Symbolic Computation of Variational Symmetries in Optimal Control

We use a computer algebra system to compute, in an efficient way, optimal control variational symmetries up to a gauge term. The symmetries are then used to obtain families of Noether's first integrals, possibly in the presence of nonconservative external forces. As an application, we obtain eight independent first integrals for the sub-Riemannian nilpotent problem (2,3,5,8).Comment: Presented at the 4th Junior European Meeting on "Control and Optimization", Bialystok Technical University, Bialystok, Poland, 11-14 September 2005. Accepted (24-Feb-2006) to Control & Cybernetic

Modulation of charge-density waves by superlattice structures

We discuss the interplay between electronic correlations and an underlying superlattice structure in determining the period of charge density waves (CDW's), by considering a one-dimensional Hubbard model with a repeated (non-random) pattern of repulsive (U>0) and free (U=0) sites. Density matrix renormalization group diagonalization of finite systems (up to 120 sites) is used to calculate the charge-density correlation function and structure factor in the ground state. The modulation period can still be predicted through effective Fermi wavevectors, k_F*, and densities, and we have found that it is much more sensitive to electron (or hole) doping, both because of the narrow range of densities needed to go from q*=0 to \pi, but also due to sharp 2k_F*-4k_F* transitions; these features render CDW's more versatile for actual applications in heterostructures than in homogeneous systems.Comment: 4 pages, 5 figures, to appear in Phys Rev

Numerical study of inflow turbulence distortion and noise for airfoils

In this work, the interaction of grid-generated turbulence with airfoils of different thicknesses, namely, a National Advisory Committee for Aeronautics (NACA) 0008 and a NACA 0018, is investigated, leading to a deeper understanding of the influence of the airfoil geometry on the near-field flow and on the far-field pressure fluctuations. Experimentally validated lattice-Boltzmann simulations are used to analyze the flow properties in the leading-edge (LE) vicinity. The analysis of the velocity fluctuations near the LE shows that momentum is transferred from the streamwise to the transverse velocity for the NACA 0008 airfoil interacting with a large turbulence length scale. This mechanism changes with the increase in the airfoil thickness because the inflow turbulence length scale becomes comparable to the airfoil thickness in the LE region, resulting in a higher concentration of vortices near the LE oriented in the transverse direction, creating high-velocity fluctuations in the spanwise direction. The near- and far-field pressure fluctuations are analyzed to understand the impact of the inflow turbulence distortion on these parameters and the limitations of analytical methods for real airfoils. Results show that the wall-pressure fluctuations are affected by the turbulence distortion in the LE region. Thick airfoils have noise directivity patterns significantly different compared to the Amiet predictions for higher frequencies, radiating higher noise levels upstream of the LE than the thin airfoil. This is likely associated with a drastic change in the pressure fluctuation distribution near the airfoil LE region, attributed to the change in the distortion of the vortical structures in the LE area.</p

The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)

Skates, Chondrichthyes fishes from order Rajiformes, are the most species-rich group of all Batoidea. However, their phylogenetic relationships and systematics is still a highly discussed and controversial subject. The use of complete mitogenome has shown to be a promising tool to fill this gap of knowledge. Here, the complete mitogenome of the Iberian pygmy skate Neoraja iberica (Stehmann, Séret, Costa & Baro 2008) was sequenced and assembled. The mitogenome is 16,723 bp long and its gene content (i.e. 13 protein-coding genes, 22 transfer RNA, and 2 ribosomal RNA genes) and arrangement are the expected for Batoidea. Phylogenetic reconstructions, including 89 Rajiformes and two outgroup Rhinopristiformes, recovered family Rajidae as monophyletic, and further divided in the monophyletic tribe Rajini, sister to tribes Amblyrajini and Rostrorajini. The newly sequenced N. iberica mitogenome is the first representative of the tribe Rostrorajini.FCT: PTDC/ART-DAQ/29537/2017/ FEDER: POCI-01-0145-FEDER-029537/ PT2020 COMPETE 2020 – FCT: UIDB/04423/2020, UIDP/04423/2020 / SFRH/BD/137935/2018/ SFRH/BD/147493/2019 PTDC/ASP-PES/28053/2017info:eu-repo/semantics/publishedVersio

The gill transcriptome of threatened European freshwater mussels

Genomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with high conservation concern: Margaritifera margaritifera, Unio crassus, Unio pictorum, Unio mancus and Unio delphinus. The final assemblies, with N50 values ranging from 1069–1895 bp and total BUSCO scores above 90% (Eukaryote and Metazoan databases), were structurally and functionally annotated, and made available. The transcriptomes here produced represent a valuable resource for future studies on these species’ biology and ultimately guide their conservation.AGS was funded by the Portuguese Foundation for Science and Technology (FCT) under the grant SFRH/ BD/137935/2018, that also supported MLL (2020.03608.CEECIND) and EF (CEECIND/00627/2017). This research was developed under the project EdgeOmics - Freshwater Bivalves at the edge: Adaptation genomics under climate-change scenarios (PTDC/CTA-AMB/3065/2020) funded by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020.info:eu-repo/semantics/publishedVersio

Comparative Analysis of Viperidae Venoms Antibacterial Profile: a Short Communication for Proteomics

Bacterial infections involving multidrug-resistant strains are one of the ten leading causes of death and an important health problem in need for new antibacterial sources and agents. Herein, we tested and compared four snake venoms (Agkistrodon rhodostoma, Bothrops jararaca, B. atrox and Lachesis muta) against 10 Gram-positive and Gram-negative drug-resistant clinical bacteria strains to identify them as new sources of potential antibacterial molecules. Our data revealed that, as efficient as some antibiotics currently on the market (minimal inhibitory concentration (MIC) = 1–32 μg mL−1), A. rhodostoma and B. atrox venoms were active against Staphylococcus epidermidis and Enterococcus faecalis (MIC = 4.5 μg mL−1), while B. jararaca inhibited S. aureus growth (MIC = 13 μg ml−1). As genomic and proteomic technologies are improving and developing rapidly, our results suggested that A. rhodostoma, B. atrox and B. jararaca venoms and glands are feasible sources for searching antimicrobial prototypes for future design new antibiotics against drug-resistant clinical bacteria. They also point to an additional perspective to fully identify the pharmacological potential of these venoms by using different techniques

The crown pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species’ unique biological and evolutionary features, helping promote its conservation.AGS was funded by the Portuguese Foundation for Science and Technology (FCT) under the grant SFRH/BD/137935/2018 and COVID/DB/152933/2022, which also supported MLL (2020.03608.CEECIND) and EF (CEECINST/00027/2021). This research was developed under the project EdgeOmics - Freshwater Bivalves at the Edge: Adaptation genomics under climate-change scenarios (PTDC/CTA-AMB/3065/2020) funded by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020.info:eu-repo/semantics/publishedVersio