Det hjemløse menneske : en studie av sykdom og lidelse

The overall aim of this study was to achieve a deeper understanding of the relationship between human suffering, disease and illness. The study is rooted in the health-care scientific research tradition as developed by Eriksson and her co-researchers at Åbo Akademi. The over-riding methodological initiative was Gadamer's hermeneutic philosophy. The main research question is: What is suffering of illness and disease? Sub-questions: Which characteristics occur when people experience being acutely ill (Article I)? What do the concepts acute, critical and chronic mean semantically (Article II)? In which way does the relation between the human being's experience of disease, illness and suffering, be manifested and understood? How does one characterize the relationship between the experience of contracting disease, illness and suffering (Article III)? How can the hermeneutical conversation contribute to the understanding of suffering caused by disease and illness (Article IV)? The results of sub-study 1 showed that patients with acute myocardial infarction saw themselves as coping, competent, and autonomous individuals. They were used to exercising control, and it was difficult for them to relinquish control. The semantic analysis of acute in sub-study 2 revealed that the concept acute has had an unclear content in the Norwegian language over the past 65 years. Acute, as a concept, says something about the way a situation arises, but not much about what it is that arises. In sub-study, 3 the relation between disease, illness and suffering is discussed. The expression of illness and suffering as verbs can convey more clearly what it is that occurs with persons who experience disease, illness and suffering. The discussion in sub-study 4 focuses on trustworthiness in hermeneutical studies.

Scientific creativity and diversity of physical work environment: framework development

The aim of this research was to develop a framework to analyze how physical environment influences scientific creativity. Due to the relative novelty of this topic, there is still a gap in the unified method to study connection between physical environment and creativity. Therefore, in order to study this issue deeply, the qualitative method was used (interviews and qualitative questionnaire). Scientists (PhD students and senior researchers) of Graduate School of Management were interviewed to build the model and one expert interview was conducted to assess its validity. The model highlights several dimensions via which physical environment can influence scientific creativity: Comfort, Instruments and Diversity. Comfort and Instruments are considered to be related mostly to productivity, an initial requirement for creativity, while Diversity is the factor responsible for supporting all the stages of scientific creative process. Thus, creative physical environment is not one place by its nature, but an aggregative phenomenon. Due to two levels of analysis, the model is named the two-level model of creative physical environment.

Targeted Annotation of Scientific Literature and Data Resources in Invenio Digital Libraries

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

Self-deposit, discovery, and delivery of scientific GIS datasets using GeoHydra

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

A Rights Expression Language for Federated Repositories

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.

Making the impact on research and society : nichesourcing of Uralic language material for the benefit of linguistic research and native-speakers

Presentation at the 12th Bibliotheca Baltica Symposium at Södertörn University Library

Language of the Future, Language of the PRC –Representations of Putonghua in South China Morning Post

As the national language of the PRC, the world's growing economic power and the sovereign of Hong Kong, Putonghua is a language with multiple facets of relevance for the current Special Administrative Region. This paper seeks to explore and explain different representations of Putonghua in Hong Kong's leading English-language newspaper South China Morning Post in articles published between January 2012 and February 2013. The representations are studied in the context of the different discourses in which they appear, some of which feature language(s) as a central theme and some more marginally. An overview is first presented of the scholarly research on the most important developments in Hong Kong's complex language scene from the beginnings of the colony until present day, with the aim of detecting developments and attitudes with potential relevance or parallels to the context of Putonghua today. The paper then reflects on the media and its role in producing and perpetuating discourses in the society, before turning to more practical considerations on Hong Kong's English and Chinese language media and the role of South China Morning Post in it. The methods used in analysing the discourses are those of discourse analysis, with textual analysis as its starting point, in which close attention is paid to linguistic forms as the concrete representations of meanings in a text. Particularly the immediate contexts of the appearances of the word “Putonghua” in the articles were studied carefully to detect vocabulary, grammar and semantical choices as signs of different discourses, potentially also revealing fundamental underlying assumptions and other “hidden meanings” in the text. Some of the most distinctive discourses in which different representations of Putonghua appeared were the Instrumental value for the individual (in which Putonghua was represented as a form of social capital); Othering of the mainlanders (in which Putonghua served as a concrete marker of distinction); Belonging to China (Putonghua as a symbol of unity); and Cultural distinctiveness of Hong Kong (Putonghua as a threat to Hong Kong's history and culture, as embodied in Cantonese). Some of these discourses were more prominent than others, and for example the discourse of Belonging to China was relatively rarely enacted in Hongkongers' voices. In general, the findings were not surprising in the light of the history, but showed a fair degree of consistency with what has been written earlier about the languages and attitudes towards them in Hong Kong. It has often been noted that Putonghua and its relation with Cantonese is a matter linked with the social identity of the colony and its citizens. While it appeared that there were no strict taboos in the representations of Putonghua in the societal context, the possibility of self-censorship cannot be ruled out as a factor toning down political discourses in the representations.

Reporting on methods of subgroup analysis in clinical trials: a survey of four scientific journals

Results of subgroup analysis (SA) reported in randomized clinical trials (RCT) cannot be adequately interpreted without information about the methods used in the study design and the data analysis. Our aim was to show how often inaccurate or incomplete reports occur. First, we selected eight methodological aspects of SA on the basis of their importance to a reader in determining the confidence that should be placed in the author's conclusions regarding such analysis. Then, we reviewed the current practice of reporting these methodological aspects of SA in clinical trials in four leading journals, i.e., the New England Journal of Medicine, the Journal of the American Medical Association, the Lancet, and the American Journal of Public Health. Eight consecutive reports from each journal published after July 1, 1998 were included. Of the 32 trials surveyed, 17 (53%) had at least one SA. Overall, the proportion of RCT reporting a particular methodological aspect ranged from 23 to 94%. Information on whether the SA preceded/followed the analysis was reported in only 7 (41%) of the studies. Of the total possible number of items to be reported, NEJM, JAMA, Lancet and AJPH clearly mentioned 59, 67, 58 and 72%, respectively. We conclude that current reporting of SA in RCT is incomplete and inaccurate. The results of such SA may have harmful effects on treatment recommendations if accepted without judicious scrutiny. We recommend that editors improve the reporting of SA in RCT by giving authors a list of the important items to be reported.

The use and misuse of the "impact factor" as a parameter for evaluation of scientific publication quality: a proposal to rationalize its application

We present a critical analysis of the generalized use of the "impact factor". By means of the Kruskal-Wallis test, it was shown that it is not possible to compare distinct disciplines using the impact factor without adjustments. After assigning the median journal the value of one (1.000), the impact factor value for each journal was calculated by the rule of three. The adjusted values were homogeneous, thus permitting comparison among distinct disciplines.

A study of the abilities in oral language comprehension of the Boston Diagnostic Aphasia Examination - Portuguese version: a reference guide for the Brazilian population

We analyzed the performance of 162 normal subjects, subdivided into groups according to age and schooling, in the oral comprehension tasks of the Boston Diagnostic Aphasia Examination translated and adapted to Brazilian Portuguese to obtain a profile of performance for the Brazilian population, as well as cut-off scores for each task, and to determine the best combination of tasks that distinguish normal from aphasic subjects, as a guide for clinicians. The normal subjects were compared to 69 aphasics. Age alone influenced the performance in the designation of actions (subjects above 70 years showing the worst performance); schooling alone influenced the comprehension of forms, colors and numbers (subjects with less than four years of education showing a poorer performance). Both age and schooling influenced the performance in Body Part Identification (BPI) and Complex Ideational Material (CIM) with mean values of 70.5 ± 3.3 (Word Discrimination, WD), 18.9 ± 1.4 (BPI), 14.7 ± 0.9 (Commands), and 10.3 ± 1.7 (CIM) for the whole sample; the cut-off scores obtained were 65 (WD), 17.5 (BPI), 14 (Commands), and 9.5 (CIM) for the whole sample. Logistic regression showed that the combination of BPI + Commands + CIM was the most efficient in differentiating normal subjects from aphasics, with 72.5% sensitivity and 97.6% specificity. However, for low-education subjects, BPI and Commands were sufficient for this differentiation (75.7% sensitivity and 84.7% specificity). The main contribution of this study was to provide reference values that are far more representative of our population to be used by health professionals in Brazil, taking into account cultural differences.

The scientific production in health and biological sciences of the top 20 Brazilian universities

Brazilian scientific output exhibited a 4-fold increase in the last two decades because of the stability of the investment in research and development activities and of changes in the policies of the main funding agencies. Most of this production is concentrated in public universities and research institutes located in the richest part of the country. Among all areas of knowledge, the most productive are Health and Biological Sciences. During the 1998-2002 period these areas presented heterogeneous growth ranging from 4.5% (Pharmacology) to 191% (Psychiatry), with a median growth rate of 47.2%. In order to identify and rank the 20 most prolific institutions in these areas, searches were made in three databases (DataCAPES, ISI and MEDLINE) which permitted the identification of 109,507 original articles produced by the 592 Graduate Programs in Health and Biological Sciences offered by 118 public universities and research institutes. The 20 most productive centers, ranked according to the total number of ISI-indexed articles published during the 1998-2003 period, produced 78.7% of the papers in these areas and are strongly concentrated in the Southern part of the country, mainly in São Paulo State.