| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Mattos, Caio R. C., et al.
(författare)
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Rainfall and topographic position determine tree embolism resistance in AmazÃŽnia and Cerrado sites
- 2023
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Ingår i: Environmental Research Letters. - : Institute of Physics Publishing (IOPP). - 1748-9326. ; 18:11
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Tidskriftsartikel (refereegranskat)abstract
- Droughts are predicted to increase in both frequency and intensity by the end of the 21st century, but ecosystem response is not expected to be uniform across landscapes. Here we assess the importance of the hill-to-valley hydrologic gradient in shaping vegetation embolism resistance under different rainfall regimes using hydraulic functional traits. We demonstrate that rainfall and hydrology modulate together the embolism resistance of tree species in different sites and topographic positions. Although buffered by stable access to groundwater, valley plants are intrinsically more vulnerable to drought-induced embolism than those on hills. In all study sites, the variability in resistance to embolism is higher on hills than on valleys, suggesting that the diversity of strategies to cope with drought is more important for tree communities on hills. When comparing our results with previously published data across the tropics, we show greater variability at the local scale than previously reported. Our results reinforce the urgent need to extend sampling efforts across rainfall regimes and topographic positions to improve the characterization of ecosystem resistance to drought at finer spatial scales.
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| 4. |
- Castro, Jonathan Pena, et al.
(författare)
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Differential Expression of Genes Related to Sexual Determination Can Modify the Reproductive Cycle of Astyanax scabripinnis (Characiformes: Characidae) in B Chromosome Carrier Individuals
- 2019
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- The species complex Astyanax scabripinnis is one of the most studied with respect to origin, distribution, and frequency of B chromosomes, and is considered a model organism for evolutionary studies. Research using population inferences about the occurrence and frequency of the B chromosome shows seasonal variation between sexes, which is associated with the presence of this supernumerary element. We hypothesized that the B chromosome could influence the sex ratio of these animals. Based on this assumption, the present work aimed to investigate if differences exist among levels of gene expression with qRT-PCR of the amh (associated with testicular differentiation) and foxl2a (associated with ovarian differentiation) genes between B-carrier and non-B-carrier individuals. The results showed that for the amh gene, the difference in expression between animals with B chromosomes was not accentuated compared to that in animals without this chromosome. Expression of foxl2a in B-carrier females, however, was reduced by 73.56% compared to females that lacked the B chromosome. Males had no difference in expression of the amh and foxl2a genes between carriers and non-carriers of the B chromosome. Results indicate that the presence of B chromosomes is correlated with the differential expression of sex-associated genes. An analysis of these results integrated with data from other studies on the reproductive cycle in the same species reveals that this difference in expression may be expanding the reproductive cycle of the species.
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| 5. |
- Fernandes, Jorge, et al.
(författare)
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Thermal performance and comfort of vernacular earthen buildings in Egypt and Portugal
- 2017
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Ingår i: Vernacular and Earthen Architecture: Conservation and Sustainability: Proceedings of Sostierra 2017 (Valencia, Spain, 14-16 September 2017). - : CRC Press. - 9781138035461 ; , s. 95-100
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Konferensbidrag (refereegranskat)abstract
- Despite the far distance between Portugal and Egypt, it was possible to find points of similarity on the influence of Roman and Arab cultures, and on solar passive and construction techniques used in vernacular architecture. Earthen construction techniques are one of these examples, being used in both countries for thousands of years. Through an explanatory qualitative and quantitative analysis, this paper presents an overview of the effects of climate-responsive strategies on thermal performance and indoor comfort of earthen architecture from Northern Egypt and Southern Portugal. To understand the effectiveness of these strategies, measurements of hygrothermal parameters and surveys on occupants’ thermal sensation were conducted in two case studies. From the results, it has been found that the case studies have shown a good thermal performance only by passive means and that the occupants expressed as being comfortable. Thus, vernacular passive strategies still can contribute to achieve indoor comfort conditions and reduce the dependency on mechanical systems.
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| 6. |
- Forslund, Kristoffer, et al.
(författare)
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Gearing up to handle the mosaic nature of life in the quest for orthologs
- 2018
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 34:2, s. 323-329
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Tidskriftsartikel (refereegranskat)abstract
- The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.
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| 7. |
- Frischknecht, R., et al.
(författare)
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Comparison of the greenhouse gas emissions of a high-rise residential building assessed with different national LCA approaches - IEA EBC Annex 72
- 2020
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Ingår i: IOP Conference Series. - : IOP Publishing. ; , s. 022029-
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Konferensbidrag (refereegranskat)abstract
- Introduction: The international research project IEA EBC Annex 72 investigates the life cycle related environmental impacts caused by buildings. The project aims inter alia to harmonise LCA approaches on buildings. Methods: To identify major commonalities and discrepancies among national LCA approaches, reference buildings were defined to present and compare the national approaches. A residential high-rise building located in Tianjin, China, was selected as one of the reference buildings. The main construction elements are reinforced concrete shear walls, beams and floor slabs. The building has an energy reference area of 4566 m2 and an operational heating energy demand of 250 MJ/m2a. An expert team provided information on the quantities of building materials and elements required for the construction, established a BIM model and quantified the operational energy demand. Results: The greenhouse gas emissions and environmental impacts of the building were quantified using 17 country-specific national assessment methods and LCA databases. Comparisons of the results are shown on the level of building elements as well as the complete life cycle of the building. Conclusions: The results of these assessments show that the main differences lie in the LCA background data used, the scope of the assessment and the reference study period applied. Despite the variability in the greenhouse gas emissions determined with the 17 national methods, the individual results are relevant in the respective national context of the method, data, tool and benchmark used. It is important that environmental benchmarks correspond to the particular LCA approach and database of a country in which the benchmark is applied. Furthermore, the results imply to include building technologies as their contribution to the overall environmental impacts is not negligible. Grant support: The authors thank the IEA for its organizational support and the funding organizations in the participating countries for their financial support.
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| 8. |
- Glover, Natasha, et al.
(författare)
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Advances and Applications in the Quest for Orthologs
- 2019
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 36:10, s. 2157-2164
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Forskningsöversikt (refereegranskat)abstract
- Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
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| 9. |
- Liu, Jianguo, et al.
(författare)
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Spillover systems in a telecoupled Anthropocene : typology, methods, and governance for global sustainability
- 2018
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435. ; 33, s. 58-69
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Forskningsöversikt (refereegranskat)abstract
- The world has become increasingly telecoupled through distant flows of information, energy, people, organisms, goods, and matter. Recent advances suggest that telecouplings such as trade and species invasion often generate spillover systems with profound effects. To untangle spillover complexity, we make the first attempt to develop a typology of spillover systems based on six criteria: flows from and to sending and receiving systems, distances from sending and receiving systems, types of spillover effects, sizes of spillover systems, roles of agents in spillover systems, and the origin of spillover systems. Furthermore, we highlight a portfolio of qualitative and quantitative methods for detecting the often-overlooked spillover systems. To effectively govern spillover systems for global sustainability, we propose an overall goal (minimize negative and maximize positive spillover effects) and three general principles (fairness, responsibility, and capability).
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| 10. |
- Peixoto, Mariana, et al.
(författare)
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On Understanding How Developers Perceive and Interpret Privacy Requirements Research Preview
- 2020
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Ingår i: Lecture Notes in Computer Science. - Cham : Springer. - 9783030444280 ; , s. 116-123
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Konferensbidrag (refereegranskat)abstract
- [Context and motivation] Ensuring privacy of users’ data has become a top concern in software development, either to satisfy users’ needs or to comply with privacy laws. The problem may increase by the time a new law is in the vacancy period, and companies are working to understand how to comply with it. In addition, research has shown that many developers do not have sufficient knowledge about how to develop privacy-sensitive software. [Question/problem] Motivated by this scenario, this research investigates the personal factors affecting the developers’ understanding of privacy requirements during the vacancy period of a data protection law. [Principal ideas/results] We conducted thirteen interviews in six different private companies. As a result, we found nine personal factors affecting how software developers perceive and interpret privacy requirements. [Contribution] The identification of the personal factors contributes to the elaboration of effective methods for promoting proper privacy-sensitive software development. © 2020, Springer Nature Switzerland AG.
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| 11. |
- Peixoto, Mariana, et al.
(författare)
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The perspective of Brazilian software developers on data privacy
- 2023
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Ingår i: Journal of Systems and Software. - : Elsevier. - 0164-1212 .- 1873-1228. ; 195
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Tidskriftsartikel (refereegranskat)abstract
- Context: Maintaining the privacy of user data is a concern in software development to satisfy customer needs or to comply with privacy laws. Recent studies have shown that software development approaches still neglect non-functional requirements, including privacy. Concern about privacy may increase in the period between when a privacy law is initially announced and when it is passed into law. During this period, companies will be challenged to comply with the new law. Research has shown that many developers do not have sufficient knowledge to develop privacy-preserving software systems.Objective: We investigate the level of knowledge and understanding that developers possess regarding privacy. We explore the personal, behavioural, and external environmental factors affecting a developer's decision-making regarding privacy requirements.Methods: We replicated a study by means of in-depth, semi-structured interviews with thirteen practitioners at six companies. Our data analysis is based on the principles of ‘grounded theory codification’.Results: We identified nine personal factors, five behavioural factors, and seven external environment factors that are relevant to how software developers make decisions regarding.Conclusion: Our identification of factors that influence the development of privacy-preserving software systems can be seen as a contribution to the specification of effective methods for securing privacy. © 2022 Elsevier Inc.
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| 12. |
- Rostami, Ahmad, et al.
(författare)
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An end-to-end programmable platform for dynamic service creation in 5g networks
- 2017
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Ingår i: 2017 Optical Fiber Communications Conference and Exhibition, OFC 2017 - Proceedings. - : IEEE. - 9781943580231
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Konferensbidrag (refereegranskat)abstract
- We demonstrate how SDN and NFV can bring end-to-end programmability to heterogeneous technology domains including optical transport, radio and cloud networks, which can in turn be leveraged for agile and resource-optimized service creation.
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