Formal development and quantitative verification of dependable systems

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Vaikutukseen perustuvat operaatiot merellisessä kriisinhallinnassa

Tutkimustyön tavoitteena on muodostaa selkeä käsitys vaikutukseen perustuvien operaatioiden teoriasta ja tutkia merellisen kriisinhallintaoperaation kehittämisperiaatteita vaikutukseen perustuvien operaatioiden kontekstissa. Kriisinhallintaoperaatioita tarkastellaan Euroopan unionin sotilaallisen kriisinhallinnan toimintaympäristössä ja merivoimakomponentin näkökulmasta. Vaikutusperusteisia operaatioita ei ole Suomessa systemaattisesti tutkittu. Euroopan turvallisuusympäristö on muuttumassa entistä haasteellisemmaksi. Uudet uhkat, joita Eurooppa kohtaa ovat entistä moninaisempia, näkymättömämpiä ja vaikeammin ennustettavissa. Merivoimilla on tulevaisuudessa keskeinen rooli ehkäistäessä levottomuuksien rantautuminen Eurooppaan. Asevoimien näkökulmasta tämän hetkinen kehitystrendi on vaikutukseen perustuvat operaatiot (Effects-Based Approach to Operations, EBAO) ja verkostokeskeinen sodankäynti (Network Centric Warfare, NCW). EBAO:n käytettävyyttä kriisinhallinnassa kehitetään voimakkaasti ja konsepti nähdään mahdollisena ratkaisuna moniin nykyaikaisen kriisinhallinnan haasteisiin ja ongelmiin. Virallisen määritelmän mukaan vaikutukseen perustuvat operaatiot ovat prosessi haluttujen strategisten vaikutusten tai lopputulosten tuottamiseksi vastustajassa. Se pitää sisällään täyden skaalan sotilaallisen voiman ja ei sotilaallisen voiman monipuolista ja kumulatiivista käyttöä taktisella, operatiivisella ja strategisella tasolla.1 Tutkimusongelmana on: Mitkä ovat vaikutusperusteisen operaatiomallin (Effects-Based Approach to Operations, EBAO) tarjoamat edut tai haitat EU:n merellisessä sotilaallisessa kriisinhallintaoperaatiossa? Tutkimusongelma ratkaistaan vastaamalla seuraaviin alaongelmiin: 1. Mikä on vaikutukseen perustuvien operaatioiden teorian sisältö sotilaallisen toiminnan näkökulmasta? 2. Mikä on vaikutukseen perustuvan operoinnin näkökulma monikansalliseen kriisinhallintaoperaatioon? 3. Mitä ovat (EU:n sotilaallisen kriisinhallinnan) mukaiset merelliset kriisinhallintaoperaatiot ja mitkä ovat Suomen intressit EU:n sotilaalliseen kriisinhallintaan? 4. Miten vaikutukseen perustuva toimintamalli ilmenee esimerkin mukaisessa merellisessä kriisinhallintaoperaatiossa? Tutkimus on luonteeltaan laadullinen tutkimus. Tutkimusmenetelmänä on käytetty sisällönanalyysia sekä käsiteanalyysia. Vaikutukseen perustuvia operaatioita käsittelevä lähdeaineisto perustuu suurelta osin 2000-luvun alussa Yhdysvalloissa aloitettuun tutkimukseen ja siitä saatuun aineistoon. Kriisinhallintaa koskeva aineisto koostuu pääosin virallisista asiakirjoista sekä aiheeseen liittyvistä uusimmista julkaisuista ja tutkimuksista. Ajankohtaisten julkaisujen ja asiakirjojen tietoa on täydennetty lehtiartikkeleiden ja internetistä saatavilla olevien tietojen avulla. Tutkimusta lähestytään taktiikan näkökulmasta. Tutkielman johtopäätöksinä ilmeni, että keskeisiä EBAO:n etuja merellisessä sotilaallisessa kriisinhallintaoperaatiossa ovat nopea reagointikyky sekä EBAO:n mukainen laajempi näkökulma, jossa huomioidaan liittolaiset, puolueettomat toimijat ja mahdolliset vastustajat entistä paremmin. EBAO on kehitysasteella oleva konsepti, jonka suurimpana potentiaalina pidetään pyrkimystä sotilaiden ja siviilien saumattomaan yhteistyöhön kriisinhallinnan moninaisessa toimintaympäristössä. Konsepti pitää kuitenkin sisällään monta epävarmuustekijää, kuten vaikutusten ja operatiivisen ympäristön ennustamisen. Nykyisellään EBAO ei välttämättä muuttaisi operaatioiden toteutusta konkreettisesti. EU on Suomen kannalta tärkeä foorumi kansainväliseen kriisinhallintaan osallistumiseksi. Kansainväliseen kriisinhallintaan osallistuminen on keskeinen osa Suomen ulko- ja turvallisuuspolitiikkaa. Kansainvälisen ulottuvuuden kehittäminen palvelee myös kansallisen puolustuksen kehittämistä. Suomen puolustusvoimien näkökulmasta on syytä muistaa, että Yhdysvaltojen kaltaisen sotilasmahdin tarpeisiin ja resursseihin suunnitellun konseptin tarkastelussa tulee olla hyvin kriittinen ja realistinen.

Switchable Lanthanide Luminescence for Detection of Biomolecules

Binary probes are oligonucleotide probe pairs that hybridize adjacently to a complementary target nucleic acid. In order to detect this hybridization, the two probes can be modified with, for example, fluorescent molecules, chemically reactive groups or nucleic acid enzymes. The benefit of this kind of binary probe based approach is that the hybridization elicits a detectable signal which is distinguishable from background noise even though unbound probes are not removed by washing before measurement. In addition, the requirement of two simultaneous binding events increases specificity. Similarly to binary oligonucleotide probes, also certain enzymes and fluorescent proteins can be divided into two parts and used in separation-free assays. Split enzyme and fluorescent protein reporters have practical applications among others as tools to investigate protein-protein interactions within living cells. In this study, a novel label technology, switchable lanthanide luminescence, was introduced and used successfully in model assays for nucleic acid and protein detection. This label technology is based on a luminescent lanthanide chelate divided into two inherently non-luminescent moieties, an ion carrier chelate and a light harvesting antenna ligand. These form a highly luminescent complex when brought into close proximity; i.e., the label moieties switch from a dark state to a luminescent state. This kind of mixed lanthanide complex has the same beneficial photophysical properties as the more typical lanthanide chelates and cryptates - sharp emission peaks, long emission lifetime enabling time-resolved measurement, and large Stokes’ shift, which minimize the background signal. Furthermore, the switchable lanthanide luminescence technique enables a homogeneous assay set-up. Here, switchable lanthanide luminescence label technology was first applied to sensitive, homogeneous, single-target nucleic acid and protein assays with picomolar detection limits and high signal to background ratios. Thereafter, a homogeneous four-plex nucleic acid array-based assay was developed. Finally, the label technology was shown to be effective in discrimination of single nucleotide mismatched targets from fully matched targets and the luminescent complex formation was analyzed more thoroughly. In conclusion, this study demonstrates that the switchable lanthanide luminescencebased label technology can be used in various homogeneous bioanalytical assays.

Vakavaraisuussääntelyn muutosten vaikutukset paikallispankille

Tutkielman tavoitteena on selvittää muuttuvan pankkisääntelyn vaikutukset vähittäispankkitoimintaa harjoittavalle paikallispankille vakavaraisuuden näkökulmasta. Vaikutuksia vakavaraisuuteen mitataan luottoriskin osalta, sen muodostaessa merkittävimmän osan kohdepankin vakavaraisuusvaatimuksesta. Tarkoituksena on selvittää käytössä olevan standardimenetelmän ja vaihtoehtoisen sisäisten luottoluokitusten menetelmän erot luottoriskin mittaamisessa ja vaikutukset vakavaraisuuteen sekä Basel II että Basel III-säännöksillä mitattuina. Tutkielmassa huomioidaan myös Basel III -säännöksen mukaiset uudet sääntelyinstrumentit ja analysoidaan niiden vaikutusta liiketoimintaan. Sekä Basel II että Basel III -säännöksellä mitattuna sisäisten luottoluokitusten menetelmä paransi kohdepankin vakavaraisuutta. Basel III -säännöksen suurimmat vaikutukset kohdistuivat kohdepankilla omien varojen laatuvaatimuksiin, jotka heikensivät vakavaraisuutta. Laatuvaatimuksista ja nousseista pääomavaatimuksista huolimatta kohdepankin vakavaraisuus säilyi hyvällä ja vaatimukset ylittävällä tasolla. Uusien sääntelyinstrumenttien vaatimukset täyttyivät nykyisellä taserakenteella vähimmäisomavaraisuusasteen ja pysyvän varainhankinnan vaatimuksen osalta. Maksuvalmiusvaatimuksen täyttämiseksi sijoitussalkkuun pitää tehdä muutoksia, minkä odotetaan vaikuttavan heikentävästi kohdepankin tulokseen.

Expression analysis of miRNA and target mRNAs in esophageal cancer

We aimed to investigate miRNAs and related mRNAs through a network-based approach in order to learn the crucial role that they play in the biological processes of esophageal cancer. Esophageal squamous-cell carcinoma (ESCC) and adenocarcinoma (EAC)-related miRNA and gene expression data were downloaded from the Gene Expression Omnibus database, and differentially expressed miRNAs and genes were selected. Target genes of differentially expressed miRNAs were predicted and their regulatory networks were constructed. Differentially expressed miRNA analysis selected four miRNAs associated with EAC and ESCC, among which hsa-miR-21 and hsa-miR-202 were shared by both diseases. hsa-miR-202 was reported for the first time to be associated with esophageal cancer in the present study. Differentially expressed miRNA target genes were mainly involved in cancer-related and signal-transduction pathways. Functional categories of these target genes were related to transcriptional regulation. The results may indicate potential target miRNAs and genes for future investigations of esophageal cancer.

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Pankkien vakavaraisuussääntelyn vaikutus startup-yritysten rahoitukseen

Tutkielman tavoitteena on määrittää, miten pankkien vakavaraisuussääntelyn muuttuminen on vaikuttanut startup-yritysten lainan hintaan ja ehtoihin, sekä tarkastella startup-yritysten muiden rahoitusmahdollisuuksien kehittymistä. Startup-yritysten eri rahoituslähteiden kasvu kootaan lähteiden vuositilastoista. Pankkien vakavaraisuussääntelyä tarkastellaan vertailemalla lainsäädännön tilaa eri vuosina. Sääntelyn vaikutuksia arvioidaan suorittamalla laskuesimerkkejä tietynlaisten pankkien ja startup-yritysten tilanteessa. Lähtöarvot kootaan lainsäädännöstä, tilastoista, tieteellisistä julkaisuista tai asiantuntijahaastattelujen pohjalta. Startup-yritysten luottoluokitukset määritetään käyttämällä Suomen Asiakastieto Oy:n luokitusmallia. Tuloksena tutkielma luo kattavan kuvan pankkien vakavaraisuussääntelyn kehittymisestä ja startup-yritysten rahoituslähteistä. Pankkisektorin ulkopuolinen rahoitus startupeille on kasvanut 2,5 %:n vuosivauhtia vuodesta 2008, josta vertaislainat ovat olleet suuressa roolissa. Lähes 72 % pankkien vähittäislainojen markkinoista on siirtynyt sisäisten luokitusten menetelmään vastuiden riskipainojen laskennassa. Siirtymä uuteen menetelmään aiheuttaa korkopaineita viidesosalle startupeista. 58 %:lle startupeista muutos ei ole ongelma. 42 % startupeista ei voi pienentää potentiaalisen lainan korkoaan edes lainan kokoisella vakuudella. Pääomavaatimusten kasvu ja pankkien siirtyminen uusiin laskentamenetelmiin voi nostaa startup-yrityksen lainan korkoa jopa 15 %.

Public-private partnership investments in dry ports – Russian logistics markets and risks

The investments have always been considered as an essential backbone and so-called ‘locomotive’ for the competitive economies. However, in various countries, the state has been put under tight budget constraints for the investments in capital intensive projects. In response to this situation, the cooperation between public and private sector has grown based on public-private mechanism. The promotion of favorable arrangement for collaboration between public and private sectors for the provision of policies, services, and infrastructure in Russia can help to address the problems of dry ports development that neither municipalities nor the private sector can solve alone. Especially, the stimulation of public-private collaboration is significant under the exposure to externalities that affect the magnitude of the risks during all phases of project realization. In these circumstances, the risk in the projects also is becoming increasingly a part of joint research and risk management practice, which is viewed as a key approach, aiming to take active actions on existing global and specific factors of uncertainties. Meanwhile, a relatively little progress has been made on the inclusion of the resilience aspects into the planning process of a dry ports construction that would instruct the capacity planner, on how to mitigate the occurrence of disruptions that may lead to million dollars of losses due to the deviation of the future cash flows from the expected financial flows on the project. The current experience shows that the existing methodological base is developed fragmentary within separate steps of supply chain risk management (SCRM) processes: risk identification, risk evaluation, risk mitigation, risk monitoring and control phases. The lack of the systematic approach hinders the solution of the problem of risk management processes of dry port implementation. Therefore, management of various risks during the investments phases of dry port projects still presents a considerable challenge from the practical and theoretical points of view. In this regard, the given research became a logical continuation of fundamental research, existing in the financial models and theories (e.g., capital asset pricing model and real option theory), as well as provided a complementation for the portfolio theory. The goal of the current study is in the design of methods and models for the facilitation of dry port implementation through the mechanism of public-private partnership on the national market that implies the necessity to mitigate, first and foremost, the shortage of the investments and consequences of risks. The problem of the research was formulated on the ground of the identified contradictions. They rose as a continuation of the trade-off between the opportunities that the investors can gain from the development of terminal business in Russia (i.e. dry port implementation) and risks. As a rule, the higher the investment risk, the greater should be their expected return. However, investors have a different tolerance for the risks. That is why it would be advisable to find an optimum investment. In the given study, the optimum relates to the search for the efficient portfolio, which can provide satisfaction to the investor, depending on its degree of risk aversion. There are many theories and methods in finance, concerning investment choices. Nevertheless, the appropriateness and effectiveness of particular methods should be considered with the allowance of the specifics of the investment projects. For example, the investments in dry ports imply not only the lump sum of financial inflows, but also the long-term payback periods. As a result, capital intensity and longevity of their construction determine the necessity from investors to ensure the return on investment (profitability), along with the rapid return on investment (liquidity), without precluding the fact that the stochastic nature of the project environment is hardly described by the formula-based approach. The current theoretical base for the economic appraisals of the dry port projects more often perceives net present value (NPV) as a technique superior to other decision-making criteria. For example, the portfolio theory, which considers different risk preference of an investor and structures of utility, defines net present value as a better criterion of project appraisal than discounted payback period (DPP). Meanwhile, in business practice, the DPP is more popular. Knowing that the NPV is based on the assumptions of certainty of project life, it cannot be an accurate appraisal approach alone to determine whether or not the project should be accepted for the approval in the environment that is not without of uncertainties. In order to reflect the period or the project’s useful life that is exposed to risks due to changes in political, operational, and financial factors, the second capital budgeting criterion – discounted payback period is profoundly important, particularly for the Russian environment. Those statements represent contradictions that exist in the theory and practice of the applied science. Therefore, it would be desirable to relax the assumptions of portfolio theory and regard DPP as not fewer relevant appraisal approach for the assessment of the investment and risk measure. At the same time, the rationality of the use of both project performance criteria depends on the methods and models, with the help of which these appraisal approaches are calculated in feasibility studies. The deterministic methods cannot ensure the required precision of the results, while the stochastic models guarantee the sufficient level of the accuracy and reliability of the obtained results, providing that the risks are properly identified, evaluated, and mitigated. Otherwise, the project performance indicators may not be confirmed during the phase of project realization. For instance, the economic and political instability can result in the undoing of hard-earned gains, leading to the need for the attraction of the additional finances for the project. The sources of the alternative investments, as well as supportive mitigation strategies, can be studied during the initial phases of project development. During this period, the effectiveness of the investments undertakings can also be improved by the inclusion of the various investors, e.g. Russian Railways’ enterprises and other private companies in the dry port projects. However, the evaluation of the effectiveness of the participation of different investors in the project lack the methods and models that would permit doing the particular feasibility study, foreseeing the quantitative characteristics of risks and their mitigation strategies, which can meet the tolerance of the investors to the risks. For this reason, the research proposes a combination of Monte Carlo method, discounted cash flow technique, the theory of real options, and portfolio theory via a system dynamics simulation approach. The use of this methodology allows for comprehensive risk management process of dry port development to cover all aspects of risk identification, risk evaluation, risk mitigation, risk monitoring, and control phases. A designed system dynamics model can be recommended for the decision-makers on the dry port projects that are financed via a public-private partnership. It permits investors to make a decision appraisal based on random variables of net present value and discounted payback period, depending on different risks factors, e.g. revenue risks, land acquisition risks, traffic volume risks, construction hazards, and political risks. In this case, the statistical mean is used for the explication of the expected value of the DPP and NPV; the standard deviation is proposed as a characteristic of risks, while the elasticity coefficient is applied for rating of risks. Additionally, the risk of failure of project investments and guaranteed recoupment of capital investment can be considered with the help of the model. On the whole, the application of these modern methods of simulation creates preconditions for the controlling of the process of dry port development, i.e. making managerial changes and identifying the most stable parameters that contribute to the optimal alternative scenarios of the project realization in the uncertain environment. System dynamics model allows analyzing the interactions in the most complex mechanism of risk management process of the dry ports development and making proposals for the improvement of the effectiveness of the investments via an estimation of different risk management strategies. For the comparison and ranking of these alternatives in their order of preference to the investor, the proposed indicators of the efficiency of the investments, concerning the NPV, DPP, and coefficient of variation, can be used. Thus, rational investors, who averse to taking increased risks unless they are compensated by the commensurate increase in the expected utility of a risky prospect of dry port development, can be guided by the deduced marginal utility of investments. It is computed on the ground of the results from the system dynamics model. In conclusion, the outlined theoretical and practical implications for the management of risks, which are the key characteristics of public-private partnerships, can help analysts and planning managers in budget decision-making, substantially alleviating the effect from various risks and avoiding unnecessary cost overruns in dry port projects.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Functional genomics of O-glucosyltransferases from Concord grape (Vitis labrusca)

Grape (Vitis spp.) is a culturally and economically important crop plant that has been cultivated for thousands of years, primarily for the production of wine. Grape berries accumulate a myriad of phenylpropanoid secondary metabolites, many of which are glucosylated in plantae More than 90 O-glucosyltransferases have been cloned and biochemically characterized from plants, only two of which have been isolated from Vitis spp. The world-wide economic importance of grapes as a crop plant, the human health benefits associated with increased consumption of grape-derived metabolites, the biological relevance of glucosylation, and the lack of information about Vitis glucosyltransferases has inspired the identification, cloning and biochemical characterization of five novel "family 1" O-glucosyltransferases from Concord grape (Vitis labrusca cv. Concord). Protein purification and associated protein sequencIng led to the molecular cloning of UDP-glucose: resveratrollhydroxycinnamic acid O-glucosyltransferase (VLRSGT) from Vitis labrusca berry mesocarp tissue. In addition to being the first glucosyltransferase which accepts trans-resveratrol as a substrate to be characterized in vitro, the recombinant VLRSGT preferentially produces the glucose esters of hydroxycinnamic acids at pH 6.0, and the glucosides of trans-resveratrol and flavonols at 'pH 9.0; the first demonstration of pH-dependent bifunctional glucosylation for this class of enzymes. Gene expression and metabolite profiling support a role for this enzyme in the bifuncitonal glucosylation ofstilbenes and hydroxycinnamic acids in plantae A homology-based approach to cloning was used to identify three enzymes from the Vitis vinifera TIGR grape gene index which had high levels of protein sequence iii identity to previously characterized UDP-glucose: anthocyanin 5-0-glucosyltransferases. Molecular cloning and biochemical characterization demonstrated that these enzymes (rVLOGTl, rVLOGT2, rVLOGT3) glucosylate the 7-0-position of flavonols and the xenobiotic 2,4,5-trichlorophenol (TCP), but not anthocyanins. Variable gene expression throughout grape berry development and enzyme assays with native grape berry protein are consistent with a role for these enzymes in the glucosylation of flavonols; while the broad substrate specificity, the ability of these enzymes to glucosylate TCP and expression of these genes in tissues which are subject to pathogen attack (berry, flower, bud) is consistent with a role for these genes in the plant defense response. Additionally, the Vitis labrusca UDP-glucose: flavonoid 3-0-glucosyltransferase (VL3GT) was identified, cloned and characterized. VL3GT has 96 % protein sequence identity to the previously characterized Vitis vinifera flavonoid 3-0-glucosyltransferase (VV3GT); and glucosylates the 3-0-position of anthocyanidins and flavonols in vitro. Despite high levels of protein sequence identity, VL3GT has distinct biochemical characteristics (as compared to VV3GT), including a preference for B-ring methylated flavonoids and the inability to use UDP-galactose as a donor substrate. RT-PCR analysis of VL3GT gene expression and enzyme assays with native grape protein is consistent with an in planta role for this enzyme in the glucosylation of anthocyanidins,but not flavonols. These studies reveal the power of combining several biochemistry- and molecular biology-based tools to identify, clone, biochemically characterize and elucidate the in planta function of several biologically relevant O-glucosyltransferases from Vitis spp.

An exploratory study for the discovery of non-invasive hepatocellular carcinoma biomarkers among high-risk hepatitis C virus infected patients

Hepatocellular Carcinoma (HCC) is a major healthcare problem, representing the third most common cause of cancer-related mortality worldwide. Chronic infections with Hepatitis B virus (HBV) and/or Hepatitis C virus (HCV) are the major risk factors for the development of HCC. The incidence of HBV -associated HCC is in decline as a result of an effective HBV vaccine; however, since an equally effective HCV vaccine has not yet been developed, there are 130 million HCV infected patients worldwide who are at a high-risk for developing HCC. Because reliable parameters and/or tools for the early detection of HCC among high-risk individuals are severely lacking, HCC patients are always diagnosed at a late stage where surgical solutions or effective treatment are not possible. Using urine as a non-invasive sample source, two different approaches (proteomic-based and genomic-based approaches) were pursued with the common goal of discovering potential biomarker candidates for the early detection of HCC among high-risk chronic HCV infected patients. Urine was collected from 106 HCV infected Egyptian patients, 32 of whom had already developed HCC and 74 patients who were diagnosed as HCC-free at the time of initial sample collection. In addition to these patients, urine samples were also collected from 12 healthy control individuals. Total urinary proteins, Trans-renal nucleic acid (Tr-NA) and microRNA (miRNA) were isolated from urine using novel methodologies and silicon carbide-loaded spin columns. In the first, "proteomic-based", approach, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify potential candidates from pooled urine samples. This was followed by validating relative expression levels of proteins present in urine among all the patients using quantitative real time-PCR (qRT-PCR). This approach revealed that significant over-expression of three proteins: DJ-1, Chromatin Assembly Factor-1 (CAF-1) and 11 Moemen Abdalla HCC Biomarkers Heat Shock Protein 60 (HSP60), were characteristic events among HCC-post HCV infected patients. As a single-based HCC biomarker, CAF-1 over-expression identified HCC among HCV infected patients with a specificity of 90%, sensitivity of 66% and with an overall diagnostic accuracy of 78%. Moreover, the CAF-lIHSP60 tandem identified HCC among HCV infected patients with a specificity of 92%, sensitivity of 61 % and with an overall diagnostic accuracy of 77%. In the second genomic-based approach, two different approaches were processed. The first approach was the miRNA-based approach. The expression levels of miRNAs isolated from urine were studied using the Illumina MicroRNA Expression Profiling Assay. This was followed by qRT-PCR-based validation of deregulated expression of identified miRNA candidates among all the patients. This approach shed the light on the deregulated expression of a number of miRNAs, which may have a role in either the development of HCC among HCV infected patients (i.e. miR-640, miR-765, miR-200a, miR-521 and miR-520) or may allow for a better understanding of the viral-host interaction (miR-152, miR-486, miR-219, miR452, miR-425, miR-154 and miR-31). Moreover, the deregulated expression of both miR-618 and miR-650 appeared to be a common event among HCC-post HCV infected patients. The results of the search for putative targets of these two miRNA suggested that miR-618 may be a potent oncogene, as it targets the tumor-suppressor gene Low density lipoprotein-related protein 12 (LPR12), while miR-650 may be a potent tumor-suppressor gene, as it is supposed to downregulate the TNF receptor-associated factor-4 (TRAF4) oncogene. The specificity of miR-618 and miR-650 deregulated expression patterns for the early detection of HCC among HCV infected patients was 68% and 58%, respectively, whereas the sensitivity was 64% and 72%, respectively. When the deregulated expression of both miRNAs was combined as a tandem biomarker, the specificity and the sensitivity were 75% and 58% respectively. 111 Moemen Abdalla HCC Biomarkers In the second, "Trans-renal nucleic acid-based", approach, the urinary apoptotic nucleic acid (uaNA) levels of 70ng/mL or more were found to be a good predictor of HCC among chronic HCV infected patients. The specificity and the sensitivity of this diagnostic approach were 76% and 86%, respectively, with an overall diagnostic value of 81 %. The uaNA levels positively correlated to HCC disease progression as monitored by epigenetic changes of a panel of eight tumor-suppressor genes (TSGs) using methylation-sensitive PCR. Moreover, the pairing of high uaNA levels (:::: 70 ng/mL) and CAF-1 over-expreSSIOn produced a highly specific (l 00%) multiple-based HCC biomarker with an acceptable sensitivity of 64%, and with a diagnostic accuracy of 82%. In comparison to the previous pairing, the uaNA levels (:::: 70 ng/mL) in tandem with HSP60 over-expression was less specific (89%) but highly sensitive (72%), resulting in a diagnostic accuracy of 64%. The specificities of miR-650 deregulated expression in combination with either high uaNA content or HSP 60 over-expression were 82% and 79%, respectively, whereas, the sensitivities of these combinations were 64% and 58%, respectively. The potential biomarkers identified in this study compare favorably with the diagnostic accuracy of the a-fetoprotein levels test, which has a specificity of 75%, sensitivity of 68% and an overall diagnostic accuracy of 70%. Here we present an intriguing study which shows the significance of using urine as a noninvasive sample source for the identification of promising HCC biomarkers. We have also introduced new techniques for the isolation of different urinary macromolecules, especially miRNA, from urine. Furthermore, we strongly recommend the potential biomarkers indentified in this study as focal points of any future research on HCC diagnosis. A larger testing pool will determine if their use is practical for mass population screening. This explorative study identified potential targets that merit further investigation for the development of diagnostically accurate biomarkers isolated from 1-2 mL urine samples that were acquired in a non-invasive manner.

Aboriginal women in education : Honouring our experiences a vision of access to and success within the university

This thesis explores Aboriginal women's access to and success within universities through an examination of Aboriginal women's educational narratives, along with input from key service providers from both the Aboriginal and non-Aboriginal community. Implemented through the Wildfire Research Method, participants engaged in a consensusbased vision of accessible education that honours the spiritual, emotional, intellectual, and physical elements necessary for the success of Aboriginal women in university. This study positions Aboriginal women as agents of social change by allowing them to define their own needs and offer viable solutions to those needs. Further, it connects service providers from the many disconnected sectors that implicate Aboriginal women's education access. The realities of Aboriginal women are contextualized through historical, sociocultural, and political analyses, revealing the need for a decolonizing educational approach. This fosters a shift away from a deficit model toward a cultural and linguistic assets based approach that emphasizes the need for strong cultural identity formation. Participants revealed academic, cultural, and linguistic barriers and offered clear educational specifications for responsive and culturally relevant programming that will assist Aboriginal women in developing and maintaining strong cultural identities. Findings reveal the need for curriculum that focuses on decolonizing and reclaiming Aboriginal women's identities, and program outcomes that encourage balance between two worldviews-traditional and academic-through the application of cultural traditions to modern contexts, along with programming that responds to the immediate needs of Aboriginal women such as childcare, housing, and funding, and provide an opportunity for universities and educators to engage in responsive and culturally grounded educational approaches.

Sport Values of Bantam, Midget and Intermediate Female Hockey Players and Their Minor Hockey Associations

The sport values of female hockey players and their minor hockey associations were explored to better inform a values-based approach for adult-managed minor hockey. Data were collected from 294 participatory HL and competitive Rep players (12-22 years of age) using the Youth Sport Values Questionnaire-2 and from 30 hockey association board members using a modified YSVQ-2. Results indicated player importance (VI) ratings for Moral (M = 4.08) and Competence (M = 4.15) values were not significantly different but were significantly higher than Status (M = 2.11) value. Significant weak relationships between age and competition level versus VI ratings were found. There were medium/ high Moral, medium/ low Competence and high/ high Status value congruence between Rep and HL Player-Board Members, respectively. Based upon the findings, girls’ minor hockey associations need to recognize the values female youth players prioritize, and ensure each is considered within a values-based decision-making approach to governance.

Investigation of Theories Supporting Engagement of Resistant Learners in Formal Academic Settings and Curriculum

This study sought to explore ways to work with a group of young people through an arts-based approach to the teaching of literacy. Through the research, the author integrated her own reflexivity applying arts methods over the past decade. The author’s past experiences were strongly informed by theories such as caring theory and maternal pedagogy, which also informed the research design. The study incorporated qualitative data collection instruments comprising interviews, journals, sketches, artifacts, and teacher field notes. Data were collected by 3 student participants for the duration of the research. Study results provide educators with data on the impact of creating informal and alternative ways to teach literacy and maintain student engagement with resistant learners.

Effets de l'application de charges aux membres inférieurs sur le patron de marche des personnes hémiparétiques chroniques

Placer une charge au niveau du membre inférieur est une approche sans fondement scientifique, utilisée par les cliniciens, pour renforcer certains muscles clés de la marche. Cette étude a déterminé les modifications du patron de marche lors de l’ajout d’une charge à la cheville parétique ou non parétique chez des personnes ayant une hémiparésie suite à un accident vasculaire cérébral et a comparé les résultats à ceux d’un groupe témoin. Il est supposé qu’une charge placée à la jambe parétique/non dominante (charge ipsilatérale) augmenterait les efforts (moments et puissance) à la hanche parétique/non dominante lors de l’oscillation et qu’une charge placée controlatéralement augmenterait les efforts lors de la phase d’appui principalement pour les abducteurs de hanche stabilisant le bassin dans le plan frontal. La marche avec et sans charge de cinq individus hémiparétiques chroniques et 5 personnes en santé a été analysée en laboratoire par l’enregistrement des forces de réaction du sol et des mouvements des membres inférieurs. Ces informations ont permis de calculer les paramètres temps-distance, les angles à la hanche parétique/non dominante et au tronc, les moments nets, les puissances et le travail mécanique à la hanche parétique/non dominante. Des tests statistiques non-paramétriques ont servi à déterminer l’effet de la condition, avec charge (ipsi- et controlatérale) ou sans charge et à comparer les résultats entre les deux groupes. L’ajout d’une charge n’a pas modifié la vitesse de marche des sujets. Les phases d’appui et d’oscillation étaient rendus plus symétriques par la charge, même si peu de différences apparaissaient dans le plan sagittal avec ou sans la charge. Dans le plan frontal, le moment abducteur de hanche des sujets hémiparétiques a diminué avec la charge controlatérale, tandis qu'il a augmenté chez les sujets en santé. L’utilisation d’une stratégie posturale ou dynamique au tronc pourrait expliquer la différence de l’effet de la charge sur le moment abducteur à la hanche. Au vu de ces résultats, il est nécessaire de poursuivre l’évaluation de cette approche de renforcement musculaire spécifique à la tâche avant d’en recommander son utilisation.