An Interactive Tool for Automatic Predimensioning and Numerical Modeling of Arch Dams

The construction of double-curvature arch dams is an attractive solution from an economic viewpoint due to the reduced volume of concrete necessary for their construction as compared to conventional gravity dams. Due to their complex geometry, many criteria have arisen for their design. However, the most widespread methods are based on recommendations of traditional technical documents without taking into account the possibilities of computer-aided design. In this paper, an innovative software tool to design FEM models of double-curvature arch dams is presented. Several capabilities are allowed: simplified geometry creation (interesting for academic purposes), preliminary geometrical design, high-detailed model construction, and stochastic calculation performance (introducing uncertainty associated with material properties and other parameters). This paper specially focuses on geometrical issues describing the functionalities of the tool and the fundamentals of the design procedure with regard to the following aspects: topography, reference cylinder, excavation depth, crown cantilever thickness and curvature, horizontal arch curvature, excavation and concrete mass volume, and additional elements such as joints or spillways. Examples of application on two Spanish dams are presented and the results obtained analyzed

Next-generation mitogenomics: A comparison of approaches applied to caecilian amphibian phylogeny

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case

Physical and numerical modeling of labyrinth weirs with polyhedral bottom

[EN] In order to comply with the new safety regulations a significant number of Spanish dam spillways must be upgraded. In this scenario and with the aim of increasing the discharge capacity with a reduced investment innovative designs become interesting solutions. One of these innovative designs are the labyrinth weirs. Project POLILAB is carrying out with the objective of optimize the design of labyrinth weirs, physical and numerical tests exposed in this article were developed within this framework. The most relevant results are related with the discharge capacity, the flow pattern and the structural reinforcement achieved by the implementation of a polyhedral bottom.[ES] Un número importante de presas en España deben ampliar sus aliviaderos para cumplir criterios de seguridad distintos a los de su construcción. En este contexto, cobran interés soluciones de aliviaderos no convencionales como los aliviaderos en laberinto, que permiten aumentar la capacidad de desagüe de estructuras existentes con una inversión moderada. Para la optimización del diseño de este tipo de aliviaderos se desarrolla el proyecto POLILAB, en cuyo marco se llevaron a cabo las campañas de modelación física y numérica que se exponen en este artículo. Se describen los resultados más relevantes en lo relativo a la inclusión de fondos poliédricos en aliviaderos en laberinto como refuerzo estructural, contemplando además las modificaciones que implican con respecto a soluciones en laberinto con fondo plano, en lo relativo a capacidad de desagüe, patrón de flujo y acciones hidrodinámicas sobre los contornos del laberinto.Los autores desean expresar su agradecimiento al Ministerio de Economía y Competitividad por su apoyo en la financiación del proyecto: “POLILAB. Diseño del prototipo de una compuerta fusible recuperable tipo laberinto de fondo poliédrico para la mejora de la seguridad hidrológica de las presas”. En el marco del Plan Nacional de Investigación Científica, Desarrollo e Innovación Tecnológica (2008-2011). Programa Nacional de Cooperación Público-Privada. Subprograma INNPACTO (IPT- 2012- 0185-380000). Proyecto co-financiado por el Fondo Europeo de Desarrollo Regional (FEDER). También se desea agradecer a Carlos Granell y Luis Ruano su disponibilidad y activa colaboración en el proyecto POLILAB.San Mauro, J.; Salazar, F.; Toledo, MÁ.; Caballero, FJ.; Ponce-Farfán, C.; Ramos, T. (2016). Modelación física y numérica de aliviaderos en laberinto con fondo poliédrico. Ingeniería del Agua. 20(3):127-138. https://doi.org/10.4995/ia.2016.4614SWORD127138203Blanc, P., Lempérière, F. (2001). Labyrinth spillways have a promising future. International Journal on Hydropower and Dams, 8(4), 129-131.Codina, R. (2000). Stabilization of incompressibility and convection through orthogonal sub-scales in finite element method. Computer Methods in Applied Mechanics and Engineering, 190(13-14), 1579-1599. doi:10.1016/S0045-7825(00)00254-1Cordero, D., Elviro, V., Granell, C. (2007). Aliviaderos en laberinto: presa de María Cristina. Revista de Ingeniería Civil. ISSN: 0213-8468, 146, 5-20.Crookston, B., Tullis, B. (2012). Labyrinth weirs: Nappe interference and local submergence. Journal of Irrigation and Drainage Engineering, 138(8), 757-765. doi:10.1061/(ASCE)IR.1943-4774.0000466Crookston, B., Tullis, B. (2013). Hydraulic design and analysis of labyrinth weirs. I: Discharge relationships. Journal of Irrigation and Drainage Engineering, 139(5), 363-370. doi:10.1061/(ASCE)IR.1943-4774.0000558Dadvand, P., Rossi, R., Oñate, E. (2010). An object-oriented environment for developing finite element codes for multi-disciplinary applications. Archives of Computational Methods in Engineering, 17(3), 253-297. doi:10.1007/s11831-010-9045-2Kratos, multiphysics open source FEM code, (2012). http://www.cimne.com/kratos [Acceso: junio 2016].Larese, A., Rossi, R., Oñate, E. (2015). Finite element modeling of free surface flow in variable porosity media. Archives of Computational Methods in Engineering, 22(4), 637-653. doi:10.1007/s11831-014-9140-xOsher, S., Fedkiw, R.P. (2001). Level set methods: An overview and some recent results. Journal of Computational Physics, 169(2), 463-502. doi:10.1006/jcph.2000.6636Pfister, M., Battisacco, E., De Cesare, G., Schleiss, A. J. (2013). Scale effects related to the rating curve of cylindrically crested Piano Key weirs. Labyrinth and Piano Key Weirs II, 73. CRC BALKEMA. ISBN: 9781138000858Principe, J., Codina, R., Henke, F. (2010). The dissipative structure of variational multiscale methods for incompressible flows. Computer Methods in Applied Mechanics and Engineering, 199(13), 791-801. doi:10.1016/j.cma.2008.09.007Rossi, R., Larese, A., Dadvand, P., Oñate, E. (2013). An efficient edge-based level set finite element method for free surface flow problems. International Journal of Numerical Methods in Fluids, 71(6), 687-716. doi:10.1002/fld.3680Salazar, F., Morán, R., Rossi, R., y Oñate, E. (2013). Analysis of the discharge capacity of radial-gated spillways using CFD and ANN-Oliana Dam case study. Journal of Hydraulic Research, 51(3), 244-252. Doi: 10.1080/00221686.2012.755714Salazar, F., San Mauro, J., Oñate, E. y Toledo, M.A. (2015). CFD analysis of flow pattern in labyrinth weirs. Dam Protections against Overtopping and Accidental Leakage, 287. CRC BALKEMA. ISBN: 9781138028081Vasquez, V., Boyd, M., Wolfhope, J., Garret, R. (2007). A labyrinth rises in the heart of Texas. Proc., 28th Annual USSD Conf., USSD, Denver, CO, 813-826. Disponible en: http://ussdams.com/proceedings/2008Proc/813-826.pdf [Acceso: junio 2016].Zienkiewicz, O.C., Taylor, R.L., Nithiarasu, P. (2005). The finite element method for fluid dynamics, ed. 6. Elsevier Butterworth-Heinemann, Oxford, UK. ISBN: 978-0-7506-6431-

Venezuelan Equine Encephalitis Replicon Particles Can Induce Rapid Protection against Foot-and-Mouth Disease Virus

We have previously shown that delivery of the porcine type I interferon gene (poIFN-α/β) with a replication-defective human adenovirus vector (adenovirus 5 [Ad5]) can sterilely protect swine challenged with foot-and-mouth disease virus (FMDV) 1 day later. However, the need of relatively high doses of Ad5 limits the applicability of such a control strategy in the livestock industry. Venezuelan equine encephalitis virus (VEE) empty replicon particles (VRPs) can induce rapid protection of mice against either homologous or, in some cases, heterologous virus challenge. As an alternative approach to induce rapid protection against FMDV, we have examined the ability of VRPs containing either the gene for green fluorescent protein (VRP-GFP) or poIFN-α (VRP-poIFN- α) to block FMDV replication in vitro and in vivo. Pretreatment of swine or bovine cell lines with either VRP significantly inhibited subsequent infection with FMDV as early as 6 h after treatment and for at least 120 h posttreatment. Furthermore, mice pretreated with either 107 or 108 infectious units of VRP-GFP and challenged with a lethal dose of FMDV 24 h later were protected from death. Protection was induced as early as 6 h after treatment and lasted for at least 48 h and correlated with induction of an antiviral response and production of IFN- α. By 6 h after treatment several genes were upregulated, and the number of genes and the level of induction increased at 24 h. Finally, we demonstrated that the chemokine IP-10, which is induced by IFN- α and VRP-GFP, is directly involved in protection against FMDV

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae

<p>Abstract</p> <p>Background</p> <p>Evolutionary novelties often appear by conferring completely new functions to pre-existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a central role in the behavior of frogs, which use their calls to delimit territories and attract mates. Therefore, frogs have evolved complex vocal structures capable of producing a wide variety of advertising sounds. It is generally acknowledged that most frogs call by moving an air column from the lungs through the glottis with the remarkable exception of the family Pipidae, whose members share a highly specialized sound production mechanism independent of air movement.</p> <p>Results</p> <p>Here, we performed behavioral observations in the poorly known African pipid genus <it>Pseudhymenochirus </it>and document that the sound production in this aquatic frog is almost certainly air-driven. However, morphological comparisons revealed an indisputable pipid nature of <it>Pseudhymenochirus </it>larynx. To place this paradoxical pattern into an evolutionary framework, we reconstructed robust molecular phylogenies of pipids based on complete mitochondrial genomes and nine nuclear protein-coding genes that coincided in placing <it>Pseudhymenochirus </it>nested among other pipids.</p> <p>Conclusions</p> <p>We conclude that although <it>Pseudhymenochirus </it>probably has evolved a reversal to the ancestral non-pipid condition of air-driven sound production, the mechanism through which it occurs is an evolutionary innovation based on the derived larynx of pipids. This strengthens the idea that evolutionary solutions to functional problems often emerge based on previous structures, and for this reason, innovations largely depend on possibilities and constraints predefined by the particular history of each lineage.</p

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

BACKGROUND: Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. METHODOLOGY/PRINCIPAL FINDINGS: We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. CONCLUSIONS/SIGNIFICANCE: Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels

What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades

<p>Abstract</p> <p>Background</p> <p>The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for <it>Plethodon </it>salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals).</p> <p>Results</p> <p>We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that <it>Plethodon </it>have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled).</p> <p>Conclusions</p> <p>Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like <it>Plethodon</it>, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.</p

The Gaia-ESO Survey: the inner disk intermediate-age open cluster NGC 6802

Milky Way open clusters are very diverse in terms of age, chemical composition, and kinematic properties. Intermediate-age and old open clusters are less common, and it is even harder to find them inside the solar Galactocentric radius, due to the high mortality rate and strong extinction inside this region. NGC 6802 is one of the inner disk open clusters (IOCs) observed by the Gaia-ESO survey (GES). This cluster is an important target for calibrating the abundances derived in the survey due to the kinematic and chemical homogeneity of the members in open clusters. Using the measurements from Gaia-ESO internal data release 4 (iDR4), we identify 95 main-sequence dwarfs as cluster members from the GIRAFFE target list, and eight giants as cluster members from the UVES target list. The dwarf cluster members have a median radial velocity of 13.6 ± 1.9 km s‾¹ , while the giant cluster members have a median radial velocity of 12.0 ± 0.9 km s‾¹ and a median [Fe/H] of 0.10 ± 0.02 dex. The color-magnitude diagram of these cluster members suggests an age of 0.9 ± 0.1 Gyr, with (m − M)₀ = 11.4 and E(B − V) = 0.86. We perform the first detailed chemical abundance analysis of NGC 6802, including 27 elemental species. To gain a more general picture about IOCs, the measurements of NGC 6802 are compared with those of other IOCs previously studied by GES, that is, NGC 4815, Trumpler 20, NGC 6705, and Berkeley 81. NGC 6802 shows similar C, N, Na, and Al abundances as other IOCs. These elements are compared with nucleosynthetic models as a function of cluster turn-off mass. The α, iron-peak, and neutron-capture elements are also explored in a self-consistent way.Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 188.B-3002. These data products have been processed by the Cambridge Astronomy Survey Unit (CASU) at the Institute of Astronomy, University of Cambridge, and by the FLAMES/UVES reduction team at INAF/Osservatorio Astrofisico di Arcetri. These data have been obtained from the Gaia-ESO Survey Data Archive, prepared and hosted by the Wide Field Astronomy Unit, Institute for Astronomy, University of Edinburgh, which is funded by the UK Science and Technology Facilities Council. This work was partly supported by the European Union FP7 programme through ERC grant number 320360 and by the Leverhulme Trust through grant RPG-2012-541. We acknowledge the support from INAF and Ministero dell’ Istruzione, dell’ Università’ e della Ricerca (MIUR) in the form of the grant "Premiale VLT 2012". The results presented here benefit from discussions held during the Gaia-ESO workshops and conferences supported by the ESF (European Science Foundation) through the GREAT Research Network Programme. We thank the anonymous referee for insightful comments. D.G. , S.V., and B.T. gratefully acknowledges support from the Chilean BASAL Centro de Excelencia en Astrofísica y Tecnologías Afines (CATA) grant PFB-06/2007. C.M. acknowledges support from CONICYT-PCHA/Doctorado Nacional/2014-21141057. R.E.C. acknowledges funding from Gemini-CONICYT for Project 32140007. F.M. gratefully acknowledges the support provided by Fondecyt for project 314017. This work was partly supported (A.R.C.) by the European Union FP7 programme through grant number 320360. This work was partly supported (A.D., G.T., R.Ž.) by the grant from the Research Council of Lithuania (MIP-082/2015). S.G.S. acknowledge the support from FCT through Investigador FCT contract of reference IF/00028/2014 and the support from FCT through the project PTDC/FIS-AST/7073/2014. C.L. gratefully acknowledges financial support from the European Research Council (ERC-CoG-646928, Multi-Pop, PI: N. Bastian). V.A. acknowledges the support from the FCT (Portugal) in the form of the grant SFRH/BPD/70574/2010, the support by FCT through national funds (ref. PTDC/FIS-AST/7073/2014 and ref. PTDC/FIS-AST/1526/2014) and by FEDER through COMPETE2020 (ref. POCI-01-0145-FEDER-016880 and ref. POCI-01-0145-FEDER-016886)