VI Workshop on Computational Data Analysis and Numerical Methods: Book of Abstracts

The VI Workshop on Computational Data Analysis and Numerical Methods (WCDANM) is going to be held on June 27-29, 2019, in the Department of Mathematics of the University of Beira Interior (UBI), Covilhã, Portugal and it is a unique opportunity to disseminate scientific research related to the areas of Mathematics in general, with particular relevance to the areas of Computational Data Analysis and Numerical Methods in theoretical and/or practical field, using new techniques, giving especial emphasis to applications in Medicine, Biology, Biotechnology, Engineering, Industry, Environmental Sciences, Finance, Insurance, Management and Administration. The meeting will provide a forum for discussion and debate of ideas with interest to the scientific community in general. With this meeting new scientific collaborations among colleagues, namely new collaborations in Masters and PhD projects are expected. The event is open to the entire scientific community (with or without communication/poster)

VII Workshop on Computational Data Analysis and Numerical Methods

Dear participants, colleagues and friends, it is a great honour and a privilege to give you all a warmest welcome to the VII Workshop on Computational Data Analysis and Numerical Methods (VII WCDANM), which is organized by the Polytechnic Institute of Tomar (located in the center of Portugal in the beautiful city of Tomar), with the support of some Portuguese research centers, hoping that the final result may exceed the expectations of the participants, sponsors and organizers. Due to the worldwide pandemic caused by the COVID-19 virus, for the first time, this meeting will be transmitted through videoconference (webminar). Nevertheless, the important contributions of Adélia Sequeira (University of Lisbon, Portugal), Sílvia Barbeiro (University of Coimbra, Portugal), Malay Banerjee (Indian Instituto of Techonology Kampur, India) and Indranhil Ghosh (University of North Carolina at Wilmington, USA) as Plenary Speakers, the high scientific level of oral and poster presentations and an active audience will certainly contribute to the success of the meeting. Part of the accepted papers (theoretical and applied) by the VII WCDANM involve big data, data mining, data science and machine learning, in different areas of research, some giving emphasis to coronavirus. A very special thanks to this small, yet important, scientific community, since this event could not be possible without any of these essential and complementary parts. This year, there is also the possibility to attend a course on ŞModeling Partial Least Squares Structural Equations (PLS-SEM) using SmartPLSŤ given by Christian M. Ringle ((TUHH) Hamburg University of Technology, Germany), who kindly and readily accepted our invitation and to whom we are very grateful. A special acknowledgment is also due to the Members of the Executive, Scientific and Organizing Committees. In particular, Anuj Mubayi (Arizona StateUniversity,USA),MilanStehlík(Johannes KeplerUniversity,Austria), AnaNata,IsabelPitacasandManuelaFernandes(hostsfromthePolytechnic Institute of Tomar, Portugal), A. Manuela Gonçalves (University of Minho, Portugal), Teresa Oliveira (Aberta University) and Fernando Carapau (University of Évora, Portugal) have been relentless in search for a balanced, broad and interesting program, having achieved an excellent result. For the third consecutive year, the Journal of Applied Statistics (Taylor & Francis) and Neural Computing and Applications (Springer) are also associated to the event, being extremely important in the dissemination of the scientific results achieved at the meeting. Given the above, it is a pleasure to be ”together” with all of you in this web conference, hoping it may provide an intellectual stimulus and an opportunity for the scientific community to jointly work and disseminate scientific research, namely presenting approaches that may contribute to the solution of the pandemic we are experiencing in the expectation that the present might be past in the near future

Population persistence in landscapes fragmented by roads: disentangling isolation, mortality and the effect of dispersal

Linear infrastructures, one of several forms of land-use, are a major driver of biodiversity loss. Roads impact populations at many levels, with direct road mortality and barrier effect contributing to decreased population abundance, higher isolation and subdivision, and therefore to increased extinction risk. In this paper, we compared the effect of road mortality and of the barrier effect on population isolation, persistence and size, and assessed the interaction of these effects with dispersal. We used a spatially explicit, process-based model of population dynamics in landscapes fragmented by varying levels of road density. We modelled a barrier effect independently from road mortality by varying the probability with which individuals avoid crossing roads. Both road mortality and the barrier effect caused population isolation. While road mortality alone had stronger negative effects than the barrier effect without extra mortality, the latter also resulted in decreased population size. Yet, road avoidance could, in some cases, rescue populations from extinction. Populations with a large dispersal distance were more negatively affected as road mortality increased. However, when there was no road mortality they maintained larger sizes than populations with a short dispersal distance. Our results highlight the much higher relative importance of road mortality than the barrier effect for population size and persistence, and the importance of assessing relevant species traits for effective long-term transportation planning and conservation management. Our model can be used in species-specific situations and with real landscape configurations in applications such as conservation planninginfo:eu-repo/semantics/publishedVersio

K- and L-shell theoretical fluorescence yields for the Fe isonuclear sequence

Funding Information: This research was funded in part by FCT (Portugal) under research center grant UID/FIS/04559/2020 (LIBPhys). This work was also funded through the project PTDC/FIS-AQM/31969/2017, “Ultra-high-accuracy X-ray spectroscopy of transition metal oxides and rare earths”. F.G. acknowledges support from FCT, Portugal through contract UI/BD/151000/2021 . J. M and J.P.S acknowledge the support of EMPIR, Germany , under Contract No. 20FUN04 PrimA-LTD. The EMPIR initiative is co-funded by the European Union’s Horizon 2020 research and innovation programme and the EMPIR, Germany participating States. Part of this work has been carried out under the High Performance Computing Chair - a R&D infrastructure (based at the University of Évora; PI: M. Avillez), endorsed by Hewlett Packard Enterprise (HPE), and involving a consortium of higher education institutions (University of Algarve, University of Évora, NOVA University Lisbon, and University of Porto), research centres (CIAC, CIDEHUS, CHRC), enterprises (HPE, ANIET, ASSIMAGRA, Cluster Portugal Mineral Resources, DECSIS, FastCompChem, GeoSense, GEOtek, Health Tech, Starkdata), and public/private organizations (Alentejo Tourism-ERT, KIPT Colab). Funding Information: This research was funded in part by FCT (Portugal) under research center grant UID/FIS/04559/2020 (LIBPhys). This work was also funded through the project PTDC/FIS-AQM/31969/2017, “Ultra-high-accuracy X-ray spectroscopy of transition metal oxides and rare earths”. F.G. acknowledges support from FCT, Portugal through contract UI/BD/151000/2021. J. M and J.P.S acknowledge the support of EMPIR, Germany, under Contract No. 20FUN04 PrimA-LTD. The EMPIR initiative is co-funded by the European Union's Horizon 2020 research and innovation programme and the EMPIR, Germany participating States. Part of this work has been carried out under the High Performance Computing Chair - a R&D infrastructure (based at the University of Évora; PI: M. Avillez), endorsed by Hewlett Packard Enterprise (HPE), and involving a consortium of higher education institutions (University of Algarve, University of Évora, NOVA University Lisbon, and University of Porto), research centres (CIAC, CIDEHUS, CHRC), enterprises (HPE, ANIET, ASSIMAGRA, Cluster Portugal Mineral Resources, DECSIS, FastCompChem, GeoSense, GEOtek, Health Tech, Starkdata), and public/private organizations (Alentejo Tourism-ERT, KIPT Colab). Publisher Copyright: © 2022 The Author(s)In this work, we present K- and L- shell fluorescence yield values of the full isonuclear sequence of Fe ions, using a state-of-the-art multiconfiguration Dirac–Fock approach. These results may be of importance for spectral fitting and plasma modeling, both in laboratory and astrophysical studies, where Fe is an important benchmark element. The K-shell fluorescence yields were found to be very similar up to the removal of 14 electrons.publishersversionpublishe

Building a Portuguese Coalition for Biodiversity Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.info:eu-repo/semantics/publishedVersio

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications