Asymptotic and Lyapunov stability of Poisson equilibria

This paper includes results centered around three topics, all of them related with the nonlinear stability of equilibria in Poisson dynamical systems. Firstly, we prove an energy-Casimir type sufficient condition for stability that uses functions that are not necessarily conserved by the flow and that takes into account certain asymptotically stable behavior that may occur in the Poisson category. This method is adapted to Poisson systems obtained via a reduction procedure and we show in examples that the kind of stability that we propose is appropriate when dealing with the stability of the equilibria of some constrained systems. Finally, we discuss two situations in which the use of continuous Casimir functions in stability studies is equivalent to the topological stability methods introduced by Patrick {\it et al.}Comment: 23 pages, 2 figure

Bilinear softening parameters and equivalent LEFM R-curve in quasibrittle failure

For composites and adhesive joints, the determination of the cohesive zone parameters from Double Cantilever Beam specimens loaded with pure moments is now well established and documented. However, for quasibrittle materials used in Civil Engineering such as concrete or wood, the difficulty to apply a pure bending moment lies inappropriated the method used for composites. Nevertheless, the one-to-one correspondence which exists between the R-curve and the softening curve is here revisited and adapted for any kind of specimen geometry and for the bilinear approximation of the softening function, well-known to successfully describe the failure of a wide group of quasibrittle materials. It is shown that even though the connections between the cohesive parameters and the ‘equivalent LEFM’ R-curve are geometry and material dependent, their trends are preserved whatever the specimen geometry and the material are. The outline of a general estimation procedure of the cohesive zone parameters funded on the equivalent LEFM R-curve is proposed

Adaptive Dispersion Compensation for Remote Fiber Delivery of NIR Femtosecond Pulses

We report on remote delivery of 25 pJ broadband near-infrared femtosecond light pulses from a Ti:sapphire laser through 150 meters of single-mode optical fiber. Pulse distortion due to dispersion is overcome with pre-compensation using adaptive pulse shaping techniques, while nonlinearities are mitigated using an SF10 rod for the final stage of pulse compression. Near transform limited pulse duration of 130 fs is measured after the final compression.Comment: 3 pages, 4 figure

ATM: approximate task memoization in the runtime system

Redundant computations appear during the execution of real programs. Multiple factors contribute to these unnecessary computations, such as repetitive inputs and patterns, calling functions with the same parameters or bad programming habits. Compilers minimize non useful code with static analysis. However, redundant execution might be dynamic and there are no current approaches to reduce these inefficiencies. Additionally, many algorithms can be computed with different levels of accuracy. Approximate computing exploits this fact to reduce execution time at the cost of slightly less accurate results. In this case, expert developers determine the desired tradeoff between performance and accuracy for each application. In this paper, we present Approximate Task Memoization (ATM), a novel approach in the runtime system that transparently exploits both dynamic redundancy and approximation at the task granularity of a parallel application. Memoization of previous task executions allows predicting the results of future tasks without having to execute them and without losing accuracy. To further increase performance improvements, the runtime system can memoize similar tasks, which leads to task approximate computing. By defining how to measure task similarity and correctness, we present an adaptive algorithm in the runtime system that automatically decides if task approximation is beneficial or not. When evaluated on a real 8-core processor with applications from different domains (financial analysis, stencil-computation, machine-learning and linear-algebra), ATM achieves a 1.4x average speedup when only applying memoization techniques. When adding task approximation, ATM achieves a 2.5x average speedup with an average 0.7% accuracy loss (maximum of 3.2%).This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the Spanish Government (grant SEV2015-0493 of the Severo Ochoa Program), by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316), by Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272) and the European HiPEAC Network of Excellence. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047. M. Casas is supported by the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia and the Cofund programme of the Marie Curie Actions of the 7th R&D Framework Programme of the European Union (Contract 2013 BP B 00243). I. Brumar has been partially supported by the Spanish Ministry of Education, Culture and Sports under grant FPU2015/12849.Peer ReviewedPostprint (author's final draft

A process centred virtual approach to support cost estimating along product life cycle

The application of engineering practices and scientific principles to the creation of cost estimates along a product life cycle is one of the basic aspects of Cost Engineering. Cost estimates are used as fundamental criteria to make design decisions in the development stage and also to make business decisions in collaboration between OEMs and their supply chain. The achievement of an estimate requires experience and knowledge of different techniques and methodologies. Key aspects on its creation are the adoption of a cost estimating process, the availability of the needed data and the proper management of the information used during the process. The collaboration between the OEM and its supplier can be facilitated by having a better common understanding of how the cost estimates have been created. The cost estimating process used is then a fundamental piece of trust. In this context, the main purpose of this paper is to present the research conducted in the definition of cost estimating processes and the virtual framework selected. They are the key elements in the development of a prototype set of virtual tools to support the creation of cost estimates, the improvement of competences of the Cost Engineering Community, and the common understanding on cost between OEMs and their supply chain

Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing

Gilthead seabream (Sparus aurata) is a teleost belonging to the family Sparidae with a high economical relevance in the Mediterranean countries. Although genomic tools have been developed in this species in order to investigate its physiology at the molecular level and consequently its culture, genomic information on post-embryonic development is still scarce. In this study, we have investigated the transcriptome of a marine teleost during the larval stage (from hatching to 60 days after hatching) by the use of 454 pyrosequencing technology. We obtained a total of 68,289 assembled contigs, representing putative transcripts, belonging to 54,606 different clusters. Comparison against all S. aurata expressed sequenced tags (ESTs) from the NCBI database revealed that up to 34,722 contigs, belonging to about 61% of gene clusters, are sequences previously not described. Contigs were annotated through an iterative Blast pipeline by comparison against databases such as NCBI RefSeq from Danio rerio, SwissProt or NCBI teleost ESTs. Our results indicate that we have enriched the number of annotated sequences for this species by more than 50% compared with previously existing databases for the gilthead seabream. Gene Ontology analysis of these novel sequences revealed that there is a statistically significant number of transcripts with key roles in larval development, differentiation, morphology, and growth. Finally, all information has been made available online through user-friendly interfaces such as GBrowse and a Blast server with a graphical frontend

AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication–informed collinear anchor identification between genomes and performs base pair–resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor–binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.This project is supported by the United States Department of Agriculture Agricultural Research Service, NSF No. 1822330, NSF No. 1854828, the European Union's Horizon 2020 Framework Programme under the DeepHealth project [825111], the European Union Regional Development Fund within the framework of The European Regional Development Fund Operational Program of Catalonia 2014 to 2020 with a grant of 50% of total cost eligible under the DRAC project [001-P-001723], and National Natural Science Foundation of China No. 31900486. M.C.S. was supported by NSF Postdoctoral Research Fellowship in Biology No. 1907343. M.M. was partially supported by the Spanish Ministry of Economy, Industry, and Competitiveness under Ramón y Cajal (RYC) fellowship number RYC-2016-21104.Peer ReviewedPostprint (published version

Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin

Background: Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity of the region, protracted human presence has obscured the biogeographic processes that shaped current diversity. Loxosceles rufescens (Araneae, Sicariidae) is an ideal example: native to the Mediterranean, the species has dispersed worldwide via cohabitation with humans. A previous study revealed considerable molecular diversity, suggesting cryptic species, but relationships among lineages did not correspond to geographic location. Results: Delimitation analyses on cytochrome c oxidase subunit I identified 11 different evolutionary lineages, presenting two contrasting phylogeographic patterns: (1) lineages with well-structured populations in Morocco and Iberia, and (2) lineages lacking geographic structure across the Mediterranean Basin. Dating analyses placed main diversification events in the Pleistocene, and multiple Pleistocene refugia, identified using ecological niche modeling (ENM), are compatible with allopatric differentiation of lineages. Human-mediated transportation appears to have complicated the current biogeography of this medically important and synanthropic spider. Conclusions: We integrated ecological niche models with phylogeographic analyses to elucidate the evolutionary history of L. rufescens in the Mediterranean Basin, with emphasis on the origins of mtDNA diversity. We found support for the hypothesis that northern Africa was the center of origin for L. rufescens, and that current genetic diversity originated in allopatry, likely promoted by successive glaciations during the Pleistocene. We corroborated the scenario of multiple refugia within the Mediterranean, principally in northern Africa, combining results from eight atmosphereocean general circulation models (AOGCMs) with two different refugium-delimitation methodologies. ENM results were useful for providing general views of putative refugia, with fine-scale details depending on the level of stringency applied for agreement among models

Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases

Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (PA) that cannot be controlled when the oligomers are produced by chemical hydrolysis. To determine the influence of the PA on the biological activities, defined chitosan oligomers in sufficient amounts are needed. Chitosan oligomers with specific PA can be produced by enzymatic deacetylation of chitin oligomers, but the diversity is limited by the low number of chitin deacetylases available. We have produced specific chitosan oligomers which are deacetylated at the first two units starting from the non-reducing end by the combined use of two different chitin deacetylases, namely NodB from Rhizobium sp. GRH2 that deacetylates the first unit and COD from Vibrio cholerae that deacetylates the second unit starting from the non-reducing end. Both chitin deacetylases accept the product of each other resulting in production of chitosan oligomers with a novel and defined PA. When extended to further chitin deacetylases, this approach has the potential to yield a large range of novel chitosan oligomers with a fully defined architecture