Optimal transportation meshfree method in geotechnical engineering problems under large deformation regime

Meshfree methods have been demonstrated as suitable and strong alternatives to the more standard numerical schemes such as finite elements or finite differences. Moreover, when formulated in a Lagrangian approach, they are appropriate for capturing soil behavior under high‐strain levels. In this paper, the optimal transportation meshfree method has been applied for the first time to geotechnical problems undergoing large deformations. All the features employed in the current methodology (ie, F‐bar, explicit viscoplastic integration, and master‐slave contact) are described and validated separately. Finally, the model is applied to the particular case of shallow foundations by using von Mises and Drucker‐Prager yield criteria to find the load at failure in the. The presented methodology is demonstrated to be robust and accurate when solving this type of problems

Example-based generation of graphical modelling environments

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-42061-5_7Domain-Specific Languages (DSLs) present numerous benefits like powerful domain-specific primitives, an intuitive syntax for domain experts, and the possibility of advanced code generation for narrow domains. While a graphical syntax is sometimes desired for a DSL, constructing graphical modelling environments is a costly and highly technical task. This relegates domain experts to play a passive role in their development and hinders a wider adoption of graphical DSLs. Targeting a simpler DSL construction process, we propose an example based technique for the automatic generation of modelling environments for graphical DSLs. This way, starting from examples of the DSL likely provided by domain experts using drawing tools like yED, our system is able to synthesize a graphical modelling environment that mimics the syntax of the provided examples. This includes a meta-model for the abstract syntax of the DSL, and a graphical concrete syntax supporting spatial relationships like containment or attachment. The system is implemented as an Eclipse plugin, and we demonstrate its usage on a running example in the home networking domain.Work supported by the Spanish Ministry of Economy and Competitivity (TIN2014-52129-R), the Madrid Region (S2013/ICE-3006), and the EU Commission (FP7-ICT-2013-10, #611125)

Explicit meshfree solution for large deformation dynamic problems in saturated porous media

In this paper a new methodology to simulate saturated soils subjected to dynamic loadings under large deformation regime (locally up to 40% in equivalent plastic strain) is presented. The coupling between solid and fluid phases is solved through the complete formulation of the Biot’s equations. The additional novelty lies in the employment of an explicit time integration scheme of the u−w (solid displacement–relative fluid displacement) formulation which enables us to take advantage of such explicit schemes. Shape functions based on the principle of maximum entropy implemented in the framework of Optimal Transportation Meshfree schemes are utilized to solve both elastic and plastic problems

u–w formulation for dynamic problems in large deformation regime solved through an implicit meshfree scheme

Solving dynamic problems for fluid saturated porous media at large deformation regime is an interesting but complex issue. An implicit time integration scheme is herein developed within the framework of the u–w (solid displacement–relative fluid displacement) formulation for the Biot’s equations. In particular, liquid water saturated porous media is considered and the linearization of the linear momentum equations taking into account all the inertia terms for both solid and fluid phases is for the first time presented. The spatial discretization is carried out through a meshfree method, in which the shape functions are based on the principle of local maximum entropy LME. The current methodology is firstly validated with the dynamic consolidation of a soil column and the plastic shear band formulation of a square domain loaded by a rigid footing. The feasibility of this new numerical approach for solving large deformation dynamic problems is finally demonstrated through the application to an embankment problem subjected to an earthquake

Unveiling the nature of the "Green Pea" galaxies

We review recent results on the oxygen and nitrogen chemical abundances in extremely compact, low-mass starburst galaxies at redshifts between 0.1-0.3 recently named to as "Green Pea" galaxies. These galaxies are genuine metal-poor galaxies ($\sim$ one fifth solar) with N/O ratios unusually high for galaxies of the same metallicity. In combination with their known general properties, i.e., size, stellar mass and star-formation rate, these findings suggest that these objects could be experiencing a short and extreme phase in their evolution. The possible action of both recent and massive inflow of gas, as well as stellar feedback mechanisms are discussed here as main drivers of the starburst activity and their oxygen and nitrogen abundances.Comment: To appear in JENAM Symposium "Dwarf Galaxies: Keys to Galaxy Formation and Evolution", P. Papaderos, G. Hensler, S. Recchi (eds.). Lisbon, September 2010, Springer Verlag, in pres

Living on the Edge: Assessing the Extinction Risk of Critically Endangered Bonelli’s Eagle in Italy

Background: The population of Bonelli’s eagle (Aquila fasciata) has declined drastically throughout its European range due to habitat degradation and unnatural elevated mortality. There are less than 1500 breeding pairs accounted for in Europe, and the species is currently catalogued as Critically Endangered in Italy, where the 22 territories of Sicily, represent nearly 95% of the entire Italian population. However, despite national and European conservation concerns, the species currently lacks a specific conservation plan, and no previous attempts to estimate the risk of extinction have been made. Methodology/Principal Findings: We incorporated the most updated demographic information available to assess the extinction risk of endangered Bonelli’s eagle in Italy through a Population Viability Analysis. Using perturbation analyses (sensitivity and elasticity), and a combination of demographic data obtained from an assortment of independent methods, we evaluated which demographic parameters have more influence on the population’s fate. We also simulated different scenarios to explore the effects of possible management actions. Our results showed that under the current conditions, Bonelli’s eagle is expected to become extinct in Italy in less than 50 years. Stand-alone juvenile mortality was the most critical demographic parameter with the strongest influence on population persistence with respect to other demographic parameters. Measures aimed at either decreasing juvenile mortality, adult mortality or decreasing both juvenile and adult mortality resulted in equivalent net positive effects on population persistence (population growth rate l.1). In contrast, changes aimed at increasing breeding success had limited positive effects on demographic trends. Conclusions/Significance: Our PVA provides essential information to direct the decision-making process and exposes gaps in our previous knowledge. To ensure the long-term persistence of the species in Italy, measures are urgently needed to decrease both adult mortality due to poaching and juvenile mortality due to nest plundering, the top ranking mortality causes.PLL is supported by a “Juan de la Cierva” postdoctoral grant of the Spanish Ministry of Economy and Competitiveness (reference JCI-2011–09588)

Microbial catabolic activities are naturally selected by metabolic energy harvest rate

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate

FI on-line chemiluminescence reaction for determination of MCPA in water samples

This paper reports an economic, simple, and rapid FI-CL method for the determination of MCPA. This method requires simple instrumentation and it is fast enough to be used in routine analyses. A chemiluminescence signal is generated by reaction between photodegraded MCPA and ferricyanide solution in alkaline medium. All physical and chemical parameters in the flow injection chemiluminescence system were optimized in the experimental setting. To eliminate interference, a solid-phase extraction stage with SDB-1 cartridges and ethanol elution is applied. The signal-MCPA concentration relation is linear in concentration intervals between 0.0015 and 0.6 ¿g¿mL -1. The calibration lines are statistically similar in different working conditions: standards with ethanol without extraction and standards with ethanol and extraction, allowing standards to be excluded from the extraction step, which simplifies the process. The detection limit (DL) is 0.5 ng¿mL -1, which is the same order as the maximum limit established in legislation regarding pesticide limits in water destined for human consumption. A DL of 0.13 ng¿mL -1 can be reached if a sample of 100 mL is preconcentrated. The interday variance coefficient is 3% and the sample throughput is 90 h -1. The water analysis method is efficient with relative error percentages lower than 5% with respect to the added concentration. © 2011 Springer-Verlag.Authors acknowledge to the "Ministerio de Educacion y Ciencia" of Spain and FEDER funds for financial support (Project CTM2006-11991)Torres Cartas, S.; Gómez Benito, C.; Meseguer-Lloret, S. (2012). FI on-line chemiluminescence reaction for determination of MCPA in water samples. Analytical and Bioanalytical Chemistry. 402:1289-1296. https://doi.org/10.1007/s00216-011-5567-1S12891296402Navarro JS (2008) Utilización de plaguicidas en las asociaciones de tratamientos integrados en agricultura en la región de Murcia. Consejería de Sanidad Región de MurciaBarceló D, Hennion MC (1997) Trace determination of pesticide and their degradation products in water. Elsevier, AmsterdamKöck M, Farré M, Martínez E, Gajda-Schrantz K, Ginebreda A, Navarro A, López de Alda M, Barceló D (2010) J Hydrol 383(1–2):73–82Woudneh MB, Sekela M, Tuominen T, Gledhill M (2007) J Chromatogr A 1139(1):121–129Laganà A, Bacaloni A, De-Leva I, Faberi A, Fago G, Marino A (2002) Anal Chim Acta 462:187–198Comoretto L, Arfib B, Chiron S (2007) Sci Total Environ 380(1–3):124–132Kuster M, de Alda MJL, Barata C, Raldá D, Barceló D (2008) Talanta 75(2):390–401Kuster M, de Alda MJL, Hernando MD, Petrovic M, Martín-Alonso J, Barceló D (2008) J Hydrol 358(1–2):112–123Gervais G, Brosillon S, Laplanche A, Helen C (2008) J Chromatogr A 1202(2):163–172Housari F, Höhener P, Chiron S (2011) Sci Total Environ 409(3):582–587Delhomme O, Raeppel C, Briand O, Millet M (2011) Anal Bioanal Chem 399:1325–1334Royal decree 140/2003, 7th of February that establishes the health criteria for the water quality for human consumption. (BOE 21 February 2003)von-der-Ohe PC, Dulio V, Slobodnik J, de-Deckere E, Köhne R, Ebert RU, Ginebreda A, de-Cooman de-Cooman W, Schüürmann G, Brack W (2011) Sci Total Environ 409(11):2064–2077Horwitz W (ed) (2000) Official methods of analysis of AOAC International, 17th edn. AOAC International, GaithersburgMoret S, Sánchez JM, Salvadó V, Hidalgo M (2005) J Chromatogr A 1099(1–2):55–63Tran ATK, Hyne RV, Doble P (2007) Chemosphere 67(5):944–953Long F, Shi HC, He M, Zhu AN (2008) Biosens Bioelectron 23:1361–1366Meulenberg EP, Stoks PG (1995) Anal Chim Acta 311:407–413Chuang JC, Van Emon JM, Durnford J, Thomas K (2005) Talanta 67:658–666Boro RC, Kaushal J, Nangia Y, Wangoo N, Bhashi A, Suri CR (2011) Analyst 136(10):2125–2130Eremin SA, Laassis P, Aaron JJ (1996) Talanta 43:295–301Almansa-López EM, García-Campaña AM, Aaron JJ, Cuadros-Rodriguez L (2003) Talanta 60:355–367García LF, Eremin S, Aaron JJ (1996) Anal Lett 29(8):1447–1461García-Campaña AM, Aaron JJ, Bosque-Sendra JM (2002) Luminescence 17:285–287Lara FJ, García-Campaña AM, Aaron JJ (2010) Anal Chim Acta 679:17–30López-Paz J, Catalá-Icardo M (2011) Anal Lett 44(1–3):146–175Mbaye M, Gaye-Seye M, Aaron JJ, Coly A, Tine A (2011) Anal Bioanal Chem 400(2):403–410López-Paz JL, Catalá-Icardo M, Antón-Garrido B (2009) Anal Bioanal Chem 394:1073–1079López-Paz J, Catalá-Icardo M (2008) Anal Chim Acta 625(2):173–179Chen X, Lin Z, Cai Z, Chen X, Wang X (2008) Talanta 76(5):1083–1087Meseguer-Lloret S, Torres-Cartas S, Gómez-Benito M (2010) Anal Bioanal Chem 398:3175–3182Catalá-Icardo M, Martínez-Calatayud J (2008) Crit Rev Anal Chem 38(2):118–13

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

Feeding spectra and activity of the freshwater crab Trichodactylus kensleyi (Decapoda: Brachyura: Trichodactylidae) at La Plata basin

Background: In inland water systems, it is important to characterize the trophic links in order to identify the ‘trophic species’ and, from the studies of functional diversity, understand the dynamics of matter and energy in these environments. The aim of this study is to analyze the natural diet of Trichodactylus kensleyi of subtropical rainforest streams and corroborate the temporal variation in the trophic activity during day hours. Results: A total of 15 major taxonomic groups were recognized in gut contents. The index of relative importance identified the following main prey items in decreasing order of importance: vegetal remains, oligochaetes, chironomid larvae, and algae. A significant difference was found in the amount of full stomachs during day hours showing a less trophic activity at midday and afternoon. The index of relative importance values evidenced the consumption of different prey according to day moments. Results of the gut content indicate that T. kensleyi is an omnivorous crab like other trichodactylid species. Opportunistic behavior is revealed by the ingestion of organisms abundant in streams such as oligochaetes and chironomid larvae. The consumption of allochthonous plant debris shows the importance of this crab as shredder in subtropical streams. However, the effective assimilation of plant matter is yet unknown in trichodactylid crabs. Conclusions: This research provides knowledge that complements previous studies about trophic relationships of trichodactylid crabs and supported the importance of T. kensleyi in the transference of energy and matter from benthic community and riparian sources to superior trophic levels using both macro- and microfauna.Fil: Williner, Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; ArgentinaFil: de Azevedo Carvalho, Debora. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; ArgentinaFil: Collins, Pablo Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; Argentina. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentin