Geo-enabling repositories - techniques, tools, and challenges

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.

Development of remote monitoring process tools for biomass fired bubbling fluidized bed boilers

Remote monitoring of a power boiler allows the supplying company to make sure that equipment is used as supposed to and gives a good chance for process optimization. This improves co-operation between the supplier and the customer and creates an aura of trust that helps securing future contracts. Remote monitoring is already in use with recovery boilers but the goal is to expand especially to biomass-fired BFB-boilers. To make remote monitoring possible, data has to be measured reliably on site and the link between the power plant and supplying company’s server has to work reliably. Data can be gathered either with the supplier’s sensors or with measurements originally installed in the power plant if the plant in question is not originally built by the supplying company. Main goal in remote monitoring is process optimization and avoiding unnecessary accidents. This can be achieved for instance by following the efficiency curves and fouling in different parts of the process and comparing them to past values. The final amount of calculations depends on the amount of data gathered. Sudden changes in efficiency or fouling require further notice and in such a case it’s important that dialogue toward the power plant in question also works.

Macroalgae across environmental gradients : tools for managing rocky coastal areas of the northern Baltic Sea

Macroalgae are the main primary producers of the temperate rocky shores providing a three-dimensional habitat, food and nursery grounds for many other species. During the past decades, the state of the coastal waters has deteriorated due to increasing human pressures, resulting in dramatic changes in coastal ecosystems, including macroalgal communities. To reverse the deterioration of the European seas, the EU has adopted the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD), aiming at improved status of the coastal waters and the marine environment. Further, the Habitats Directive (HD) calls for the protection of important habitats and species (many of which are marine) and the Maritime Spatial Planning Directive for sustainability in the use of resources and human activities at sea and by the coasts. To efficiently protect important marine habitats and communities, we need knowledge on their spatial distribution. Ecological knowledge is also needed to assess the status of the marine areas by involving biological indicators, as required by the WFD and the MSFD; knowledge on how biota changes with human-induced pressures is essential, but to reliably assess change, we need also to know how biotic communities vary over natural environmental gradients. This is especially important in sea areas such as the Baltic Sea, where the natural environmental gradients create substantial differences in biota between areas. In this thesis, I studied the variation occurring in macroalgal communities across the environmental gradients of the northern Baltic Sea, including eutrophication induced changes. The aim was to produce knowledge to support the reliable use of macroalgae as indicators of ecological status of the marine areas and to test practical metrics that could potentially be used in status assessments. Further, the aim was to develop a methodology for mapping the HD Annex I habitat reefs, using the best available data on geology and bathymetry. The results showed that the large-scale variation in the macroalgal community composition of the northern Baltic Sea is largely driven by salinity and exposure. Exposure is important also on smaller spatial scales, affecting species occurrence, community structure and depth penetration of algae. Consequently, the natural variability complicates the use of macroalgae as indicators of human-induced changes. Of the studied indicators, the number of perennial algal species, the perennial cover, the fraction of annual algae, and the lower limit of occurrence of red and brown perennial algae showed potential as usable indicators of ecological status. However, the cumulated cover of algae, commonly used as an indicator in the fully marine environments, showed low responses to eutrophication in the area. Although the mere occurrence of perennial algae did not show clear indicator potential, a distinct discrepancy in the occurrence of bladderwrack, Fucus vesiculosus, was found between two areas with differing eutrophication history, the Bothnian Sea and the Archipelago Sea. The absence of Fucus from many potential sites in the outer Archipelago Sea is likely due to its inability to recover from its disappearance from the area 30-40 years ago, highlighting the importance of past events in macroalgal occurrence. The methodology presented for mapping the potential distribution and the ecological value of reefs showed, that relatively high accuracy in mapping can be achieved by combining existing available data, and the maps produced serve as valuable background information for more detailed surveys. Taken together, the results of the theses contribute significantly to the knowledge on macroalgal communities of the northern Baltic Sea that can be directly applied in various management contexts.

Cardiac Troponin Specific Autoantibodies: Analytical Tools for Exploring Their Impact on Cardiac Troponin I Testing

Cardiac troponin (cTn) I and T are the recommended biomarkers for the diagnosis and risk stratification of patients with suspected acute coronary syndrome (ACS), a major cause of cardiovascular death and disability worldwide. It has recently been demonstrated that cTn-specific autoantibodies (cTnAAb) can negatively interfere with cTnI detection by immunoassays to the extent that cTnAAb-positive patients may be falsely designated as cTnI-negative. The aim of this thesis was to develop and optimize immunoassays for the detection of both cTnI and cTnAAb, which would eventually enable exploring the clinical impact of these autoantibodies on cTnI testing and subsequent patient management. The extent of cTnAAb interference in different cTnI assay configurations and the molecular characteristics of cTnAAbs were investigated in publications I and II, respectively. The findings showed that cTnI midfragment targeting immunoassays used predominantly in clinical practice are affected by cTnAAb interference which can be circumvented by using a novel 3+1-type assay design with three capture antibodies against the N-terminus, midfragment and C-terminus and one tracer antibody against the C-terminus. The use of this assay configuration was further supported by the epitope specificity study, which showed that although the midfragment is most commonly targeted by cTnAAbs, the interference basically encompasses the whole molecule, and there may be remarkable individual variation at the affected sites. In publications III and IV, all the data obtained in previous studies were utilized to develop an improved version of an existing cTnAAb assay and a sensitive cTnI assay free of this specific analytical interference. The results of the thesis showed that approximately one in 10 patients with suspected ACS have detectable amounts of cTnAAbs in their circulation and that cTnAAbs can inhibit cTnI determination when targeted against the binding sites of assay antibodies used in its immunological detection. In the light of these observations, the risk of clinical misclassification caused by the presence of cTnAAbs remains a valid and reasonable concern. Because the titers, affinities and epitope specificities of cTnAAbs and the concentration of endogenous cTnI determine the final effect of circulating cTnAAbs, appropriately sized studies on their clinical significance are warranted. The new cTnI and cTnAAb assays could serve as analytical tools for establishing the impact of cTnAAbs on cTnI testing and also for unraveling the etiology of cTn-related autoimmune responses.

Parasitic Order Machine. A Sociology and Ontology of Information Securing

This study examines information security as a process (information securing) in terms of what it does, especially beyond its obvious role of protector. It investigates concepts related to ‘ontology of becoming’, and examines what it is that information securing produces. The research is theory driven and draws upon three fields: sociology (especially actor-network theory), philosophy (especially Gilles Deleuze and Félix Guattari’s concept of ‘machine’, ‘territory’ and ‘becoming’, and Michel Serres’s concept of ‘parasite’), and information systems science (the subject of information security). Social engineering (used here in the sense of breaking into systems through non-technical means) and software cracker groups (groups which remove copy protection systems from software) are analysed as examples of breaches of information security. Firstly, the study finds that information securing is always interruptive: every entity (regardless of whether or not it is malicious) that becomes connected to information security is interrupted. Furthermore, every entity changes, becomes different, as it makes a connection with information security (ontology of becoming). Moreover, information security organizes entities into different territories. However, the territories – the insides and outsides of information systems – are ontologically similar; the only difference is in the order of the territories, not in the ontological status of entities that inhabit the territories. In other words, malicious software is ontologically similar to benign software; they both are users in terms of a system. The difference is based on the order of the system and users: who uses the system and what the system is used for. Secondly, the research shows that information security is always external (in the terms of this study it is a ‘parasite’) to the information system that it protects. Information securing creates and maintains order while simultaneously disrupting the existing order of the system that it protects. For example, in terms of software itself, the implementation of a copy protection system is an entirely external addition. In fact, this parasitic addition makes software different. Thus, information security disrupts that which it is supposed to defend from disruption. Finally, it is asserted that, in its interruption, information security is a connector that creates passages; it connects users to systems while also creating its own threats. For example, copy protection systems invite crackers and information security policies entice social engineers to use and exploit information security techniques in a novel manner.

Digitization Project of Kindred Languages : materials, methods and tools for researchers

Presentation at "Soome-ugri keelte andmebaasid ja e-leksikograafia" at Eesti Keele Instituut (Institution of Estonian Languages) in Tallnn on the 18th of November 2014.

RNA and DNA aptamers as potential tools to prevent cell adhesion in disease

Recent research has shown that receptor-ligand interactions between surfaces of communicating cells are necessary prerequisites for cell proliferation, cell differentiation and immune defense. Cell-adhesion events have also been proposed for pathological conditions such as cancer growth, metastasis, and host-cell invasion by parasites such as Trypanosoma cruzi. RNA and DNA aptamers (aptus = Latin, fit) that have been selected from combinatorial nucleic acid libraries are capable of binding to cell-adhesion receptors leading to a halt in cellular processes induced by outside signals as a consequence of blockage of receptor-ligand interactions. We outline here a novel approach using RNA aptamers that bind to T. cruzi receptors and interrupt host-cell invasion in analogy to existing procedures of blocking selectin adhesion and function in vitro and in vivo.

pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

Slöjd som process och produkt : Talking Tools som dokumentations- och utvärderingsverktyg

Syftet med denna studie är att granska hur användningen av smarttelefoner kan stöda elevens reflektion av sin egen slöjdprocess och samtidigt se hur eleven dokumenterar sin slöjdprocess med hjälp av Talking Tools (TT). Fokus i denna studie ligger på dokumentation av elevens slöjdprocess, men jag behandlar även presentation av slöjdprodukter och olika möjligheter till och sätt på hur eleverna använder TT på en smarttelefon i slöjdundervisningen. En förändring i hur informations- och kommunikationsteknik (IKT) används sker och kommer även att ske i fortsättningen i grundskolan. Då en ny läroplan för den grundläggande utbildningen tas i bruk år 2016 kommer IKT att ha en avsevärt större roll. Denna förändring lägger press på lärare och på skolan överlag för att skapa ändamålsenliga metoder i användningen av IKT. Studien baserar sig på intervjuer med elever som använt TT under ett arbetsområde i slöjden. Elva elever presenterade först sina slöjdprodukter för forskaren varefter eleverna intervjuades. Eleverna hade tillgång till sina slöjdbloggar gjorda i TT under intervjutillfällena. Intervjuerna filmades och lades ihop med bloggarna för att förenkla analysen av materialet. I den här undersökningen framkom att dokumentationen av slöjdprocessen bidrog till en reflektion av när bilder och texter från bloggarna användes under presentationerna. Då kraven på dokumenteringen av arbetet i skolan blir högre i och med läroplanen 2016 tror jag att Talking Tools kan vara ett hjälpmedel för elever och lärare i förverkligandet av bland annat användningen av IKT i arbetet i skolan. Detta förutsätter att eleverna ges tid för användningen samt att tekniken fungerar.

Possibility of press forming wood films into primary packaging

In recent times the packaging industry is finding means to maximize profit. Wood used to be the most advantageous and everyday material for packaging, worktables, counters, constructions, interiors, tools and as materials and utensils in the food companies in the world. The use of wood has declined vigorously, and other materials like plastic, ceramic, stainless steel, concrete, and aluminum have taken its place. One way that the industry could reduce its cost is by finding possibilities of using wood for primary packaging after which it can be safely recycled or burned as a carbon source for energy. Therefore, the main objective of this thesis is to investigate the possibility of press-forming a wood film into primary packaging. In order to achieve the stated objectives, discussion on major characteristics of wood in terms of structure, types and application were studied. Two different wood species, pine and birch were used for the experimental work. These were provided by a local carpentry workshop in Lappeenranta and a workshop in Ruokolahti supervised by Professor Timo Kärki. Laboratory tests were carried out at Lappeenranta University of Technology FMS workshop on Stenhøj EPS40 M hydraulic C-frame press coupled with National Instruments VI Logger and on the Adjustable packaging line machine at LUT Packaging laboratory. The tests succeeded better on the LUT packaging line than on the Stenhoj equipment due to the integrated heating system in the machine. However, there is much work to be done before the quality of a tray produced from the wood film is comparable to that of the wood plastic composite tray.

Inductance Calculation of Tooth-Coil Permanent-Magnet Synchronous Machines

Analytical calculation methods for all the major components of the synchronous inductance of tooth-coil permanentmagnet synchronous machines are reevaluated in this paper. The inductance estimation is different in the tooth-coil machine compared with the one in the traditional rotating field winding machine. The accuracy of the analytical torque calculation highly depends on the estimated synchronous inductance. Despite powerful finite element method (FEM) tools, an accurate and fast analytical method is required at an early design stage to find an initialmachine design structure with the desired performance. The results of the analytical inductance calculation are verified and assessed in terms of accuracy with the FEM simulation results and with the prototype measurement results.

MARKETING COMMUNICATIONS IN B2B COMPANIES – The Roles of Marketing Communication Tools in the Digital Age

Marketing communications has gone through significant changes during the last decades and new online tools have been leading this change for the last decade. Now, in the digital age, if wanting to be successful companies need to experiment new things and seize the opportunities online provides and adapt to the new environment. However, during this time the marketing communication mix and the meanings given to the various components of it have not changed dramatically, and personal selling, direct marketing, sales promotion, advertising and public relations activities are still regarded as important tools in the marketing communications mix. The purpose of this study was to examine business-to-business marketing communications and the tools used by companies in their marketing communications efforts in the digital age and in a global environment. The research questions dealt with the marketing communication tools and their roles as well as the role of online marketing communication and the way it has shaped the field of b2b marketing communications. In order to answer these questions, qualitative approach was chosen and the data was collected by theme interviews with six representatives of Finnish global companies from the b2b sector being interviewed. The theoretical framework covers the general field of b2b marketing communications and its main elements. The online environment as well as the concept of a global marketplace and integrated approach to marketing communication activities is also discussed. The theory was supported by the interviews regarding the activities and roles of the marketing communication tools and both theory as well as the interviews found personal selling to be a vital tool. However, the importance of online has grown and online marketing activities have risen right next to personal selling. The use of analytics and marketing automation was found to be of great interest in the interviews and they were seen as a growing domain in b2b marketing communications. The importance of targeted and personalised messages from relevant medias was a repeating theme as was the customer-centric approach in marketing communication activities. Also, offline and online tools and channels were seen as something that should be treated together as an entity rather than as separate activities. Relevant content created according to the needs of the customer with the gathered data from analytics were seen as the future of b2b marketing communications. Online has added its input to the more traditionally perceived tools and they are executed within the framework of the digital age. Nevertheless, even though online has increased its presence in the b2b marketing communications mix, the more traditionally perceived marketing communication tools, especially personal selling, have not lost their meaning or place in the b2b marketing communication mix.

Replacing Copper with New Carbon Nanomaterials in Electrical Machine Windings

Electrical machines have significant improvement potential. Nevertheless, the field is characterized by incremental innovations. Admittedly, steady improvement has been achieved, but no breakthrough development. Radical development in the field would require the introduction of new elements, such that may change the whole electrical machine industry system. Recent technological advancements in nanomaterials have opened up new horizons for the macroscopic application of carbon nanotube (CNT) fibres. With values of 100 MS/m measured on individual CNTs, CNT fibre materials hold promise for conductivities far beyond those of metals. Highly conductive, lightweight and strong CNT yarn is finally within reach; it could replace copper as a potentially better winding material. Although not yet providing low resistivity, the newest CNT yarn offers attractive perspectives for accelerated efficiency improvement of electrical machines. In this article, the potential for using new CNT materials to replace copper in machine windings is introduced. It does so, firstly, by describing the environment for a change that could revolutionize the industry and, secondly, by presenting the breakthrough results of a prototype construction. In the test motor, which is to our knowledge the first in its kind, the presently most electrically conductive carbon nanotube yarn replaces usual copper in the windings.

Design and Drive-Cycle Based Analysis of Direct-Driven Permanent Magnet Synchronous Machine for a Small Urban Use Electric Vehicle

A direct-driven permanent magnet synchronous machine for a small urban use electric vehicle is presented. The measured performance of the machine at the test bench as well as the performance over the modified New European Drive Cycle will be given. The effect of optimal current components, maximizing the efficiency and taking into account the iron loss, is compared with the simple id=0 – control. The machine currents and losses during the drive cycle are calculated and compared with each other.