311 research outputs found

    Methodology for high resolution spatial analysis of the physical flood susceptibility of buildings in large river floodplains

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    The impacts of floods on buildings in urban areas are increasing due to the intensification of extreme weather events, unplanned or uncontrolled settlements and the rising vulnerability of assets. There are some approaches available for assessing the flood damage to buildings and critical infrastructure. To this point, however, it is extremely difficult to adapt these methods widely, due to the lack of high resolution classification and characterisation approaches for built structures. To overcome this obstacle, this work presents: first, a conceptual framework for understanding the physical flood vulnerability and the physical flood susceptibility of buildings, second, a methodological framework for the combination of methods and tools for a large-scale and high-resolution analysis and third, the testing of the methodology in three pilot sites with different development conditions. The conceptual framework narrows down an understanding of flood vulnerability, physical flood vulnerability and physical flood susceptibility and its relation to social and economic vulnerabilities. It describes the key features causing the physical flood susceptibility of buildings as a component of the vulnerability. The methodological framework comprises three modules: (i) methods for setting up a building topology, (ii) methods for assessing the susceptibility of representative buildings of each building type and (iii) the integration of the two modules with technological tools. The first module on the building typology is based on a classification of remote sensing data and GIS analysis involving seven building parameters, which appeared to be relevant for a classification of buildings regarding potential flood impacts. The outcome is a building taxonomic approach. A subsequent identification of representative buildings is based on statistical analyses and membership functions. The second module on the building susceptibility for representative buildings bears on the derivation of depth-physical impact functions. It relates the principal building components, including their heights, dimensions and materials, to the damage from different water levels. The material’s susceptibility is estimated based on international studies on the resistance of building materials and a fuzzy expert analysis. Then depth-physical impact functions are calculated referring to the principal components of the buildings which can be affected by different water levels. Hereby, depth-physical impact functions are seen as a means for the interrelation between the water level and the physical impacts. The third module provides the tools for implementing the methodology. This tool compresses the architecture for feeding the required data on the buildings with their relations to the building typology and the building-type specific depth-physical impact function supporting the automatic process. The methodology is tested in three flood plains pilot sites: (i) in the settlement of the Barrio Sur in MaganguĂ© and (ii) in the settlement of La Peña in Cicuco located on the flood plain of Magdalena River, Colombia and (iii) in a settlement of the city of Dresden, located on the Elbe River, Germany. The testing of the methodology covers the description of data availability and accuracy, the steps for deriving the depth-physical impact functions of representative buildings and the final display of the spatial distribution of the physical flood susceptibility. The discussion analyses what are the contributions of this work evaluating the findings of the methodology’s testing with the dissertation goals. The conclusions of the work show the contributions and limitations of the research in terms of methodological and empirical advancements and the general applicability in flood risk management.:1 INTRODUCTION 1 1.1 Background 1 1.2 State of the art 2 1.3 Problem statement 6 1.4 Objectives 6 1.5 Approach and outline 6 2 CONCEPTUAL FRAMEWORK 9 2.1 Flood vulnerability 10 2.2 Physical flood vulnerability 12 2.3 Physical flood susceptibility 14 3 METHODOLOGICAL FRAMEWORK 23 3.1 Module 1: Building taxonomy for settlements 24 3.1.1 Extraction of building features 24 3.1.2 Derivation of building parameters for setting up a building taxonomy 38 3.1.3 Selection of representative buildings for a building susceptibility assessment 51 3.2 Module 2: Physical susceptibility of representative buildings 57 3.2.1 Identification of building components 57 3.2.2 Qualification of building material susceptibility 62 3.2.3 Derivation of a depth-physical impact function 71 3.3 Module 3: Technological integration 77 3.3.1 Combination of the depth-physical impact function with the building taxonomic code 77 3.3.2 Tools supporting the physical susceptibility analysis 78 3.3.3 The users and their requirements 79 4 RESULTS OF THE METHODOLOGY TESTING 83 4.1 Pilot site “Kleinzschachwitz” – Dresden, Germany – Elbe River 83 4.1.1 Module 1: Building taxonomy – “Kleinzschachwitz” 85 4.1.2 Module 2: Physical susceptibility of representative buildings – “Kleinzschachwitz” 97 4.1.3 Module 3: Technological integration – “Kleinzschachwitz” 103 4.2 Pilot site “La Peña” – Cicuco, Colombia – Magdalena River 107 4.2.1 Module 1: Building taxonomy – “La Peña” 108 4.2.2 Module 2: Physical susceptibility of representative buildings – “La Peña” 121 4.2.3 Module 3: Technological integration– “La Peña” 129 4.3 Pilot site “Barrio Sur” – MaganguĂ©, Colombia – Magdalena River 133 4.3.1 Module 1: Building taxonomy – “Barrio Sur” 133 4.3.2 Module 2: Physical susceptibility of representative buildings – “Barrio Sur” 141 4.3.3 Module 3: Technological integration – “Barrio Sur” 147 4.4 Empirical findings 151 4.4.1 Empirical findings of Module 1 151 4.4.2 Empirical findings of Module 2 155 4.4.3 Empirical findings of Module 3 157 4.4.4 Guidance of the methodology 157 5 DISCUSSION 161 5.1 Discussion on the conceptual framework 161 5.2 Discussion on the methodological framework 161 5.2.1 Discussion on Module 1: the building taxonomic approach 162 5.2.2 Discussion on Module 2: the depth-physical impact function 164 6 CONCLUSIONS AND OUTLOOK 167 6.1 Conclusions 167 6.2 Outlook 168 REFERENCES 171 INDEX OF FIGURES 199 INDEX OF TABLES 201 APPENDICES 203In vielen StĂ€dten nehmen die Auswirkungen von Hochwasser auf GebĂ€ude aufgrund immer extremerer Wetterereignisse, unkontrollierbarer Siedlungsbauten und der steigenden VulnerabilitĂ€t von BesitztĂŒmern stetig zu. Es existieren zwar bereits AnsĂ€tze zur Beurteilung von WasserschĂ€den an GebĂ€uden und Infrastrukturknotenpunkten. Doch ist es bisher schwierig, diese Methoden großrĂ€umig anzuwenden, da es an einer prĂ€zisen Klassifizierung und Charakterisierung von GebĂ€uden und anderen baulichen Anlagen fehlt. Zu diesem Zweck sollen in dieser Arbeit erstens ein Konzept fĂŒr ein genaueres VerstĂ€ndnis der physischen VulnerabilitĂ€t von GebĂ€uden gegenĂŒber Hochwasser dargelegt, zweitens ein methodisches Verfahren zur Kombination der bestehenden Methoden und Hilfsmittel mit dem Ziel einer großrĂ€umigen und hochauflösenden Analyse erarbeitet und drittens diese Methode an drei Pilotstandorten mit unterschiedlichem Ausbauzustand erprobt werden. Die Rahmenbedingungen des Konzepts grenzen die Begriffe der VulnerabilitĂ€t, der physischen VulnerabilitĂ€t und der physischen AnfĂ€lligkeit gegenĂŒber Hochwasser ein und erörtern deren Beziehung zur sozialen und ökonomischen VulnerabilitĂ€t. Es werden die Merkmale der physischen AnfĂ€lligkeit von GebĂ€uden gegenĂŒber Hochwasser als Bestandteil der VulnerabilitĂ€t definiert. Das methodische Verfahren umfasst drei Module: (i) Methoden zur Erstellung einer GebĂ€udetypologie, (ii) Methoden zur Bewertung der AnfĂ€lligkeit reprĂ€sentativer GebĂ€ude jedes GebĂ€udetyps und (iii) die Kombination der beiden Module mit Hilfe technologischer Hilfsmittel. Das erste Modul zur GebĂ€udetypologie basiert auf der Klassifizierung von Fernerkundungsdaten und GIS-Analysen anhand von sieben GebĂ€udeparametern, die sich fĂŒr die Klassifizierung von GebĂ€uden bezĂŒglich ihres Risikopotenzials bei Hochwasser als wichtig erweisen. Daraus ergibt sich ein Ansatz zur GebĂ€udeklassifizierung. Die anschließende Ermittlung reprĂ€sentativer GebĂ€ude beruht auf statistischen Analysen und Zugehörigkeitsfunktionen. Das zweite Modul zur AnfĂ€lligkeit reprĂ€sentativer GebĂ€ude beruht auf der Ableitung von Funktion von Wasserstand und physischer Einwirkung. Es setzt die relevanten GebĂ€udemerkmale, darunter Höhe, Maße und Materialien, in Beziehung zum erwartbaren Schaden bei unterschiedlichen WasserstĂ€nden. Die MaterialanfĂ€lligkeit wird aufgrund internationaler Studien zur Festigkeit von Baustoffen sowie durch Anwendung eines Fuzzy-Logic-Expertensystems eingeschĂ€tzt. Anschließend werden Wasserstand-Schaden-Funktionen unter Einbeziehung der HauptgebĂ€udekomponenten berechnet, die durch unterschiedliche WasserstĂ€nde in Mitleidenschaft gezogen werden können. Funktion von Wasserstand und physischer Einwirkung dienen hier dazu, den jeweiligen Wasserstand und die physischen Auswirkung in Beziehung zueinander zu setzen. Das dritte Modul stellt die zur Umsetzung der Methoden notwendigen Hilfsmittel vor. Zur UnterstĂŒtzung des automatisierten Verfahrens dienen Hilfsmittel, die die GebĂ€udetypologie mit der Funktion von Wasserstand und physischer Einwirkung fĂŒr GebĂ€ude in Hochwassergebieten kombinieren. Die Methoden wurden anschließend in drei hochwassergefĂ€hrdeten Pilotstandorten getestet: (i) in den Siedlungsgebieten von Barrio Sur in MaganguĂ© und (ii) von La Pena in Cicuco, zwei Überschwemmungsgebiete des Magdalenas in Kolumbien, und (iii) im Stadtgebiet von Dresden, das an der Elbe liegt. Das Testverfahren umfasst die Beschreibung der DatenverfĂŒgbarkeit und genauigkeit, die einzelnen Schritte zur Analyse der. Funktion von Wasserstand und physischer Einwirkung reprĂ€sentativer GebĂ€ude sowie die Darstellung der rĂ€umlichen Verteilung der physischen AnfĂ€lligkeit fĂŒr Hochwasser. In der Diskussion wird der Beitrag dieser Arbeit zur Beurteilung der Erkenntnisse der getesteten Methoden anhand der Ziele dieser Dissertation analysiert. Die Folgerungen beleuchten abschließend die Fortschritte und auch Grenzen der Forschung hinsichtlich methodischer und empirischer Entwicklungen sowie deren allgemeine Anwendbarkeit im Bereich des Hochwasserschutzes.:1 INTRODUCTION 1 1.1 Background 1 1.2 State of the art 2 1.3 Problem statement 6 1.4 Objectives 6 1.5 Approach and outline 6 2 CONCEPTUAL FRAMEWORK 9 2.1 Flood vulnerability 10 2.2 Physical flood vulnerability 12 2.3 Physical flood susceptibility 14 3 METHODOLOGICAL FRAMEWORK 23 3.1 Module 1: Building taxonomy for settlements 24 3.1.1 Extraction of building features 24 3.1.2 Derivation of building parameters for setting up a building taxonomy 38 3.1.3 Selection of representative buildings for a building susceptibility assessment 51 3.2 Module 2: Physical susceptibility of representative buildings 57 3.2.1 Identification of building components 57 3.2.2 Qualification of building material susceptibility 62 3.2.3 Derivation of a depth-physical impact function 71 3.3 Module 3: Technological integration 77 3.3.1 Combination of the depth-physical impact function with the building taxonomic code 77 3.3.2 Tools supporting the physical susceptibility analysis 78 3.3.3 The users and their requirements 79 4 RESULTS OF THE METHODOLOGY TESTING 83 4.1 Pilot site “Kleinzschachwitz” – Dresden, Germany – Elbe River 83 4.1.1 Module 1: Building taxonomy – “Kleinzschachwitz” 85 4.1.2 Module 2: Physical susceptibility of representative buildings – “Kleinzschachwitz” 97 4.1.3 Module 3: Technological integration – “Kleinzschachwitz” 103 4.2 Pilot site “La Peña” – Cicuco, Colombia – Magdalena River 107 4.2.1 Module 1: Building taxonomy – “La Peña” 108 4.2.2 Module 2: Physical susceptibility of representative buildings – “La Peña” 121 4.2.3 Module 3: Technological integration– “La Peña” 129 4.3 Pilot site “Barrio Sur” – MaganguĂ©, Colombia – Magdalena River 133 4.3.1 Module 1: Building taxonomy – “Barrio Sur” 133 4.3.2 Module 2: Physical susceptibility of representative buildings – “Barrio Sur” 141 4.3.3 Module 3: Technological integration – “Barrio Sur” 147 4.4 Empirical findings 151 4.4.1 Empirical findings of Module 1 151 4.4.2 Empirical findings of Module 2 155 4.4.3 Empirical findings of Module 3 157 4.4.4 Guidance of the methodology 157 5 DISCUSSION 161 5.1 Discussion on the conceptual framework 161 5.2 Discussion on the methodological framework 161 5.2.1 Discussion on Module 1: the building taxonomic approach 162 5.2.2 Discussion on Module 2: the depth-physical impact function 164 6 CONCLUSIONS AND OUTLOOK 167 6.1 Conclusions 167 6.2 Outlook 168 REFERENCES 171 INDEX OF FIGURES 199 INDEX OF TABLES 201 APPENDICES 203El impacto de las inundaciones sobre los edificios en zonas urbanas es cada vez mayor debido a la intensificaciĂłn de los fenĂłmenos meteorolĂłgicos extremos, asentamientos no controlados o no planificados y su creciente vulnerabilidad. Hay mĂ©todos disponibles para evaluar los daños por inundaciĂłn en edificios e infraestructuras crĂ­ticas. Sin embargo, es muy difĂ­cil implementar estos mĂ©todos sistemĂĄticamente en grandes ĂĄreas debido a la falta de clasificaciĂłn y caracterizaciĂłn de estructuras construidas en resoluciones detalladas. Para superar este obstĂĄculo, este trabajo se enfoca, en primer lugar, en desarrollar un marco conceptual para comprender la vulnerabilidad y susceptibilidad fĂ­sica de edificios por inudaciones, en segundo lugar, en desarrollar un marco metodolĂłgico para la combinaciĂłn de los mĂ©todos y herramientas para una anĂĄlisis de alta resoluciĂłn y en tercer lugar, la prueba de la metodologĂ­a en tres sitios experimentales, con distintas condiciones de desarrollo. El marco conceptual se enfoca en comprender la vulnerabilidad y susceptibility de las edificaciones frente a inundaciones, y su relaciĂłn con la vulnerabilidad social y econĂłmica. En Ă©l se describen las principales caracterĂ­sticas fĂ­sicas de la susceptibilidad de edificicaiones como un componente de la vulnerabilidad. El marco metodolĂłgico consta de tres mĂłdulos: (i) mĂ©todos para la derivaciĂłn de topologĂ­a de construcciones, (ii) mĂ©todos para evaluar la susceptibilidad de edificios representativos y (iii) la integraciĂłn de los dos mĂłdulos a travĂ©s herramientas tecnolĂłgicas. El primer mĂłdulo de topologĂ­a de construcciones se basa en una clasificaciĂłn de datos de sensoramiento rĂ©moto y procesamiento SIG para la extracciĂłn de siete parĂĄmetros de las edficaciones. Este mĂłdulo parece ser aplicable para una clasificaciĂłn de los edificios en relaciĂłn con los posibles impactos de las inundaciones. El resultado es una taxonomĂ­a de las edificaciones y una posterior identificaciĂłn de edificios representativos que se basa en anĂĄlisis estadĂ­sticos y funciones de pertenencia. El segundo mĂłdulo consiste en el anĂĄlisis de susceptibilidad de las construcciones representativas a travĂ©s de funciones de profundidad del impacto fĂ­sico. Las cuales relacionan los principales componentes de la construcciĂłn, incluyendo sus alturas, dimensiones y materiales con los impactos fĂ­sicos a diferentes niveles de agua. La susceptibilidad del material se calcula con base a estudios internacionales sobre la resistencia de los materiales y un anĂĄlisis a travĂ©s de sistemas expertos difusos. AquĂ­, las funciones de profundidad de impacto fĂ­sico son considerados como un medio para la interrelaciĂłn entre el nivel del agua y los impactos fĂ­sicos. El tercer mĂłdulo proporciona las herramientas necesarias para la aplicaciĂłn de la metodologĂ­a. Estas herramientas tecnolĂłgicas consisten en la arquitectura para la alimentaciĂłn de los datos relacionados a la tipologĂ­a de construcciones con las funciones de profundidad del impacto fĂ­sico apoyado en procesos automĂĄticos. La metodologĂ­a es probada en tres sitios piloto: (i) en el Barrio Sur en MaganguĂ© y (ii) en la barrio de La Peña en Cicuco situado en la llanura inundable del RĂ­o Magdalena, Colombia y (iii) en barrio Kleinzschachwitz de la ciudad de Dresden, situado a orillas del rĂ­o Elba, en Alemania. Las pruebas de la metodologĂ­a abarca la descripciĂłn de la disponibilidad de los datos y la precisiĂłn, los pasos a seguir para obtener las funciones profundidad de impacto fĂ­sico de edificios representativos y la presentaciĂłn final de la distribuciĂłn espacial de la susceptibilidad fĂ­sica frente inundaciones El discusiĂłn analiza las aportaciones de este trabajo y evalua los resultados de la metodologĂ­a con relaciĂłn a los objetivos. Las conclusiones del trabajo, muestran los aportes y limitaciones de la investigaciĂłn en tĂ©rminos de avances metodolĂłgicos y empĂ­ricos y la aplicabilidad general de gestiĂłn del riesgo de inundaciones.:1 INTRODUCTION 1 1.1 Background 1 1.2 State of the art 2 1.3 Problem statement 6 1.4 Objectives 6 1.5 Approach and outline 6 2 CONCEPTUAL FRAMEWORK 9 2.1 Flood vulnerability 10 2.2 Physical flood vulnerability 12 2.3 Physical flood susceptibility 14 3 METHODOLOGICAL FRAMEWORK 23 3.1 Module 1: Building taxonomy for settlements 24 3.1.1 Extraction of building features 24 3.1.2 Derivation of building parameters for setting up a building taxonomy 38 3.1.3 Selection of representative buildings for a building susceptibility assessment 51 3.2 Module 2: Physical susceptibility of representative buildings 57 3.2.1 Identification of building components 57 3.2.2 Qualification of building material susceptibility 62 3.2.3 Derivation of a depth-physical impact function 71 3.3 Module 3: Technological integration 77 3.3.1 Combination of the depth-physical impact function with the building taxonomic code 77 3.3.2 Tools supporting the physical susceptibility analysis 78 3.3.3 The users and their requirements 79 4 RESULTS OF THE METHODOLOGY TESTING 83 4.1 Pilot site “Kleinzschachwitz” – Dresden, Germany – Elbe River 83 4.1.1 Module 1: Building taxonomy – “Kleinzschachwitz” 85 4.1.2 Module 2: Physical susceptibility of representative buildings – “Kleinzschachwitz” 97 4.1.3 Module 3: Technological integration – “Kleinzschachwitz” 103 4.2 Pilot site “La Peña” – Cicuco, Colombia – Magdalena River 107 4.2.1 Module 1: Building taxonomy – “La Peña” 108 4.2.2 Module 2: Physical susceptibility of representative buildings – “La Peña” 121 4.2.3 Module 3: Technological integration– “La Peña” 129 4.3 Pilot site “Barrio Sur” – MaganguĂ©, Colombia – Magdalena River 133 4.3.1 Module 1: Building taxonomy – “Barrio Sur” 133 4.3.2 Module 2: Physical susceptibility of representative buildings – “Barrio Sur” 141 4.3.3 Module 3: Technological integration – “Barrio Sur” 147 4.4 Empirical findings 151 4.4.1 Empirical findings of Module 1 151 4.4.2 Empirical findings of Module 2 155 4.4.3 Empirical findings of Module 3 157 4.4.4 Guidance of the methodology 157 5 DISCUSSION 161 5.1 Discussion on the conceptual framework 161 5.2 Discussion on the methodological framework 161 5.2.1 Discussion on Module 1: the building taxonomic approach 162 5.2.2 Discussion on Module 2: the depth-physical impact function 164 6 CONCLUSIONS AND OUTLOOK 167 6.1 Conclusions 167 6.2 Outlook 168 REFERENCES 171 INDEX OF FIGURES 199 INDEX OF TABLES 201 APPENDICES 20

    Model atmospheres of chemically peculiar stars: Self-consistent empirical stratified model of HD24712

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    High-resolution spectra of some chemically peculiar stars clearly demonstrate the presence of strong abundance gradients in their atmospheres. However, these inhomogeneities are usually ignored in the standard scheme of model atmosphere calculations, braking the consistency between model structure and spectroscopically derived abundance pattern. In this paper we present first empirical self-consistent stellar atmosphere model of roAp star HD24712, with stratification of chemical elements included, and which is derived directly from the observed profiles of spectral lines without time-consuming simulations of physical mechanisms responsible for these anomalies. We used the LLmodels stellar model atmosphere code and DDAFIT minimization tool for analysis of chemical elements stratification and construction of self-consistent atmospheric model. Empirical determination of Pr and Nd stratification in the atmosphere of HD24712 is based on NLTE line formation for Prii/iii and Ndii/iii with the use of the DETAIL code. Based on iterative procedure of stratification analysis and subsequent re-calculation of model atmosphere structure we constructed a self-consistent model of HD24712, i.e. the model which temperature-pressure structure is consistent with results of stratification analysis. It is shown that stratification of chemical elements leads to the considerable changes in model structure as to compare with non-stratified homogeneous case. We find that accumulation of REE elements allows for the inverse temperature gradient to be present in upper atmosphere of the star with the maximum temperature increase of about 600K.Comment: Comments: Accepted by A&A, 16 pages, 10 figures, 3 table

    Multi-substrate flavonol O-glucosyltransferases from strawberry (Fragaria×ananassa) achene and receptacle

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    In an effort to characterize fruit ripening-related genes functionally, two glucosyltransferases, FaGT6 and FaGT7, were cloned from a strawberry (Fragaria×ananassa) cDNA library and the full-length open reading frames were amplified by rapid amplification of cDNA ends. FaGT6 and FaGT7 were expressed heterologously as fusion proteins in Escherichia coli and target protein was purified using affinity chromatography. Both recombinant enzymes exhibited a broad substrate tolerance in vitro, accepting numerous flavonoids, hydroxycoumarins, and naphthols. FaGT6 formed 3-O-glucosides and minor amounts of 7-O-, 4â€Č-O-, and 3â€Č-O-monoglucosides and one diglucoside from flavonols such as quercetin. FaGT7 converted quercetin to the 3-O-glucoside and 4â€Č-O-glucoside and minor levels of the 7- and 3â€Č-isomers but formed no diglucoside. Gene expression studies showed that both genes are strongly expressed in achenes of small-sized green fruits, while the expression levels were generally lower in the receptacle. Significant levels of quercetin 3-O-, 7-O-, and 4â€Č-O-glucosides, kaempferol 3-O- and 7-O-glucosides, as well as isorhamnetin 7-O-glucoside, were identified in achenes and the receptacle. In the receptacle, the expression of both genes is negatively controlled by auxin which correlates with the ripening-related gene expression in this tissue. Salicylic acid, a known signal molecule in plant defence, induces the expression of both genes. Thus, it appears that FaGT6 and FaGT7 are involved in the glucosylation of flavonols and may also participate in xenobiotic metabolism. The latter function is supported by the proven ability of strawberries to glucosylate selected unnatural substrates injected in ripe fruits. This report presents the first biochemical characterization of enzymes mainly expressed in strawberry achenes and provides the foundation of flavonoid metabolism in the seeds

    Automatic Determination of Stellar Atmospheric Parameters and Construction of Stellar Spectral Templates of the Guoshoujing Telescope (LAMOST)

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    A number of spectroscopic surveys have been carried out or are planned to study the origin of the Milky Way. Their exploitation requires reliable automated methods and softwares to measure the fundamental parameters of the stars. Adopting the ULySS package, we have tested the effect of different resolutions and signal-to-noise ratios (SNR) on the measurement of the stellar atmospheric parameters (effective temperature Teff, surface gravity log g, and metallicity [Fe/H]). We show that ULySS is reliable to determine these parameters with medium-resolution spectra (R~2000). Then, we applied the method to measure the parameters of 771 stars selected in the commissioning database of the Guoshoujing Telescope (GSJT). The results were compared with the SDSS/SEGUE Stellar Parameter Pipeline (SSPP), and we derived precisions of 167 K, 0.34 dex, and 0.16 dex for Teff, log g and [Fe/H] respectively. Furthermore, 120 of these stars are selected to construct the primary stellar spectra template library (Version 1.0) of GSJT, and will be deployed as basic ingredients for the GSJT automated parametrization pipeline.Comment: 23 pages, 15 figures, accepted by RA

    MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome

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    Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes. Such deletion mapping is usually conducted using polymerase chain reaction (PCR) assays for the presence or absence of a series of Y-chromosomal DNA markers, or sequence-tagged sites (STSs). In the course of mapping intact and aberrant Y chromosomes during the past two decades, we and our colleagues have developed robust PCR assays for 1287 Y-specific STSs. These PCR assays amplify 1698 loci at an average spacing of <14 kb across the MSY euchromatin. To facilitate mapping of deletions, we have compiled a database of these STSs, MSY Breakpoint Mapper (http://breakpointmapper.wi.mit.edu/). When queried, this online database provides regionally targeted catalogs of STSs and nearby genes. MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.National Institutes of Health (U.S.)Howard Hughes Medical Institut

    <i>Gaia</i> Data Release 1. Summary of the astrometric, photometric, and survey properties

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    Context. At about 1000 days after the launch of Gaia we present the first Gaia data release, Gaia DR1, consisting of astrometry and photometry for over 1 billion sources brighter than magnitude 20.7. Aims. A summary of Gaia DR1 is presented along with illustrations of the scientific quality of the data, followed by a discussion of the limitations due to the preliminary nature of this release. Methods. The raw data collected by Gaia during the first 14 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into an astrometric and photometric catalogue. Results. Gaia DR1 consists of three components: a primary astrometric data set which contains the positions, parallaxes, and mean proper motions for about 2 million of the brightest stars in common with the HIPPARCOS and Tycho-2 catalogues – a realisation of the Tycho-Gaia Astrometric Solution (TGAS) – and a secondary astrometric data set containing the positions for an additional 1.1 billion sources. The second component is the photometric data set, consisting of mean G-band magnitudes for all sources. The G-band light curves and the characteristics of ∌3000 Cepheid and RR-Lyrae stars, observed at high cadence around the south ecliptic pole, form the third component. For the primary astrometric data set the typical uncertainty is about 0.3 mas for the positions and parallaxes, and about 1 mas yr−1 for the proper motions. A systematic component of ∌0.3 mas should be added to the parallax uncertainties. For the subset of ∌94 000 HIPPARCOS stars in the primary data set, the proper motions are much more precise at about 0.06 mas yr−1. For the secondary astrometric data set, the typical uncertainty of the positions is ∌10 mas. The median uncertainties on the mean G-band magnitudes range from the mmag level to ∌0.03 mag over the magnitude range 5 to 20.7. Conclusions. Gaia DR1 is an important milestone ahead of the next Gaia data release, which will feature five-parameter astrometry for all sources. Extensive validation shows that Gaia DR1 represents a major advance in the mapping of the heavens and the availability of basic stellar data that underpin observational astrophysics. Nevertheless, the very preliminary nature of this first Gaia data release does lead to a number of important limitations to the data quality which should be carefully considered before drawing conclusions from the data

    Combining magnetic hyperthermia and dual T1/T2 MR imaging using highly versatile iron oxide nanoparticles

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    [EN] Magnetic hyperthermia and magnetic resonance imaging (MRI) are two of the most important biomedical applications of magnetic nanoparticles (MNPs). However, the design of MNPs with good heating performance for hyperthermia and dual T1/T2 contrast for MRI remains a considerable challenge. In this work, ultrasmall superparamagnetic iron oxide nanoparticles (USPIONs) are synthesized through a simple one-step methodology. A post-synthetic purification strategy has been implemented in order to separate discrete nanoparticles from aggregates and unstable nanoparticles, leading to USPIONs that preserve chemical and colloidal stability for extended periods of time. The optimized nanoparticles exhibit high saturation magnetization and show good heating efficiency in magnetic hyperthermia experiments. Remarkably, the evaluation of the USPIONs as MRI contrast agents revealed that the nanoparticles are also able to provide significant dual T1/T2 signal enhancement. These promising results demonstrate that USPIONs are excellent candidates for the development of theranostic nanodevices with potential application in both hyperthermia and dual T1/T2 MR imaging.We are grateful to the Spanish Government (projects MAT2015-64139-C4-1-R and AGL2015-70235-C2-2-R (MINECO/FEDER)) and the Generalitat Valenciana (Projects PROMETEO/2018/024 and PROMETEOII/2014/047) for financial support. S. S. C. is grateful to the Spanish MEC for his FPU grant. JG acknowledges funding from FCT and the ERDF through NORTE2020 through the project Self-reporting immunestimulating formulation for on-demand cancer therapy with real-time treatment response monitoring (028052).SĂĄnchez-Cabezas, S.; Montes-Robles, R.; Gallo, J.; SancenĂłn Galarza, F.; MartĂ­nez-Måñez, R. (2019). Combining magnetic hyperthermia and dual T1/T2 MR imaging using highly versatile iron oxide nanoparticles. Dalton Transactions. 48(12):3883-3892. https://doi.org/10.1039/c8dt04685aS388338924812Lee, J.-H., Jang, J., Choi, J., Moon, S. H., Noh, S., Kim, J., 
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    Crosstalk between cAMP and MAP Kinase Signaling in the Regulation of Cell Proliferation

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    Hormonal stimulation of cyclic adenosine monophosphate (cAMP) and the cAMP-dependent protein kinase PKA regulates cell growth by multiple mechanisms. A hallmark of cAMP is its ability to stimulate cell growth in many cell types while inhibiting cell growth in others. In this review, the cell type-specific effects of cAMP on the mitogen-activated protein (MAP) kinase (also called extracellular signal-regulated kinase, or ERK) cascade and cell proliferation are examined. Two basic themes are discussed. First, the capacity of cAMP for either positive or negative regulation of the ERK cascade accounts for many of the cell type-specific actions of cAMP on cell proliferation. Second, there are several specific mechanisms involved in the inhibition or activation of ERKs by cAMP. Emerging new data suggest that one of these mechanisms might involve the activation of the GTPase Rap1, which can activate or inhibit ERK signaling in a cell-specific manner

    The Relevance of Marine Chemical Ecology to Plankton and Ecosystem Function: An Emerging Field

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    Marine chemical ecology comprises the study of the production and interaction of bioactive molecules affecting organism behavior and function. Here we focus on bioactive compounds and interactions associated with phytoplankton, particularly bloom-forming diatoms, prymnesiophytes and dinoflagellates. Planktonic bioactive metabolites are structurally and functionally diverse and some may have multiple simultaneous functions including roles in chemical defense (antipredator, allelopathic and antibacterial compounds), and/or cell-to-cell signaling (e.g., polyunsaturated aldehydes (PUAs) of diatoms). Among inducible chemical defenses in response to grazing, there is high species-specific variability in the effects on grazers, ranging from severe physical incapacitation and/or death to no apparent physiological response, depending on predator susceptibility and detoxification capability. Most bioactive compounds are present in very low concentrations, in both the producing organism and the surrounding aqueous medium. Furthermore, bioactivity may be subject to synergistic interactions with other natural and anthropogenic environmental toxicants. Most, if not all phycotoxins are classic secondary metabolites, but many other bioactive metabolites are simple molecules derived from primary metabolism (e.g., PUAs in diatoms, dimethylsulfoniopropionate (DMSP) in prymnesiophytes). Producing cells do not seem to suffer physiological impact due to their synthesis. Functional genome sequence data and gene expression analysis will provide insights into regulatory and metabolic pathways in producer organisms, as well as identification of mechanisms of action in target organisms. Understanding chemical ecological responses to environmental triggers and chemically-mediated species interactions will help define crucial chemical and molecular processes that help maintain biodiversity and ecosystem functionality
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