| 1. |
- Elsik, Christine G., et al.
(author)
-
The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
Journal article (peer-reviewed)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
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| 3. |
- Householder, John Ethan, et al.
(author)
-
One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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In: NATURE ECOLOGY & EVOLUTION. - 2397-334X.
-
Journal article (peer-reviewed)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 4. |
- Luize, Bruno Garcia, et al.
(author)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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In: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
-
Journal article (peer-reviewed)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 5. |
- Stanaway, Jeffrey D., et al.
(author)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
-
In: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
-
Journal article (peer-reviewed)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 6. |
- ter Steege, Hans, et al.
(author)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
-
In: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
-
Journal article (peer-reviewed)abstract
- Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
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| 7. |
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| 8. |
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| 9. |
- Aad, G., et al.
(author)
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Readiness of the ATLAS Tile Calorimeter for LHC collisions
- 2010
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:4, s. 1193-1236
-
Journal article (peer-reviewed)abstract
- The Tile hadronic calorimeter of the ATLAS detector has undergone extensive testing in the experimental hall since its installation in late 2005. The readout, control and calibration systems have been fully operational since 2007 and the detector has successfully collected data from the LHC single beams in 2008 and first collisions in 2009. This paper gives an overview of the Tile Calorimeter performance as measured using random triggers, calibration data, data from cosmic ray muons and single beam data. The detector operation status, noise characteristics and performance of the calibration systems are presented, as well as the validation of the timing and energy calibration carried out with minimum ionising cosmic ray muons data. The calibration systems' precision is well below the design value of 1%. The determination of the global energy scale was performed with an uncertainty of 4%.
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| 10. |
- Aad, G., et al.
(author)
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Studies of the performance of the ATLAS detector using cosmic-ray muons
- 2011
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 71:3
-
Journal article (peer-reviewed)abstract
- Muons from cosmic-ray interactions in the atmosphere provide a high-statistics source of particles that can be used to study the performance and calibration of the ATLAS detector. Cosmic-ray muons can penetrate to the cavern and deposit energy in all detector subsystems. Such events have played an important role in the commissioning of the detector since the start of the installation phase in 2005 and were particularly important for understanding the detector performance in the time prior to the arrival of the first LHC beams. Global cosmic-ray runs were undertaken in both 2008 and 2009 and these data have been used through to the early phases of collision data-taking as a tool for calibration, alignment and detector monitoring. These large datasets have also been used for detector performance studies, including investigations that rely on the combined performance of different subsystems. This paper presents the results of performance studies related to combined tracking, lepton identification and the reconstruction of jets and missing transverse energy. Results are compared to expectations based on a cosmic-ray event generator and a full simulation of the detector response.
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| 11. |
- Aad, G., et al.
(author)
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The ATLAS Inner Detector commissioning and calibration
- 2010
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 787-821
-
Journal article (peer-reviewed)abstract
- The ATLAS Inner Detector is a composite tracking system consisting of silicon pixels, silicon strips and straw tubes in a 2 T magnetic field. Its installation was completed in August 2008 and the detector took part in data-taking with single LHC beams and cosmic rays. The initial detector operation, hardware commissioning and in-situ calibrations are described. Tracking performance has been measured with 7.6 million cosmic-ray events, collected using a tracking trigger and reconstructed with modular pattern-recognition and fitting software. The intrinsic hit efficiency and tracking trigger efficiencies are close to 100%. Lorentz angle measurements for both electrons and holes, specific energy-loss calibration and transition radiation turn-on measurements have been performed. Different alignment techniques have been used to reconstruct the detector geometry. After the initial alignment, a transverse impact parameter resolution of 22.1 +/- 0.9 mu m and a relative momentum resolution sigma (p) /p=(4.83 +/- 0.16)x10(-4) GeV(-1)xp (T) have been measured for high momentum tracks.
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| 12. |
- Aad, G., et al.
(author)
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The ATLAS Simulation Infrastructure
- 2010
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 823-874
-
Journal article (peer-reviewed)abstract
- The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.
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| 13. |
- Alexandre, Rui Carlos Josino, et al.
(author)
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Cybersecurity Risk Assessment for Medium-Risk Drones : A Systematic Literature Review
- 2023
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In: IEEE Aerospace and Electronic Systems Magazine. - : Institute of Electrical and Electronics Engineers (IEEE). - 0885-8985 .- 1557-959X. ; 38:6, s. 28-43
-
Research review (peer-reviewed)abstract
- The increased demand for Remotely Piloted Aircraft Systems (RPAS) in Beyond Visual Line-Of-Sight (BVLOS) operations gives rise to a set of concerns regarding cybersecurity that, if not addressed, can lead to the unsafe operation of RPASs. To assist the airworthiness evaluation that is performed by Civil Aviation Authorities (CAAs), we identified several processes that are used to evaluate the cybersecurity of RPAS. We conducted a Systematic Literature Review (SLR) by selecting 30 papers (out of 211 screened) that were published during the past five years. The results of our SLR indicate the importance of cybersecurity to the safe operation of RPAS. It is evident that there is a lack of a systematic process to enable a cybersecurity review of RPAS. We observe that common cyber threats to RPAS are related to jamming, spoofing, and DOS/DDOS (Denial of Service/Distributed Denial of Service). Processes relevant to the assessment of RPAS cybersecurity exist, however they differ in safety concerns from our perspective. In addition, with only one exception, the methods have not been used, and/or the use has not been reported as pertaining to industrial application. The most frequently cited vulnerabilities are those related to GPS and datalinks.
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| 14. |
- Araujo, Mario Jorge, et al.
(author)
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Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species
- 2021
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In: Proteomes. - : MDPI. - 2227-7382. ; 9:4
-
Journal article (peer-reviewed)abstract
- Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC-MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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| 15. |
- Araújo, Mário J, et al.
(author)
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Proteomics reveals multiple effects of titanium dioxide and silver nanoparticles in the metabolism of turbot, Scophthalmus maximus
- 2022
-
In: Chemosphere. - : Pergamon-Elsevier Science Ltd. - 0045-6535 .- 1879-1298. ; 308
-
Journal article (peer-reviewed)abstract
- Titanium dioxide (TiO2) and silver (Ag) NPs are among the most used engineered inorganic nanoparticles (NPs); however, their potential effects to marine demersal fish species, are not fully understood. Therefore, this study aimed to assess the proteomic alterations induced by sub-lethal concentrations citrate-coated 25 nm ("P25") TiO2 or polyvinylpyrrolidone (PVP) coated 15 nm Ag NPs to turbot, Scophthalmus maximus. Juvenile fish were exposed to the NPs through daily feeding for 14 days. The tested concentrations were 0, 0.75 or 1.5 mg of each NPs per kg of fish per day. The determination of NPs, Titanium and Ag levels (sp-ICP-MS/ICP-MS) and histological alterations (Transmission Electron Microscopy) supported proteomic analysis performed in the liver and kidney. Proteomic sample preparation procedure (SP3) was followed by LC-MS/MS. Label-free MS quantification methods were employed to assess differences in protein expression. Functional analysis was performed using STRING web-tool. KEGG Gene Ontology suggested terms were discussed and potential biomarkers of exposure were proposed. Overall, data shows that liver accumulated more elements than kidney, presented more histological alterations (lipid droplets counts and size) and proteomic alterations. The Differentially Expressed Proteins (DEPs) were higher in Ag NPs trial. The functional analysis revealed that both NPs caused enrichment of proteins related to generic processes (metabolic pathways). Ag NPs also affected protein synthesis and nucleic acid transcription, among other processes. Proteins related to thyroid hormone transport (Serpina7) and calcium ion binding (FAT2) were suggested as biomarkers of TiO2 NPs in liver. For Ag NPs, in kidney (and at a lower degree in liver) proteins related with metabolic activity, metabolism of exogenous substances and oxidative stress (e.g.: NADH dehydrogenase and Cytochrome P450) were suggested as potential biomarkers. Data suggests adverse effects in turbot after medium/long-term exposures and the need for additional studies to validate specific biological applications of these NPs.
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| 16. |
- Aronsson, Daniel, et al.
(author)
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EU FP7 INFSO-ICT-247223 ARTIST4G, D3.4 Relay configurations
- 2011
-
Reports (other academic/artistic)abstract
- The following document contains proposals for innovations on relay configurations made by partners involved in the Artist4G project WP3, Task 3.3. The different relay configurations are for in-band and out-band relays, multi-hop relays, and moving relays. For each innovation, a description, the potential deviation from a defined baseline architecture, and simulation results (as far as available) are included. Important issues regarding the innovations impact on the architecture are pointed out and analysed in detail. This analysis will also be forwarded to WP4.
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| 17. |
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| 18. |
- Bruneau, Anne, et al.
(author)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
-
In: PhytoKeys. - Sofia : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
-
Journal article (peer-reviewed)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 19. |
- Bäck-Wiklund, Margareta, 1944, et al.
(author)
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Os hospitais são organizações saudáveis? Qualidade de vida no trabalho hospitalar no norte e no sul da Europa : Are healthcare organizations healthy? Quality of life in healthcare work in Northern and Southern Europe
- 2018
-
In: Sociologia, Problemas e Práticas. - 0873-6529. ; 86, s. 45-67
-
Research review (peer-reviewed)abstract
- From a gender perspective, this article analyses the concept of "healthy organization" through the study of the "dual agenda" of healthcare organizations. Based in the EU funded project "Quality of Life in a Changing Europe", which priviledged a multi-method approach, we analyse data from an extensive survey applied in eight European countries (Germany, Bulgaria, Finland, The Netherlands, Hungary, Portugal, United Kingdom and Sweden) and present two case studies undergone at university public hospitals in Sweden and in Portugal. Results show that the perceptions of what is a healthy organization are developed around the notions of social support, life satisfaction, work engagement and work-life reconciliation. Gender variations are a common feature in each of these dimensions. Organizational policies, professional trajectories and family resources are directly related to these variations.
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| 20. |
- Carl, Johannes, et al.
(author)
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Physical Literacy in Europe: The Current State of Implementation in Research, Practice, and Policy
- 2023
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In: Journal of Exercise Science and Fitness. - : Elsevier BV. - 1728-869X .- 2226-5104. ; 21:1, s. 165-176
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Journal article (peer-reviewed)abstract
- The holistic concept of physical literacy (PL) embraces different person-centered qualities (physical, cognitive, affective/psychological) necessary to lead physically active lifestyles. PL has recently gained increasing attention globally and Europe is no exception. However, scientific endeavors summarizing the current state of PL in Europe are lacking. Therefore, the goal of this study was to comprehensively assess and compare the implementation of PL in research, policy, and practice across the continent. We assembled a panel of experts representing 25 European countries. Employing a complementary mixed-methods design, the experts first prepared reviews about the current state of PL in their countries (categories: research, practice/policy). The reviews underwent comparative document analysis ensuring a transnational foureyes principle. For re-validation purposes, the representatives completed a quantitative survey with questions reflecting the inductive themes from the document analysis. The document analysis resulted in ten disjunct themes (related to “concept”, “research”, “practice/policy”, “future/prospect”) and yielded a heterogenous PL situation in Europe. The implementation state was strongly linked to conceptual discussions (e.g., existence of competing approaches), linguistic issues (e.g., translations), and country-specific traditions. Despite growing scholarly attention, PL hesitantly permeates practice and policy in most countries. Nevertheless, the experts largely anticipate increasing popularity of PL for the future. Despite the heterogeneous situation across Europe, the analysis has uncovered similarities among the countries, such as the presence of established yet not identical concept. Research should intensify academic activities (conceptuallinguistic elaborations, empirical work) before PL may gain further access into practical and political spheres in the long term.
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| 21. |
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| 22. |
- de Albuquerque, Gabriela E., et al.
(author)
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Evaluation of Bacteria and Fungi DNA Abundance in Human Tissues
- 2022
-
In: Genes. - : MDPI. - 2073-4425. ; 13:2
-
Journal article (peer-reviewed)abstract
- Whereas targeted and shotgun sequencing approaches are both powerful in allowing the study of tissue-associated microbiota, the human: microorganism abundance ratios in tissues of interest will ultimately determine the most suitable sequencing approach. In addition, it is possible that the knowledge of the relative abundance of bacteria and fungi during a treatment course or in pathological conditions can be relevant in many medical conditions. Here, we present a qPCR-targeted approach to determine the absolute and relative amounts of bacteria and fungi and demonstrate their relative DNA abundance in nine different human tissue types for a total of 87 samples. In these tissues, fungi genomes are more abundant in stool and skin samples but have much lower levels in other tissues. Bacteria genomes prevail in stool, skin, oral swabs, saliva, and gastric fluids. These findings were confirmed by shotgun sequencing for stool and gastric fluids. This approach may contribute to a more comprehensive view of the human microbiota in targeted studies for assessing the abundance levels of microorganisms during disease treatment/progression and to indicate the most informative methods for studying microbial composition (shotgun versus targeted sequencing) for various samples types.
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| 23. |
- de Jong, Yde, et al.
(author)
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PESI - a taxonomic backbone for Europe
- 2015
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In: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 3, s. 1-51
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Journal article (peer-reviewed)abstract
- Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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| 24. |
- Edpalm, Viktor, et al.
(author)
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Camera networks dimensioning and scheduling with quasi worst-case transmission time
- 2018
-
In: 30th Euromicro Conference on Real-Time Systems, ECRTS 2018. - 9783959770750 ; 106
-
Conference paper (peer-reviewed)abstract
- This paper describes a method to compute frame size estimates to be used in quasi Worst-Case Transmission Times (qWCTT) for cameras that transmit frames over IP-based communication networks. The precise determination of qWCTT allows us to model the network access scheduling problem as a multiframe problem and to re-use theoretical results for network scheduling. The paper presents a set of experiments, conducted in an industrial testbed, that validate the qWCTT estimation. We believe that a more precise estimation will lead to savings for network infrastructure and to better network utilization.
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| 25. |
- Edpalm, Viktor, et al.
(author)
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H.264 Video Frame Size Estimation
- 2018
-
Reports (other academic/artistic)abstract
- This report describes a method to estimate the video bandwidth for IP cameras using the H.264 standard. The precise determination of bandwidth allows us to model the network access as a scheduling problem and/or estimate the amount of data that would traverse it during different periods. The paper is written to be as didactic as possible and presents a set of experiments, conducted in an industrial testbed, that validate the estimation. We believe that a more precise estimation will lead to savings for network infrastructure and to better network utilization
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| 26. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 27. |
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| 28. |
- Martins, Alexandre, et al.
(author)
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Control-Based Resource Management for Storage of Video Streams
- 2020
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In: IFAC Proceedings Volumes (IFAC-PapersOnline). - : Elsevier BV. - 2405-8963. ; 53:2, s. 5542-5549
-
Journal article (peer-reviewed)abstract
- Distributed surveillance systems typically consist of multiple cameras that need to store some fraction of their video streams at a central storage node. The disk space of this node constitutes a shared resource. In the paper the disk space allocation is formulated as a PI control problem and a new method for enforcing global resource constraints inspired by anti-windup tracking is proposed. The approach is evaluated by simulations.
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| 29. |
- Martins, Alexandre, et al.
(author)
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Dynamic Management of Multiple Resources in Camera Surveillance Systems*
- 2021
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In: 2021 American Control Conference, ACC 2021. - 0743-1619. - 9781665441971 - 9781728197043 ; 2021-May, s. 2061-2068
-
Conference paper (peer-reviewed)abstract
- Distributed camera surveillance systems typically consist of multiple cameras that need to store some fraction of their video streams in a central storage node. The disk space of this node as well as the network between the cameras and this central node constitute shared resources. In the paper the disk space allocation as well as the network bandwidth reservation are solved using techniques normally associated with process control. These include mid-range control and tracking-based control of global shared resources. The approach is evaluated by simulations.
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| 30. |
- Martins, Alexandre
(author)
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Resource Management in Distributed Camera Systems
- 2022
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Doctoral thesis (other academic/artistic)abstract
- The aim of this work is to investigate different methods to solve the problem of allocating the correct amount of resources (network bandwidth and storage space) to video camera systems. Here we explore the intersection between two research areas: automatic control and game theory. Camera systems are a good example of the emergence of the Internet of Things (IoT) and its impact on our daily lives and the environment. We aim to improve today’s systems, shift from resources over-provisioning to allocate dynamically resources where they are needed the most. We optimize the storage and bandwidth allocation of camera systems to limit the impact on the environment as well as provide the best visual quality attainable with the resource limitations. This thesis is written as a collection of papers. It begins by introducing the problem with today’s camera systems, and continues with background information about resource allocation, automatic control and game theory. The third chapter de- scribes the models of the considered systems, their limitations and challenges. It then continues by providing more background on the automatic control and game theory techniques used in the proposed solutions. Finally, the proposed solutions are provided in five papers.Paper I proposes an approach to estimate the amount of data needed by surveillance cameras given camera and scenario parameters. This model is used for calculating the quasi Worst-Case Transmission Times of videos over a network. Papers II and III apply control concepts to camera network storage and bandwidth assignment. They provide simple, yet elegant solutions to the allocation of these resources in distributed camera systems. Paper IV com- bines pricing theory with control techniques to force the video quality of cam- era systems to converge to a common value based solely on the compression parameter of the provided videos. Paper V uses the VCG auction mechanism to solve the storage space allocation problem in competitive camera systems. It allows for a better system-wide visual quality than a simple split allocation given the limited system knowledge, trust and resource constraints.
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| 31. |
- Martins, Alexandre, et al.
(author)
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Storage Allocation for Camera Sensor Networks using Feedback-based Price Discrimination
- 2022
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In: Storage Allocation for Camera Sensor Networks using Feedback-based Price Discrimination. - : SCITEPRESS - Science and Technology Publications. ; , s. 34-44
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Conference paper (peer-reviewed)abstract
- Camera sensor networks, mainly with surveillance cameras, are growing in size and complexity. Storage space is the prime resource in such systems but current surveillance setups are still very much centralized and limited in resources due to cost and security constraints. Allocating the correct amount of storage to each camera sensor considering their large difference in characteristics and video content is challenging. In this paper we propose a framework using feedback-based price discrimination of storage resources in order to guarantee a uniform quality level of the videos in camera sensor networks, regardless of the specific camera sensor parameters. We designed a lightweight solution using simple video quality metrics, cascade control and PI (Proportional and Integral) controllers to define the optimal price of resources per camera.
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| 32. |
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| 33. |
- Martins, Ernane de Freitas, et al.
(author)
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A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent
- 2022
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:39, s. 24404-24412
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Journal article (peer-reviewed)abstract
- Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.
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| 34. |
- Martins, Ernane de Freitas, et al.
(author)
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Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates
- 2019
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In: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:5
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Journal article (peer-reviewed)abstract
- In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.
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| 35. |
- Martins, Ernane de Freitas, et al.
(author)
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The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing
- 2020
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In: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 158, s. 314-319
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Journal article (peer-reviewed)abstract
- Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a nitrogen-terminated nanogap on a graphene sheet with the aqueous environment fully taken into account. Our investigation is performed using a hybrid methodology combining quantum and classical mechanics coupled to non-equilibrium Green's functions for solving the electron transport across the device. The obtained results show that the DNA nucleotides can be both detected and distinguished in such a device, which indicates that it can be used as a DNA sequencing device providing very high sensitivity and selectivity. Furthermore, our results show that water plays a major role in electronic transport in nanoscopic tunneling devices, not only from an electrostatics point of view, but also by providing states that significantly increase the conductance in nanogap-based DNA sequencing devices.
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| 36. |
- Martins, Vasco Alexandre, et al.
(author)
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Go for Lipids! Food Preferences and Nutrient Composition in Zoo-Housed White-Faced Sakis, Pithecia pithecia
- 2023
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In: International journal of primatology. - : SPRINGER. - 0164-0291 .- 1573-8604. ; 44, s. 341-356
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Journal article (peer-reviewed)abstract
- The role that single nutrients may play for food choices in nonhuman primates is not fully understood. White-faced sakis (Pithecia pithecia) are unusual among frugivorous primates as they do not serve as seed dispersers but rather exploit the seeds they consume, presumably for their high contents of lipids and proteins. Therefore, we assessed the occurrence of spontaneous food preferences in zoo-housed white-faced sakis and analyzed whether these preferences correlate with nutrient composition. Using a two-alternative choice test, we repeatedly presented three female and two male sakis with all possible binary combinations of 15 types of food that are part of their diet under human care, and found them to display the following rank order of preference: peanut > hazelnut > avocado > melon > egg > apple > mealworms > beetroot > carrot > cucumber > cabbage > tomato > sweet potato > broccoli > eggplant. This preference ranking significantly and positively correlated with the total energy content of the food items. However, we found the strongest positive correlation among the three macronutrients providing metabolic energy between the sakis food preferences and lipid content. This is remarkable as all other primate species tested so far using this method displayed the strongest correlation with carbohydrates instead. Together with our finding that the sakis significantly preferred foods high in mono-unsaturated fatty acids, the building blocks of lipids, these results support the notion that white-faced sakis exploit the lipids contained in seeds to meet their requirements of metabolic energy.
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| 37. |
- Niskanen, Tuula, et al.
(author)
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Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi
- 2023
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In: ANNUAL REVIEW OF ENVIRONMENT AND RESOURCES. - 1543-5938 .- 1545-2050. ; 48, s. 149-176
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Research review (peer-reviewed)abstract
- Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected.We aim to flip this situation by synthesizing current knowledge.We present a revised estimate of 2-3 million fungal species with a "best estimate" at 2.5 million. To name the unknown >90% of these by the end of this century, we propose recognition of species known only from DNA data and call for large-scale sampling campaigns.We present an updated global map of fungal richness, highlighting tropical and temperate ecoregions of high diversity. We call for further Red List assessments and enhanced management guidelines to aid fungal conservation. Given that fungi play an inseparable role in our lives and in all ecosystems, and considering the fascinating questions remaining to be answered, we argue that fungi constitute the next frontier of biodiversity research.
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| 38. |
- Oliveira, Flavio, et al.
(author)
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Physiological and Metabolic Responses of Marine Mussels Exposed to Toxic Cyanobacteria Microcystis aeruginosa and Chrysosporum ovalisporum
- 2020
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In: Toxins. - : MDPI. - 2072-6651. ; 12:3
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Journal article (peer-reviewed)abstract
- Toxic cyanobacterial blooms are a major contaminant in inland aquatic ecosystems. Furthermore, toxic blooms are carried downstream by rivers and waterways to estuarine and coastal ecosystems. Concerning marine and estuarine animal species, very little is known about how these species are affected by the exposure to freshwater cyanobacteria and cyanotoxins. So far, most of the knowledge has been gathered from freshwater bivalve molluscs. This work aimed to infer the sensitivity of the marine mussel Mytilus galloprovincialis to single as well as mixed toxic cyanobacterial cultures and the underlying molecular responses mediated by toxic cyanobacteria. For this purpose, a mussel exposure experiment was outlined with two toxic cyanobacteria species, Microcystis aeruginosa and Chrysosporum ovalisporum at 1 x 10(5) cells/mL, resembling a natural cyanobacteria bloom. The estimated amount of toxins produced by M. aeruginosa and C. ovalisporum were respectively 0.023 pg/cell of microcystin-LR (MC-LR) and 7.854 pg/cell of cylindrospermopsin (CYN). After 15 days of exposure to single and mixed cyanobacteria, a depuration phase followed, during which mussels were fed only non-toxic microalga Parachlorella kessleri. The results showed that the marine mussel is able to filter toxic cyanobacteria at a rate equal or higher than the non-toxic microalga P. kessleri. Filtration rates observed after 15 days of feeding toxic microalgae were 1773.04 mL/ind.h (for M. aeruginosa), 2151.83 mL/ind.h (for C. ovalisporum), 1673.29 mL/ind.h (for the mixture of the 2 cyanobacteria) and 2539.25 mL/ind.h (for the non-toxic P. kessleri). Filtering toxic microalgae in combination resulted in the accumulation of 14.17 ng/g dw MC-LR and 92.08 ng/g dw CYN. Other physiological and biochemical endpoints (dry weight, byssus production, total protein and glycogen) measured in this work did not change significantly in the groups exposed to toxic cyanobacteria with regard to control group, suggesting that mussels were not affected with the toxic microalgae. Nevertheless, proteomics revealed changes in metabolism of mussels related to diet, specially evident in those fed on combined cyanobacteria. Changes in metabolic pathways related with protein folding and stabilization, cytoskeleton structure, and gene transcription/translation were observed after exposure and feeding toxic cyanobacteria. These changes occur in vital metabolic processes and may contribute to protect mussels from toxic effects of the toxins MC-LR and CYN.
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| 39. |
- Prasongkit, Jariyanee, et al.
(author)
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Topological Line Defects Around Graphene Nanopores for DNA Sequencing
- 2018
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In: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 122:13, s. 7094-7099
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Journal article (peer-reviewed)abstract
- Topological line defects in graphene represent an ideal way to produce highly controlled structures with reduced dimensionality that can be used in electronic devices. In this work, we propose using extended line defects in graphene to improve nucleobase selectivity in nanopore-based DNA sequencing devices. We use a combination of quantum mechanics/molecular mechanics and nonequilibrium Green's function methods to investigate the conductance modulation, fully accounting for solvent effects. By sampling over a large number of different orientations generated from molecular dynamics simulations, we theoretically demonstrate that distinguishing between the four nucleobases using line defects in a graphene-based electronic device appears possible. The changes in conductance are associated with transport across specific molecular states near the Fermi level and their coupling to the pore. Through the application of a specifically tuned gate voltage, such a device would be able to discriminate the four types of nucleobases more reliably than that of graphene sensors without topological line defects.
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| 40. |
- Ruuskanen, Johan, et al.
(author)
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Latency prediction in 5G for control with deadtime compensation
- 2019
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In: IoT-Fog '19 Proceedings of the Workshop on Fog Computing and the IoT. - 9781450366984 ; , s. 51-55
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Conference paper (peer-reviewed)abstract
- With the promise of increased responsiveness and robustness of the emerging 5G technology, it is suddenly becoming feasible to deploy latency-sensitive control systems over the cloud via a mobile network. Even though 5G is herald to give lower latency and jitter than current mobile networks, the effect of the delay would still be non-negligible for certain applications.In this paper we explore and demonstrate the possibility of compensating for the unknown and time-varying latency introduced by a 5G mobile network for control of a latency-sensitive plant. We show that the latency from a prototype 5G test bed lacks significant short-term correlation, making accurate latency prediction a difficult task. Further, because of the unknown and time-varying latency our used simple interpolation-based model experiences some troubling theoretical properties, limiting its usability in real world environments. Despite this, we give a demonstration of the strategy which seems to increase robustness in a simulated plant.
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| 41. |
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| 42. |
- van Leeuwen, F., et al.
(author)
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Gaia Data Release 1 : Open cluster astrometry: Performance, limitations, and future prospects
- 2017
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 601
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Journal article (peer-reviewed)abstract
- Context. The first Gaia Data Release contains the Tycho-Gaia Astrometric Solution (TGAS). This is a subset of about 2 million stars for which, besides the position and photometry, the proper motion and parallax are calculated using Hipparcos and Tycho-2 positions in 1991.25 as prior information. Aims. We investigate the scientific potential and limitations of the TGAS component by means of the astrometric data for open clusters. Methods. Mean cluster parallax and proper motion values are derived taking into account the error correlations within the astrometric solutions for individual stars, an estimate of the internal velocity dispersion in the cluster, and, where relevant, the effects of the depth of the cluster along the line of sight. Internal consistency of the TGAS data is assessed. Results. Values given for standard uncertainties are still inaccurate and may lead to unrealistic unit-weight standard deviations of least squares solutions for cluster parameters. Reconstructed mean cluster parallax and proper motion values are generally in very good agreement with earlier Hipparcos-based determination, although the Gaia mean parallax for the Pleiades is a significant exception. We have no current explanation for that discrepancy. Most clusters are observed to extend to nearly 15 pc from the cluster centre, and it will be up to future Gaia releases to establish whether those potential cluster-member stars are still dynamically bound to the clusters. Conclusions. The Gaia DR1 provides the means to examine open clusters far beyond their more easily visible cores, and can provide membership assessments based on proper motions and parallaxes. A combined HR diagram shows the same features as observed before using the Hipparcos data, with clearly increased luminosities for older A and F dwarfs.
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| 43. |
- Yabuta, Hikaru, et al.
(author)
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Macromolecular organic matter in samples of the asteroid (162173) Ryugu
- 2023
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In: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 379:6634
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Journal article (peer-reviewed)abstract
- Samples of the carbonaceous asteroid (162173) Ryugu were collected and brought to Earth by the Hayabusa2 spacecraft. We investigated the macromolecular organic matter in Ryugu samples and found that it contains aromatic and aliphatic carbon, ketone, and carboxyl functional groups. The spectroscopic features of the organic matter are consistent with those in chemically primitive carbonaceous chondrite meteorites that experienced parent-body aqueous alteration (reactions with liquid water). The morphology of the organic carbon includes nanoglobules and diffuse carbon associated with phyllosilicate and carbonate minerals. Deuterium and/or nitrogen-15 enrichments indicate that the organic matter formed in a cold molecular cloud or the presolar nebula. The diversity of the organic matter indicates variable levels of aqueous alteration on Ryugus parent body.
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| 44. |
- Aad, G., et al.
(author)
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- 2013
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In: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 73:1
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Journal article (peer-reviewed)
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| 45. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 46. |
- Aad, G., et al.
(author)
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- 2010
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swepub:Mat__t
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| 47. |
- Aad, G., et al.
(author)
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- 2011
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Journal article (peer-reviewed)
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