| 1. |
- Bataille, Christopher, et al.
(author)
-
Net-zero deep decarbonization pathways in Latin America : Challenges and opportunities
- 2020
-
In: Energy Strategy Reviews. - : Elsevier BV. - 2211-467X .- 2211-4688. ; 30
-
Journal article (peer-reviewed)abstract
- This synthesis paper presents the objectives, approach and cross-cutting results of the Latin American Deep Decarbonization Pathways project (DDP-LAC). It synthesizes and compares detailed national and sectoral deep decarbonization pathways (DDPs) to 2050 compatible with the Paris Agreement objectives and domestic development priorities in Argentina, Colombia, Costa Rica, Ecuador, Mexico and Peru. The first five countries analysed in detail the energy system and agriculture, forestry and land use (AFOLU) at a high level, while Peru focussed on a detailed analysis of AFOLU given its predominance in its GHG emissions. While economy-wide results were produced, this paper focuses on the electricity, passenger transport, and AFOLU results because of their current emissions, potential to grow, and identification of successful strategies for decarbonization (e.g. switching to clean electricity and other net-zero emissions fuels across the economy; urban planning, mode shifting, and electrification in passenger transport; and intensive sustainable agriculture, assignment of land use rights and their enforcement and afforestation in AFOLU). It also highlights where significant emissions remain in 2050, notably in industry, AFOLU, freight, and oil and gas production, all areas for future research. It derives insights for the design of domestic policy packages and identifies priorities for international cooperation. This analysis provides critical information for Long-Term Strategies, Nationally Determined Contributions and Global Stocktaking in the context of the Paris Agreement.
|
|
| 2. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
|
|
| 3. |
- Askarpour, Mehrnoosh, et al.
(author)
-
RoboMAX: Robotic Mission Adaptation eXemplars
- 2021
-
In: Proceedings - 2021 International Symposium on Software Engineering for Adaptive and Self-Managing Systems, SEAMS 2021. ; , s. 245-251
-
Conference paper (peer-reviewed)abstract
- Emerging and future applications of robotic systems pose unique self-adaptation challenges. To support the research needed to address these challenges, we provide an extensible repository of robotic mission adaptation exemplars. Co-designed with robotic application stakeholders including researchers, developers, operators, and end-users, our repository captures key sources of uncertainty, adaptation concerns, and other distinguishing characteristics of such applications. An online form enables external parties to supply new exemplars for curation and inclusion into the repository. We envisage that our RoboMAX repository will enable the development, evaluation, and comparison of self-adaptation approaches for the robotic systems domain.
|
|
| 4. |
- Esquinas, Cristina, et al.
(author)
-
Gene and miRNA expression profiles in PBMCs from patients with severe and mild emphysema and PiZZ alpha I-antitrypsin deficiency
- 2017
-
In: International Journal of COPD. - 1176-9106. ; 12, s. 3381-3390
-
Journal article (peer-reviewed)abstract
- Introduction: COPD has complex etiologies involving both genetic and environmental determinants. Among genetic determinants, the most recognized is a severe PiZZ (Glu342Lys) inherited alpha1-antitrypsin deficiency (AATD). Nonetheless, AATD patients present a heterogeneous clinical evolution, which has not been completely explained by sociodemographic or clinical factors. Here we performed the gene expression profiling of blood cells collected from mild and severe COPD patients with PiZZ AATD. Our aim was to identify differences in messenger RNA (mRNA) and microRNA (miRNA) expressions that may be associated with disease severity. Materials and methods: Peripheral blood mononuclear cells from 12 COPD patients with PiZZ AATD (6 with severe disease and 6 with mild disease) were used in this pilot, high-throughput microarray study. We compared the cellular expression levels of RNA and miRNA of the 2 groups, and performed functional and enrichment analyses using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene-ontology (GO) terms. We also integrated the miRNA and the differentially expressed putative target mRNA. For data analyses, we used the R statistical language R Studio (version 3.2.5). Results: The severe and mild COPD-AATD groups were similar in terms of age, gender, exacerbations, comorbidities, and use of augmentation therapy. In severe COPD-AATD patients, we found 205 differentially expressed genes (DEGs) (114 upregulated and 91 downregulated) and 28 miRNA (20 upregulated and 8 downregulated) compared to patients with mild COPD-AATD disease. Of these, hsa-miR-335-5p was downregulated and 12 target genes were involved in cytokine signaling, MAPK/mk2, JNK signaling cascades, and angiogenesis were much more highly expressed in severe compared with mild patients. Conclusions: Despite the small sample size, we identified downregulated miRNA (hsa-miR-335) and the activation of pathways related to inflammation and angiogenesis on comparing patients with severe vs mild COPD-AATD. Nonetheless, our findings warrant further validation in large studies.
|
|
| 5. |
- Fernández-Pozo, Noé, et al.
(author)
-
EuroPineDB : a high-coverage web database for maritime pine transcriptome
- 2011
-
In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 12, s. 366-
-
Journal article (peer-reviewed)abstract
- BACKGROUND: Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. DESCRIPTION: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. CONCLUSIONS: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.
|
|
| 6. |
- Gonzalez-Acuna, Daniel, et al.
(author)
-
Health evaluation of wild gentoo penguins (Pygoscelis papua) in the Antarctic Peninsula
- 2013
-
In: Polar Biology. - : Springer Science and Business Media LLC. - 0722-4060 .- 1432-2056. ; 36:12, s. 1749-1760
-
Journal article (peer-reviewed)abstract
- Historically wildlife conservation was based on habitat protection and exploitation control. Only recently have diseases been considered an important issue. However, pathogens are usually described during or after disease outbreaks, but to determine which pathogens may be emerging, surveys of wildlife health are critical in a given time. This study deals with the health status of gentoo penguins Pygoscelis papua in two localities at the Antarctica Peninsula and one at Ardley Island off the South Shetland Islands. Cloacal swaps, fresh fecal samples, ectoparasites, and blood smears were collected. We examined and dissected 14 penguin corpses found dead. Fecal samples were positive for Campylobacter, Escherichia coli and in the carcasses four endoparasitic species were found: Diphyllobothrium sp. and Parorchites zederi, Corynosoma shackletoni and Stegophorus adeliae. The tick Ixodes uriae occurred in five of the examined penguins, and the louse Austrogoniodes gressitti on six birds. From the colony grounds, we collected 1,184 I. uriae. We recorded antibiotic-resistant bacteria, such as E. coli, in ecosystems where gentoo penguins breed. Cloacal samples (300) were negative for Chlamydia, as well as for Salmonella, Campylobacter, E. coli, Newcastle and Influenza viruses.
|
|
| 7. |
- Householder, John Ethan, et al.
(author)
-
One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
-
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.
|
|
| 8. |
- Llorens, Carlos, et al.
(author)
-
The Gypsy Database (GyDB) of mobile genetic elements : release 2.0.
- 2011
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 39:Database issue
-
Journal article (peer-reviewed)abstract
- This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.
|
|
| 9. |
- Luize, Bruno Garcia, et al.
(author)
-
Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
-
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.
|
|
| 10. |
- Queiroz, Rodrigo, et al.
(author)
-
A Driver-Vehicle Model for ADS Scenario-Based Testing
- 2024
-
In: IEEE Transactions on Intelligent Transportation Systems. - 1524-9050 .- 1558-0016. ; In Press
-
Journal article (peer-reviewed)abstract
- Scenario-based testing for automated driving systems (ADS) must be able to simulate traffic scenarios that rely on interactions with other vehicles. Although many languages for high-level scenario modelling have been proposed, they lack the features to precisely and reliably control the required micro-simulation, while also supporting behavior reuse and test reproducibility for a wide range of interactive scenarios. To fill this gap between scenario design and execution, we propose the Simulated Driver-Vehicle (SDV) model to represent and simulate vehicles as dynamic entities with their behavior being constrained by scenario design and goals set by testers. The model combines driver and vehicle as a single entity. It is based on human-like driving and the mechanical limitations of real vehicles for realistic simulation. The model leverages behavior trees to express high-level behaviors in terms of lower-level maneuvers, affording multiple driving styles and reuse. Furthermore, optimization-based maneuver planners guide the simulated vehicles towards the desired behavior. Our extensive evaluation shows the model’s design effectiveness using NHTSA pre-crash scenarios, its motion realism in comparison to naturalistic urban traffic, and its scalability with traffic density. Finally, we show the applicability of our SDV model to test a real ADS and to identify crash scenarios, which are impractical to represent using predefined vehicle trajectories. The SDV model instances can be injected into existing simulation environments via co-simulation.
|
|
| 11. |
- ter Steege, Hans, et al.
(author)
-
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.
|
|
