Comparative pathogenicity of Coxsackievirus A16 circulating and noncirculating strains in vitro and in a neonatal mouse model

An enterovirus 71 (EV71) vaccine for the prevention of hand, foot, and mouth disease (HMFD) is available, but it is not known whether the EV71 vaccine cross-protects against Coxsackievirus (CV) infection. Furthermore, although an inactivated circulating CVA16 Changchun 024 (CC024) strain vaccine candidate is effective in newborn mice, the CC024 strain causes severe lesions in muscle and lung tissues. Therefore, an effective CV vaccine with improved pathogenic safety is needed. The aim of this study was to evaluate the in vivo safety and in vitro replication capability of a noncirculating CVA16 SHZH05 strain. The replication capacity of circulating CVA16 strains CC024, CC045, CC090 and CC163 and the noncirculating SHZH05 strain was evaluated by cytopathic effect in different cell lines. The replication capacity and pathogenicity of the CC024 and SHZH05 strains were also evaluated in a neonatal mouse model. Histopathological and viral load analyses demonstrated that the SHZH05 strain had an in vitro replication capacity comparable to the four CC strains. The CC024, but not the SHZH05 strain, became distributed in a variety of tissues and caused severe lesions and mortality in neonatal mice. The differences in replication capacity and in vivo pathogenicity of the CC024 and SHZH05 strains may result from differences in the nucleotide and amino acid sequences of viral functional polyproteins P1, P2 and P3. Our findings suggest that the noncirculating SHZH05 strain may be a safer CV vaccine candidate than the CC024 strain.

Scalable Feature Selection Applications for Genome-Wide Association Studies of Complex Diseases

Personalized medicine will revolutionize our capabilities to combat disease. Working toward this goal, a fundamental task is the deciphering of geneticvariants that are predictive of complex diseases. Modern studies, in the formof genome-wide association studies (GWAS) have afforded researchers with the opportunity to reveal new genotype-phenotype relationships through the extensive scanning of genetic variants. These studies typically contain over half a million genetic features for thousands of individuals. Examining this with methods other than univariate statistics is a challenging task requiring advanced algorithms that are scalable to the genome-wide level. In the future, next-generation sequencing studies (NGS) will contain an even larger number of common and rare variants. Machine learning-based feature selection algorithms have been shown to have the ability to effectively create predictive models for various genotype-phenotype relationships. This work explores the problem of selecting genetic variant subsets that are the most predictive of complex disease phenotypes through various feature selection methodologies, including filter, wrapper and embedded algorithms. The examined machine learning algorithms were demonstrated to not only be effective at predicting the disease phenotypes, but also doing so efficiently through the use of computational shortcuts. While much of the work was able to be run on high-end desktops, some work was further extended so that it could be implemented on parallel computers helping to assure that they will also scale to the NGS data sets. Further, these studies analyzed the relationships between various feature selection methods and demonstrated the need for careful testing when selecting an algorithm. It was shown that there is no universally optimal algorithm for variant selection in GWAS, but rather methodologies need to be selected based on the desired outcome, such as the number of features to be included in the prediction model. It was also demonstrated that without proper model validation, for example using nested cross-validation, the models can result in overly-optimistic prediction accuracies and decreased generalization ability. It is through the implementation and application of machine learning methods that one can extract predictive genotype–phenotype relationships and biological insights from genetic data sets.

Fiber-reinforced composite fixed dental prostheses: Studies of the materials used as pontics

Fiber-reinforced composite fixed dental prostheses – Studies of the materials used as pontics University of Turku, Faculty of Medicine, Institute of Dentistry, Department of Biomaterials Science, Finnish Doctoral Program in Oral Sciences – FINDOS, Annales Universitatis Turkuensis, Turku, Finland 2015 Fiber-reinforced composites (FRC), a non-metallic biomaterial, represent a suitable alternative in prosthetic dentistry when used as a component of fixed dental prostheses (FDPs). Some drawbacks have been identified in the clinical performance of FRC restorations, such as delamination of the veneering material and fracture of the pontic. Therefore, the current series of studies were performed to investigate the possibilities of enhancing the mechanical and physical properties of FRC FDPs by improving the materials used as pontics, to then heighten their longevity. Four experiments showed the importance of the pontic design and surface treatment in the performance of FRC FDPs. In the first, the load-bearing capacities of inlay-retained FRC FDPs with pontics of various materials and thicknesses were evaluated. Three different pontic materials were assessed with different FRC framework vertical positioning. Thicker pontics showed increased load-bearing capacities, especially ceramic pontics. A second study was completed investigating the influence of the chemical conditioning of the ridge-lap surface of acrylic resin denture teeth on their bonding to a composite resin. Increased shear bond strength demonstrated the positive influence of the pretreatment of the acrylic surfaces, indicating dissolution of the denture surfaces, and suggesting potential penetration of the monomer systems into the surface of denture teeth. A third study analyzed the penetration depth of different monomer systems on the acrylic resin denture teeth surfaces. The possibility of establishing a durable bond between acrylic pontics and FRC frameworks was demonstrated by the ability of monomers to penetrate the surface of acrylic resin denture teeth, measured by a confocal scanning type microscope. A fourth study was designed to evaluate the load-bearing capacities of FRC FDPs using the findings of the previous three studies. In this case, the performance of pre-shaped acrylic resin denture teeth used as pontics with different composite resins as filling materials was evaluated. The filling material influenced the load-bearing capacities, providing more durable FRC FDPs. It can be concluded that the mechanical and physical properties of FRC FDPs can be improved as has been shown in the development of this thesis. The improvements reported then might provide long lasting prosthetic solutions of this kind, positioning them as potentially permanent rehabilitation treatments. Key words: fiber-reinforced composite, fixed dental prostheses, inlay-retained bridges, adhesion, acrylic resin denture teeth, dental material.

Comparative antiproliferation of human prostate cancer cells by ethanolic extracts of two groups of Brazilian propolis

Two groups of propolis, group 12, which was collected in the southeastern Brazil and group 13, which was collected in the northeastern Brazil, were examined for antiproliferation of primary malignant tumor (RC-58T/h/SA#4)-derived human prostate cancer cells and human prostate epithelial cells. The strongest inhibition of RC-58T/h/SA#4 cells was observed in propolis group 13 extracts, whereas moderate growth inhibition was observed in human prostate epithelial cells in comparison with group 12. It can be said that the Brazilian propolis of group 13 contains important chemical ingredients.

Studies of chemical and enzymatic characteristics of Yacon (Smallanthus sonchifolius) and its flours

Due to the importance of studies on yacon related to health, its in natura pulp, in natura peel, pulp flour, and peel flour were chemically analyzed in terms of its centesimal composition, specific minerals, total dietary fiber and fractions, pH, total soluble solids, total titratable acidity, tannins, oxalic acid, and nitrate. The polyphenoloxidase and peroxidase enzymatic activities were evaluated for in natura pulp and peel only. Yacon pulp and peel flour presented average yield of 7.94% and 10.86%, respectively. The in natura pulp presented a higher moisture and carboydrate content and lower lipid, protein, total dietary fiber, and ash than those of the peel flour. The same pattern was observed for pulp flour when compared to peel flour. The highest tannin, nitrate, and oxalic acid levels were found in the peel flour, 15,304.5 mg.kg-1, 1,578.3 mg.kg-1, and 7,925.0 mg.kg-1 (wet weight), respectively. The polyphenoloxidase and peroxidase enzymes presented higher enzymatic activity in the yacon peel. Based on the results obtained, it can be said that the yacon and its derivatives are important dietary carbohydrate and mineral sources and contain antinutritional substance contents lower than those harmful to health.

Assessing environmental impacts using a comparative LCA of industrial and artisanal production processes: "Minas Cheese" case

This study uses the Life Cycle Assessment (LCA) methodology to evaluate and compare the environmental impacts caused by both the artisanal and the industrial manufacturing processes of "Minas cheese". This is a traditional cheese produced in the state of Minas Gerais (Brazil), and it is considered a "cultural patrimony" in the country. The high participation of artisanal producers in the market justifies this research, and this analysis can help the identification of opportunities to improve the environmental performance of several stages of the production system. The environmental impacts caused were also assessed and compared. The functional unit adopted was 1 kilogram (Kg) of cheese. The system boundaries considered were the production process, conservation of product (before sale), and transport to consumer market. The milk production process was considered similar in both cases, and therefore it was not included in the assessment. The data were collected through interviews with the producers, observation, and a literature review; they were ordered and processed using the SimaPro 7 LCA software. According to the impact categories analyzed, the artisanal production exerted lower environmental impacts. This can be justified mainly because the industrial process includes the pasteurization stage, which uses dry wood as an energy source and refrigeration.

Post-transaction brand and model line-up integration in the automotive industry: Case studies of European companies as target of acquisitions by Chinese and Indian multinational corporations

Corporations practice company acquisitions in order to create shareholder’s value. During the last few decades, the companies in emerging markets have become active in the acquisition business. During the last decade, large and significant acquisitions have occurred especially in automotive industry. While domestic markets have become too competitive and companies are lacking required capabilities, they seek possibilities to expand into Western markets by attaining valuable assets through acquisitions of developed country corporations. This study discusses the issues and characteristics of these acquisitions through case studies. The purpose of this study was to identify the acquisition motives and strategies for post-transaction brand and product integration as well as analyze the effect of the motives to the integration strategy. The cases chosen for the research were Chinese Geely acquiring Swedish Volvo in 2010 and Indian Tata Motors buying British Jaguar Land Rover in 2008. The main topics were chosen according to their significance for companies in automotive industry as well as those are most visible parts for consumers. The study is based on qualitative case study methods, analyzing secondary data from academic papers and news articles as well as companies’ own announcements e.g. stock exchange and press releases. The study finds that the companies in the cases mainly possessed asset-seeking and market-seeking motives. In addition, the findings refer to rather minimal post-acquisition brand and product integration strategies. Mainly the parent companies left the target company autonomous to make their own business strategies and decisions. The most noticeable integrations were in the product development and production processes. Through restructuring the product architectures, the companies were able to share components and technology between product families and brands, which results in cutting down costs and in increase of profitability and efficiency. In the Geely- Volvo case, the strategy focused more on component sharing and product development know-how, whereas in Tata Motors-Jaguar Land Rover case, the main actions were to cut down costs through component sharing and combine production and distribution networks especially in Asian markets. However, it was evident that in both cases the integration and technology sharing were executed cautiously to prevent on harming the valuable image of the luxury brand. This study has concluded that the asset-seeking motives have significant influence on the posttransaction brand and model line-up integration strategies. By taking a cautious approach in acquiring assets, such as luxury brand, the companies in the cases have implemented a successful post-acquisition strategy and managed to create value for the shareholders at least in short-term. Yritykset harjoittavat yritysostoja luodakseen osakkeenomistajille lisäarvoa. Viimeisten muutamien vuosikymmenien aikana yritykset kehittyvissä maissa ovat myös aktivoituneet yritysostoissa. Viimeisen vuosikymmenen aikana erityisesti autoteollisuudessa on esiintynyt suuria ja merkittäviä yritysostoja. Koska kilpailu kotimaan markkinoilla on kiristynyt ja yritykset ovat vailla vaadittavia valmiuksia, ne etsivät mahdollisuuksiaan laajentaa länsimaisiin markkinoihin hankkimalla arvokkaita etuja kehittyneiden maiden yrityksistä yritysostojen avulla. Tämä tutkimus pohtii näiden yritysostojen olennaisia kysymyksiä ja ominaisuuksia casetutkimuksien kautta. Tutkimuksen tarkoitus oli tunnistaa sekä yritysostojen motiiveja ja brändi- ja mallisto-integraation strategioita että analysoida kyseisten motiivien vaikutusta integraatiostrategiaan. Tapaus-tutkimuksiksi valittiin kiinalaisen Geelyn yritysosto ruotsalaisesta Volvosta vuonna 2010 ja intialaisen Tata Motorsin yritysosto englantilaisesta Jaguar Land Roverista vuonna 2008. Tutkimus on kvalitatiivinen case-tutkimus ja siinä analysoidaan toissijaista tietoa sekä akateemisten ja uutisartikkeleiden että yritysten omien ilmoitusten, kuten pörssi- ja lehdistötiedotteiden, kautta. Tutkimuksen tulokset osoittavat, että tutkittujen yritysten toiminnat perustuivat motiiveihin, joita ajoivat etujen and uusien markkinoiden tarve. Sen lisäksi tutkimustulokset osoittivat, että yritysoston jälkeinen brändi- ja mallisto-integraatio pidettiin minimaalisena. Pääasiallisesti kohdeyrityksille jätettiin autonomia tehdä omat liikkeenjohdolliset päätökset yritysstrategioihin liittyen. Huomattavimmat integraatiot koskivat tuotekehityksellisiä ja tuotannollisia prosesseja. Kehittämällä uudelleen tuotearkkitehtuureja, yritykset pystyivät jakamaan komponentteja ja teknologiaa tuoteperheiden ja brändien välillä. Tämä mahdollisti kustannusleikkauksia sekä kannattavuuden ja tehokkuuden parantamista. Geely-Volvo –tapauksessa integraatiostrategia keskittyi komponenttien jakamiseen yhteisten tuotearkkitehtuurien avulla ja tuotekehityksen ammattitaitoon, kun taas Tata Motors-JLR –tapauksessa päätoiminnat olivat kustannuksien leikkaus sekä tuotannon ja jakeluverkoston yhdistäminen erityisesti Aasian maissa. Yhteistä yrityskaupoissa oli, että brändi- ja mallisto-integraatio sekä teknologian jakaminen suoritettiin varoen ehkäistäkseen arvokkaiden luksus-brändien tuotekuvan vahingoittamista. Tutkimuksen lopputulokset osoittavat, että yrityskaupan motiiveilla on huomattava vaikutus brändija mallisto-integraation strategiaan. Toteuttamalla varovaista lähestymistapaa luksus-brändin hankinnassa ja integraatiossa, yritykset ovat onnistuneet luomaan lisäarvoa osakkeenomistajille vähintään lyhyellä aikavälillä.

Studies of rotor dynamics using a multibody simulation approach

The non-idealities in a rotor-bearing system may cause undesirable subcritical superharmonic resonances that occur when the rotating speed of the rotor is a fraction of the natural frequency of the system. These resonances arise partly from the non-idealities of the bearings. This study introduces a novel simulation approach that can be used to study the superharmonic vibrations of rotor-bearing systems. The superharmonic vibrations of complex rotor-bearing systems can be studied in an accurate manner by combining a detailed rotor and bearing model in a multibody simulation approach. The research looks at the theoretical background of multibody formulations that can be used in the dynamic analysis of flexible rotors. The multibody formulations currently in use are suitable for linear deformation analysis only. However, nonlinear formulation may arise in high-speed rotor dynamics applications due to the cenrrifugal stiffening effect. For this reason, finite element formulations that can describe nonlinear deformation are also introduced in this work. The description of the elastic forces in the absolute nodal coordinate formulation is studied and improved. A ball bearing model that includes localized and distributed defects is developed in this study. This bearing model could be used in rotor dynamics or multibody code as an interface elements between the rotor and the supporting structure. The model includes descriptions of the nonlinear Hertzian contact deformation and the elastohydrodynamic fluid film. The simulation approaches and models developed here are applied in the analysis of two example rotor-bearing systems. The first example is an electric motor supported by two ball bearings and the second is a roller test rig that consists of the tube roll of a paper machine supported by a hard-bearing-type balanceing machine. The simulation results are compared to the results available in literature as well as to those obtained by measuring the existing structure. In both practical examples, the comparison shows that the simulation model is capable of predicting the realistic responses of a rotor system. The simulation approaches developed in this work can be used in the analysis of the superharmonic vibrations of general rotor-bearing systems.

Structural and Mechanistic Studies of Phosphoserine Aminotransferase

Phosphoserine aminotrasferase (PSAT: EC 2.6.1.52) is a vitamin B6-dependent enzyme and a member of the subgroup IV in the aminotransferase superfamily. Here, X-ray crystallography was used to determine the structure of PSAT from Bacillus alcalophilus with pyridoxamine 5′-phosphate (PMP) at high resolution (1.57 Å). In addition, analysis of active residues and their conformational changes was performed. The structure is of good quality as indicated, for example, by the last recorded Rwork and Rfree numbers (0.1331 and 0.1495, respectively). The enzyme was initially crystallized in the presence of substrate L-glutamate with the idea to produce the enzyme-substrate complex. However, the structure determination revealed no glutamate bound at the active site. Instead, the Schiff base between Lys196 and PLP appeared broken, resulting in the formation of PMP owing to the excess of the donor substrate used during co-crystallization. Structural comparison with the free PSAT enzyme and the PSAR-PSER complex showed that the aromatic ring of the co-factor remains in almost the same place in all structures. A flexible nearby loop in the active site was found in the same position as in the free PSAT structure while in the PSAT-PSER structure it moves inwards to interact with PSER. B-factors comparison in all three structures (PSAT-PMP complex, free PSAT, and PSAT-PSER complex) showed elevated loop flexibility in the absence of the substrate, indicating that loop flexibility plays an important role during substrate binding. The reported structure provides mechanistic details into the reaction mechanism of PSAT and may help in understanding better the role of various parts in the structure towards the design of novel compounds as potential disruptors of PSAT function. This may lead to the development of new drugs which could target the human and bacterial PSAT active site.

Geographical Studies of Underwater Light Dynamics in the Coastal Archipelago of SW Finland, Baltic Sea

The underwater light field is an important environmental variable as it, among other things, enables aquatic primary production. Although the portion of solar radiation that is referred to as visible light penetrates water, it is restricted to a limited surface water layer because of efficient absorption and scattering processes. Based on the varying content of optical constituents in the water, the efficiency of light attenuation changes in many dimensions and over various spatial and temporal scales. This thesis discusses the underwater light dynamics of a transitional coastal archipelago in south-western Finland, in the Baltic Sea. While the area has long been known to have a highly variable underwater light field, quantified knowledge on the phenomenon has been scarce, patchy, or non-existent. This thesis focuses on the variability in the underwater light field through euphotic depths (1% irradiance remaining), which were derived from in situ measurements of vertical profiles of photosynthetically active radiation (PAR). Spot samples were conducted in the archipelago of south-western Finland, mainly during the ice-free growing seasons of 2010 and 2011. In addition to quantifying both the seasonal and geographical patterns of euphotic depth development, the need and usability of underwater light information are also discussed. Light availability was found to fluctuate in multiple dimensions and scales. The euphotic depth was shown to have combined spatio-temporal dynamics rather than separate changes in spatial and temporal dimensions. Such complexity in the underwater light field creates challenges in data collection, as well as in its utilisation. Although local information is needed, in highly variable conditions spot sampled information may only poorly represent its surroundings. Moreover, either temporally or spatially limited sampling may cause biases in understanding underwater light dynamics. Consequently, the application of light availability data, for example in ecological modelling, should be made with great caution.

Systematic studies of the effect of pressure on magnetic and electronic properties of La2/3Ca1/3MnO3 thin films with various thicknesses /

Interest in mixed-valent perovskite manganese oxides of La\-xAxMnO^ (v4-divalent alkaline earth Ca, Sr or Ba), whose unusual properties were discovered nearly a half century ago, has recently been revived. The discovery of the colossal magnetoresistance and pressure effects introduced new questions concerning the complex interplay between lattice structure, magnetism and transport in doped perovskite manganites. In this study, we report our experimental investigations of pressure and magnetic field dependencies of La-i/sCai/sMnOs (LCMO) epitaxial films with various thickness on SrTiO$ substrate. An analysis of film thickness dependency of the resistivity of LCMO epitaxial films under pressure and magnetic field has been performed by taking into account substrate contributions. This verifies the correlation of lattice distortion with magnetic and transport properties. Strong dependencies of Mn — O — Mn bond bending and Mn — O bond stretching with pressure as well as Mn spin alignment with magnetic field, and the lattice distortion induced by the substrate are discussed.