In search of information systems value : a case study of the EHR benefits realisation efforts of three Swedish hospitals.

The Swedish public health care organisation could very well be undergoing its most significant change since its specialisation during the late 19th and early 20th century. At the heart of this change is a move from using manual patient journals to electronic health records (EHR). EHR are complex integrated organisational wide information systems (IS) that promise great benefits and value as well as presenting great challenges to the organisation. The Swedish public health care is not the first organisation to implement integrated IS, and by no means alone in their quest for realising the potential benefits and value that it has to offer. As organisations invest in IS they embark on a journey of value-creation and capture. A journey where a costbased approach towards their IS-investments is replaced with a value-centric focus, and where the main challenges lie in the practical day-to-day task of finding ways to intertwine technology, people and business processes. This has however proven to be a problematic task. The problematic situation arises from a shift of perspective regarding how to manage IS in order to gain value. This is a shift from technology delivery to benefits delivery; from an ISimplementation plan to a change management plan. The shift gives rise to challenges related to the inability of IS and the elusiveness of value. As a response to these challenges the field of IS-benefits management has emerged offering a framework and a process in order to better understand and formalise benefits realisation activities. In this thesis the benefits realisation efforts of three Swedish hospitals within the same county council are studied. The thesis focuses on the participants of benefits analysis projects; their perceptions, judgments, negotiations and descriptions of potential benefits. The purpose is to address the process where organisations seek to identify which potential IS-benefits to pursue and realise, this in order to better understand what affects the process, so that realisation actions of potential IS-benefits could be supported. A qualitative case study research design is adopted and provides a framework for sample selection, data collection, and data analysis. It also provides a framework for discussions of validity, reliability and generalizability. Findings displayed a benefits fluctuation, which showed that participants’ perception of what constituted potential benefits and value changed throughout the formal benefits management process. Issues like structure, knowledge, expectation and experience affected perception differently, and this in the end changed the amount and composition of potential benefits and value. Five dimensions of benefits judgment were identified and used by participants when finding accommodations of potential benefits and value to pursue. Identified dimensions affected participants’ perceptions, which in turn affected the amount and composition of potential benefits. During the formal benefits management process participants shifted between judgment dimensions. These movements emerged through debates and interactions between participants. Judgments based on what was perceived as expected due to one’s role and perceived best for the organisation as a whole were the two dominant benefits judgment dimensions. A benefits negotiation was identified. Negotiations were divided into two main categories, rational and irrational, depending on participants’ drive when initiating and participating in negotiations. In each category three different types of negotiations were identified having different characteristics and generating different outcomes. There was also a benefits negotiation process identified that displayed management challenges corresponding to its five phases. A discrepancy was also found between how IS-benefits are spoken of and how actions of IS benefits realisation are understood. This was a discrepancy between an evaluation and a realisation focus towards IS value creation. An evaluation focus described IS-benefits as well-defined and measurable effects and a realisation focus spoke of establishing and managing an on-going place of value creation. The notion of valuescape was introduced in order to describe and support the understanding of IS value creation. Valuescape corresponded to a realisation focus and outlined a value configuration consisting of activities, logic, structure, drivers and role of IS.

Search advertising for small Finnish tourism company in Russian Internet – Experimental study: Google AdWords versus Yandex.Direct

Yandex is the dominant search engine in Russia, followed by the world leader Google. This study focuses on the performance differences between the two in search advertising in the context of tourism, by running two identical campaigns and measuring the KPI’s, such as CPA (cost-per-action), on both campaigns. Search engine advertising is a new and fast changing form of advertising, which should be studied frequently in order to keep up with the changes. Research was done as an experimental study in cooperation with a Finnish tourism company and the data is gathered from the clickstream and not from questionnaires, which is recommended method by the literature. The results of the study suggests that Yandex.Direct performed better in the selected niche and that the individual campaign planning for Yandex.Direct and Google AdWords is an important part of the optimization of search advertising in Russia.

AgEcon Search: Evolution of a Subject Repository

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

Elasticsearch as a new search engine for Invenio and more

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

Tag Cloud of Search Queries for Repository System

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.

A Business continuity management maturity model : the search for an ISO 22301 Compliant BCM Maturity model

BCM (business continuity Management) is a holistic management process aiming at ensuring business continuity and building organizational resilience. Maturity models offer organizations a tool for evaluating their current maturity in a certain process. In the recent years BCM has been subject to international ISO standardization, while the interest of organizations to bechmark their state of BCM agains standards and the use of maturity models for these asessments has increased. However, although new standards have been introduced, very little attention has been paid to reviewing the existing BCM maturity models in research - especially in the light of the new ISO 22301 standard for BCM. In this thesis the existing BCM maturily models are carefully evaluated to determine whetherthey could be improved. In order to accomplish this, the compliance of the existing models to the ISO 22301 standard is measured and a framework for assessing a maturitymodel´s quality is defined. After carefully evaluating the existing frameworks for maturity model development and evaluation, an approach suggested by Becker et al. (2009) was chosen as the basis for the research. An additionto the procedural model a set of seven research guidelines proposed by the same authors was applied, drawing on the design-science research guidelines as suggested by Hevner et al. (2004). Furthermore, the existing models´ form and function was evaluated to address their usability. Based on the evaluation of the existing BCM maturity models, the existing models were found to have shortcomings in each dimension of the evaluation. Utilizing the best of the existing models, a draft version for an enhanced model was developed. This draft model was then iteratively developed by conducting six semi-structured interviews with BCM professionals in finland with the aim of validating and improving it. As a Result, a final version of the enhanced BCM maturity model was developed, conforming to the seven key clauses in the ISO 22301 standard and the maturity model development guidelines suggested by Becker et al. (2009).

A search for RFLP markers to identify genes for aluminum tolerance in maize

The objective of this study was to identify restriction fragment length polymorphism (RFLP) markers linked to QTLs that control aluminum (Al) tolerance in maize. The strategy used was bulked segregant analysis (BSA) and the genetic material utilized was an F2 population derived from a cross between the Al-susceptible inbred line L53 and Al-tolerant inbred line L1327. Both lines were developed at the National Maize and Sorghum Research Center - CNPMS/EMBRAPA. The F2 population of 1554 individuals was evaluated in a nutrient solution containing a toxic concentration of Al and relative seminal root length (RSRL) was used as a phenotypic measure of tolerance. The RSRL frequency distribution was continuous, but skewed towards Al-susceptible individuals. Seedlings of the F2 population which scored the highest and the lowest RSRL values were transplanted to the field and subsequently selfed to obtain F3 families. Thirty F3 families (15 Al-susceptible and 15 Al-tolerant) were evaluated in nutrient solution, using an incomplete block design, to identify those with the smallest variances for aluminum tolerance and susceptibility. Six Al-susceptible and five Al-tolerant F3 families were chosen to construct one pool of Al-susceptible individuals, and another of Al-tolerant, herein referred as "bulks", based on average values of RSRL and genetic variance. One hundred and thirteen probes were selected, with an average interval of 30 cM, covering the 10 maize chromosomes. These were tested for their ability to discriminate the parental lines. Fifty-four of these probes were polymorphic, with 46 showing codominance. These probes were hybridized with DNA from the two contrasting bulks. Three RFLPs on chromosome 8 distinguished the bulks on the basis of band intensity. DNA of individuals from the bulks was hybridized with these probes and showed the presence of heterozygous individuals in each bulk. These results suggest that in maize there is a region related to aluminum tolerance on chromosome 8

Semantic and fuzzy modelling for human behaviour recognition in smart spaces : a case study on ambient assisted living.

Human activity recognition in everyday environments is a critical, but challenging task in Ambient Intelligence applications to achieve proper Ambient Assisted Living, and key challenges still remain to be dealt with to realize robust methods. One of the major limitations of the Ambient Intelligence systems today is the lack of semantic models of those activities on the environment, so that the system can recognize the speci c activity being performed by the user(s) and act accordingly. In this context, this thesis addresses the general problem of knowledge representation in Smart Spaces. The main objective is to develop knowledge-based models, equipped with semantics to learn, infer and monitor human behaviours in Smart Spaces. Moreover, it is easy to recognize that some aspects of this problem have a high degree of uncertainty, and therefore, the developed models must be equipped with mechanisms to manage this type of information. A fuzzy ontology and a semantic hybrid system are presented to allow modelling and recognition of a set of complex real-life scenarios where vagueness and uncertainty are inherent to the human nature of the users that perform it. The handling of uncertain, incomplete and vague data (i.e., missing sensor readings and activity execution variations, since human behaviour is non-deterministic) is approached for the rst time through a fuzzy ontology validated on real-time settings within a hybrid data-driven and knowledgebased architecture. The semantics of activities, sub-activities and real-time object interaction are taken into consideration. The proposed framework consists of two main modules: the low-level sub-activity recognizer and the high-level activity recognizer. The rst module detects sub-activities (i.e., actions or basic activities) that take input data directly from a depth sensor (Kinect). The main contribution of this thesis tackles the second component of the hybrid system, which lays on top of the previous one, in a superior level of abstraction, and acquires the input data from the rst module's output, and executes ontological inference to provide users, activities and their in uence in the environment, with semantics. This component is thus knowledge-based, and a fuzzy ontology was designed to model the high-level activities. Since activity recognition requires context-awareness and the ability to discriminate among activities in di erent environments, the semantic framework allows for modelling common-sense knowledge in the form of a rule-based system that supports expressions close to natural language in the form of fuzzy linguistic labels. The framework advantages have been evaluated with a challenging and new public dataset, CAD-120, achieving an accuracy of 90.1% and 91.1% respectively for low and high-level activities. This entails an improvement over both, entirely data-driven approaches, and merely ontology-based approaches. As an added value, for the system to be su ciently simple and exible to be managed by non-expert users, and thus, facilitate the transfer of research to industry, a development framework composed by a programming toolbox, a hybrid crisp and fuzzy architecture, and graphical models to represent and con gure human behaviour in Smart Spaces, were developed in order to provide the framework with more usability in the nal application. As a result, human behaviour recognition can help assisting people with special needs such as in healthcare, independent elderly living, in remote rehabilitation monitoring, industrial process guideline control, and many other cases. This thesis shows use cases in these areas.

A search for RNA insertions and NS3 gene duplication in the genome of cytopathic isolates of bovine viral diarrhea virus

Calves born persistently infected with non-cytopathic bovine viral diarrhea virus (ncpBVDV) frequently develop a fatal gastroenteric illness called mucosal disease. Both the original virus (ncpBVDV) and an antigenically identical but cytopathic virus (cpBVDV) can be isolated from animals affected by mucosal disease. Cytopathic BVDVs originate from their ncp counterparts by diverse genetic mechanisms, all leading to the expression of the non-structural polypeptide NS3 as a discrete protein. In contrast, ncpBVDVs express only the large precursor polypeptide, NS2-3, which contains the NS3 sequence within its carboxy-terminal half. We report here the investigation of the mechanism leading to NS3 expression in 41 cpBVDV isolates. An RT-PCR strategy was employed to detect RNA insertions within the NS2-3 gene and/or duplication of the NS3 gene, two common mechanisms of NS3 expression. RT-PCR amplification revealed insertions in the NS2-3 gene of three cp isolates, with the inserts being similar in size to that present in the cpBVDV NADL strain. Sequencing of one such insert revealed a 296-nucleotide sequence with a central core of 270 nucleotides coding for an amino acid sequence highly homologous (98%) to the NADL insert, a sequence corresponding to part of the cellular J-Domain gene. One cpBVDV isolate contained a duplication of the NS3 gene downstream from the original locus. In contrast, no detectable NS2-3 insertions or NS3 gene duplications were observed in the genome of 37 cp isolates. These results demonstrate that processing of NS2-3 without bulk mRNA insertions or NS3 gene duplications seems to be a frequent mechanism leading to NS3 expression and BVDV cytopathology.

Westerners in search of the legendary potion : ayahuasca travel in the borderland between tourism and pilgrimage

The thesis examines the phenomenon most commonly known as “ayahuasca tourism” – i.e. the practice of westerners traveling to South America and partaking in ceremonies in which a powerful entheogenic brew, ayahuasca, is consumed. While this popular phenomenon has been steadily increasing during the last decades, it has, however, been insufficiently studied by scholars. An important question which has not been properly addressed in earlier studies is how ayahuasca tourism relates to the wider occurrence of travel and how it should be perceived with reference to the theoretical frameworks on the subject of travel. Drawing on theories regarding pilgrimage and tourism, the main purpose of this thesis is to examine the relationship between ayahuasca tourism and the broader spectrum of travel. In particular, the study tests the designations “pilgrimage”, “religious tourism” and “spiritual tourism” with reference to ayahuasca tourism. Utilizing earlier literature as well as ayahuasca tourists‟ reports obtained from an Internet forum as a basis for analysis, I search for a suitable terminology to be used for the phenomenon. The study lays special emphasis on the protagonists‟ motivations, experiences and outcomes in order to take note of various aspects of the wide-ranging occurrence of ayahuasca tourism. Key findings indicate that ayahuasca tourism is best understood as a combination of pilgrimage and tourism. On the basis of the analysis I argue that ayahuasca tourism should be labeled as “pilgrimage” and/or “spiritual tourism”, and the tourists respectively as “pilgrims” and/or “spiritual tourists”. The category of “religious tourism/tourist”, on the other hand, turns out to be an inappropriate designation when describing the phenomenon. In general, through my study I show that the results are consistent with the present trend in the study of travel to perceive pilgrimage and tourism as theoretically similar phenomena. The study of ayahuasca tourism serves thus as living proof of contemporary travel, in which the categories of pilgrimage and tourism are often indistinguishable. I suggest that ayahuasca tourism is by no means exceptional on this point, but can rather be used as an illustration of modern travel forms on a general level. Thus, the present study does not only add to the research of ayahuasca tourism, but also provides additional insights into the study of travel.

Oral verrucous lesions – a search for PVL

Proliferatiivinen verrukoottinen leukoplakia (PVL) esiintyy yhtenä laajana tai useampana verrukoottisena, valkoisena muutoksena suun limakalvoilla. PVL on aggressiivinen limakalvomuutos, joka ei usein vastaa hoitoihin, uusii herkästi ja sillä on muita leukoplakioita suurempi pahanlaatuistumistaipumus. Tutkimuksen tarkoitus on lisätä tietoa PVL:sta ja sen ilmentymisestä ja kehittymisestä sekä arvioida kriittisesti PVL:n diagnostiikkaa. Systemaattinen kirjallisuuskatsaus suoritettiin etsimällä Pubmed-tietokannan kirjallisuushaulla kaikki englannin kielellä raportoidut ja vertaisarvioidut PVL- potilastapaukset 2000 – 2013. PVL voi histologisesti esiintyä myös verrukoottisena hyperplasiana (VH), joten myös nämä tapaukset sisällytettiin aineistoon. Kaikkiaan 54 artikkelia täytti sisäänottokriteerit. Näissä oli yhteensä 388 PVL- ja 848 VH-tapausta. Lisäksi kerättiin kaikki Turun yliopiston hammaslääketieteen laitoksen suupatologian osastolla histologisesti diagnosoidut vastaavat suun VH-muutokset 2000 – 2013. Kirjallisuudesta havaittiin, että PVL esiintyi useammin naisilla (2,2 : 1), kun taas VH esiintyi useammin miehillä (1 : 3,8). Tupakointi ei näyttänyt liittyvän PVL:aan (30 %), kun taas VH:aan se näytti selkeämmin liittyvän (83 %). PVL:n yleisin sijainti oli ikenellä (59 %) ja suurin osa VH-muutoksista esiintyi posken limakalvolla (51 %). PVL-potilaista 47 %:lla ja VH-potilaista 5 %:lla todettiin seurannassa pahanlaatuinen kasvain. Turun yliopiston suupatologian osastolla diagnosoituja VH-tapauksia oli 13 vuoden aikana 29. Naisten osuus sairastuneista oli suurempi kuin miesten (1,4 : 1). Muutokset esiintyivät yleisimmin kielen limakalvolla (48 %) ja poskessa (34 %). Yhdessä tapauksessa kehittyi pahanlaatuinen kasvain (3 %). Tutkimuksessa todettiin, että PVL- ja VH-muutokset poikkeavat toisistaan sukupuolijakauman, tupakoinnin ja pahanlaatuistumisen osalta. Ongelmana katsauksessa olivat tietojen puutteellisuus ja raportoinnin heterogeenisyys kirjallisuudessa. PVL- ja VH-tutkimuksessa tulisikin panostaa yhteneviin diagnostisiin kriteereihin, jotta materiaalit olisivat vertailukelpoisia. Potilaan kannalta PVL:n ja VH:n varhainen diagnosointi ja huolellinen seuranta ovat olennaisen tärkeitä asioita.

The search for circadian clock components in humans: new perspectives for association studies

Individual circadian clocks entrain differently to environmental cycles (zeitgebers, e.g., light and darkness), earlier or later within the day, leading to different chronotypes. In human populations, the distribution of chronotypes forms a bell-shaped curve, with the extreme early and late types _ larks and owls, respectively _ at its ends. Human chronotype, which can be assessed by the timing of an individual's sleep-wake cycle, is partly influenced by genetic factors - known from animal experimentation. Here, we review population genetic studies which have used a questionnaire probing individual daily timing preference for associations with polymorphisms in clock genes. We discuss their inherent limitations and suggest an alternative approach combining a short questionnaire (Munich ChronoType Questionnaire, MCTQ), which assesses chronotype in a quantitative manner, with a genome-wide analysis (GWA). The advantages of these methods in comparison to assessing time-of-day preferences and single nucleotide polymorphism genotyping are discussed. In the future, global studies of chronotype using the MCTQ and GWA may also contribute to understanding the influence of seasons, latitude (e.g., different photoperiods), and climate on allele frequencies and chronotype distribution in different populations.

Utility of a novel risk score for prediction of ventricular tachycardia and cardiac death in chronic Chagas disease - the SEARCH-RIO study

The SEARCH-RIO study prospectively investigated electrocardiogram (ECG)-derived variables in chronic Chagas disease (CCD) as predictors of cardiac death and new onset ventricular tachycardia (VT). Cardiac arrhythmia is a major cause of death in CCD, and electrical markers may play a significant role in risk stratification. One hundred clinically stable outpatients with CCD were enrolled in this study. They initially underwent a 12-lead resting ECG, signal-averaged ECG, and 24-h ambulatory ECG. Abnormal Q-waves, filtered QRS duration, intraventricular electrical transients (IVET), 24-h standard deviation of normal RR intervals (SDNN), and VT were assessed. Echocardiograms assessed left ventricular ejection fraction. Predictors of cardiac death and new onset VT were identified in a Cox proportional hazard model. During a mean follow-up of 95.3 months, 36 patients had adverse events: 22 new onset VT (mean±SD, 18.4±4‰/year) and 20 deaths (26.4±1.8‰/year). In multivariate analysis, only Q-wave (hazard ratio, HR=6.7; P<0.001), VT (HR=5.3; P<0.001), SDNN<100 ms (HR=4.0; P=0.006), and IVET+ (HR=3.0; P=0.04) were independent predictors of the composite endpoint of cardiac death and new onset VT. A prognostic score was developed by weighting points proportional to beta coefficients and summing-up: Q-wave=2; VT=2; SDNN<100 ms=1; IVET+=1. Receiver operating characteristic curve analysis optimized the cutoff value at >1. In 10,000 bootstraps, the C-statistic of this novel score was non-inferior to a previously validated (Rassi) score (0.89±0.03 and 0.80±0.05, respectively; test for non-inferiority: P<0.001). In CCD, surface ECG-derived variables are predictors of cardiac death and new onset VT.