Multi-source ingestion of publisher articles - The SCOAP3 repository experience

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

Ecophysiology

An attempt to delineate rather than to precisely define what we mean by "ecophysiology" is based on a brief historical overview of what eventually led to development of instrumentation and sampling strategies for analyses that allow description of physiological performance in the field. These techniques are surveyed. Ecophysiology originally is aut-ecology dedicated to the behaviour of individual plants, species or higher taxa, viz. "physiotypes", in particular habitats. Examples of ecophysiological diversity are developed, which illustrate gradual merging with more integrative considerations of functions and dynamics of habitats or ecosystems, i.e. a trend of research towards physiological syn-ecology. The latter is exemplified by studies with comparisons of a variety of morphotypes and physiotypes within a given habitat or ecosystem and across a range of habitats or ecosystems. The high demand and complexity as well as the excitement of ecology and ecophysiology arise from the quest to cover all conditions of the existence of organisms according to Ernst Haeckel's original definition of "ecology".

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.

Value-based Reference Marketing in a Small Process Industry Software and Service Company

This master’s thesis was done for a small company, Vipetec Oy, which offers specialized technological services for companies mainly in forest industry. The study was initiated partly because the company wants to expand its customer base to a new industry. There were two goals connected to each other. First was to find out how much and what kind of value current customers have realized from ATA Process Event Library, one of the products that the company offers. Second was to determine the best way to present this value and its implications for future value potential to both current and potential customers. ATA helps to make grade and product changes, starting after machine downtime, and recovery from production break faster for customers. All three events sometimes occur in production line. The faster operation results to savings in time and material. In addition to ATA Vipetec also offers other services related to development of automation and optimization of controls. Theoretical part concentrates on the concept of value, how it can be delivered to customers, and what kind of risk customer faces in industrial purchasing. Also the function of reference marketing towards customers is discussed. In the empirical part the realized value for existing customers is evaluated based on both numerical data and interviews. There’s also a brief case study about one customer. After that the value-based reference marketing for a target industry is examined through interviews of these potential customers. Finally answers to the research questions are stated and compared also to the theoretical knowledge about the subject. Results show that those customers’ machines which use the full service concept of ATA usually are able to save more time and material than the machines which use only some features of the product. Interviews indicated that sales arguments which focus on improved competitive status are not as effective as current arguments which focus on numerical improvements. In the case of potential customers in the new industry, current sales arguments likely work best for those whose irregular production situations are caused mainly by fault situations. When the actions of Vipetec were compared to ten key elements of creating customer references, it was seen that many of them the company has either already included in its strategy or has good chances to include them with the help of the results of this study.

ERP-järjestelmän käyttöönoton vaikutuksia johdon laskentatoimeen: näkökulmia suomalaisista yrityksistä

The objective of this study is to examine effects of ERP-system implementations to management accounting in Finnish companies. Study also explores if ERP-system implementation has influenced to development of management accounting role in companies. Theory part of study examines ERP-system projects and ERP-systems influence to management accounting development. Research is qualitative and empirical material has been collected by interviews from three companies and they ERP-system vendor. According to results ERP-system implementation has affected positively to companies management accounting in many different ways and also influenced to development of management accounting role in companies.

Framework for Regional Heating Energy Efficiency Assessment

The aim of this project was to develop general framework for systematic assessment of energy efficiency of heating on regional level in Russia. The framework created during this project includes two main instruments, namely: general regional heating energy efficiency assessment model (REEMod) and general regional heating energy efficiency assessment criteria for housing areas (REECrit). Framework pays extreme attention to realization of energy saving, overall cost efficiency and comfortable indoor climate. Life-cycle ideology was applied during creation of the framework. Application of the framework can provide decision-making process with systematically collected and processed information on current state of areas energy efficiency. Such information will help decision makers to evaluate current situation of the whole energy chain, to compare different development scenarios and to identify the most efficient improvement methods, thus supporting realization of regions efficient energy management. Simultaneous pursuit of energy savings, cost efficiency and indoor air quality can contribute to development of sustainable community. Presented instruments should be continuously developed further as an iterative process based on knew experience, development of technology and overall understanding of energy efficiency issues.

Nasopharyngeal colonization by pathogenic bacteria: effect of polymorphisms in innate immune genes of young children

Nasopharyngeal bacteria can asymptomatically colonize the nasopharynx of infants and young children but are also associated with the development of respiratory infections and diseases. Such nasopharyngeal bacteria include Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae and Staphylococcus aureus. The host defense against invading pathogens is largely relies germline-encoded pattern recognition receptors (PRR), which are expressed on the cells of innate immunity, and different cytokines. These include toll-like receptors (TLR), mannose-binding lectin (MBL) and different cytokines such as IL-17A. Single nucleotide polymorphisms (SNP) in these receptors and cytokines have been reported. The aim of this study was to investigate genetic polymorphisms in the genes for TLR2, 3 and 4, MBL as well as for IL-17A and their associations with nasopharyngeal pathogenic bacterial colonization during a two-year follow-up. The study revealed that polymorphisms in TLRs, MBL2 and IL17A are associated with the nasopharyngeal bacterial colonization in young children. Healthy young (2.6 months of age) children with variant types of MBL2, TLR2 R753Q or TLR4 D299G had an increased risk to be colonized by S. pneumonia, S. aureus or M. catarrhalis, respectively. Moreover, variant types of MBL2 in healthy children with might facilitate human rhinovirus (HRV)-induced S. pneumoniae colonization at 2.6 months of age. The polymorphism of TLR4 D299G was shown to be associated with M. catarrhalis colonization throughout the whole two-year follow-up (2.6, 13 and 24 months of age) and also with the bacterial load of this pathogen. Also, the polymorphism of IL17A G152A was shown to be associated with increased risk to be colonized by S. pneumoniae at 13 and 24 months of age. Furthermore, the results suggest that IL17A G152A has an effect on production of serum IL-17A already at young age. In conclusion, the results of this study indicate that polymorphisms in the key PRRs and IL17A seem to play an important role to colonization of S. pneumoniae, M. catarrhalis, and S. aureus in healthy young Finnish children. The nasopharyngeal colonization by these pathogenic bacteria may further promote the development of respiratory infections and may be related to development of asthma and allergy in the later life of children. These findings offer a possible explanation why some children have more respiratory infections than other children and provide a rational basis for future studies in this field.

Distribution of small proteoglycans and glycosaminoglycans in humerus-related articular cartilage of chickens

The expression of components present in the cartilaginous extracellular matrix is related to development, gender, and genotype, as well as to the biomechanical properties of each type of cartilage. In the present study, we analyzed small proteoglycans and glycosaminoglycans present in different cartilages of the chicken wing after extraction with guanidine hydrochloride or papain. Quantitative analysis of glycosaminoglycans showed a larger amount in humeral cartilage (around 200 mg/g tissue) than in articular cartilage of the radius and ulna, with 138 and 80 mg/g tissue, respectively. Non-collagenous proteins isolated were predominantly from cartilage in the proximal regions of the humerus and radius. D4 fractions obtained by ultracentrifugation were separated by DEAE-Sephacel and Octyl-Sepharose chromatography and analyzed by SDS-PAGE. Two bands of 57 and 70-90 kDa were observed for all samples treated with ß-mercaptoethanol. Immunoblotting of these proteins was positive for the small proteoglycans fibromodulin and decorin, respectively. Apparently, the 57-kDa protein is present in macromolecular complexes of 160 and 200 kDa. Chondroitin sulfate was detected in all regions. HPLC analysis of the products formed by chondroitinase AC and ABC digestion mainly revealed ß-D-glucuronic acid and N-acetyl ß-D-galactosamine residues. The 4-sulfation/6-sulfation ratio was close to 3, except for the proximal cartilage of the radius (2.5). These results suggest functional differences between the scapula-humerus, humerus-ulna, and humerus-radius joints of the chicken wing. This study contributes to the understanding of the physiology of cartilage and joints of birds under different types of mechanical stress.

Tuotekehitysprosessin alkupään järjestäminen pelialan yrityksessä

Tämän diplomityön tarkoitus on rakentaa mobiilipeliyritykselle tuotekehitysprosessin alkupään prosessi tuotekehityksen tehostamiseksi. Toimialan dynaamisuudesta ja hyperkilpailullisuudesta johtuen sekä projektien abstraktin luonteen takia tulee mobiilipelikehitysyritysten erityisesti panostaa tuotekehityksen alkuvaiheisiin. Työ tutkii yleisiä tuotekehityksen periaatteita sekä yleisiä olemassaolevia tuotekehitysprosesseja. Tarkastelun kohteena ovat erityisesti innovatiivinen organisaatio ja benchmarking tuotekehityksen apuna. Yleisesti tuotekehitysprosesseista tutustutaan yleisimpiin malleihin, jotka ovat olleet valtavirran käytössä jo pitkään. Prosessien tarkastelun lisäksi niitä tutkitaan kriittisesti ja löydetään osa-alueita, joihin tulee keskittyä erityisesti tuotekehitysprosessin alkupään järjestämisessä. Lisäksi työssä paneudutaan alan menestyneiden yritysten toimintatapoihin, joista haetaan oppia rakennettavaan malliin. Työssä käsitellään myös toimialan ominaispiirteitä, joista johtuen perinteiset tuotekehitysprosessit eivät ole optimaalisia alalle. Työn tuloksena saadaan virtaviivainen prosessimalli, joka maksimoi luovuuden, mutta säästää resursseja ja luo selkeät linjat prosessin läpivientiin. Rakennettuun malliin pohditaan myös kehitysehdotuksia, ja sille on laadittu kevyt jatkokehityssuunnitelma. Malli menee suoraan yrityksen käyttöön, joten lopullinen malli tulee myös hioutumaan tuotekehitysprojektien edetessä. Työssä on erityistä se, että työn tekijä on toiminut alalla työtehtävissä, ja malli on hioutunut pitkän ajan kuluessa. Täten suuri osa työstä on tekijän hiljaisen tiedon avaamista ja pohtimista.

Polymorphism of the promoter region and exon 1 of the CTLA4 gene in endemic pemphigus foliaceus (fogo selvagem)

Endemic pemphigus foliaceus (EPF) is an autoimmune bullous skin disease characterized by acantholysis and antibodies against a desmosomal protein, desmoglein 1. Genetic and environmental factors contribute to development of this multifactorial disease. HLA class II and some cytokine gene polymorphisms are the only genetic markers thus far known to be associated with susceptibility to or protection from EPF. The cytotoxic T-lymphocyte antigen-4 gene (CTLA4) encodes a key immunoreceptor molecule that regulates and inhibits T-cell proliferation. It participates in the regulatory process controlling autoreactivity and therefore has been considered a strong candidate gene in autoimmune diseases. In the search for genes that might influence EPF pathogenesis, we analyzed variants of the CTLA4 gene in a sample of 118 patients and 291 controls from a Brazilian population. This is the first study investigating the possible role of polymorphisms of the 2q33 chromosomal region in differential susceptibility to pemphigus foliaceus. Promoter region and exon 1 single nucleotide polymorphisms -318 (C,T) and 49 (A,G) were genotyped using sequence-specific oligonucleotide probes after amplification by the polymerase chain reaction. The allelic and genotypic frequencies did not differ significantly between the patient and the control groups (-318T: 9.8 and 10.9%, 49G: 33.0 and 35.2% were the allelic frequencies in patients and controls, respectively). In addition, no significant difference was found when the patient and control population samples were stratified by the presence of HLA-DRB1 alleles. We conclude that the CTLA4 -318 (C,T) and 49 (A,G) polymorphisms do not play a major role in EPF development.

Apply of energy storages in electricity distribution networks and reserve capacity applications

The Thesis is dedicated to development of an operative tool to support decision making of battery energy storages implementation in distribution networks. The basics of various battery technologies, their perspectives and challenges are represented in the Thesis. Mathematical equations that describe economic effect from battery energy storage installation are offered. The main factors that influence profitability of battery settings have been explored and mathematically defined. Mathematical model and principal trends of battery storage profitability under an impact of the major factors are determined. The meaning of annual net value was introduced to show the difference between savings and required costs. The model gives a clear vision for dependencies between annual net value and main factors. Proposals for optimal network and battery characteristics are suggested.

Suomalaisen pienpanimon kansainvälistymismahdollisuudet Ruotsissa

Työn tavoitteena on kartoittaa suomalaisen pienpanimon kansainvälistymismahdollisuuksia valitulla kohdemarkkina-alueella, hankkia kattavasti informaatiota kansainvälistymiseen vaadittavista asioista, sekä arvioida toimeksiantajayrityksen valmiuksia kansainvälistymiseen. Tarkoituksena on näiden asioiden perusteella muodostaa suomalaiselle pienpanimolle sopiva kansainvälistymispolku, valita operaatiomuoto kohdemarkkinoilla toimimiseksi sekä hahmotella jo ensimmäiset askeleet kansainvälisen toiminnan aloittamiseksi. Kansainvälistyminen on kokonaisvaltainen oppimis- ja muutosprosessi, jonka tuloksena yritys laajentaa omaa toimintaansa kansainvälisille markkinoille. Pienpanimolle kansainvälistyminen asettaa haasteita etenkin resurssien rajallisuuteen liittyen, mutta resursseja voidaan kehittää ja lisätä yritysten välisen verkostoitumisen ja muiden organisaatioiden avulla. Tietämyksen kasvattaminen ja verkostoaseman parantaminen syventää yrityksen kansainvälistä toimintaa ja vie kansainvälistymisprosessia eteenpäin. Suomalaisen pienpanimon kansainvälistymisessä avainasemaan nousee oikean yhteistyökumppanin löytäminen. Huolellinen valmistautuminen parantaa mahdollisuuksia onnistua, mutta kansainvälistymistä voi myös harjoitella ja samalla verkostoitua kohdemarkkinoilla hyödyntämällä pienpanimoille tyypillisiä kansainvälisiä yhteistyömuotoja.

Risk management in transportation companies: Russian and Finnish practices

Development of risk management practices became significant part of transportation companies’ strategy. Evolution from insurance management into enterprise risk management (ERM) led to development of risk management tools and methods. The purpose of this thesis is to design technique for evaluation of risk management practices of national transportation companies. The empirical research is made on the example of Russian and Finnish transportation companies. The required data was conducted with a help of survey. The result of the thesis is designed technique for risk management practices evaluation that allows to compare practices of different countries and organizations with different characteristics. The Master thesis has novelty in theoretical and practical contribution. It was designed new technique based on realization of the method of APIS. Moreover, it has practical implication as managers can utilize this method for comparison of practices between different countries, different organization and even different units within particular organization.

The human rights dilemma : an east-west encounter : Germany and China in 1996 /

Conflicts over human rights in relations between East Asia and the West have increased since the end of the Cold War. Western governments express concern about human rights standards in East Asian countries. In the East, these expressions have been perceived as interference in internal affairs. Due to dramatic economic development, East Asian nations recently have gained in pride and self-confidence as global actors. Such development is observed with suspicion in the West. Concerned about the decline of global U.S. influence, some American scholars have re-invented the notion of "culture" to point at an alleged East Asian threat. Also East Asian statesmen use the cultural argument by claiming the existence of so-called 'Asian values', which they allege are the key to Eastern economic success. This thesis argues that issues of human rights in East-West relations are not only a consequence of well-intended concern by Western governments regarding the human rights and welfare of the citizens of East Asian nations, but are in fact dominated by and used as a pawn in interplay with more complicated questions of global power and economic relations between East and West. The thesis reviews the relevance of culture in East-West relations. In the West, particularly Samuel P. Huntington with his prediction of the Clash of Civilizations stands out. Singapore's Lee Kuan Yew has been very vocal on the Eastern side. Whereas the West tries to cope with its decrease of global influence, after hundreds of years under Western hegemonism, the East believes in an Asian way of development without interference form the West. Most of this dispute revolves around the issue of human rights. The West claims the universality of rights which in fact emphasizes political and civil rights. Western countries critizise poor human rights standards in East Asia. The East, in return, accuses the West of hypocritical policies that seek global dominance. East Asian governments assert that due to a different stage of development they have to stress first their rights to development in order to assure stability. In particular, China argues this way. The country's leadership, however, shows concern about human rights and has already improved its human rights record over the past years. This thesis analyses the dispute over human rights in a case study on Germany and China. Both countries have a mutual interest in trade relations which has conflicted with Germany's criticism of China's problematic human rights record. In 1996, the two countries clashed after the German parliament passed a resolution condemning China's treatment of Tibet. This caused a lot of damage to the Chinese-German relationship which in the course of the year went back to normality. In the light of these frictions a German human rights policy that focuses on unspectacular grass-roots support of China, for example in strengthening China's legal system, would be preferable. Such co-operation must be based on mutual respect.

Canadian Shredded Wheat Company Fonds

In 1893 Attorney Henry Drushel Perky and William H. Ford invented a machine for the preparation of cereals for food. Perky soon realized that the actual cereal biscuits were more popular than the machines and he opened Shredded Wheat plants in Massachusetts and Niagara Falls, New York. In 1904, the Niagara Falls, Canada plant was opened. These factories also served as tourist attractions. In 1907, one hundred thousand people visited the plants on both sides of the border. In 1928, the company was sold to The National Biscuit Company and the product name changed to Nabisco Shredded Wheat. The name of the plant was changed to Nabisco Foods in 1956 to reflect the variety of foods that were being produced at that time. In 1985, Nabisco was purchased by J.R. Reynolds thus forming RJR Nabisco. In 1994, RJR sold its breakfast cereal business to Kraft Foods and the international licenses to General Mills. Shredded Wheat is now integrated into the Post Foods portfolio. with information from: Niagara Falls Canada a History by The Kiwanis Club of Stamford, Ontario Inc. and Business Source Complete