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

The genomic environment around the Aromatase gene: evolutionary insights

BACKGROUND: The cytochrome P450 aromatase (CYP19), catalyses the aromatisation of androgens to estrogens, a key mechanism in vertebrate reproductive physiology. A current evolutionary hypothesis suggests that CYP19 gene arose at the origin of vertebrates, given that it has not been found outside this clade. The human CYP19 gene is located in one of the proposed MHC-paralogon regions (HSA15q). At present it is unclear whether this genomic location is ancestral (which would suggest an invertebrate origin for CYP19) or derived (genomic location with no evolutionary meaning). The distinction between these possibilities should help to clarify the timing of the CYP19 emergence and which taxa should be investigated. RESULTS: Here we determine the "genomic environment" around CYP19 in three vertebrate species Homo sapiens, Tetraodon nigroviridis and Xenopus tropicalis. Paralogy studies and phylogenetic analysis of six gene families suggests that the CYP19 gene region was structured through "en bloc" genomic duplication (as part of the MHC-paralogon formation). Four gene families have specifically duplicated in the vertebrate lineage. Moreover, the mapping location of the different paralogues is consistent with a model of "en bloc" duplication. Furthermore, we also determine that this region has retained the same gene content since the divergence of Actinopterygii and Tetrapods. A single inversion in gene order has taken place, probably in the mammalian lineage. Finally, we describe the first invertebrate CYP19 sequence, from Branchiostoma floridae. CONCLUSION: Contrary to previous suggestions, our data indicates an invertebrate origin for the aromatase gene, given the striking conservation pattern in both gene order and gene content, and the presence of aromatase in amphioxus. We propose that CYP19 duplicated in the vertebrate lineage to yield four paralogues, followed by the subsequent loss of all but one gene in vertebrate evolution. Finally, we suggest that agnathans and lophotrocozoan protostomes should be investigated for the presence of aromatase

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

Basal gnathostomes provide unique insights into the evolution of vitamin B12 binders

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 7 (2015): 457-464, doi:10.1093/gbe/evu289.The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket.This work was funded by the Fundação para a Ciência e a Tecnologia (FCT) project PEst-C/MAR/LA0015/2013. PhD grant SFRH/BD/84238/2012 awarded to M.L-.M. Postdoctoral grant SFRH/BPD/72519/2010 awarded to R.R

Deep learning for the classification of quenched jets

An important aspect of the study of Quark-Gluon Plasma (QGP) in ultra-relativistic collisions of heavy ions is the ability to identify, in experimental data, a subset of the jets that were strongly modified by the interaction with the QGP. In this work, we propose studying deep learning techniques for this purpose. Samples of $Z+$jet events were simulated in vacuum and medium and used to train deep neural networks with the objective of discriminating between medium- and vacuum-like jets. Dedicated Convolutional Neural Networks, Dense Neural Networks and Recurrent Neural Networks were developed and trained, and their performance was studied. Our results show the potential of these techniques for the identification of jet quenching effects induced by the presence of the QGP.Fundação para a Ciência e a Tecnologiainfo:eu-repo/semantics/publishedVersio

Trophic ecology of common bottlenose dolphins in a pelagic insular environment inferred by stable isotopes

The common bottlenose dolphin (Tursiops truncatus) is a top marine predator widely dispersed in coastal and pelagic habitats and with a generalist feeding behavior. Yet, information on the trophic ecology of animals inhabiting pelagic environments is still scarce. Using carbon (& delta;C-13: C-13/C-12) and nitrogen (& delta;N-15: N-15/N-14) stable isotope ratios, we identified and quantified the main groups of prey assimilated by bottlenose dolphins inhabiting an oceanic habitat (Madeira Island, East Atlantic). Bottlenose dolphins assimilated pelagic, schooling fish (such as blue jack mackerel, Trachurus picturatus) and mesopelagic and demersal squids, which reinforces the pelagic dietary composition of insular/oceanic dolphins. Also, intra-seasonal differences were found in their stable isotope ratios, which suggest intraspecific variability in the feeding behavior among individuals living in the same area. Sex was not the main factor contributing to these differences, suggesting the lack of trophic niche segregation between adult males and females in this offshore environment. Nonetheless, further studies including different life stages and information on the ecophysiological requirements are necessary to disclose the factors responsible for the observed variability. This study showed that insular dolphins fed primarily on economically important pelagic prey, highlighting the need of developing management strategies that integrate conservation in fisheries plans.NORTE01-0145-FEDER-000031; M1420-01-0145-FEDER-000001-OOM; LA/P/0069/2020; M1420-09-5369-FSE-000002info:eu-repo/semantics/publishedVersio

En busca de un horizonte común para la Biblioteca digital de arqueología náutica (NADL). Reflexiones sobre ciencia, método, teoría y plantillas

[EN] Data sharing is a fundamental process for the advancement of both natural and social sciences. Starting from the idea that computers and the internet have drastically changed the world in the last decades, this paper advocates for the creation of a space where archaeologists from around the world can share information about maritime history and exchange data with colleagues. Following the principles of open access, we argue that raw data publication is necessary and significant for the development and democratization of the discipline. This study explains the fundamental aspects of the Nautical Archaeology Digital Library (NADL) and its efforts to standardize information collection for shipwrecks and related sites, so that scholars can create a community to disseminate both raw data and complete information in the field of maritime archaeology. To achieve this, our purpose is to facilitate the development of common-ground methodology and terminology that promotes an intelligible dialogue within the global community of nautical archaeologists. This paper addresses some considerations on terminology and systematization in scientific disciplines and discusses the theoretical and methodological issues linked to the process of making a template for recording shipwrecks. Furthermore, this article analyses some of the problems related to the standardization of description processes and the necessity to create a flexible system that accounts for data diversity. The third section discusses how science is greatly enhanced by publishing information in open access platforms.Highlights:Standardization of data allows robust comparative and inter-subjective analysis of coastal and maritime projects, shipwrecks and nautical technology.Research is strongly benefited by sharing information underlying publications and raw data generated within a project in open source platforms.Digital databases such as NADL enhance cooperative research, as well as teaching and outreach strategies.[ES] Compartir información es un proceso fundamental para el desarrollo de las ciencias naturales y sociales. Partiendo de la idea de que las computadoras e Internet han cambiado drásticamente el mundo en las últimas décadas, este trabajo aboga por la creación de un espacio en el que arqueólogos de alrededor del mundo puedan compartir información sobre historia marítima e intercambiar datos con otros colegas. Siguiendo los principios del libre acceso, sostenemos que la publicación de datos en bruto es necesaria y significativa para el desarrollo y democratización de la disciplina. Este artículo explica los fundamentos de la Biblioteca Digital de Arqueología Náutica (NADL: https://nadl.tamu.edu/) y sus esfuerzos por estandarizar el registro de la información sobre naufragios y sitios relacionados, para que los investigadores puedan crear una comunidad de divulgación, tanto de datos primarios como de información completa en el campo de la arqueología marítima. Para lograrlo, nuestro propósito es contribuir al desarrollo de una metodología y terminología común que promueva un diálogo inteligible entre la comunidad global de arqueólogos náuticos. En este artículo presentamos algunas consideraciones sobre la terminología y la sistematización en las disciplinas científicas y discutimos los problemas teóricos y metodológicos vinculados al proceso de creación de una plantilla para el registro de naufragios. Además, reflexionamos sobre algunos de los problemas relacionados con la estandarización de los procesos descriptivos y la necesidad de crear un sistema flexible que refleje la diversidad de los datos. Finalmente, discutimos cómo la ciencia se ve enormemente favorecida por la publicación de información en plataformas de libre acceso.This paper is a result of a T3 Texas A&M University grant. We want to thank the NADL community for their input. This paper is based on extensive discussions among the community. We would also like to thank Prof. José Luis Lerma, the editorial team of VAR and the reviewers for their insightful comments.Borrero L., R.; Schwindingera, P.; Castelli, A.; Ciarlo, NC.; Torres, R.; Manders, M.; Castro, F.... (2021). Seeking a common ground for the Nautical Archaeology Digital Library (NADL). Reflections on science, method, theory and templates. Virtual Archaeology Review. 12(24):11-24. https://doi.org/10.4995/var.2021.14331OJS11241224Adams, J. (2001). Ships and Boats as Archaeological Source Material. World Archaeology, 32(3), 292-310. https://doi.org/10.1080/00438240120048644Bailey, G. (2007). Time perspectives, palimpsests, and the archaeology of time. Journal of Anthropological Archaeology, 26(2), 198-223. https://doi.org/10.1016/j.jaa.2006.08.002Berkeley, G. (1998). A Treatise Concerning the Principles of Human Knowledge. Oxford University Press.Campbell, R. N. (2009). What is Science? London: Cornell University Library.Castro, F., Bendig, C., Bérubé, M., Borrero, R., Budsberg, N., Dostal, C., Monteiro, A., Smith, C., Torres, R., & Yamafune, K. (2018). Recording, Publishing, and Reconstructing Wooden Shipwrecks. Journal of Maritime Archaeology, 13(1), 55-66. https://doi.org/10.1007/s11457-017-9185-8Coseriu, E. (1977). Principios de semántica structural. Madrid: Gredos.Doerr, M., Bekiari, C., Bruseker, G., Ore, C-E., Stead, & Velios, S. T. (Eds.). (2020). Definition of the CIDOC Conceptual Reference Model. Volume A. ICOM/CIDOC Documentation Standards Group and CRM Special Interest Group. Version 7.1, October 2020. Retrieved 28th October, 2020, from: http://www.cidoc-crm.org/sites/default/files/CIDOC%20CRM_v.7.0.1_%2018-10-2020.pdfEerkens, J. W. & Bettinger, R. L. (2001). Techniques for Assessing Standardization in Artifact Assemblages: Can we Scale Material Variability? American Antiquity, 66(3), 493 -504. https://doi.org/10.2307/2694247Eiteljorg, H. (2004). 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A Dynamic Context Recording and Modeling System for Archaeology. International Journal of Nautical Archaeology, 23(2), 141-145. https://doi.org/10.1111/j.1095-9270.1994.tb00453.xHuggett, J. (2012a). Lost in information? Ways of knowing and modes of representation in e-archaeology. World Archaeology, 44(4), 538-552. https://doi.org/10.1080/00438243.2012.736274Huggett, J. (2012b). Core or periphery? Digital Humanities from an archaeological perspective. Historische Sozialforschung, 37 (3), 86-105. https://doi.org/10.12759/hsr.37.2012.3.86-105Klimovsky, G. (2005). Las desventuras del conocimiento científico. Buenos Aires: A-Z Editora.Kuhn, T. S. (1977). La tensión esencial: tradición e innovación en la investigación científica. In T. Kuhn (Ed.), La tensión esencial. Estudios selectos sobre la tradición y el cambio en el ámbito de la ciencia (pp. 248-262). México, D.F.: Fondo de Cultura Económica.Lock, G. (2003). Using computers in Archaeology: Towards virtual pasts. Routledge, New York. https://doi.org/10.1080/00665983.2003.11078213Lock, G., & Molyneaux, B. (Eds.) (2006). Confronting Scale in Archaeology. Springer, New York. https://doi.org/10.1007/0-387-32773-8Losee, J. (1981). Introducción histórica a la filosofía de la ciencia. Madrid: Alianza. Translation of the 1st Edition.Mach, E., (1959). The Analysis of Sensations. New York: Dover Publications.Manders, M., Oosting, R., & Brouwers, W. (2009). MACHU Final Report Nr. 3. Rotterdam: Educom Publishers B.V.Menéndez, E. (1999). Uso y desuso de conceptos: ¿dónde quedaron los olvidos? Alteridades, 9(17): 147-164.Mill, J. S. (2002). A System of Logic. Honolulu: University Press of the Pacific.Monroy, C., Parks, N., Furuta, R., & Castro, F. (2006). The Nautical Archaeology Digital Library. In Gonzalo et al. (Eds.), European Conference on Digital Libraries 2006 LNCS 4172 (pp. 544-547). Berlin and Heidelberg: Springer-Verlag.Monroy, C., Furuta, R., & Castro, F., (2007). 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Two alternative pathways for docosahexaenoic acid (DHA, 22:6n-3) biosynthesis are widespread among teleost fish

Docosahexaenoic acid (DHA) plays important physiological roles in vertebrates. Studies in rats and rainbow trout confirmed that DHA biosynthesis proceeds through the so-called &ldquo;Sprecher pathway&rdquo;, a biosynthetic process requiring a &Delta;6 desaturation of 24:5n-3 to 24:6n-3. Alternatively, some teleosts possess fatty acyl desaturases 2 (Fads2) that enable them to biosynthesis DHA through a more direct route termed the &ldquo;&Delta;4 pathway&rdquo;. In order to elucidate the prevalence of both pathways among teleosts, we investigated the &Delta;6 ability towards C24 substrates of Fads2 from fish with different evolutionary and ecological backgrounds. Subsequently, we retrieved public databases to identify Fads2 containing the YXXN domain responsible for the &Delta;4 desaturase function, and consequently enabling these species to operate the &Delta;4 pathway. We demonstrated that, with the exception of &Delta;4 desaturases, fish Fads2 have the ability to operate as &Delta;6 desaturases towards C24 PUFA enabling them to synthesise DHA through the Sprecher pathway. Nevertheless, the &Delta;4 pathway represents an alternative route in some teleosts and we identified the presence of putative &Delta;4 Fads2 in a further 11 species and confirmed the function as &Delta;4 desaturases of Fads2 from medaka and Nile tilapia. Our results demonstrated that two alternative pathways for DHA biosynthesis exist in teleosts

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