

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

HIMALDOC: A Tool for a Regional Open Repository on Sustainable Mountain Development Issues in the Hindu Kush Himalaya

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

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

The Pay-Off Method as a Tool for Evaluating the Risk and Profitability of Public Real Estate Investments

Real option valuation, in particular the fuzzy pay-off method, has proven to be useful in defining risk and visualizing imprecision of investments in various industry applications. This study examines whether the evaluation of risk and profitability for public real estate investments can be improved by using real option methodology. Firstly, the context of real option valuation in the real estate industry is examined. Further, an empirical case study is performed on 30 real estate investments of a Finnish government enterprise in order to determine whether the presently used investment analysis system can be complemented by the pay-off method. Despite challenges in the application of the pay-off method to the case company’s large investment base, real option valuation is found to create additional value and facilitate more robust risk analysis in public real estate applications.