Hydraulic and stability analysis of the supporting layer of wedge-shaped blocks

Presented at the Protections 2016: 2nd international seminar on dam protection against overtopping: concrete dams, embankment dams, levees, tailings dams held on 7th-9th September, 2016, at Colorado State University in Fort Collins, Colorado, USA. The increasing demand for dam and levee safety and flood protection has motivated new research and advancements and a greater need for cost-effective measures in overtopping protection as a solution for overtopping concerns at levees and dams. This seminar will bring together leading experts from practice, research, development, and implementation for two days of knowledge exchange followed by a technical tour of the Colorado State University Hydraulic Laboratory with overtopping flume and wave simulator. This seminar will focus on: Critical issues related to levees and dams; New developments and advanced tools; Overtopping protection systems; System design and performance; Applications and innovative solutions; Case histories of overtopping events; Physical modeling techniques and recent studies; and Numerical modeling methods.Includes bibliographical references.Wedge shaped blocks (WSB) are attracting increasing attention as protection against overtopping for earth and rock-fill dams. However, there are limited examples of application and some aspects of the technology merit additional research and improvement. One key issue is the design of drainage and supporting layer for WSB protections. During overtopping, part of the overflow leaks through the joints between blocks, hence circulating through the granular material. The permeability and thickness of the supporting layer must be sufficient to prevent the flow from generating pressure on the bottom side of the blocks, which contributes to its destabilization. However, it must also be structurally stable to avoid undesirable deformations on the downstream face. Both the material permeability and the layer thickness determine the hydraulic behavior of this element. These, together with the weight of the blocks and the slope of the downstream face, directly influence mass and block stability. These aspects should be taken into account for the numerical modeling of seepage through the supporting layer. To this end, an application of the open source software Kratos Multi-physics was employed. A parametric study was conducted to quantify the influence of each design variable in the safety factor against mass sliding of the supporting and drainage layer

Orientability of vector bundles over real flag manifolds

We investigate the orientability of a class of vector bundles over flag manifolds of real semi-simple Lie groups, which include the tangent bundle and also stable bundles of certain gradient flows. Closed formulas, in terms of roots, are provided.Comment: 26 page

Applications of numerical methods in design and evaluation of overtopping protection systems

Presented at the Protections 2016: 2nd international seminar on dam protection against overtopping: concrete dams, embankment dams, levees, tailings dams held on 7th-9th September, 2016, at Colorado State University in Fort Collins, Colorado, USA. The increasing demand for dam and levee safety and flood protection has motivated new research and advancements and a greater need for cost-effective measures in overtopping protection as a solution for overtopping concerns at levees and dams. This seminar will bring together leading experts from practice, research, development, and implementation for two days of knowledge exchange followed by a technical tour of the Colorado State University Hydraulic Laboratory with overtopping flume and wave simulator. This seminar will focus on: Critical issues related to levees and dams; New developments and advanced tools; Overtopping protection systems; System design and performance; Applications and innovative solutions; Case histories of overtopping events; Physical modeling techniques and recent studies; and Numerical modeling methods.Includes bibliographical references.The development of overtopping protection systems often requires detailed analyses of complex physical phenomena. This hinders the comprehensive knowledge of their behavior, and therefore the development of suitable design criteria. In recent years, the authors have developed and validated different methods, combining continuous, particle and discrete numerical techniques, to obtain accurate and reliable solutions of different numerical problems involving fluid-soil-structure interaction. In this contribution, some applications of these methods to the study of dam protection against overtopping are presented. The main advantages of this approach include the ability to extract results of the governing variables (pressure, velocity) at any location of the domain, and the possibility to consider scenarios without the restrictions of the experimental facilities (flow rates, size, scale effects). In particular, the contribution gathers examples of application of numerical methods in a) analysis of rockfill dam stability against overtopping, including seepage evolution and deformation of the downstream shoulder, and b) stability analysis of wedge-shaped-blocks subjected to vandalism

What Lies Beneath? Molecular Evolution During the Radiation of Caecilian Amphibians

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates

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

Inadvertent paralog inclusion drives artifactual topologies and timetree estimates in phylogenomics

Increasingly, large phylogenomic datasets include transcriptomic data from non-model organisms. This has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. While this may be expected to result in decreased phylogenetic support it is not clear if it could also drive highly supported artefactual relationships. Many groups, including the hyper-diverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events, small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated datasets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasises the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa

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-

Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation & diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians

What lies beneath? Molecular evolution during the radiation of caecilian amphibians

Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians

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