Experimental insight into the domain decomposition method for a finite element method code

The use of Domain Decomposition Methods (DDM) for a Finite Element Method (FEM) framework was a hot topic in the past decade, leading to very powerful results in terms of scalability and widening the problems that could be full-wave simulated with the FEM, [1–3]. However, despite the promising results shown in these references, it seems not to be a widespread use of the DDM in commercial FEM softwares or publications, whereas the common research topics (adaptivity, higher-order basis functions, different element shapes) in FEM have not been explored together with DDM. In this communication, we share experimental details with different non-overlapping DDM within FEM. We explore the use of different finite element shapes with up to fourth-order basis functions. We propose a propagation problem through a rectangular waveguide as a benchmark, and we show the different implementation choices available and their impact in the performance of the code

Strategies to parallelize a finite element mesh truncation technique on multi-core and many-core architectures

Achieving maximum parallel performance on multi-core CPUs and many-core GPUs is a challenging task depending on multiple factors. These include, for example, the number and granularity of the computations or the use of the memories of the devices. In this paper, we assess those factors by evaluating and comparing different parallelizations of the same problem on a multiprocessor containing a CPU with 40 cores and four P100 GPUs with Pascal architecture. We use, as study case, the convolutional operation behind a non-standard finite element mesh truncation technique in the context of open region electromagnetic wave propagation problems. A total of six parallel algorithms implemented using OpenMP and CUDA have been used to carry out the comparison by leveraging the same levels of parallelism on both types of platforms. Three of the algorithms are presented for the first time in this paper, including a multi-GPU method, and two others are improved versions of algorithms previously developed by some of the authors. This paper presents a thorough experimental evaluation of the parallel algorithms on a radar cross-sectional prediction problem. Results show that performance obtained on the GPU clearly overcomes those obtained in the CPU, much more so if we use multiple GPUs to distribute both data and computations. Accelerations close to 30 have been obtained on the CPU, while with the multi-GPU version accelerations larger than 250 have been achieved.Funding for open access charge: CRUE-Universitat Jaume

Structural, photoluminescent properties and Judd-Ofelt analysis of Eu3+-activated CaF2 nanocubes

Eu3+-doped CaF2 nanocubes with variable europium concentration, [Eu3+] = 0, 0.6, 1.3, 1.7, 2.2 and 5.4 mol%, have been synthesized by a direct precipitation route. It has been found that, within this concentration range, the nanoparticles present the fluoride-type crystalline structure and the characteristic cubic shape of CaF2 crystals. The nanoparticle size follows a log-normal distribution with a mean value decreasing with the Eu3+ content. Rietveld refinement has been performed to calculate the lattice parameter and crystallite size. Eu3+ concentration affects both parameters giving rise to an increase in the lattice parameter and a reduction of crystallite size. The luminescent properties of Eu3+ ions in these nanostructures have been investigated under CW and pulsed excitation. A Judd-Ofelt analysis, as function of the Eu3+ content, has been performed to determine the transition probabilities, radiative lifetimes and branching ratios of the 5D0 emitting level. It was found that and Judd-Ofelt intensity parameters are dependent on the doping level, showing an evolution that indicates a decrease in the Eu3+ site local symmetry with increasing Eu3+ concentration. Finally, it has been observed that the characteristic luminescence decay time of the 5D0 manifold is reduced with increasing Eu3+ concentration. This effect is partially due to an increase of radiative transition probability, associated with a reduction in the local symmetry of the lanthanide ions, and also to the occurrence of concentration quenching effectsThis work has been partially supported by Ministerio de Economía y Competitividad and Ministerio de Ciencia, Innovación y Universidades under projects MAT2016-75716-2-2-R and RTI2018- 101020-B-I00

Análisis del comportamiento de los gases de escape del vehículo nissan sentra wagon previo a la revisión técnica vehicular

En este artículo se presenta el comportamiento de los gases de escape de un vehículo en función del adelanto al encendido, para cumplir los parámetros establecidos por la normativa INEN 2204. Con ello se busca disminuir al mínimo la contaminación producida por la combustión interna en el motor y de esta manera aprobar la revisión técnica vehicular. Se realizaron 6 pruebas, para conocer en que ángulo de encendido el motor emite la menor cantidad de gases contaminantes. Se obtuvo como resultado que a 1°, próximo al Punto Muerto Superior (PMS), las emisiones se encuentran dentro de lo establecido en la norma INEN 2204

On the use of many-core machines for the acceleration of a mesh truncation technique for FEM

Finite element method (FEM) has been used for years for radiation problems in the field of electromagnetism. To tackle problems of this kind, mesh truncation techniques are required, which may lead to the use of high computational resources. In fact, electrically large radiation problems can only be tackled using massively parallel computational resources. Different types of multi-core machines are commonly employed in diverse fields of science for accelerating a number of applications. However, properly managing their computational resources becomes a very challenging task. On the one hand, we present a hybrid message passing interface + OpenMP-based acceleration of a mesh truncation technique included in a FEM code for electromagnetism in a high-performance computing cluster equipped with 140 compute nodes. Results show that we obtain about 85% of the theoretical maximum speedup of the machine. On the other hand, a graphics processing unit has been used to accelerate one of the parts that presents high fine-grain parallelism.This work has been fnancially supported by TEC2016-80386-P, TIN2017-82972-R, CAM S2013/ICE-3004 projects and “Ayudas para contratos predoctorales de Formación del Profesorado Universitario FPU”

A non-coding RNA network involved in KSHV tumorigenesis

Regulatory pathways involving non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNA), have gained great relevance due to their role in the control of gene expression modulation. Using RNA sequencing of KSHV Bac36 transfected mouse endothelial cells (mECK36) and tumors, we have analyzed the host and viral transcriptome to uncover the role lncRNA-miRNA-mRNA driven networks in KSHV tumorigenesis. The integration of the differentially expressed ncRNAs, with an exhaustive computational analysis of their experimentally supported targets, led us to dissect complex networks integrated by the cancer-related lncRNAs Malat1, Neat1, H19, Meg3, and their associated miRNA-target pairs. These networks would modulate pathways related to KSHV pathogenesis, such as viral carcinogenesis, p53 signaling, RNA surveillance, and cell cycle control. Finally, the ncRNA-mRNA analysis allowed us to develop signatures that can be used to an appropriate identification of druggable gene or networks defining relevant AIDS-KS therapeutic targets.Fil: Naipauer, Julian. Miami University. School Of Medicine; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Garcia Sola, Martin Emilio. Miami University. School Of Medicine; Estados Unidos. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Salyakina, Daria. Miami University. School Of Medicine; Estados UnidosFil: Rosario, Santas. Miami University. School Of Medicine; Estados UnidosFil: Williams, Sion. Miami University. School Of Medicine; Estados UnidosFil: Coso, Omar Adrian. Miami University. School Of Medicine; Estados Unidos. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Abba, Martín Carlos. Miami University. School Of Medicine; Estados Unidos. Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Inmunológicas Básicas y Aplicadas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Mesri, Enrique Alfredo. Miami University. School Of Medicine; Estados UnidosFil: Lacunza, Ezequiel. Miami University. School Of Medicine; Estados Unidos. Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Inmunológicas Básicas y Aplicadas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentin

Rethinking entrenched narratives about protected areas and human wellbeing in the Global South

Attempts to link human development and biodiversity conservation goals remain a constant feature of policy and practice related to protected areas (PAs). Underlying these approaches are narratives that simplify assumptions, shaping how interventions are designed and implemented. We examine evidence for five key narratives: 1) conservation is pro-poor; 2) poverty reduction benefits conservation; 3) compensation neutralises costs of conservation; 4) local participation is good for conservation; 5) secure tenure rights for local communities support effective conservation. Through a mixed-method synthesis combining a review of 100 peer-reviewed papers and 25 expert interviews, we examined if and how each narrative is supported or countered by the evidence. The first three narratives are particularly problematic. PAs can reduce material poverty, but exclusion brings substantial local costs to wellbeing, often felt by the poorest. Poverty reduction will not inevitably deliver on conservation goals and trade-offs are common. Compensation (for damage due to human wildlife conflict, or for opportunity costs), is rarely sufficient or commensurate with costs to wellbeing and experienced injustices. There is more support for narratives 4 and 5 on participation and secure tenure rights, highlighting the importance of redistributing power towards Indigenous Peoples and Local Communities in successful conservation. In light of the proposed expansion of PAs under the post-2020 Global Biodiversity Framework, we outline implications of our review for the enhancement and implementation of global targets in order to proactively integrate social equity into conservation and the accountability of conservation actors

Fragmentary Blue: Resolving the Rarity Paradox in Flower Colors

Blue is a favored color of many humans. While blue skies and oceans are a common visual experience, this color is less frequently observed in flowers. We first review how blue has been important in human culture, and thus how our perception of blue has likely influenced the way of scientifically evaluating signals produced in nature, including approaches as disparate as Goethe’s Farbenlehre, Linneaus’ plant taxonomy, and current studies of plant-pollinator networks. We discuss the fact that most animals, however, have different vision to humans; for example, bee pollinators have trichromatic vision based on UV-, Blue-, and Green-sensitive photoreceptors with innate preferences for predominantly short-wavelength reflecting colors, including what we perceive as blue. The subsequent evolution of blue flowers may be driven by increased competition for pollinators, both because of a harsher environment (as at high altitude) or from high diversity and density of flowering plants (as in nutrient-rich meadows). The adaptive value of blue flowers should also be reinforced by nutrient richness or other factors, abiotic and biotic, that may reduce extra costs of blue-pigments synthesis. We thus provide new perspectives emphasizing that, while humans view blue as a less frequently evolved color in nature, to understand signaling, it is essential to employ models of biologically relevant observers. By doing so, we conclude that short wavelength reflecting blue flowers are indeed frequent in nature when considering the color vision and preferences of bees.publishedVersio

R-Spondin3 is associated with basal-progenitor behavior in normal and tumor mammary cells

R-spondin3 (RSPO3) is a member of a family of secreted proteins that enhance Wnt signaling pathways in diverse processes, including cancer. However, the role of RSPO3 in mammary gland and breast cancer development remains unclear. In this study, we show that RSPO3 is expressed in the basal stem cell–enriched compartment of normal mouse mammary glands but is absent from committed mature luminal cells in which exogenous RSPO3 impairs lactogenic differentiation. RSPO3 knockdown in basal-like mouse mammary tumor cells reduced canonical Wnt signaling, epithelial-to-mesenchymal transition-like features, migration capacity, and tumor formation in vivo. Conversely, RSPO3 overexpression, which was associated with some LGR and RUNX factors, highly correlated with the basal-like subtype among patients with breast cancer. Thus, we identified RSPO3 as a novel key modulator of breast cancer development and a potential target for treatment of basal-like breast cancers. Significance: These findings identify RSPO3 as a potential therapetuic target in basal-like breast cancers. Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/16/4497/F1.large.jpg.Fil: Tocci, Johanna Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Felcher, Carla María. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Garcia Sola, Martin Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Goddio, Maria Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Zimberlin, Maria Noel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Rubinstein, Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Srebrow, Anabella. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Coso, Omar Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Abba, Martín Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Meissl, Roberto Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Kordon, Edith Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentin

EVC-EVC2 complex stability and ciliary targeting are regulated by modification with ubiquitin and SUMO

Ellis van Creveld syndrome and Weyers acrofacial dysostosis are two rare genetic diseases affecting skeletal development. They are both ciliopathies, as they are due to malfunction of primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae and are required for Hedgehog signaling, a key pathway during skeletal morphogenesis. These ciliopathies are caused by mutations affecting the EVC-EVC2 complex, a transmembrane protein heterodimer that regulates Hedgehog signaling from inside primary cilia. Despite the importance of this complex, the mechanisms underlying its stability, targeting and function are poorly understood. To address this, we characterized the endogenous EVC protein interactome in control and Evc-null cells. This proteomic screen confirmed EVC’s main known interactors (EVC2, IQCE, EFCAB7), while revealing new ones, including USP7, a deubiquitinating enzyme involved in Hedgehog signaling. We therefore looked at EVC-EVC2 complex ubiquitination. Such ubiquitination exists but is independent of USP7 (and of USP48, also involved in Hh signaling). We did find, however, that monoubiquitination of EVC-EVC2 cytosolic tails greatly reduces their protein levels. On the other hand, modification of EVC-EVC2 cytosolic tails with the small ubiquitin-related modifier SUMO3 has a different effect, enhancing complex accumulation at the EvC zone, immediately distal to the ciliary transition zone, possibly via increased binding to the EFCAB7-IQCE complex. Lastly, we find that EvC zone targeting of EVC-EVC2 depends on two separate EFCAB7-binding motifs within EVC2’s Weyers-deleted peptide. Only one of these motifs had been characterized previously, so we have mapped the second herein. Altogether, our data shed light on EVC-EVC2 complex regulatory mechanisms, with implications for ciliopathies