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

Superclasses and supercharacters of normal pattern subgroups of the unipotent upper triangular matrix group

Let $U_n$ denote the group of $n\times n$ unipotent upper-triangular matrices over a fixed finite field \FF_q, and let U_\cP denote the pattern subgroup of $U_n$ corresponding to the poset \cP. This work examines the superclasses and supercharacters, as defined by Diaconis and Isaacs, of the family of normal pattern subgroups of $U_n$. After classifying all such subgroups, we describe an indexing set for their superclasses and supercharacters given by set partitions with some auxiliary data. We go on to establish a canonical bijection between the supercharacters of U_\cP and certain \FF_q-labeled subposets of \cP. This bijection generalizes the correspondence identified by Andr\'e and Yan between the supercharacters of $U_n$ and the \FF_q-labeled set partitions of $\{1,2,...,n\}$. At present, few explicit descriptions appear in the literature of the superclasses and supercharacters of infinite families of algebra groups other than \{U_n : n \in \NN\}. This work signficantly expands the known set of examples in this regard.Comment: 28 page

The role of poroelasticity on the biomechanics of the intervertebral disc : a finite element study

The major goal for the present work is to evaluate a biomimetic Finite Element (FE) model of the Intervertebral Disc (IVD). Recent studies have emphasized the importance of an accurate biomechanical modeling of the IVD, which is a highly complex biphasic medium. A novel biphasic poroelastic model was implemented and coupled with Wilson’s model (2005) for biphasic osmotic swelling behavior. Numerical tests were devoted to the analysis of the time- dependent behavior of the IVD. The results show good agreement with literature experimental data (Heuer et al., 2007 or O’Connell et al., 2011) and also with other numerical studies (Galbusera et al., 2011). In brief, this in-development IVD FE model aims to be a valuable tool to study the biomechanics of the IVD and its pathways for degeneration.Fundação para a Ciência e a Tecnologia (FCT

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

A resource for sustainable management:<i>De novo</i> assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, <i>Scomber colias</i>

Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management. Keywords: RNA-Seq, Scombridae, Stock management, Atlantic chub mackerel, Live

Aerobic and anoxic growth and nitrate removal capacity of a marine denitrifying bacterium isolated from a recirculation aquaculture system

Bacterial biofilters used in marine recirculation aquaculture systems need improvements to enhance nitrogen removal efficiency. Relatively little is known about biofilter autochthonous population structure and function. The present study was aimed at isolating and characterizing an Autochthonous denitrifying bacterium from a marine biofilter installed at a recirculation aquaculture system. Colonization of four different media in a marine fish farm was followed by isolation of various denitrifying strains and molecular classification of the most promising one, strain T2, as a novel member of the Pseudomonas fluorescens cluster. This strain exhibits high metabolic versatility regarding N and C source utilization and environmental conditions for growth. It removed nitrate through aerobic assimilatory metabolism at a specific rate of 116.2 mg NO3-N g dw _1 h _1. Dissimilatory NO3-N removal was observed under oxic conditions at a limited rate, where transient NO2-N formed represented 22% (0.17 mg L _1) of the maximum transient NO2-N observed under anoxic conditions. Dissimilatory NO3-N removal under anoxic conditions occurred at a specific rate of 53.5 mgNO3-N g dw _1 h _1. The isolated denitrifying strain was able to colonize different materials, such as granular activated carbon (GAC), Filtralite and Bioflow plastic rings, which allow the development of a prototype bioreactor for strain characterization under dynamic conditions and mimicking fish-farm operating conditions

Quantification of GHB and GHB-GLUC in an 1,4-butanediol intoxication: a case report

Gamma-hydroxybutyric acid (GHB) is an endogenous compound with known action at the neural level. Its psychoactive effects led to an illicit use context including recreational purposes, muscle building effects in bodybuilders and drug-facilitated crimes, specifically in sexual assaults. Besides the misuse of the main compound, there are precursors like Gammabutyrolactone (GBL) and 1,4-butanediol (1,4-BD), usually non controlled substances, becoming a much easier way to obtain the target-compound. The authors present the first reported intoxication case in Portugal with 1,4-Butanediol, including the quantification of GHB and GHB-GLUC in serum, by GC-MS/MS TQD. A suspicious liquid and a serum sample were sent by an hospital ER and analysed by GC-MS-single quadrupole and GC-MS/MS TQD, respectively. A methodology including protein precipitation and GC-MS/MS TQD analysis was used to detect and quantify GHB and GHB-GLUC in serum. Toxicological analysis revealed the presence of 1,4-Butanediol in the liquid and GHB [171 mg/L] and GHB-GLUC [13,7 mg/L] in serum. The victim reverted the coma with no neurological sequelae. This was the first detected case, in Portugal, with 1,4-Butanediol, suggesting that it is important to be aware that consumers have different options to obtain illicit compounds, such as GHB. On the other hand, GHB-GLUC was identified and quantified for the first time in a real case, due to intoxication. This case highlights the importance of analysing all samples for active compounds, precursors and metabolites that can lead to the main intoxication origin.publishe

AgEx: A Financial Market Simulation Tool for Software Agents

Abstract. Many researchers in the software agent field use the financial domain as a test bed to develop adaptation, cooperation and learning skills of software agents. However, there are no open source financial market simulation tools available, that are able to provide a suitable environment for agents with real information about assets and order execution service. In order to address such demand, this paper proposes an open source financial market simulation tool, called AgEx. This tool allows traders launched from distinct computers to act in the same market. The communication among agents is performed through FIPA ACL and uses a market ontology created specifically to be used for trader agents. We implemented several traders using AgEx and performed many simulations using data from real markets. The achieved results allowed to test and assess comparatively trader&apos;s performance against each other in terms of risk and return. We verified that the effort to implement and test trader agents was significantly diminished by the use of AgEx. Furthermore, such results indicated new directions in trader strategy design

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