Practical preservation with Arkivum & Eprints

Presentation 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.

Entrepreneurship Education in Basic and Upper Secondary Education – Measurement and Empirical Evidence

The starting point of this study is to direct more attention to the teacher and those entrepreneurship education practices taking place in formal school to find out solutions for more effective promotion of entrepreneurship education. For this objective, the strategy-level aims of entrepreneurship education need to be operationalised into measurable and understandable teacher-level practices. Furthermore, to enable the effective development of entrepreneurship education in basic and upper secondary level education, more knowledge is needed of the state of affairs of entrepreneurship education in teaching. The purpose of the study is to increase the level of understanding of teachers’ entrepreneurship education practices, and through this to develop entrepreneurship education. This study builds on the literature on entrepreneurship education and especially those elements referring to the aims, resources, benefits, methods, and practises of entrepreneurship education. The study comprises five articles highlighting teachers’ role in entrepreneurship education. In the first article the concept of entrepreneurship and the teachers role in reflection upon his/hers approaches to entrepreneurship education are considered. The second article provides a detailed analysis of the process of developing a measurement tool to depict the teachers’ activities in entrepreneurship education. The next three articles highlight the teachers’ role in directing the entrepreneurship education in basic and upper secondary level education. Furthermore, they analyse the relationship between the entrepreneurship education practises and the teachers’ background characteristics. The results of the study suggest a wide range of conclusions and implications. First, in spite of many outspoken aims connected to entrepreneurship education, teachers have not set any aims for themselves. Additionally, aims and results seem to mix. However, it is possible to develop teachers’ target orientation by supporting their reflection skills, and through measurement and evaluation increase their understanding of their own practices. Second, applying a participatory action process it is possible to operationalise teachers’entrepreneurship education practices. It is central to include the practitioners’ perspective in the development of measures to make sure that the concepts and aims of entrepreneurship education are understood. Third, teachers’ demographic or tenure-related background characteristics do not affect their entrepreneurship education practices, but their training related to entrepreneurship education, participation in different school-level or regional planning, and their own capabilities support entrepreneurship education. Fourth, a large number of methods are applied to entrepreneurship education, and the most often used methods were different kinds of discussions, which seem to be an easy, low-threshold way for teachers to include entrepreneurship education regularly in their teaching. Field trips to business enterprises or inviting entrepreneurs to present their work in schools are used fairly seldom. Interestingly, visits outside the school are more common than visitors invited to the school. In line, most of the entrepreneurship education practices take place in a classroom. Therefore it seems to be useful to create and encourage teachers towards more in-depth cooperation with companies (e.g. via joint projects) and to network systematically. Finally, there are plenty of resources available for entrepreneurship education, such as ready-made materials, external stakeholders, support organisations, and learning games, but teachers have utilized them only marginally.

Co-creating value with customers as a new approach of entering new market

Global trends associated with development of information technology, globalization, industrial and economic changes are influencing on company and customer domains and thus transforming company-customer relationship. The company centric paradigm with a strong product focus shifts to a customer oriented one with a strong emphasis on customer collaboration. As a result, the customer role changes from a passive observer to an active player. Moreover, global trends contribute to transformation of competitive environment making it tougher and simplifying an access to resources previously considered as unique. All that factors push the companies towards cooperation with customers in order to identify unarticulated needs and finding the best possible solution to existing customer problems. The Master’s Thesis is done for Outotec (Lappeenranta) which considers extension of dewatering business in Russian coal market. Research aims to identify key features of coal preparation and dewatering of fine coal and tailings in Russian preparation plants; analyze the state of Russian coal market and evaluate market potential for Outotec dewatering solutions. The study has a qualitative nature and implements an action research methodology that involves both creation of knowledge and introduction of changes into the system. The base for taking actions is formed by theoretical framework that targets on describing company - customer interaction and has selected co-creation as the most appropriate method of customer involvement. The integration of co-creation approach into an action research cycle allows not only fulfilling the research objectives but also facilitates organizational learning and intraorganizational collaboration, assists in establishing customer contacts and making the first steps into the market, bringing new joint projects to the company and opening real business opportunities.

Learning information technology business in a changing industry landscape. Introducing Team Entrepreneurship in Renewing Bachelor Education in Renewing Bachelor Education in Information

Speed, uncertainty and complexity are increasing in the business world all the time. When knowledge and skills become quickly irrelevant, new challenges are set for information technology (IT) education. Meta-learning skills – learning how to learn rapidly - and innovation skills have become more essential than single technologies or other specific issues. The drastic changes in the information and communications technology (ICT) sector have caused a need to reconsider how IT Bachelor education in Universities of Applied Sciences should be organized and employed to cope with the change. The objective of the study was to evaluate how a new approach to IT Bachelor education, the ICT entrepreneurship study path (ICT-ESP) fits IT Bachelor education in a Finnish University of Applied Sciences. This kind of educational arrangement has not been employed elsewhere in the context of IT Bachelor education. The study presents the results of a four-year period during which IT Bachelor education was renewed in a Finnish University of Applied Sciences. The learning environment was organized into an ICT-ESP based on Nonaka’s knowledge theory and Kolb’s experiental learning. The IT students who studied in the ICT-ESP established a cooperative and learned ICT by running their cooperative at the University of Applied Sciences. The students (called team entrepreneurs) studied by reading theory in books and other sources of explicit information, doing projects for their customers, and reflecting in training sessions on what was learnt by doing and by studying the literature. Action research was used as the research strategy in this study. Empirical data was collected via theme-based interviews, direct observation, and participative observation. Grounded theory method was utilized in the data analysis and the theoretical sampling was used to guide the data collection. The context of the University of Applied Sciences provided a good basis for fostering team entrepreneurship. However, the results showed that the employment of the ICT-ESP did not fit into the IT Bachelor education well enough. The ICT-ESP was cognitively too tough for the team entrepreneurs because they had two different set of rules to follow in their studies. The conventional courses engaged lot of energy which should have been spent for professional development in the ICT-ESP. The amount of competencies needed in the ICT-ESP for professional development was greater than those needed for any other ways of studying. The team entrepreneurs needed to develop skills in ICT, leadership and self-leadership, team development and entrepreneurship skills. The entrepreneurship skills included skills on marketing and sales, brand development, productization, and business administration. Considering the three-year time the team entrepreneurs spent in the ICT-ESP, the challenges were remarkable. Changes to the organization of IT Bachelor education are also suggested in the study. At first, it should be admitted that the ICT-ESP produces IT Bachelors with a different set of competencies compared to the conventional way of educating IT Bachelors. Secondly, the number of courses on general topics in mathematics, physics, and languages for team entrepreneurs studying in the ICTESP should be reconsidered and the conventional course-based teaching of the topics should be reorganized to support the team coaching process of the team entrepreneurs with their practiceoriented projects. Third, the upcoming team entrepreneurs should be equipped with relevant information about the ICT-ESP and what it would require in practice to study as a team entrepreneur. Finally, the upcoming team entrepreneurs should be carefully selected before they start in the ICT-ESP to have a possibility to eliminate solo players and those who have a too romantic view of being a team entrepreneur. The results gained in the study provided answers to the original research questions and the objectives of the study were met. Even though the IT degree programme was terminated during the research process, the amount of qualitative data gathered made it possible to justify the interpretations done.

Changing teachers´ practices in regular schools enrolling children with visual impairment

The number of persons with visual impairment in Tanzania is estimated to over 1.6 million. About half a million of these persons are children aged 7-13. Only about 1% of these children are enrolled in schools. The special schools and units are too few and in most cases they are far away from the children’s homes. More and more regular schools are enrolling children with visual impairment, but the schools lack financial resources, tactile teaching materials and trained special education teachers. Children with visual impairment enrolled in regular schools seldom get enough support and often fail in examinations. The general aim of this study was to contribute to increased knowledge and understanding about how teachers can change their teaching practices and thus facilitate the learning of children with visual impairment included in regular classrooms as they participate in an action research project. The project was conducted in a primary school in a poor rural region with a high frequency of blindness and visual impairment. The school was poorly resourced and the average number of pupils per class was 90. The teachers who participated in the collaborative action research project were the 14 teachers who taught blind or visually impaired pupils in grades 4 and 6, in total 6 pupils. The action research project was conducted during a period of 6 months and was carried out in five cycles. The teachers were actively involved in all the project activities; identifying challenges, planning solutions, producing teaching materials, reflecting on outcomes, collaborating and evaluating. Empirical data was collected with questionnaires, interviews, observations and focus group discussions. The findings of the study show that the teachers managed to change their teaching practices through systematic reflection, analysis and collaboration. The teachers produced a variety of tactile teaching materials, which facilitated the learning of the pupils with visual impairment. The pupils learned better and felt more included in the regular classes. The teachers gained new knowledge and skills. They grew professionally and started to collaborate with each other. The study contributes to new knowledge of how collaborative action research can be conducted in the area of special education in a Tanzanian school context. The study has also relevance to the planning of school-based professional development programs and teacher education programs in Tanzania and in other low-income countries. The results also point at strategies which can promote inclusion of children with disabilities in regular schools.

Diagnostic investigation of ventilator-associated pneumonia using bronchoalveolar lavage: comparative study with a postmortem lung biopsy

The purpose of the present study was to validate the quantitative culture and cellularity of bronchoalveolar lavage (BAL) for the diagnosis of ventilator-associated pneumonia (VAP). A prospective validation test trial was carried out between 1992 and 1997 in a general adult intensive care unit of a teaching hospital. Thirty-seven patients on mechanical ventilation with suspected VAP who died at most three days after a BAL diagnostic procedure were submitted to a postmortem lung biopsy. BAL effluent was submitted to Gram staining, quantitative culture and cellularity count. Postmortem lung tissue quantitative culture and histopathological findings were considered to be the gold standard exams for VAP diagnosis. According to these criteria, 20 patients (54%) were diagnosed as having VAP and 17 (46%) as not having the condition. Quantitative culture of BAL effluent showed 90% sensitivity (18/20), 94.1% specificity (16/17), 94.7% positive predictive value and 88.8% negative predictive value. Fever and leukocytosis were useless for VAP diagnosis. Gram staining of BAL effluent was negative in 94.1% of the patients without VAP (16/17). Regarding the total cellularity of BAL, a cut-off point of 400,000 cells/ml showed a specificity of 94.1% (16/17), and a cut-off point of 50% of BAL neutrophils showed a sensitivity of 90% (19/20). In conclusion, BAL quantitative culture, Gram staining and cellularity might be useful in the diagnostic investigation of VAP.

Inducing mutations in the mouse genome with the chemical mutagen ethylnitrosourea

When compared to other model organisms whose genome is sequenced, the number of mutations identified in the mouse appears extremely reduced and this situation seriously hampers our understanding of mammalian gene function(s). Another important consequence of this shortage is that a majority of human genetic diseases still await an animal model. To improve the situation, two strategies are currently used: the first makes use of embryonic stem cells, in which one can induce knockout mutations almost at will; the second consists of a genome-wide random chemical mutagenesis, followed by screening for mutant phenotypes and subsequent identification of the genetic alteration(s). Several projects are now in progress making use of one or the other of these strategies. Here, we report an original effort where we mutagenized BALB/c males, with the mutagen ethylnitrosourea. Offspring of these males were screened for dominant mutations and a three-generation breeding protocol was set to recover recessive mutations. Eleven mutations were identified (one dominant and ten recessives). Three of these mutations are new alleles (Otop1mlh, Foxn1sepe and probably rodador) at loci where mutations have already been reported, while 4 are new and original alleles (carc, eqlb, frqz, and Sacc). This result indicates that the mouse genome, as expected, is far from being saturated with mutations. More mutations would certainly be discovered using more sophisticated phenotyping protocols. Seven of the 11 new mutant alleles induced in our experiment have been localized on the genetic map as a first step towards positional cloning.

Developing construction site operations for EPC power plant projects

The purpose of this thesis is to find development areas for site operations in power plant construction projects delivered by Wärtsilä. The inspected operations are subcontractor management, site material management and work scheduling. The contractor's role in EPC project is to respond for engineering, procurement, and construction supervision. Geographical and cultural differences brings challenges for finding development areas as Wärtsilä delivers projects world-wide. Searching for development area is mainly made with survey, which answers were collected from the target company's site personnel. Based on the results, with good planning and preparation various problems would be avoided. An external view for the thesis was collected by an expert interview, which was held to three expe-rienced construction operating executives. Interviewees believed that with the se-lection of right site personnel and clearly defined areas of responsibility will great-ly affect the outcome of the project. Some of the theory has been collected from areas, which have helped to under-stand the inspected operations on site. Improving competence knowledge has been important due to the broad scope of work and the author’s inexperience of the topic. Also generally effective practices from construction projects has been col-lected to the theory part. Functionality of general practices have been reflected together with the results of empirically collected data for Wärtsilä's projects. As a result, a model was generated where development proposals and the benefits from new procedures were presented.

Peritoneal and serum interleukin-18 levels are not increased in women with minimum or mild endometriosis

Interleukin-18 (IL-18) is a cytokine that belongs to the IL-1 family. Endometriosis is strongly associated with sub-fertility, and affects about 15% of women of reproductive age. IL-18 may favor the progression of endometriosis. The objective of the present study was to determine the concentration of IL-18 in the serum and peritoneal fluid of infertile women with endometriosis. Forty infertile and 25 fertile women were screened in a teaching hospital. Thirty-four infertile patients with minimal or mild endometriosis and 22 fertile controls were enrolled in the study. The primary outcome was the estimate of IL-18 levels and the secondary outcome was the correlation between serum and peritoneal levels of IL-18. There were no differences between the two groups regarding age, body mass index and levels of peritoneal fluid IL-18 (mean ± SD): 290.85 ± 173.02 pg/mL for infertile women vs 374.21 ± 330.15 pg/mL for controls; or serum IL-18: 391.07 ± 119.71 pg/mL for infertile women vs 373.42 ± 129.11 pg/mL for controls. However, a positive association was found between serum and peritoneal IL-18 levels in patients with endometriosis: r = 0.794, P = 0.0001. All measurements were carried out at the same time by the Human IL-18 Immuno Assay ELISA kit (MBL Co. Ltd., Japan). The present study did not find evidence supporting the hypothesis that IL-18 levels are associated with infertility in women with minimal and mild endometriosis, although a positive correlation was detected in these women between peritoneal and serum levels of IL-18.

Study of the comprehension of the scientific method by members of a university health research laboratory

In Brazil, scientific research is carried out mainly at universities, where professors coordinate research projects with the active participation of undergraduate and graduate students. However, there is no formal program for the teaching/learning of the scientific method. The objective of the present study was to evaluate the comprehension of the scientific method by students of health sciences who participate in scientific projects in an academic research laboratory. An observational descriptive cross-sectional study was conducted using Edgar Morin complexity as theoretical reference. In a semi-structured interview, students were asked to solve an abstract logical puzzle - TanGram. The collected data were analyzed using the hermeneutic-dialectic analysis method proposed by Minayo and discussed in terms of the theoretical reference of complexity. The students’ concept of the scientific method is limited to participation in projects, stressing the execution of practical procedures as opposed to scientific thinking. The solving of the TanGram puzzle revealed that the students had difficulties in understanding questions and activities focused on subjects and their processes. Objective answers, even when dealing with personal issues, were also reflected on the students’ opinions about the characteristics of a successful researcher. Students’ difficulties concerning these issues may affect their scientific performance and result in poorly designed experiments. This is a preliminary study that should be extended to other centers of scientific research.

Development of Piping Stress Analysis Guideline for Neste Jacobs' Projects

The aim of this research was to develop a piping stress analysis guideline to be widely used in Neste Jacobs Oy’s domestic and foreign projects. The company’s former guideline to performing stress analysis was partial and lacked important features, which were to be fixed through this research. The development of the guideline was based on literature research and gathering of existing knowledge from the experts in piping engineering. Case study method was utilized by performing stress analysis on an existing project with help of the new guideline. Piping components, piping engineering in process industry, and piping stress analysis were studied in the theory section of this research. Also, the existing piping standards were studied and compared with one another. By utilizing the theory found in literature and the vast experience and know-how collected from the company’s employees, a new guideline for stress analysis was developed. The guideline would be widely used in various projects. The purpose of the guideline was to clarify certain issues such as which of the piping would have to be analyzed, how are different material values determined and how will the results be reported. As a result, an extensive and comprehensive guideline for stress analysis was created. The new guideline more clearly defines formerly unclear points and creates clear parameters to performing calculations. The guideline is meant to be used by both new and experienced analysts and with its aid, the calculation process was unified throughout the whole company’s organization. Case study was used to exhibit how the guideline is utilized in practice, and how it benefits the calculation process.

High-Tech Commercialization Research Projects: A Pragmatic View

In the Finnish university society the commercialization research projects has not been a focus of interest until now. The reasons for the growing interest towards commercialization research projects are their possibility to develop our economy simultaneously by providing new technologies and products. This study focuses on the examination of what kind of high-technology oriented research can be commercialized and how. The aim is to generate understanding of how commercialization research projects should proceed and to find concrete ways of improving the of commercialization research projects. As its research method, the study analyzes four different university high-technology research projects which have been commercially oriented and have to some degree been able to commercialize the product or technology developed during the research phase. The data has been gathered mainly by semi-structured interviews of people involved in these particular projects or cases. The findings from the interviews have been reflected to the final reports of the projects, provided by TEKES, and later on the data gained has been compared to each other. Also a literature review has been produced about the subject of commercializing university research with the purpose of providing known theories and framework connected with the subject. The study reveals five main factors related to commercializing high-tech research. These factors are: The Team, Market potential and competitiveness, Product and technology, Funding and Steering Group. Also the uncertainties related to these factors have been addressed. As a conclusion the study provides the main aspects that should be considered when starting a commercialization research project. Also a combining hierarchical framework has been provided related to the five factors presented. In Chapter 5 the study addresses the main tasks or steps to be taken in order to get public funding for a commercially oriented research project and later on the actual steps to be executed in order to successfully commercialize these high-tech research projects.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Prevalence of Chronic Kidney Disease in newly diagnosed patients with Human immunodeficiency virus in Ilorin, Nigeria

AbstractIntroduction:Human immunodeficiency virus (HIV) the causative agent of Acquired immunodeficiency syndrome (AIDS) is an important cause of renal diseases in sub-Saharan Africa. There is paucity of studies on the burden of chronic kidney disease (CKD) among patients with HIV/AIDS in the North-Central zone of Nigeria.Methods:This is a cross-sectional study of 227 newly-diagnosed, antiretroviral naïve patients with HIV/AIDS seen at the HIV clinic of the Medical Out-patient Department (MOPD) of University of Ilorin Teaching Hospital (UITH). They were matched with 108 control group. Laboratory investigations were performed for the participants. CKD was defined as estimated glomerular filtration rate (eGFR) < 60 ml/min/1.73 m2 and/or albumin creatinine ratio (ACR) > 30 mg/g.Results:There were 100 (44%) males among the patients and 47 (43.5%) among the control group. The mean ages of the patients and controls were 40.3 ± 10.3 years and 41.8 ± 9.5 years respectively. CKD was observed in 108 (47.6%) among the patients and 18 (16.7%) of the controls (p = 0.01). The median CD4 T-cell count was significantly lower in patients with CKD. Ninety-three (41.0%) of the patients had dipstick proteinuria of > 2 +. The median albumin creatinine ratio (ACR) was significantly higher among the HIV-positive patients (272.3 mg/g) compared with the HIV-negative controls (27.22 mg/g) p = 0.01. The CD4 T-cell count correlates positively with eGFR (r = 0.463, p = 0.001) and negatively with ACR (r = -0.806, p = 0.001).Conclusions:CKD is very common among patients with HIV/AIDS in Ilorin. Screening and early intervention for CKD should be part of the protocols in the management of these patients.