In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads

2018

Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., "sequencing reads"). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., "RNA-Seq") has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample's (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt's lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3.

2018

Patients with inflammatory bowel disease (IBD) are susceptible to thromboembolism. Interestingly, IBD occurs less frequently in patients with inherited bleeding disorders. Therefore, we analyzed whether F9-deficiency is protective against the onset of acute colitis in a genetic hemophilia B mouse model. In the 3.5% dextran sulfate sodium (DSS)-induced colitis model, F9-deficient mice were protected from body-weight loss and had a reduced disease activity score. We detected decreased colonic myeloperoxidase activity and decreased CXCL1 levels in DSS-treated F9-deficient mice compared with wild-type (WT) littermate controls, indicating decreased neutrophil infiltration. Remarkably, we identif…

Regional Innovation System as a Framework for the Co-generation of Policy: An Action Research Approach

2018

Policy makers in regional development often relate their policies to frameworks proposed by researchers in the field. Of these frameworks, the regional innovation system (RIS) has been one of the most influential. This chapter focuses on the difficulties that arise when policy makers try to enact the RIS and other related frameworks and proposes action research—and, more specifically, a co-generative approach—to help face these challenges. The starting point for this proposal is an analysis of the differences and similarities between the observer and co-generative research approaches. Most research in this field has been developed with researchers positioned as outside observers, and co-gen…

Electronic Supplementary Material from Ecological conditions alter cooperative behaviour and its costs in a chemically defended sawfly.

2018

The evolution of cooperation and social behaviour is often studied in isolation from the ecology of organisms. Yet, the selective environment under which individuals evolve is much more complex in nature, consisting of ecological and abiotic interactions in addition to social ones. Here, we measured the life-history costs of cooperative chemical defence in a gregarious social herbivore, Diprion pini pine sawfly larvae, and how these costs vary under different ecological conditions. We ran a rearing experiment where we manipulated diet (resin content) and attack intensity by repeatedly harassing larvae to produce a chemical defence. We show that forcing individuals to allocate more to cooper…

High-Pressure High-Temperature Stability and Thermal Equation of State of Zircon-Type Erbium Vanadate.

2018

Inorganic chemistry 57(21), 14005 - 14012 (2018). doi:10.1021/acs.inorgchem.8b01808

Rapid evaluation of notch stress intensity factors using the peak stress method: Comparison of commercial finite element codes for a range of mesh pa…

2018

The peak stress method (PSM) is an engineering, finite element (FE)-oriented method to rapidly estimate the notch stress intensity factors by using the singular linear elastic peak stresses calculated from coarse FE analyses. The average element size adopted to generate the mesh pattern can be chosen arbitrarily within a given range. Originally, the PSM has been calibrated under pure mode I and pure mode II loadings by means of Ansys FE software. In the present contribution, a round robin between 10 Italian universities has been carried out to calibrate the PSM with 7 different commercial FE codes. To this aim, several two-dimensional mode I and mode II problems have been analysed independe…

Chromophore-Protein Interplay During the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy

2018

Phytochrome proteins regulate many photoresponses of plants and microorganisms. Light absorption causes isomerization of the biliverdin chromophore, which triggers a series of structural changes to activate the signaling domains of the protein. However, the structural changes are elusive, and therefore the molecular mechanism of signal transduction remains poorly understood. Here, we apply two-color step-scan infrared spectroscopy to the bacteriophytochrome from Deinococcus radiodurans. We show by recordings in H2O and D2O that the hydrogen bonds to the biliverdin D-ring carbonyl become disordered in the first intermediate (Lumi-R) forming a dynamic microenvironment, then completely detach …

On the mend of bryophyte conservation in Spain: preparing a proposal for the inclusion of bryophytes in national species protection catalogues

2018

The Spanish bryoflora contains 1291 taxa, 272 of them included in the Spanish Red List under any threat category. Although bryophytes show a low rate of endemicity compared to vascular flora, Spanish administration’s responsibility for the conservation of these plants is very high, since the country has 63 exclusive or rare species on a European or world scale. However, the representation of this group of plants in the Spanish legislation on species conservation is merely anecdotal. Royal Decree 139/2011 of 4 February develops a list of wild protected species (LESRPE and CEEA, Spanish abbreviations) and includes only 10 species of bryophytes, all of them from the Directive Habitats and the …

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

2018

Abstract Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-deriv…

Additional file 3: of Immunocompromised patients with acute respiratory distress syndrome: secondary analysis of the LUNG SAFE database

2018

Table S2. Factors associated with the use of noninvasive ventilation. Multivariate logistic regression model describing the factors associated with the use of noninvasive ventilation. (PDF 49Â kb)

Improved meteorology and surface fluxes in mesoscale modelling using adjusted initial vertical soil moisture profiles

2018

The Regional Atmospheric Modeling System (RAMS) is being used for different and diverse purposes, ranging from atmospheric and dispersion of pollutants forecasting to agricultural meteorology and ecological modelling as well as for hydrological purposes, among others. The current paper presents a comprehensive assessment of the RAMS forecasts, comparing the results not only with observed standard surface meteorological variables, measured at FLUXNET stations and other portable and permanent weather stations located over the region of study, but also with non-standard observed variables, such as the surface energy fluxes, with the aim of evaluating the surface energy budget and its relation …

Photoluminescence and Electron Spin Resonance of Silicon Dioxide Crystal with Rutile Structure (Stishovite)

2018

This work was supported by ERANET MYND. Also, financial support provided by Scientific Research Project for Students and Young Researchers Nr. SJZ/2017/2 realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged. The authors express our gratitude to R.I. Mashkovtsev for help in ESR signal interpretation. The authors are appreciative to T.I. Dyuzheva, L.M. Lityagina, N.A. Bendeliani for stishovite single crystals and to K. Hubner and H.-J. Fitting for stishovite powder of Barringer Meteor Crater.

Les dictionnaires du commerce bilingues franco-italiens

2018

L’article analyse les caractéristiques fondamentales des premiers dictionnaires du commerce italien-français : Endimio Spezia avec son Terminologia e fraseologia commerciale italiana-francese de 1899, Mario Edmondo Dozin avec le Dizionario tecnico commerciale italiano-francese de 1910 et Pasquale De Franciscis avec le Dizionarietto commerciale italiano-francese : ad uso degli alunni delle scuole serali superiori de 1911. Ces dictionnaires combleront un vide dans le panorama éditorial scolaire commercial italien.

Bestiality: Animal Cultures

2018

Multinaturalism shouldn’t be viewed solely as the paradigmatic existence of multiple natures in different cultures – or “ontologies” as Descola refers to them – but also and most importantly as the syntagmatic presence, and the resulting contrast, of various ontologies within the same culture. From a semiotic point of view, then, the so-called ontologies are considered to be effects of meaning derived from precise discursive dispositifs. Describing such dispositifs is the aim of this paper.

Non-equilibrium thermodynamics, heat transport and thermal waves in laminar and turbulent superfluid helium

2018

This review paper puts together some results concerning non equilibrium thermodynamics and heat transport properties of superfluid He II. A one-fluid extended model of superfluid helium, which considers heat flux as an additional independent variable, is presented, its microscopic bases are analyzed, and compared with the well known two-fluid model. In laminar situations, the fundamental fields are density, velocity, absolute temperature, and heat flux. Such a theory is able to describe the thermomechanical phenomena, the propagation of two sounds in liquid helium, and of fourth sound in superleak. It also leads in a natural way to a two-fluid model on purely macroscopical grounds and allow…

Volcanic gases

2018

Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches

2018

Mercury (Hg) is a highly toxic element for living organisms and is known to bioaccumulate and biomagnify. Here, we analyze the response of benthic foraminifera communities cultured in mesocosm and exposed to different concentrations of Hg. Standard morphological analyses and environmental DNA metabarcoding show evidence that Hg pollution has detrimental effects on benthic foraminifera. The molecular analysis provides a more complete view of foraminiferal communities including the soft-walled single-chambered monothalamiids and small-sized hard-shelled rotaliids and textulariids than the morphological one. Among these taxa that are typically overlooked in morphological studies we found poten…

Bridges between Cultures: Ties and Knots

2018

Centred on the metaphor of bridges and knots, this volume investigates the dialogic and dialectical relationships between socially dissimilar and topographically distant cultures. The contributions here explore various methodological frameworks for discourses and theories that purport to conceptualize cultural spaces, which – as opposed to objective, geographical areas – are characterized by the propensity to bind topographical distances by means of symbolic ties and perimeters. The chapters address possible juxtapositions and intersections of spatial and temporal dimensions of cultural practice, religious and ethical “ties and knots” between lands and cultures, disconnections between histo…

Społeczeństwo internautów a kultura globalna. Młody użytkownik w sieci. Cz. 2

2018

Juden - Christen - Muslime. Was sie verbindet - was sie trennt

2018

Liturgy and Music in the History of the Pauline Order

2018

Does organized sport participation during youth predict healthy habits in adulthood? : A 28-year longitudinal study

2018

Health behaviors in youth can predict the same behaviors later in life, but the role of sport participation in predicting healthy lifestyle habits is unclear. This study aimed to investigate the association between participation in organized youth sport and adult healthy lifestyle habits. Data from the longitudinal Cardiovascular Risk in Young Finns Study (YFS) with a 28‐year follow‐up were used. The participation in sport‐club training sessions was self‐reported by 9‐18‐year‐olds in 1983 and 1986 (n = 1285). During 2011, participants (aged 37‐43‐year old) reported their smoking status, alcohol consumption, fruit and vegetable consumption, and physical activity. Odd ratios (OR) were calcula…

Extending the hosts of Tectiviridae into four additional genera of Gram-positive bacteria and more diverse Bacillus species

2018

Tectiviridae are composed of tailless bacteriophages with an icosahedral capsid and an inner membrane enclosing a double-stranded 15 kb linear DNA genome. Five of the seven previously studied Tectivirus isolates infect bacteria from Bacillus cereus sensu lato group (Betatectivirus), one distantly related member (PRD1) infect Enterobactericeae (Alpatectivirus) and one recently discovered virus infect Gluconobacter cerinus (Gammatectivirus). Here we expand the host spectrum of Betatectivirus elements to four additional genera (Streptococcus, Exiguobacterium, Clostridium and Brevibacillus) and to more distantly related Bacillus species (B. pumilus and B. flexus) by studying the genomes of four…

Erinomaiset matematiikan osaajat

2018

Äikkähän on oppiaine, joka syleilee maailmaa : äidinkielen ja kirjallisuuden aineenopettajien käsityksiä globaalikasvatuksesta ja sen toteuttamisesta

2018

Tutkimuksessani olen selvittänyt yläkoulun äidinkielen ja kirjallisuuden opettajien käsityksiä globaalikasvatuksesta ilmiönä sekä sen toteuttamisesta osana äidinkielen ja kirjallisuuden oppiainetta. Tutkimuksen aineisto on kerätty kolmelta vuosina 2013–2015 valmistuneelta opettajalta teemahaastatteluin. Teoreettisen viitekehyksen tälle tutkimukselle muodostavat globaalikasvatuksen käsite sekä fenomenografia analyysimenetelmänä. Sidon tutkimukseni myös perusopetuksen opetussuunnitelmaan. Pyrkimykseni oli selvittää, onko globaalikasvatuksen käsite opettajille entuudestaan tuttu ja miten he sen ymmärtävät. Myös opettajien näkemykset globaalikasvatuksen ja äidinkielen ja kirjallisuuden oppiaine…

Kansallinen yliopisto ja kansainväliset intressit : kieli-ideologiat korkeakoulupolitiikan hierarkioiden kuvaajina

2018

Methods in dress research

2018

Rungen lause ja sovelluksia inversio-ongelmiin

2018

Learning Experience Technology Usability Design framework

2018

Using information and communication technology (ICT) for learning purposes has become more ingrained in curriculums and students’ lives over the past decades. Commonly, the lack of understanding about learning and pedagogy, and more specifically their contexts, will lead to creating learning software that utilize outdated pedagogy or are lacking in critical aspects of pedagogical design. This has created a need to find cost efficient ways to address the multidimensional usability issues found in learning technology. Creating an engaging and pedagogically robust learning product is a complicated task that requires easily accessible knowledge about both the technological and learning related …

Alpha frequency discrepancy and trait anxiety, activation, and inhibition in states of anxiety and mindfulness

2018

Meditaatiotekniikat tarjovat laajalti mahdollisuuksia hyvinvoinnin ylläpitämiseen ja kehittämiseen sekä stressin lievittämiseen. Useat neurotieteelliset tutkimukset ovat osoittaneet välittömiä tuloksia meditatitiivisten tekniikoiden soveltamisen ja aivojen oskillatoristen mekanismien välisessä suhteessa. Meditaatiolla on osoitettu olevan myös pitkäaikaisia vaikutuksia, joihin sisältyy ahdistuneisuuden ja murheen väheneminen. Keskittymistä tukevan aivokäyttöliittymän alustavan suunnittelun tueksi tutkittiin alpha-aallonpituuden käyttäytymistä ahdistuneisuuden ja mindfulnessin tiloissa ja niiden välisiä eroja lähestyttiin aktivaatio-/inhibitio -persoonallisuuspiirteiden sekä ahdistuneisuuteen…

Physical Inactivity from Youth to Adulthood and Risk of Impaired Glucose Metabolism

2018

INTRODUCTION: Physical activity (PA) is important in the prevention and treatment of impaired glucose metabolism. However, association of physical inactivity during the transition between childhood and adulthood with glucose metabolism is unknown. Therefore, we studied the association of persistent physical inactivity since childhood with glucose metabolism in adulthood. METHODS: Data were drawn from the ongoing, Cardiovascular Risk in Young Finns Study with repeated follow-ups between 1980 and 2011 (baseline age, 3-18 yr; n = 3596). Impaired glucose metabolism was defined as having impaired fasting glucose (6.1-6.9 mmol·L) or type 2 diabetes in adulthood. Leisure-time PA habits were repeat…

Suomalaisten 4-luokkalaisten lukutaito : PIRLS 2016 -tutkimuksen keskeisiä tuloksia

2018

Joulukuussa 2017 julkaistiin kansainvälisen lasten lukutaitotutkimuksen (PIRLS) tulokset (ks. Leino ym. 2017). PIRLS-tutkimuksessa tarkastellaan 4.-luokkalaisten oppilaiden lukutaitoa ja lukemista monin eri tavoin. Keväällä 2016 hieman alle 5 000 oppilasta osallistui lukutaidon kokeeseen, jossa oppilaat vastasivat kaunokirjallisiin ja tietoteksteihin pohjautuviin tehtäviin. Lisäksi oppilaat täyttivät kyselyn, jonka avulla kerättiin tietoja oppilaiden asenteista, erilaisten tekstien lukemisesta ja oppilaan kotitaustasta. Tämän lisäksi tutkimuksessa oli lasten vanhemmille, opettajille ja koulujen rehtoreille omat kyselynsä, joiden avulla saatiin tietoa oppimisen ympäristöistä sekä resursseist…

Digitalisaation vaikutukset kaupunkisuunnittelussa

2018

Tämä kandidaatintutkielma on tutkimus digitalisaation vaikutuksesta kau-punkisuunnitteluun. Tutkimus on tehty kirjallisuuskatsauksena, jossa tarkastellaan ensin digitalisaatiota terminologisesti ja ilmiötasolla. Digitalisaatio on käsitteenä vielä suhteellisen uusi ja vakiintumaton, joten siitä on pyritty eri lähteiden ja kontekstien avulla saamaan kattava kuva ja käsitys informaatioteknologisena tekijänä ja ilmiönä. Digitalisaatio liittyy käsillä olevaan valtavaan tiedon määrän kasvuun, jota on vaikea jäsentää ja analysoida. Tätä tietoa voidaan kutsua massadataksi. Kaupunkisuunnittelu puolestaan on yhteiskunnallisesti säännelty ja tarkasteltu tekijä, joka on kaupunkien kehitystä määräävä ja…

I beste fall en god nummer to : Om kjønnsforskjeller i fotballen på Sørlandet

2018

Masteroppgave Sosiologi og sosialt arbeid ME522 - Universitetet i Agder 2018 Fotball er for lengst blitt Norges største og mest populære idrett for jenter og kvinner. Likevel er fotballarenaen svært mannsdominert, og idretten preges fortsatt av store kjønnsforskjeller. Formålet med denne studien er å belyse hvordan kjønnsforskjeller i fotballen kommer til uttrykk på Sørlandet. Spesielt synes jeg det kan være interessant å gjøre en slik studie i den minst likestilte landsdelen, der det viser seg at over 80 prosent av alle fotballag i Agder Fotballkrets er gutte- og herrelag. Jeg har benytta meg av to ulike tilnærminger for å belyse de store kjønnsforskjellene som finnes. Først vil jeg se på …

Muligheter og utfordringer i veiprosjekter ved bruk av Best Value Procurement i kombinasjon med totalentreprise : En casestudie av Nye Veier prosjekt…

2018

Masteroppgave industriell økonomi og teknologiledelse IND590 - Universitetet i Agder 2018 Nye Veiers project E18 Rugtvedt-Dørdal is the first project in Norway to use the procurement method Best Value Procurement. The project is carried out as a Design-Build contract, which also is fairly new in the road construction industry. The purpose of this thesis is to reveal how Nye Veiers new project execution model has influenced the project execution phase, regarding cooperation, constructability and customer value. This will be discussed in the context of theories regarding transaction costs, the principal-agent problem, network in value chains and learning. The study is based on an abductive ap…

Planificación de la producción en un entorno multifábrica

2018

Las cadenas de suministro en las que se insertan los procesos de producción son cada vez más complejas. Las empresas que cuentan con fábricas en diferentes localizaciones reparten entre ellas la fabricación de piezas y componentes. E incluso llegan a externalizar el montaje de los productos finales, enviando sus componentes a otras plantas para su montaje final. Surgen, por tanto, nuevos problemas de planificación y programación de la producción inherentes a esta forma de producción descentralizada. Se ha de asignar la producción de cada planta, programar su producción y, llegados el caso, planificar los envíos a la planta en la que se realizará el montaje. Si bien es cierto que cada uno de…