World Wide Web korpuksena kielitieteellisen tutkimusaineiston haku verkkosivuilta

Tämä tutkielma käsittelee World Wide Webin sisältämien verkkosivujen sisältöjen käyttöä korpusmaisesti kielitieteellisenä tutkimusaineistona. World Wide Web sisältää moninkertaisesti enemmän tekstiä kuin suurimmat olemassa olevat perinteiset tekstikorpukset, joten verkkosivuilta voi todennäköisesti löytää paljon esiintymiä sellaisista sanoista ja rakenteista, jotka ovat perinteisissä korpuksissa harvinaisia. Verkkosivuja voidaan käyttää aineistona kahdella eri tavalla: voidaan kerätä satunnainen otos verkkosivuista ja luoda itsenäinen korpus niiden sisällöistä, tai käyttää koko World Wide Webiä korpuksena verkkohakukoneiden kautta. Verkkosivuja on käytetty tutkimusaineistona monilla eri kielitieteen aloilla, kuten leksikograafisessa tutkimuksessa, syntaktisten rakenteiden tutkimuksessa, pedagogisena materiaalina ja vähemmistökielten tutkimuksessa. Verkkosivuilla on perinteisiin korpuksiin verrattuna useita haitallisia ominaisuuksia, jotka pitää ottaa huomioon, kun niitä käytetään aineistona. Kaikki sivut eivät sisällä kelvollista tekstiä, ja sivut ovat usein esimerkiksi HTML-muotoisia, jolloin ne pitää muuttaa helpommin käsiteltävissä olevaan muotoon. Verkkosivut sisältävät enemmän kielellisiä virheitä kuin perinteiset korpukset, ja niiden tekstityypit ja aihepiirit ovat runsaslukuisempia kuin perinteisten korpusten. Aineiston keräämiseen verkkosivuilta tarvitaan tehokkaita ohjelmatyökaluja. Näistä yleisimpiä ovat kaupalliset verkkohakukoneet, joiden kautta on mahdollista päästä nopeasti käsiksi suureen määrään erilaisia sivuja. Näiden lisäksi voidaan käyttää erityisesti kielitieteellisiin tarpeisiin kehitettyjä työkaluja. Tässä tutkielmassa esitellään ohjelmatyökalut WebCorp, WebAsCorpus.org, BootCaT ja Web as Corpus Toolkit, joiden avulla voi hakea aineistoa verkkosivuilta nimenomaan kielitieteellisiin tarkoituksiin.

Tiedonhakustrategiat World Wide Webissä

Tutkimuksen tarkoituksena on selvittää, millaisia tiedonhakustrategioita tiedonhakijatkäyttävät etsiessään tietoa Internetistä. Käyttäjät luokitellaan kolmeen ryhmään tiedonhakustrategiansa mukaan. Haku-suuntautuneet käyttäjät käyttävät enimmäkseen hakukoneita, niin koko Internetin kattavia kuin sivustojen sisäisiäkin. Linkkisuuntautuneet taas joko tietävät tai arvaavat kohdesivuston osoitteen tai käyttävät laajoja hierarkkisia hakemistoja tiedon löytämiseen. He navigoivat mielummin sivustollakin linkkejä käyttäen eivätkä yleensä käytä hakutoimintoa. Eriytyneet käyttäjät eivät säännönmukaisesti suosi kumpaakaan tapaa, vaan valitsevat strategian tehtävän mukaan. Tietoa kerättiin kahdella tavalla: WWW-sivulla olleella kyselylomakkeella ja tiedonhakutestillä, jossa käyttäjille annettiin suoritettavaksi erilaisia tiedonhakutehtäviä. Tiedonhakutehtävät lajiteltiin kolmeen ryhmään sen mukaan, mitä strategiaa ne suosivat: hakustrategiaa suosivat, linkkistrategiaa suosivat ja neutraalit tehtävät. Tutkimusongelmana oli selvittää, kuinka tehtävän tyyppi ja ATK- ja Internet-kokemus vaikuttavat tiedonhakustrategian valintaan. Kävi ilmi, ettei käyttäjien suuntautuneisuus tiettyyn strategiaan vaikuta tiedonhakustrategian valintaan, vaan ainoastaan tehtävän tyyppi oli merkitsevä tekijä. Aikaisemman tutkimustiedon valossa kokeenet suosivat haku-suuntautunutta strategiaa. Tässä tutkimuksessa havaittiin, että kokemus lisäsi molempien strategioiden käyttöä yhtäläisesti, mutta tämä ilmiö oli havaittavissa ainoastaan kysely-lomakkeen pohjalta, ei testeissä. Molempien tiedonhakustrategioiden käyttö lisääntyy kokemuksen myötä, mutta suhteelliset osuudet pysyvät samoina. Syyksi sille, että kokeneet eivät suosineet hakustrategiaa, esitetään sitä, että tehtävät olivat liian helppoja, jolloin kokemus ei pääse auttamaan. Oleellisia eroja suoritusajoissa tai hakustrategian vaihdon tiheydessä ei havaittu suhteessa kokemukseen, ainoastaan suhteessa tehtävän tyyppiin.Tämäkin selitettiin toisentyyppisten tehtävien helppoudella. Tutkimuksessa pohditaan lisäksi asiantuntijuuden syntyä tiedonhakukontekstissa sekä esitetään metatietohypoteesi, jonka mukaan tiedonhakustrategian valintaan vaikuttaa tärkeänä tekijänä käyttäjän metatieto hakupalveluista. Metatietoon kuuluu tieto siitä, mitä hakukoneita on saatavilla, mitä tietoa verkosta kannattaa hakea, millä yrityksillä ja yhteisöillä on sisältörikkaat sivut jne, ja minkä tyyppistä tietoa yleensä on saatavilla. Kaikenkaikkiaan strategian valintaan esitetään taustalle kolmen tason tiedon vaikutusta: 1) oma asiantuntemus haettavasta alasta, 2) metatieto Internetin tiedonhakupalveluista sekä 3) tekninen tieto siitä, kuinka hakukoneet toimivat. Avainsanat: tiedonhaku, tiedonhakustrategia, hakukone, WWW, metatieto, kognitiivinen psykologia

Rhizoctonia solani as a potato pathogen : Variation of isolates in Finland and host response

Rhizoctonia solani is a soil inhabiting basidiomycetous fungus able to induce a wide range of symptoms in many plant species. This genetically complex species is divided to 13 anastomosis groups (AG), of which AG-3 is specialized to infect potato. However, also a few other AGs are able to infect or live in close contact with potato. On potato, R. solani infection causes two main types of diseases including stem canker observed as a dark brown lesions on developing stems and stolons, and black scurf that develops on new tubers close to the time of harvest. These disease symptoms are collectively called a ‘Rhizoctonia disease complex’. Between the growing seasons R. solani survives in soil and plant debri as sclerotia or as the sclerotia called black scurf on potato tubers which when used as seed offer the main route for dispersal of the fungus to new areas. The reasons for the dominance of AG-3 on potato seem to be attributable to its highly specialization to potato and its ability to infect and form sclerotia efficiently at low temperatures. In this study, a large nationwide survey of R. solani isolates was made in potato crops in Finland. Almost all characterized isolates belonged to AG-3. Additionally, three other AGs (AG-2-1, AG-4 and AG-5) were found associated with symptoms on potato plants but they were weaker pathogens on potato than AG-3 as less prone to form black scurf. According to phylogenetic analysis of the internal transcribed sequences (ITS) of the ribosomal RNA genes the Finnish AG-3 isolates are closely related to each other even though a wide variation of physiological features was observed between them. Detailed analysis of the ITS regions revealed single nucleotide polymorphism in 14 nucleotide positions of ITS-1 and ITS-2. Additionally, compensatory base changes on ITS-2 were detected which suggests that potato-infecting R. solani AG-3 could be considered as a separate species instead of an AG of R. solani. For the first time, molecular defence responses were studied and detected during the early phases of interaction between R. solani AG-3 and potato. Extensive systemic signalling for defence exploiting several known defence pathways was activated as soon as R. solani came into close contact with the base of a sprout. The defence response was strong enough to protect vulnerable sprout tips from new attacks by the pathogen. These results at least partly explain why potato emergence is eventually successful even under heavy infection pressure by R. solani.

Lantibiotic Nisin and Its Detection Methods

The type A lantibiotic nisin produced by several Lactococcus lactis strains, and one Streptococcus uberis strainis a small antimicrobial peptide that inhibits the growth of a wide range of gram-positive bacteria, such as Bacillus, Clostridium, Listeria and Staphylococcus species. It is nontoxic to humans and used as a food preservative (E234) in more than 50 countries including the EU, the USA, and China. National legislations concerning maximum addition levels of nisin in different foods vary greatly. Therefore, there is a demand for non-laborious and sensitive methods to identify and quantify nisin reliably from different food matrices. The horizontal inhibition assay, based on the inhibitory effect of nisin to Micrococcus luteus is the base for most quantification methods developed so far. However, the sensitivity and accuracy of the agar diffusion method is affected by several parameters. Immunological tests have also been described. Taken into account the sensitivity of immunological methods to interfering substances within sample matrices, and possible cross-reactivities with lantibiotics structurally close to nisin, their usefulness for nisin detection from food samples remains limited. The proteins responsible for nisin biosynthesis, and producer self-immunity are encoded by genes arranged into two inducible operons, nisA/Z/QBTCIPRK and nisFEG, which also contain internal, constitutive promoters PnisI and PnisR. The transmembrane histidine kinase NisK and the response regulator NisR form a two-component signal transduction system, in which NisK autophosphorylates after exposure to extra cellular nisin, and subsequently transfers the phosphate to NisR. The phosphorylated NisR then relays the signal downstream by binding to two regulated promoters in the nisin gene cluster, i.e the nisA/Z/Qand the nisF promoters, thus activating transcription of the structural gene nisA/Z/Q and the downstream genes nisBTCIPRK from the nisA/Z/Q promoter, and the genes nisFEG from the nisF promoter. In this work two novel and highly sensitive nisin bioassays were developed. Both of these quantification methods were based on NisRK mediated, nisin induced Green Fluorescent Protein (GFP) fluorescence. The suitabilities of these assays for quantifica¬tion of nisin from food samples were evaluated in several food matrices. These bioassays had nisin sensitivities in the nanogram or picogram levels. In addition, shelf life of nisin in cooked sausages and retainment of the induction activity of nisin in intestinal chyme (intestinal content) was assessed.

Schiff Base Complexes and their Assemblies on Surfaces

Schiff bases and their transition metal complexes are of significant current interest even though they have been prepared for decades. They have been used in various applications such as catalysis, corrosion protection, and molecular sensors. In this study, N-aryl Schiff base ketimine ligands as well as numerous new, differently substituted salen and salophen-type ligands and their cobalt(II), copper(II), iron(II), manganese(II), and nickel(II) complexes were synthesised. New solid state structures of the above compounds and the dioxygen coordination properties of cobalt(II) complexes and catalytic properties of three synthesised binuclear complexes were examined. The prepared complexes were applied in the formation of self-assembled layers on a polycrystalline gold surface and liquid-graphite interface. The effect of metal ion and ligand structure on the as-formed patterns was studied. When studying gold surfaces, a unique thiol-assisted dissolution of elemental gold was observed and a new thin gold foil preparation method was introduced. In the summary, synthesis, structures, and properties of Schiff base ligands and their transition metal complexes are described in detail and the applications of these reviewed. Assemblies of other complexes on a liquid-graphite interface and on a gold surface are also presented, and the surface characterisation methods and surfaces employed are described.

Export of organic matter, sulphate and base cations from boreal headwater catchments downstream to the coast: impacts of land use and climate

The terrestrial export of dissolved organic matter (DOM) is associated with climate, vegetation and land use, and thus is under the influence of climatic variability and human interference with terrestrial ecosystems, their soils and hydrological cycles. The present study provides an assessment of spatial variation of DOM concentrations and export, and interactions between DOM, catchment characteristics, land use and climatic factors in boreal catchments. The influence of catchment characteristics, land use and climatic drivers on the concentrations and export of total organic carbon (TOC), total organic nitrogen (TON) and dissolved organic phosphorus (DOP) was estimated using stream water quality, forest inventory and climatic data from 42 Finnish pristine forested headwater catchments, and water quality monitoring, GIS land use, forest inventory and climatic data from the 36 main Finnish rivers (and their sub-catchments) flowing to the Baltic Sea. Moreover, the export of DOM in relation to land use along a European climatic gradient was studied using river water quality and land use data from four European areas. Additionally, the role of organic and minerogenic acidity in controlling pH levels in Finnish rivers and pristine streams was studied by measuring organic anion, sulphate (SO4) and base cation (Ca, Mg, K and Na) concentrations. In all study catchments, TOC was a major fraction of DOM, with much lower proportions of TON and DOP. Moreover, most of TOC and TON was in a dissolved form. The correlation between TOC and TON concentrations was strong and TOC concentrations explained 78% of the variation in TON concentrations in pristine headwater streams. In a subgroup of 20 headwater catchments with similar climatic conditions and low N deposition in eastern Finland, the proportion of peatlands in the catchment and the proportion of Norway spruce (Picea abies Karsten) of the tree stand had the strongest correlation with the TOC and TON concentrations and export. In Finnish river basins, TOC export increased with the increasing proportion of peatland in the catchment, whereas TON export increased with increasing extent of agricultural land. The highest DOP concentrations and export were recorded in river basins with a high extent of agricultural land and urban areas, reflecting the influence of human impact on DOP loads. However, the most important predictor for TOC, TON and DOP export in Finnish rivers was the proportion of upstream lakes in the catchment. The higher the upstream lake percentage, the lower the export indicating organic matter retention in lakes. Molar TOC:TON ratio decreased from headwater catchments covered by forests and peatlands to the large river basins with mixed land use, emphasising the effect of the land use gradient on the stoichiometry of rivers. This study also demonstrated that the land use of the catchments is related to both organic and minerogenic acidity in rivers and pristine headwater streams. Organic anion dominated in rivers and streams situated in northern Finland, reflecting the higher extent of peatlands in these areas, whereas SO4 dominated in southern Finland and on western coastal areas, where the extent of fertile areas, agricultural land, urban areas, acid sulphate soils, and sulphate deposition is highest. High TOC concentrations decreased pH values in the stream and river water, whereas no correlation between SO4 concentrations and pH was observed. This underlines the importance of organic acids in controlling pH levels in Finnish pristine headwater streams and main rivers. High SO4 concentrations were associated with high base cation concentrations and fertile areas, which buffered the effects of SO4 on pH.

Identification of genetic susceptibility loci for migraine

Migraine is the common cause of chronic episodic headache, affecting 12%-15% of the Caucasian population (41 million Europeans and some half a million Finns), and causes considerable loss of quality of life to its sufferers, as well as being linked to increased risk for a wide range of conditions, from depression to stroke. Migraine is the 19th most severe disease in terms of disability-adjusted life years, and 9th among women. It is characterized by attacks of headache accompanied by sensitivity to external stimuli lasting 4-72 hours, and in a third of cases by neurological aura symptoms, such as loss of vision, speech or muscle function. The underlying pathophysiology, including what triggers migraine attacks and why they occur in the first place, is largely unknown. The aim of this study was to identify genetic factors associated with the hereditary susceptibility to migraine, in order to gain a better understanding of migraine mechanisms. In this thesis, we report the results of genetic linkage and association analyses on a Finnish migraine patient collection as well as migraineurs from Australia, Denmark, Germany, Iceland and the Netherlands. Altogether we studied genetic information of nearly 7,000 migraine patients and over 50,000 population-matched controls. We also developed a new migraine analysis method called the trait component analysis, which is based on individual patient responses instead of the clinical diagnosis. Using this method, we detected a number of new genetic loci for migraine, including on chromosome 17p13 (HLOD 4.65) and 10q22-q23 (female-specific HLOD 7.68) with significant evidence of linkage, along with five other loci (2p12, 8q12, 4q28-q31, 18q12-q22, and Xp22) detected with suggestive evidence of linkage. The 10q22-q23 locus was the first genetic finding in migraine to show linkage to the same locus and markers in multiple populations, with consistent detection in six different scans. Traditionally, ion channels have been thought to play a role in migraine susceptibility, but we were able to exclude any significant role for common variants in a candidate gene study of 155 ion transport genes. This was followed up by the first genome-wide association study in migraine, conducted on 2,748 migraine patients and 10,747 matched controls followed by a replication in 3,209 patients and 40,062 controls. In this study, we found interesting results with genome-wide significance, providing targets for future genetic and functional studies. Overall, we found several promising genetic loci for migraine providing a promising base for future studies in migraine.

Identification of genetic susceptibility loci for migraine

Migraine is the common cause of chronic episodic headache, affecting 12%-15% of the Caucasian population (41 million Europeans and some half a million Finns), and causes considerable loss of quality of life to its sufferers, as well as being linked to increased risk for a wide range of conditions, from depression to stroke. Migraine is the 19th most severe disease in terms of disability-adjusted life years, and 9th among women. It is characterized by attacks of headache accompanied by sensitivity to external stimuli lasting 4-72 hours, and in a third of cases by neurological aura symptoms, such as loss of vision, speech or muscle function. The underlying pathophysiology, including what triggers migraine attacks and why they occur in the first place, is largely unknown. The aim of this study was to identify genetic factors associated with the hereditary susceptibility to migraine, in order to gain a better understanding of migraine mechanisms. In this thesis, we report the results of genetic linkage and association analyses on a Finnish migraine patient collection as well as migraineurs from Australia, Denmark, Germany, Iceland and the Netherlands. Altogether we studied genetic information of nearly 7,000 migraine patients and over 50,000 population-matched controls. We also developed a new migraine analysis method called the trait component analysis, which is based on individual patient responses instead of the clinical diagnosis. Using this method, we detected a number of new genetic loci for migraine, including on chromosome 17p13 (HLOD 4.65) and 10q22-q23 (female-specific HLOD 7.68) with significant evidence of linkage, along with five other loci (2p12, 8q12, 4q28-q31, 18q12-q22, and Xp22) detected with suggestive evidence of linkage. The 10q22-q23 locus was the first genetic finding in migraine to show linkage to the same locus and markers in multiple populations, with consistent detection in six different scans. Traditionally, ion channels have been thought to play a role in migraine susceptibility, but we were able to exclude any significant role for common variants in a candidate gene study of 155 ion transport genes. This was followed up by the first genome-wide association study in migraine, conducted on 2,748 migraine patients and 10,747 matched controls followed by a replication in 3,209 patients and 40,062 controls. In this study, we found interesting results with genome-wide significance, providing targets for future genetic and functional studies. Overall, we found several promising genetic loci for migraine providing a promising base for future studies in migraine.

Accurate mass-based analysis in human sport doping control : Application of liquid chromatography - time-of-flight mass spectrometry

Human sport doping control analysis is a complex and challenging task for anti-doping laboratories. The List of Prohibited Substances and Methods, updated annually by World Anti-Doping Agency (WADA), consists of hundreds of chemically and pharmacologically different low and high molecular weight compounds. This poses a considerable challenge for laboratories to analyze for them all in a limited amount of time from a limited sample aliquot. The continuous expansion of the Prohibited List obliges laboratories to keep their analytical methods updated and to research new available methodologies. In this thesis, an accurate mass-based analysis employing liquid chromatography - time-of-flight mass spectrometry (LC-TOFMS) was developed and validated to improve the power of doping control analysis. New analytical methods were developed utilizing the high mass accuracy and high information content obtained by TOFMS to generate comprehensive and generic screening procedures. The suitability of LC-TOFMS for comprehensive screening was demonstrated for the first time in the field with mass accuracies better than 1 mDa. Further attention was given to generic sample preparation, an essential part of screening analysis, to rationalize the whole work flow and minimize the need for several separate sample preparation methods. Utilizing both positive and negative ionization allowed the detection of almost 200 prohibited substances. Automatic data processing produced a Microsoft Excel based report highlighting the entries fulfilling the criteria of the reverse data base search (retention time (RT), mass accuracy, isotope match). The quantitative performance of LC-TOFMS was demonstrated with morphine, codeine and their intact glucuronide conjugates. After a straightforward sample preparation the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The hydrophilic interaction technique (HILIC) provided good chromatographic separation, which was critical for the morphine glucuronide isomers. A wide linear range (50-5000 ng/ml) with good precision (RSD<10%) and accuracy (±10%) was obtained, showing comparable or better performance to other methods used. In-source collision-induced dissociation (ISCID) allowed confirmation analysis with three diagnostic ions with a median mass accuracy of 1.08 mDa and repeatable ion ratios fulfilling WADA s identification criteria. The suitability of LC-TOFMS for screening of high molecular weight doping agents was demonstrated with plasma volume expanders (PVE), namely dextran and hydroxyethylstarch (HES). Specificity of the assay was improved, since interfering matrix compounds were removed by size exclusion chromatography (SEC). ISCID produced three characteristic ions with an excellent mean mass accuracy of 0.82 mDa at physiological concentration levels. In summary, by combining TOFMS with a proper sample preparation and chromatographic separation, the technique can be utilized extensively in doping control laboratories for comprehensive screening of chemically different low and high molecular weight compounds, for quantification of threshold substances and even for confirmation. LC-TOFMS rationalized the work flow in doping control laboratories by simplifying the screening scheme, expediting reporting and minimizing the analysis costs. Therefore LC-TOFMS can be exploited widely in doping control, and the need for several separate analysis techniques is reduced.

Lewis Acid-Lewis Base Mediated Metal-Free Hydrogen Activation and Catalytic Hydrogenation

Organocatalysis, the use of organic molecules as catalysts, is attracting increasing attention as one of the most modern and rapidly growing areas of organic chemistry, with countless research groups in both academia and the pharmaceutical industry around the world working on this subject. The literature review of this thesis mainly focuses on metal-free systems for hydrogen activation and organocatalytic reduction. Since these research topics are relatively new, the literature review also highlights the basic principles of the use of Lewis acid-Lewis base pairs, which do not react irreversibly with each other, as a trap for small molecules. The experimental section progresses from the first observation of the facile heterolytical cleavage of hydrogen gas by amines and B(C6F5)3 to highly active non-metal catalysts for both enantioselective and racemic hydrogenation of unsaturated nitrogen-containing compounds. Moreover, detailed studies of structure-reactivity relationships of these systems by X-ray, neutron diffraction, NMR methods and quantum chemical calculations were performed to gain further insight into the mechanism of hydrogen activation and hydrogenation by boron-nitrogen compounds.