Homogeneous Assays for Simplified Screening of HLA-conferred Genetic Disease Risk

The increasing incidence of type 1 diabetes has led researchers on a quest to find the reason behind this phenomenon. The rate of increase is too great to be caused simply by changes in the genetic component, and many environmental factors are under investigation for their possible contribution. These studies require, however, the participation of those individuals most likely to develop the disease, and the approach chosen by many is to screen vast populations to find persons with increased genetic risk factors. The participating individuals are then followed for signs of disease development, and their exposure to suspected environmental factors is studied. The main purpose of this study was to find a suitable tool for easy and inexpensive screening of certain genetic risk markers for type 1 diabetes. The method should be applicable to using whole blood dried on sample collection cards as sample material, since the shipping and storage of samples in this format is preferred. However, the screening of vast sample libraries of extracted genomic DNA should also be possible, if such a need should arise, for example, when studying the effect of newly discovered genetic risk markers. The method developed in this study is based on homogeneous assay chemistry and an asymmetrical polymerase chain reaction (PCR). The generated singlestranded PCR product is probed by lanthanide-labelled, LNA (locked nucleic acid)-spiked, short oligonucleotides with exact complementary sequences. In the case of a perfect match, the probe is hybridised to the product. However, if even a single nucleotide difference occurs, the probe is bound instead of the PCR product to a complementary quencher-oligonucleotide labelled with a dabcyl-moiety, causing the signal of the lanthanide label to be quenched. The method was applied to the screening of the well-known type 1 diabetes risk alleles of the HLA-DQB1 gene. The method was shown to be suitable as an initial screening step including thousands of samples in the scheme used in the TEDDY (The Environmental Determinants of Diabetes in the Young) study to identify those individuals at increased genetic risk. The method was further developed into dry-reagent form to allow an even simpler approach to screening. The reagents needed in the assay were in dry format in the reaction vessel, and performing the assay required only the addition of the sample and, if necessary, water to rehydrate the reagents. This allows the assay to be successfully executed even by a person with minimal laboratory experience.

Upconverting Phosphor Technology: Exceptional Photoluminescent Properties Light Up Homogeneous Bioanalytical Assays

The aim of the present study was to demonstrate the wide applicability of the novel photoluminescent labels called upconverting phosphors (UCPs) in proximity-based bioanalytical assays. The exceptional features of the lanthanide-doped inorganic UCP compounds stem from their capability for photon upconversion resulting in anti-Stokes photoluminescence at visible wavelengths under near-infrared (NIR) excitation. Major limitations related to conventional photoluminescent labels are avoided, rendering the UCPs a competitive next-generation label technology. First, the background luminescence is minimized due to total elimination of autofluorescence. Consequently, improvements in detectability are expected. Second, at the long wavelengths (>600 nm) used for exciting and detecting the UCPs, the transmittance of sample matrixes is significantly greater in comparison with shorter wavelengths. Colored samples are no longer an obstacle to the luminescence measurement, and more flexibility is allowed even in homogeneous assay concepts, where the sample matrix remains present during the entire analysis procedure, including label detection. To transform a UCP particle into a biocompatible label suitable for bioanalytical assays, it must be colloidal in an aqueous environment and covered with biomolecules capable of recognizing the analyte molecule. At the beginning of this study, only UCP bulk material was available, and it was necessary to process the material to submicrometer-sized particles prior to use. Later, the ground UCPs, with irregular shape, wide size-distribution and heterogeneous luminescence properties, were substituted by a smaller-sized spherical UCP material. The surface functionalization of the UCPs was realized by producing a thin hydrophilic coating. Polymer adsorption on the UCP surface is a simple way to introduce functional groups for bioconjugation purposes, but possible stability issues encouraged us to optimize an optional silica-encapsulation method which produces a coating that is not detached in storage or assay conditions. An extremely thin monolayer around the UCPs was pursued due to their intended use as short-distance energy donors, and much attention was paid to controlling the thickness of the coating. The performance of the UCP technology was evaluated in three different homogeneous resonance energy transfer-based bioanalytical assays: a competitive ligand binding assay, a hybridization assay for nucleic acid detection and an enzyme activity assay. To complete the list, a competitive immunoassay has been published previously. Our systematic investigation showed that a nonradiative energy transfer mechanism is indeed involved, when a UCP and an acceptor fluorophore are brought into close proximity in aqueous suspension. This process is the basis for the above-mentioned homogeneous assays, in which the distance between the fluorescent species depends on a specific biomolecular binding event. According to the studies, the submicrometer-sized UCP labels allow versatile proximity-based bioanalysis with low detection limits (a low-nanomolar concentration for biotin, 0.01 U for benzonase enzyme, 0.35 nM for target DNA sequence).

Homogeneous assay technologies in drug screening: Quenching Resonance Energy Transfer (QRET) technique

Information gained from the human genome project and improvements in compound synthesizing have increased the number of both therapeutic targets and potential lead compounds. This has evolved a need for better screening techniques to have a capacity to screen number of compound libraries against increasing amount of targets. Radioactivity based assays have been traditionally used in drug screening but the fluorescence based assays have become more popular in high throughput screening (HTS) as they avoid safety and waste problems confronted with radioactivity. In comparison to conventional fluorescence more sensitive detection is obtained with time-resolved luminescence which has increased the popularity of time-resolved fluorescence resonance energy transfer (TR-FRET) based assays. To simplify the current TR-FRET based assay concept the luminometric homogeneous single-label utilizing assay technique, Quenching Resonance Energy Transfer (QRET), was developed. The technique utilizes soluble quencher to quench non-specifically the signal of unbound fraction of lanthanide labeled ligand. One labeling procedure and fewer manipulation steps in the assay concept are saving resources. The QRET technique is suitable for both biochemical and cell-based assays as indicated in four studies:1) ligand screening study of β2 -adrenergic receptor (cell-based), 2) activation study of Gs-/Gi-protein coupled receptors by measuring intracellular concentration of cyclic adenosine monophosphate (cell-based), 3) activation study of G-protein coupled receptors by observing the binding of guanosine-5’-triphosphate (cell membranes), and 4) activation study of small GTP binding protein Ras (biochemical). Signal-to-background ratios were between 2.4 to 10 and coefficient of variation varied from 0.5 to 17% indicating their suitability to HTS use.

Methods for Region Based Paper Surface Roughness Measurement

Paperin pinnan karheus on yksi paperin laatukriteereistä. Sitä mitataan fyysisestipaperin pintaa mittaavien laitteiden ja optisten laitteiden avulla. Mittaukset vaativat laboratorioolosuhteita, mutta nopeammille, suoraan linjalla tapahtuville mittauksilla olisi tarvetta paperiteollisuudessa. Paperin pinnan karheus voidaan ilmaista yhtenä näytteelle kohdistuvana karheusarvona. Tässä työssä näyte on jaettu merkitseviin alueisiin, ja jokaiselle alueelle on laskettu erillinen karheusarvo. Karheuden mittaukseen on käytetty useita menetelmiä. Yleisesti hyväksyttyä tilastollista menetelmää on käytetty tässä työssä etäisyysmuunnoksen lisäksi. Paperin pinnan karheudenmittauksessa on ollut tarvetta jakaa analysoitava näyte karheuden perusteella alueisiin. Aluejaon avulla voidaan rajata näytteestä selvästi karheampana esiintyvät alueet. Etäisyysmuunnos tuottaa alueita, joita on analysoitu. Näistä alueista on muodostettu yhtenäisiä alueita erilaisilla segmentointimenetelmillä. PNN -menetelmään (Pairwise Nearest Neighbor) ja naapurialueiden yhdistämiseen perustuvia algoritmeja on käytetty.Alueiden jakamiseen ja yhdistämiseen perustuvaa lähestymistapaa on myös tarkasteltu. Segmentoitujen kuvien validointi on yleensä tapahtunut ihmisen tarkastelemana. Tämän työn lähestymistapa on verrata yleisesti hyväksyttyä tilastollista menetelmää segmentoinnin tuloksiin. Korkea korrelaatio näiden tulosten välillä osoittaa onnistunutta segmentointia. Eri kokeiden tuloksia on verrattu keskenään hypoteesin testauksella. Työssä on analysoitu kahta näytesarjaa, joidenmittaukset on suoritettu OptiTopolla ja profilometrillä. Etäisyysmuunnoksen aloitusparametrit, joita muutettiin kokeiden aikana, olivat aloituspisteiden määrä ja sijainti. Samat parametrimuutokset tehtiin kaikille algoritmeille, joita käytettiin alueiden yhdistämiseen. Etäisyysmuunnoksen jälkeen korrelaatio oli voimakkaampaa profilometrillä mitatuille näytteille kuin OptiTopolla mitatuille näytteille. Segmentoiduilla OptiTopo -näytteillä korrelaatio parantui voimakkaammin kuin profilometrinäytteillä. PNN -menetelmän tuottamilla tuloksilla korrelaatio oli paras.

Mass transfer and particleinteractions in granular systems and suspension flows

The purpose of this study was to investigate some important features of granular flows and suspension flows by computational simulation methods. Granular materials have been considered as an independent state ofmatter because of their complex behaviors. They sometimes behave like a solid, sometimes like a fluid, and sometimes can contain both phases in equilibrium. The computer simulation of dense shear granular flows of monodisperse, spherical particles shows that the collisional model of contacts yields the coexistence of solid and fluid phases while the frictional model represents a uniform flow of fluid phase. However, a comparison between the stress signals from the simulations and experiments revealed that the collisional model would result a proper match with the experimental evidences. Although the effect of gravity is found to beimportant in sedimentation of solid part, the stick-slip behavior associated with the collisional model looks more similar to that of experiments. The mathematical formulations based on the kinetic theory have been derived for the moderatesolid volume fractions with the assumption of the homogeneity of flow. In orderto make some simulations which can provide such an ideal flow, the simulation of unbounded granular shear flows was performed. Therefore, the homogeneous flow properties could be achieved in the moderate solid volume fractions. A new algorithm, namely the nonequilibrium approach was introduced to show the features of self-diffusion in the granular flows. Using this algorithm a one way flow can beextracted from the entire flow, which not only provides a straightforward calculation of self-diffusion coefficient but also can qualitatively determine the deviation of self-diffusion from the linear law at some regions nearby the wall inbounded flows. Anyhow, the average lateral self-diffusion coefficient, which was calculated by the aforementioned method, showed a desirable agreement with thepredictions of kinetic theory formulation. In the continuation of computer simulation of shear granular flows, some numerical and theoretical investigations were carried out on mass transfer and particle interactions in particulate flows. In this context, the boundary element method and its combination with the spectral method using the special capabilities of wavelets have been introduced as theefficient numerical methods to solve the governing equations of mass transfer in particulate flows. A theoretical formulation of fluid dispersivity in suspension flows revealed that the fluid dispersivity depends upon the fluid properties and particle parameters as well as the fluid-particle and particle-particle interactions.

Hiomon AI-järjestelmän toimivuuden arviointi

Työn tavoitteena oli uudentyyppisen hiontaprosessin ohjausjärjestelmän kehittäminen ja testaaminen UPM-Kymmene Kaukaan hiomossa. Uuden ohjausjärjestelmän perusajatuksena oli pitää yksittäistä hiomakiveä jatkuvasti optimaalisessa toimintapisteessä, ja hiomon kaikilla koneilla pyrittiin samaan kivenalusmassan laatuun. Uutta ohjaustapaa kutsuttiin Optimum operating point -strategiaksi (OOPS). Hiomakiven pitäminen optimaalisessa toimintapisteessä tapahtui pääosin vesiteräyskäsittelyllä, jonka intensiteettiä ohjasi asiantuntijajärjestelmä (AI-järjestelmä). Lisäksi testattiin ohjelmoidun anturan nopeussäädön vaikutusta hiomakoneen resurssien käyttöön. AI-järjestelmä päätteli vesiteräyskäsittelyn tarpeellisuuden CSF-mallin ja hiomakoneen resurssien perusteella. Seurannasta saatujen tulosten perusteella AI-järjestelmän käyttöönotto vesiteräyskäsittelyssä paransi tuotannon ja massan laadun tasaisuutta. Hiomakoneiden resurssien havaittiin pienenevän puunsyöttölinjan mukaisesti. Paksummat pöllit kerääntyvät linjan päähän, jolloin varsinkin hydrauliikkapaineiden tarve lisääntyy linjan päässä olevilla hiomakoneilla. Hiomakoneen resurssit saatiin paremmin käyttöön kuormittamalla konetta ohjelmoidulla anturan nopeussäädöllä (ONS) kuin vakioidulla anturan nopeussäädöllä (VNS). Kuitenkin hydraulipaineresurssien puutteellisuus rajoitti koeajon aikana ONS:n toimintaa. Resursseja ei optimoitu koeajon aikana, koska kiven pinnan haluttiin pysyvän mahdollisimman stabiilina. Kivelle ei suoritettu mekaanista käsittelyä, vaikka kivenpinnan massan kuljetuskapasiteetin havaittiin olevan huono. AI-järjestelmä otettiin ohjaamaan vesiteräyskäsittelyä vasta ONS - VNS -koeajon jälkeen. Mekaanisen rullateräyksen jälkeen massan ominaisuudet muuttuivat, koska kiven pinnan terävät särmät katkoivat kuituja alentaen massan sitoutumiskykyä. Heti rullakäsittelyn jälkeen mitattu CSF saattoi jopa alentua huomattavasti, mutta AI-järjestelmän laskema CSF nousi selvästi indikoiden energian ominaiskulutuksen (EOK) laskua. Muutaman päivän hionnan jälkeen mitattu ja laskettu CSF saavuttivat saman tason.

Business models enhancing the diffusion of mobile Internet in emerging markets

Tämän tutkimuksen päätavoitteena oli selvittää, millaiset liiketoimintamallit soveltuvat mobiilin internet-liiketoiminnan harjoittamiseen kehittyvillä markkinoilla. Tavoitteena oli myös selvittää tekijöitä, jotka vaikuttavat mobiilin internetin diffuusioon. Tutkimus tehtiin käyttäen sekä kvantitatiivista että kvalitatiivista tutkimusmenetelmää. Klusterianalyysin avulla 40 Euroopan maasta muodostettiin sisäisesti homogeenisiä maaklustereita. Näiden klustereiden avulla oli mahdollista suunnitella erityyppisille markkinoille soveltuvat liiketoimintamallit. Haastatteluissa selvitettiin asiantuntijoiden näkemyksiä tekijöistä, jotka vaikuttavat mobiilin internetin diffuusioon kehittyvillä markkinoilla. Tutkimuksessa saatiin selville, että tärkeimmät liiketoimintamallin elementit kehittyvillä markkinoilla ovat hinnoittelu, arvotarjooma ja arvoverkko. Puutteellisen kiinteän verkon todettiin olevan yksi tärkeimmistä mobiilin internetin diffuusiota edistävistä tekijöistä kehittyvillä markkinoilla.

Vaatimustiedon hallinta rakennusteollisuuden tuotanto- ja suunnitteluyrityksessä

Diplomityön ensisijaisena tavoitteena on luoda yleinen vaatimustiedon hallinnan malli, jonka avulla yrityksen toimintaympäristössä vaikuttavat vaatimukset voidaan tunnistaa ja kommunikoida koko organisaation tietoisuuteen. Kohdeyrityksen näkökulmasta mielenkiinto kohdistuu erityisesti käytännön työn kautta saataviin lopputuloksiin. Tavoitteena on luoda yritykseen pohja vaatimustiedon hallinnalle sekä samalla kehittää sähköistä vaatimustietojärjestelmää. Diplomityö on toteutettu konstruktiivisena tutkimuksena. Tutkittavasta aiheesta on saatavilla teoriatietoa hyvin rajallisesti. Tämän vuoksi vaatimustiedon hallinnan malli toteutetaan vahvasti käytännön työn havaintojen ja analysoinnin pohjalta. Lähtökohdaksi käytännön työlle esitellään laadunhallinnan, tiedonhallinnan sekä prosessien näkökulmia sekä perinteisiä vaatimusten hallinnan teorioita. Tiedot, joiden avulla valmis malli on luotu, kerättiin haastattelemalla yrityksen prosessien omistajia. Työn tuloksina esitellään vaatimustiedon hallinnan malli sekä yrityksessä saatuja käytännön työn lopputuloksia. Vaatimustiedon hallinnalla tarkoitetaan yrityksen toimintaympäristössä, prosesseissa sekä tuotteissa vaikuttavien vaatimusten saattamista organisaation tietoisuuteen mahdollisimman käyttäjäystävällisellä tavalla. Mallissa esiintyvät vaatimukset ovat sidosryhmien tai yrityksen itsensä ilmaisuja liittyen tuotteen tai palvelun ominaisuuksiin sekä suorituskykyyn. Valmis malli voidaan jakaa neljään eri vaiheeseen, jotka ovat suunnittelu ja esitutkimus, toteutus, käyttöönotto, sekä muutostenhallinta ja ylläpito. Laajimmillaan toteutettuna vaatimustiedon hallinta auttaa yritystä parhaiden käytäntöjen tunnistamisessa ja prosessien kehittämisessä, mahdollistaa tasalaatuisen toiminnan ja tuotteet sekä toimivan tiedon ja osaamisen hallinnan.

Modeling the transport phenomena within arterial wall: porous media approach

The transport of macromolecules, such as low-density lipoprotein (LDL), and their accumulation in the layers of the arterial wall play a critical role in the creation and development of atherosclerosis. Atherosclerosis is a disease of large arteries e.g., the aorta, coronary, carotid, and other proximal arteries that involves a distinctive accumulation of LDL and other lipid-bearing materials in the arterial wall. Over time, plaque hardens and narrows the arteries. The flow of oxygen-rich blood to organs and other parts of the body is reduced. This can lead to serious problems, including heart attack, stroke, or even death. It has been proven that the accumulation of macromolecules in the arterial wall depends not only on the ease with which materials enter the wall, but also on the hindrance to the passage of materials out of the wall posed by underlying layers. Therefore, attention was drawn to the fact that the wall structure of large arteries is different than other vessels which are disease-resistant. Atherosclerosis tends to be localized in regions of curvature and branching in arteries where fluid shear stress (shear rate) and other fluid mechanical characteristics deviate from their normal spatial and temporal distribution patterns in straight vessels. On the other hand, the smooth muscle cells (SMCs) residing in the media layer of the arterial wall respond to mechanical stimuli, such as shear stress. Shear stress may affect SMC proliferation and migration from the media layer to intima. This occurs in atherosclerosis and intimal hyperplasia. The study of blood flow and other body fluids and of heat transport through the arterial wall is one of the advanced applications of porous media in recent years. The arterial wall may be modeled in both macroscopic (as a continuous porous medium) and microscopic scales (as a heterogeneous porous medium). In the present study, the governing equations of mass, heat and momentum transport have been solved for different species and interstitial fluid within the arterial wall by means of computational fluid dynamics (CFD). Simulation models are based on the finite element (FE) and finite volume (FV) methods. The wall structure has been modeled by assuming the wall layers as porous media with different properties. In order to study the heat transport through human tissues, the simulations have been carried out for a non-homogeneous model of porous media. The tissue is composed of blood vessels, cells, and an interstitium. The interstitium consists of interstitial fluid and extracellular fibers. Numerical simulations are performed in a two-dimensional (2D) model to realize the effect of the shape and configuration of the discrete phase on the convective and conductive features of heat transfer, e.g. the interstitium of biological tissues. On the other hand, the governing equations of momentum and mass transport have been solved in the heterogeneous porous media model of the media layer, which has a major role in the transport and accumulation of solutes across the arterial wall. The transport of Adenosine 5´-triphosphate (ATP) is simulated across the media layer as a benchmark to observe how SMCs affect on the species mass transport. In addition, the transport of interstitial fluid has been simulated while the deformation of the media layer (due to high blood pressure) and its constituents such as SMCs are also involved in the model. In this context, the effect of pressure variation on shear stress is investigated over SMCs induced by the interstitial flow both in 2D and three-dimensional (3D) geometries for the media layer. The influence of hypertension (high pressure) on the transport of lowdensity lipoprotein (LDL) through deformable arterial wall layers is also studied. This is due to the pressure-driven convective flow across the arterial wall. The intima and media layers are assumed as homogeneous porous media. The results of the present study reveal that ATP concentration over the surface of SMCs and within the bulk of the media layer is significantly dependent on the distribution of cells. Moreover, the shear stress magnitude and distribution over the SMC surface are affected by transmural pressure and the deformation of the media layer of the aorta wall. This work reflects the fact that the second or even subsequent layers of SMCs may bear shear stresses of the same order of magnitude as the first layer does if cells are arranged in an arbitrary manner. This study has brought new insights into the simulation of the arterial wall, as the previous simplifications have been ignored. The configurations of SMCs used here with elliptic cross sections of SMCs closely resemble the physiological conditions of cells. Moreover, the deformation of SMCs with high transmural pressure which follows the media layer compaction has been studied for the first time. On the other hand, results demonstrate that LDL concentration through the intima and media layers changes significantly as wall layers compress with transmural pressure. It was also noticed that the fraction of leaky junctions across the endothelial cells and the area fraction of fenestral pores over the internal elastic lamina affect the LDL distribution dramatically through the thoracic aorta wall. The simulation techniques introduced in this work can also trigger new ideas for simulating porous media involved in any biomedical, biomechanical, chemical, and environmental engineering applications.

Liiketoimintastrategisten vaatimusten syntyminen ja niiden toteutumisen arviointi keskisuurten yritysten toiminnanohjausjärjestelmähankkeissa. Tapaustutkimus kolmesta teollisuusyrityksestä ja aineistolähtöinen teoria

Tietojärjestelmien strateginen kehittäminen on ollut niin liike-elämän kiinnostuksen kuin akateemisen tutkimuksenkin kohteena jo pitkään. Aihe on edelleen ajankohtainen, eikä ajankohtaisuus osoita laantumisen merkkejä. Valtaosa tutkimuksesta on kohdistunut suuryrityksiin ja jonkin verran pk-yrityksiin yhtenä ryhmänä. Tutkimus on kohdistunut aiheeseen tarkastelemalla onko tietojärjestelmien ja liiketoimintastrategian välillä yhteyttä, ja jos, onko sillä merkitystä yrityksen menestykselle. Tämän tutkimuksen tavoitteena oli pureutua syvemmälle siihen tapaan, jolla yritys kytkee liiketoimintastrategiansa tietojärjestelmähankintaan. Kohdetietojärjestelmäksi tutkimuksessa valittiin toiminnanohjausjärjestelmät ja yrityskooksi keskisuuret yritykset. Toiminnanohjausjärjestelmän valintaa voidaan perustella sen kattavuudella yrityksen toiminnassa eri sidosryhmien suunnasta katsottaessa. Keskisuuret yritykset valittiin osittain sen vuoksi, koska niistä ei ole paljoakaan omaa tutkimusta, osittain sen vuoksi, että niiden luonne kehityspolun epäjatkumokohdassa haluttiin nostaa esille. Tutkimuksen empiirinen osa pohjautuu kolmeen tutkimustapaukseen, kolmen keskisuuren yrityksen toiminnanohjaushankkeeseen. Tapausyritysten liiketoiminta- ja ITjohtoa haastateltiin, ja lisäksi käytettiin kaikkea saataville ollutta kirjallista arkistoaineistoa. Tutkimuksen päämenetelmä oli Grounded Theory (GT). Tutkimustavassa ei, poiketen useista muista laadullisista tutkimustavoista, ole ennalta määrättyä viitekehystä, vaan tutkimus lähtee liikkeelle ns. puhtaalta pöydältä ilman esioletuksia luoden tutkimusprosessin kuluessa uutta teoriaa. Tutkimustavan etuna voidaan pitää ennakkoluulottomuutta. Aikaisemman tutkimuksen rooli tässä tutkimuksessa oli ensinnäkin kartoittaa tutkimusaluetta ja olla johdantona tutkimukselle, toisaalta tuloksia vertailtiin aikaisempaan tutkimukseen. Tutkimusaineisto analysoitiin tarkasti. Ensin aineisto käytiin läpi koodaamalla se aineistosta esille nousseiden käsitteiden alle. Seuraavaksi saatu tulos luokiteltiin aineistosta nousseisiin luokkiin sekä muodostettiin käsitteiden ja luokkien väliset yhteydet. Lopuksi muodostumassa oleva teoria konkretisoitiin 18 hypoteesin ja hypoteesit yhdistävän mallin avulla. Tutkimuksessa saatiin uutta tietoa siitä, miten vaatimusprosessi etenee ja miten keskisuuren yrityksen ominaispiirteet vaikuttavat vaatimusprosessiin. Lisäksi saatiin uutta tietoa siitä, mitkä ovat kriittisiä menestystekijöitä keskisuuren yrityksen toiminnanohjaushankkeessa. Keskisuuretyritykset näyttävät tämän tutkimuksen aineiston perusteella osaavan asettaa vaatimuksia toiminnanohjausjärjestelmälle liiketoimintastrategian, prosessikuvausten ja toiminnanohjausjärjestelmien tarjoamien mahdollisuuksien suunnista. Vaatimusten toteutumisenarviointi on keskisuurilla yrityksillä epäsystemaattista, kuten aikaisemmassa tutkimuksessa on todettu olevan myös suurilla yrityksillä. Resurssivaje vaikeuttaa toiminnanohjausjärjestelmän liiketoimintastrategisten vaatimusten toteutumista. Tutkimusaineiston perusteella voidaan päätellä, että keskisuurissa yrityksissä – huolimatta siitä, että niissä on olemassa prosessikuvaukset – ei ole varsinaista prosessiajattelua tai prosessijohtamista. Keskisuuret yritykset eivät tämän tutkimuksen aineiston perusteella näytä muodostavan poikkeusta, vaan mittariston käyttö on epäkypsää, eikä mittaristoa pystytä hyödyntämään tietojärjestelmähankkeen tukena. Tulosten pohjalta voidaan arvioida, että strategisen johtamisen komponentit ovat keskisuuressa yrityksessä toisistaan irrallisia. Vaikka toiminnanohjaushankkeen vaatimuksia asetettaessa liiketoimintastrategia on vahvasti mukana, jää vaatimuksenasettelu karkealle tasolle, eikä konkretisoidu prosesseihin ja mittarointiin. Sen seurauksena toiminnanohjausjärjestelmästä ei saada kaikkea sitä hyötyä ja tukea liiketoimintastrategialle, mikä olisi mahdollista. Tutkimuksessa tuli myös esille resurssi- ja osaamispuutteen haittavaikutuksia keskisuurten yritysten toiminnanohjaushankkeiden vaatimusprosessissa. Puutteet yhdistettynä hajallaan oleviin strategisen johtamisen komponentteihin muodostavat yhdessä vaikean lähtökohdan strategiselle toiminnanohjaushankkeelle.

Nanoparticle Labels in Bioaffinity Assays

Nanoparticles offer adjustable and expandable reactive surface area compared to the more traditional solid phase forms utilized in bioaffinity assays due to the high surface to-volume ratio. The versatility of nanoparticles is further improved by the ability to incorporate various molecular complexes such as luminophores into the core. Nanoparticle labels composed of polystyrene, silica, inorganic crystals doped with high number of luminophores, preferably lanthanide(III) complexes, are employed in bioaffinity assays. Other label species such as semiconductor crystals (quantum dots) or colloidal gold clusters are also utilized. The surface derivatization of such particles with biomolecules is crucial for the applicability to bioaffinity assays. The effectiveness of a coating is reliant on the biomolecule and particle surface characteristics and the selected coupling technique. The most critical aspects of the particle labels in bioaffinity assays are their size-dependent features. For polystyrene, silica and inorganic phosphor particles, these include the kinetics, specific activity and colloidal stability. For quantum dots and gold colloids, the spectral properties are also dependent on particle size. This study reports the utilization of europium(III)-chelate-embedded nanoparticle labels in the development of bioaffinity assays. The experimental covers both the heterogeneous and homogeneous assay formats elucidating the wide applicability of the nanoparticles. It was revealed that the employment of europium(III) nanoparticles in heterogeneous assays for viral antigens, adenovirus hexon and hepatitis B surface antigen (HBsAg), resulted in sensitivity improvement of 10-1000 fold compared to the reference methods. This improvement was attributed to the extreme specific activity and enhanced monovalent affinity of the nanoparticles conjugates. The applicability of europium(III)-chelate-doped nanoparticles to homogeneous assay formats were proved in two completely different experimental settings; assays based on immunological recognition or proteolytic activity. It was shown that in addition to small molecule acceptors, particulate acceptors may also be employed due to the high specific activity of the particles promoting proximity-induced reabsorptive energy transfer in addition to non-radiative energy transfer. The principle of proteolytic activity assay relied on a novel dual-step FRET concept, wherein the streptavidin-derivatized europium(III)-chelate-doped nanoparticles were used as donors for peptide substrates modified with biotin and terminal europium emission compliant primary acceptor and a secondary quencher acceptor. The recorded sensitized emission was proportional to the enzyme activity, and the assay response to various inhibitor doses was in agreement with those found in literature showing the feasibility of the technique. Experiments regarding the impact of donor particle size on the extent of direct donor fluorescence and reabsorptive excitation interference in a FRET-based application was conducted with differently sized europium(III)-chelate-doped nanoparticles. It was shown that the size effect was minimal

Design and production of protein nanostructures for biomolecular detection

Particulate nanostructures are increasingly used for analytical purposes. Such particles are often generated by chemical synthesis from non-renewable raw materials. Generation of uniform nanoscale particles is challenging and particle surfaces must be modified to make the particles biocompatible and water-soluble. Usually nanoparticles are functionalized with binding molecules (e.g., antibodies or their fragments) and a label substance (if needed). Overall, producing nanoparticles for use in bioaffinity assays is a multistep process requiring several manufacturing and purification steps. This study describes a biological method of generating functionalized protein-based nanoparticles with specific binding activity on the particle surface and label activity inside the particles. Traditional chemical bioconjugation of the particle and specific binding molecules is replaced with genetic fusion of the binding molecule gene and particle backbone gene. The entity of the particle shell and binding moieties are synthesized from generic raw materials by bacteria, and fermentation is combined with a simple purification method based on inclusion bodies. The label activity is introduced during the purification. The process results in particles that are ready-to-use as reagents in bioaffinity. Apoferritin was used as particle body and the system was demonstrated using three different binding moieties: a small protein, a peptide and a single chain Fv antibody fragment that represents a complex protein including disulfide bridge.If needed, Eu3+ was used as label substance. The results showed that production system resulted in pure protein preparations, and the particles were of homogeneous size when visualized with transmission electron microscopy. Passively introduced label was stably associated with the particles, and binding molecules genetically fused to the particle specifically bound target molecules. Functionality of the particles in bioaffinity assays were successfully demonstrated with two types of assays; as labels and in particle-enhanced agglutination assay. This biological production procedure features many advantages that make the process especially suited for applications that have frequent and recurring requirements for homogeneous functional particles. The production process of ready, functional and watersoluble particles follows principles of “green chemistry”, is upscalable, fast and cost-effective.

Food Safety Testing: Rapid Molecular Methods for Chemical and Biological Hazards

The central goal of food safety policy in the European Union (EU) is to protect consumer health by guaranteeing a high level of food safety throughout the food chain. This goal can in part be achieved by testing foodstuffs for the presence of various chemical and biological hazards. The aim of this study was to facilitate food safety testing by providing rapid and user-friendly methods for the detection of particular food-related hazards. Heterogeneous competitive time-resolved fluoroimmunoassays were developed for the detection of selected veterinary residues, that is coccidiostat residues, in eggs and chicken liver. After a simplified sample preparation procedure, the immunoassays were performed either in manual format with dissociation-enhanced measurement or in automated format with pre-dried assay reagents and surface measurement. Although the assays were primarily designed for screening purposes providing only qualitative results, they could also be used in a quantitative mode. All the developed assays had good performance characteristics enabling reliable screening of samples at concentration levels required by the authorities. A novel polymerase chain reaction (PCR)-based assay system was developed for the detection of Salmonella spp. in food. The sample preparation included a short non-selective pre-enrichment step, after which the target cells were collected with immunomagnetic beads and applied to PCR reaction vessels containing all the reagents required for the assay in dry form. The homogeneous PCR assay was performed with a novel instrument platform, GenomEra^™, and the qualitative assay results were automatically interpreted based on end-point time-resolved fluorescence measurements and cut-off values. The assay was validated using various food matrices spiked with sub-lethally injured Salmonella cells at levels of 1-10 colony forming units (CFU)/25 g of food. The main advantage of the system was the exceptionally short time to result; the entire process starting from the pre-enrichment and ending with the PCR result could be completed in eight hours. In conclusion, molecular methods using state-of-the-art assay techniques were developed for food safety testing. The combination of time-resolved fluorescence detection and ready-to-use reagents enabled sensitive assays easily amenable to automation. Consequently, together with the simplified sample preparation, these methods could prove to be applicable in routine testing.

Lanthanide Chelates as Donors in Fluorescence Resonance Energy Transfer: Exciting Prospects for Bioaffinity Assay Detection

Fluorescence resonance energy transfer (FRET) is a non-radiative energy transfer from a fluorescent donor molecule to an appropriate acceptor molecule and a commonly used technique to develop homogeneous assays. If the emission spectrum of the donor overlaps with the excitation spectrum of the acceptor, FRET might occur. As a consequence, the emission of the donor is decreased and the emission of the acceptor (if fluorescent) increased. Furthermore, the distance between the donor and the acceptor needs to be short enough, commonly 10-100 Å. Typically, the close proximity between the donor and the acceptor is achieved via bioaffinity interactions e.g. antibody binding antigen. Large variety of donors and acceptors exist. The selection of the donor/acceptor pair should be done not only based on the requirements of FRET but also the performance expectancies and the objectives of the application should be considered. In this study, the exceptional fluorescence properties of the lanthanide chelates were employed to develop two novel homogeneous immunoassays: a non-competitive hapten (estradiol) assay based on a single binder and a dual-parametric total and free PSA assay. In addition, the quenching efficiencies and energy transfer properties of various donor/acceptor pairs were studied. The applied donors were either europium(III) or terbium(III) chelates; whereas several organic dyes (both fluorescent and quenchers) acted as acceptors. First, it was shown that if the interaction between the donor/acceptor complexes is of high quality (e.g. biotin-streptavidin) the fluorescence of the europium(III) chelate could be quenched rather efficiently. Furthermore, the quenching based homogeneous non-competitive assay for estradiol had significantly better sensitivity (~67 times) than a corresponding homogeneous competitive assay using the same assay components. Second, if the acceptors were chosen to emit at the emission minima of the terbium(III) chelate, several acceptor emissions could be measured simultaneously without significant cross-talk from other acceptors. Based on these results, the appropriate acceptors were chosen for the dual-parameter assay. The developed homogeneous dual-parameter assay was able to measure both total and free PSA simultaneously using a simple mix and measure protocol. Correlation of this assay to a heterogeneous single parameter assay was excellent (above 0.99 for both) when spiked human plasma samples were used. However, due to the interference of the sample material, the obtained concentrations were slightly lower with the homogeneous than the heterogeneous assay, especially for the free PSA. To conclude, in this work two novel immunoassay principles were developed, which both are adaptable to other analytes. However, the hapten assay requires a rather good antibody with low dissociation rate and high affinity; whereas the dual-parameter assay principle is applicable whenever two immunometric complexes can form simultaneously, provided that the requirements of FRET are fulfilled.

A Practical Micro Mechanical Model Based Local Approach Methodology for the Analysis of Ductile Fracture of Welded T-Joints

This thesis concentrates on developing a practical local approach methodology based on micro mechanical models for the analysis of ductile fracture of welded joints. Two major problems involved in the local approach, namely the dilational constitutive relation reflecting the softening behaviour of material, and the failure criterion associated with the constitutive equation, have been studied in detail. Firstly, considerable efforts were made on the numerical integration and computer implementation for the non trivial dilational Gurson Tvergaard model. Considering the weaknesses of the widely used Euler forward integration algorithms, a family of generalized mid point algorithms is proposed for the Gurson Tvergaard model. Correspondingly, based on the decomposition of stresses into hydrostatic and deviatoric parts, an explicit seven parameter expression for the consistent tangent moduli of the algorithms is presented. This explicit formula avoids any matrix inversion during numerical iteration and thus greatly facilitates the computer implementation of the algorithms and increase the efficiency of the code. The accuracy of the proposed algorithms and other conventional algorithms has been assessed in a systematic manner in order to highlight the best algorithm for this study. The accurate and efficient performance of present finite element implementation of the proposed algorithms has been demonstrated by various numerical examples. It has been found that the true mid point algorithm (a = 0.5) is the most accurate one when the deviatoric strain increment is radial to the yield surface and it is very important to use the consistent tangent moduli in the Newton iteration procedure. Secondly, an assessment of the consistency of current local failure criteria for ductile fracture, the critical void growth criterion, the constant critical void volume fraction criterion and Thomason's plastic limit load failure criterion, has been made. Significant differences in the predictions of ductility by the three criteria were found. By assuming the void grows spherically and using the void volume fraction from the Gurson Tvergaard model to calculate the current void matrix geometry, Thomason's failure criterion has been modified and a new failure criterion for the Gurson Tvergaard model is presented. Comparison with Koplik and Needleman's finite element results shows that the new failure criterion is fairly accurate indeed. A novel feature of the new failure criterion is that a mechanism for void coalescence is incorporated into the constitutive model. Hence the material failure is a natural result of the development of macroscopic plastic flow and the microscopic internal necking mechanism. By the new failure criterion, the critical void volume fraction is not a material constant and the initial void volume fraction and/or void nucleation parameters essentially control the material failure. This feature is very desirable and makes the numerical calibration of void nucleation parameters(s) possible and physically sound. Thirdly, a local approach methodology based on the above two major contributions has been built up in ABAQUS via the user material subroutine UMAT and applied to welded T joints. By using the void nucleation parameters calibrated from simple smooth and notched specimens, it was found that the fracture behaviour of the welded T joints can be well predicted using present methodology. This application has shown how the damage parameters of both base material and heat affected zone (HAZ) material can be obtained in a step by step manner and how useful and capable the local approach methodology is in the analysis of fracture behaviour and crack development as well as structural integrity assessment of practical problems where non homogeneous materials are involved. Finally, a procedure for the possible engineering application of the present methodology is suggested and discussed.