| 1. |
|
|
| 2. |
- Hudson, Lawrence N, et al.
(författare)
-
The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
-
Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
-
Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
|
|
| 3. |
|
|
| 4. |
- Abdallah, J., et al.
(författare)
-
Mechanical construction and installation of the ATLAS tile calorimeter
- 2013
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 8, s. T11001-
-
Tidskriftsartikel (refereegranskat)abstract
- This paper summarises the mechanical construction and installation of the Tile Calorimeter for the ATLAS experiment at the Large Hadron Collider in CERN, Switzerland. The Tile Calorimeter is a sampling calorimeter using scintillator as the sensitive detector and steel as the absorber and covers the central region of the ATLAS experiment up to pseudorapidities +/- 1.7. The mechanical construction of the Tile Calorimeter occurred over a period of about 10 years beginning in 1995 with the completion of the Technical Design Report and ending in 2006 with the installation of the final module in the ATLAS cavern. During this period approximately 2600 metric tons of steel were transformed into a laminated structure to form the absorber of the sampling calorimeter. Following instrumentation and testing, which is described elsewhere, the modules were installed in the ATLAS cavern with a remarkable accuracy for a structure of this size and weight.
|
|
| 5. |
- Abdallah, J., et al.
(författare)
-
The optical instrumentation of the ATLAS Tile Calorimeter
- 2013
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 8, s. P01005-
-
Tidskriftsartikel (refereegranskat)abstract
- The Tile Calorimeter, covering the central region of the ATLAS experiment up to pseudorapidities of +/-1.7, is a sampling device built with scintillating tiles that alternate with iron plates. The light is collected in wave-length shifting (WLS) fibers and is read out with photomultipliers. In the characteristic geometry of this calorimeter the tiles lie in planes perpendicular to the beams, resulting in a very simple and modular mechanical and optical layout. This paper focuses on the procedures applied in the optical instrumentation of the calorimeter, which involved the assembly of about 460,000 scintillator tiles and 550,000 WLS fibers. The outcome is a hadronic calorimeter that meets the ATLAS performance requirements, as shown in this paper.
|
|
| 6. |
- Osorio, A., et al.
(författare)
-
Evaluation of the XRCC1 gene as a phenotypic modifier in BRCA1/2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2
- 2011
-
Ingår i: British Journal of Cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 104:8, s. 1356-1361
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Single-nucleotide polymorphisms (SNPs) in genes involved in DNA repair are good candidates to be tested as phenotypic modifiers for carriers of mutations in the high-risk susceptibility genes BRCA1 and BRCA2. The base excision repair (BER) pathway could be particularly interesting given the relation of synthetic lethality that exists between one of the components of the pathway, PARP1, and both BRCA1 and BRCA2. In this study, we have evaluated the XRCC1 gene that participates in the BER pathway, as phenotypic modifier of BRCA1 and BRCA2. METHODS: Three common SNPs in the gene, c.-77C>T (rs3213245) p.Arg280His (rs25489) and p.Gln399Arg (rs25487) were analysed in a series of 701 BRCA1 and 576 BRCA2 mutation carriers. RESULTS: An association was observed between p.Arg280His-rs25489 and breast cancer risk for BRCA2 mutation carriers, with rare homozygotes at increased risk relative to common homozygotes (hazard ratio: 22.3, 95% confidence interval: 14.3-34, P<0.001). This association was further tested in a second series of 4480 BRCA1 and 3016 BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2. CONCLUSIONS AND INTERPRETATION: No evidence of association was found when the larger series was analysed which lead us to conclude that none of the three SNPs are significant modifiers of breast cancer risk for mutation carriers. British Journal of Cancer (2011) 104, 1356-1361. doi:10.1038/bjc.2011.91 www.bjcancer.com Published online 22 March 2011 (C) 2011 Cancer Research UK
|
|
| 7. |
|
|
| 8. |
- Aquila, A., et al.
(författare)
-
The linac coherent light source single particle imaging road map
- 2015
-
Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4
-
Tidskriftsartikel (refereegranskat)abstract
- Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.
|
|
| 9. |
- Hudson, Lawrence N., et al.
(författare)
-
The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
-
Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
-
Tidskriftsartikel (refereegranskat)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
|
|
| 10. |
- Chrysafi, Anna, et al.
(författare)
-
Quantifying Earth system interactions for sustainable food production via expert elicitation
- 2022
-
Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 5:10, s. 830-842
-
Tidskriftsartikel (refereegranskat)abstract
- Several safe boundaries of critical Earth system processes have already been crossed due to human perturbations; not accounting for their interactions may further narrow the safe operating space for humanity. Using expert knowledge elicitation, we explored interactions among seven variables representing Earth system processes relevant to food production, identifying many interactions little explored in Earth system literature. We found that green water and land system change affect other Earth system processes strongly, while land, freshwater and ocean components of biosphere integrity are the most impacted by other Earth system processes, most notably blue water and biogeochemical flows. We also mapped a complex network of mechanisms mediating these interactions and created a future research prioritization scheme based on interaction strengths and existing knowledge gaps. Our study improves the understanding of Earth system interactions, with sustainability implications including improved Earth system modelling and more explicit biophysical limits for future food production.
|
|
| 11. |
- De Palma, Adriana, et al.
(författare)
-
Predicting bee community responses to land-use changes : effects of geographic and taxonomic biases
- 2016
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6, s. 1-14
-
Tidskriftsartikel (refereegranskat)abstract
- Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.
|
|
| 12. |
- Downing, Andrea S., et al.
(författare)
-
Coupled human and natural system dynamics as key to the sustainability of Lake Victoria's ecosystem services
- 2014
-
Ingår i: Ecology and Society. - 1708-3087. ; 19:4, s. 31-
-
Tidskriftsartikel (refereegranskat)abstract
- East Africa's Lake Victoria provides resources and services to millions of people on the lake's shores and abroad. In particular, the lake's fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria's system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake's social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks' vulnerability to exploitation but reduce society's vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.
|
|
| 13. |
|
|
| 14. |
- Koschorreck, Matthias, et al.
(författare)
-
Hidden treasures : Human-made aquatic ecosystems harbour unexplored opportunities
- 2020
-
Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 49:2, s. 531-540
-
Tidskriftsartikel (refereegranskat)abstract
- Artificial water bodies like ditches, fish ponds, weirs, reservoirs, fish ladders, and irrigation channels are usually constructed and managed to optimize their intended purposes. However, human-made aquatic systems also have unintended consequences on ecosystem services and biogeochemical cycles. Knowledge about their functioning and possible additional ecosystem services is poor, especially compared to natural ecosystems. A GIS analysis indicates that currently only similar to 10% of European surface waters are covered by the European Water Framework directive, and that a considerable fraction of the excluded systems are likely human-made aquatic systems. There is a clear mismatch between the high possible significance of human-made water bodies and their low representation in scientific research and policy. We propose a research agenda to build an inventory of human-made aquatic ecosystems, support and advance research to further our understanding of the role of these systems in local and global biogeochemical cycles as well as to identify other benefits for society. We stress the need for studies that aim to optimize management of human-made aquatic systems considering all their functions and to support programs designed to overcome barriers of the adoption of optimized management strategies.
|
|
| 15. |
- Mooij, Wolf M., et al.
(författare)
-
Modeling water quality in the Anthropocene : directions for the next-generation aquatic ecosystem models
- 2019
-
Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 36, s. 85-95
-
Forskningsöversikt (refereegranskat)abstract
- Everything changes and nothing stands still (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models - and ecological models in general - as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
|
|
| 16. |
|
|
| 17. |
- Soranno, Patricia A., et al.
(författare)
-
LAGOS-NE : A multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. lakes
- 2017
-
Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 6:12, s. 1-22
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states. LAGOS-NE contains data for 51101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 datamodules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situmeasurements of lake water quality for a subset of the lakes fromthe past 3 decades for approximately 2600–12 000 lakes depending on the variable. The database contains approximately 150000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from87 lake water quality data sets fromfederal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest andmost comprehensive databases of its type because it includes both in situmeasurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales
|
|
| 18. |
- Tranvik, Lars J., et al.
(författare)
-
Lakes and reservoirs as regulators of carbon cycling and climate
- 2009
-
Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 54:6:2, s. 2298-2314
-
Forskningsöversikt (refereegranskat)abstract
- We explore the role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland waters is likely to change in response to climate. Furthermore, we project changes as global climate change in the abundance and spatial distribution of lakes in the biosphere, and we revise the estimate for the global extent of carbon transformation in inland waters. This synthesis demonstrates that the global annual emissions of carbon dioxide from inland waters to the atmosphere are similar in magnitude to the carbon dioxide uptake by the oceans and that the global burial of organic carbon in inland water sediments exceeds organic carbon sequestration on the ocean floor. The role of inland waters in global carbon cycling and climate forcing may be changed by human activities, including construction of impoundments, which accumulate large amounts of carbon in sediments and emit large amounts of methane to the atmosphere. Methane emissions are also expected from lakes on melting permafrost. The synthesis presented here indicates that (1) inland waters constitute a significant component of the global carbon cycle, (2) their contribution to this cycle has significantly changed as a result of human activities, and (3) they will continue to change in response to future climate change causing decreased as well as increased abundance of lakes as well as increases in the number of aquatic impoundments.
|
|
| 19. |
- Viljur, Mari-Liis, et al.
(författare)
-
The effect of natural disturbances on forest biodiversity : an ecological synthesis
- 2022
-
Ingår i: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 97:5, s. 1930-1947
-
Tidskriftsartikel (refereegranskat)abstract
- Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q = 0 but not for q = 1 and q = 2, indicating that diversity–disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes.
|
|
| 20. |
- Bonet, Eulàlia, et al.
(författare)
-
(In)Direct reference in the phonology-syntax interface under phase theory: a response to Modular PIC (D’Alessandro and Scheer 2015)
- 2019
-
Ingår i: Linguistic Inquiry. - : MIT Press. - 0024-3892 .- 1530-9150. ; 50:4, s. 751-777
-
Tidskriftsartikel (refereegranskat)abstract
- While the domains of phrasal phonological processes are, in many interface theories, defined in terms of prosodic constituents, D’Alessandro and Scheer (2015) argue that their proposed modification of phase theory, Modular PIC, renders prosodic constituents superfluous. Phrasal phonological domains can instead be defined directly in the syntax. In this response, we argue that Modular PIC does not provide a convincing new approach to the syntaxphonology interface, as it is both too powerful and too restrictive. We show that the analysis offered of Raddoppiamento fonosintattico in Eastern Abruzzese does not justify the loss of restrictiveness Modular PIC brings to phase theory. Modular PIC is also shown to be too restrictive to account for phenomena, from Bantu languages and others, which have received satisfactory analyses within interface theories that appeal to prosodic constituents. We conclude that Modular PIC does not successfully replace prosodic constituent approaches to the interface.
|
|
| 21. |
- Cheng, Lisa L.-S., et al.
(författare)
-
Phasal syntax = cyclic phonology?
- 2016
-
Ingår i: Syntax. - : Wiley. - 1368-0005 .- 1467-9612. ; 19:2, s. 159-191
-
Tidskriftsartikel (refereegranskat)abstract
- This paper addresses three central questions in the phonology–syntax interface: What does phonology know about syntax? Does phrasal phonology “know” about syntax directly or indirectly (i.e., mediated by prosodic constituents such as Intonation Phrase)? When does the phonology–syntax interaction take place? Most current phase-based theories of the interface assume a strict cyclic model of derivation, in which the output of each spell-out domain directly feeds the phonology. We argue instead for an indirect model in which phonology is mainly conditioned by phase edges and accesses syntax only when the syntactic derivation is complete. We motivate the model mainly with data from Bantu languages that have played a leading role in the development of current theories of the phonology–syntax interface.
|
|
| 22. |
- Cheng, Lisa L. S., et al.
(författare)
-
Recursion and the definition of universal prosodic categories
- 2021
-
Ingår i: Languages. - : MDPI AG. - 2226-471X. ; 6:3
-
Tidskriftsartikel (refereegranskat)abstract
- It is widely agreed that prosodic constituents should mirror syntactic constituents (unless high-ranking prosodic constraints interfere). Because recursion is a feature of syntactic representations, one expects recursion in prosodic representations as well. However, it is of current controversy what kinds of syntactic representation motivate prosodic recursion. In this paper, the use of Phonological Phrase recursion is reviewed in several case studies, chosen because prosodic recursion mostly does not reflect syntactic recursion as defined in current syntactic theory. We provide reanalyses that do not appeal to prosodic recursion (unless syntactically motivated), showing that Phonological Phrase recursion is not necessary to capture the relevant generalizations. The more restrictive use of prosodic recursion we argue for has the following conceptual advantages. It allows for more consistent cross-linguistic generalizations about the syntax–prosody mapping so that prosodic representations more closely reflect syntactic ones. It allows the fundamental syntactic distinctions between clause (and other phases) and phrase to be reflected in the prosodic representation, and it allows cross-linguistic generalizations to be made about the prosodic domain of intonational processes, such as downstep and continuation rise.
|
|
| 23. |
- Cheng, Lisa L-S, et al.
(författare)
-
The problems of adverbs in Zulu
- 2014
-
Ingår i: Above and Beyond the Segments. Experimental linguistics and phonetics. Caspers, Johanneke, Yiya Chen, Willemijn Heeren, Jos Pacilly, Niels O. Schiller and Ellen van Zanten (eds.). - Amsterdam : John Benjamins. - 9789027212160 ; , s. 42-59
-
Bokkapitel (refereegranskat)abstract
- Adverbs in Durban Zulu appear to have contradictory properties. On the one hand, when they appear with intransitive verbs, they phrase prosodically with the verb, just like direct objects. On the other hand, adverbs which appear with transitive verbs are like typical adjuncts, which are adjoined above νP, and they are prosodically phrased separately from the rest of the sentence. We suggest that due to the nominal character of adverbs in Zulu, they can be selected by the verb. Selected materials (including selected adverbs) are merged at the time of main structure building, while non-selected adverbs and other adjuncts are merged late. The timing of the merger of adverbs reflects their prosodic phrasing properties.
|
|
| 24. |
- Cornwallis, Charlie K., et al.
(författare)
-
Cooperation facilitates the colonization of harsh environments
- 2017
-
Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 1:3
-
Tidskriftsartikel (refereegranskat)abstract
- Animals living in harsh environments, where temperatures are hot and rainfall is unpredictable, are more likely to breed in cooperative groups. As a result, harsh environmental conditions have been accepted as a key factor explaining the evolution of cooperation. However, this is based on evidence that has not investigated the order of evolutionary events, so the inferred causality could be incorrect. We resolved this problem using phylogenetic analyses of 4,707 bird species and found that causation was in the opposite direction to that previously assumed. Rather than harsh environments favouring cooperation, cooperativebreeding has facilitated the colonization of harsh environments. Cooperative breeding was, in fact, more likely to evolve from ancestors occupying relatively cool environmental niches with predictable rainfall, which had low levels of polyandry and hence high within-group relatedness. We also found that polyandry increased after cooperative breeders invaded harsh environments,suggesting that when helpers have limited options to breed independently, polyandry no longer destabilizes cooperation. This provides an explanation for the puzzling cases of polyandrous cooperative breeding birds. More generally, this illustrates how cooperation can play a key role in invading ecological niches, a pattern observed across all levels of biological organization from cells to animal societies.
|
|
| 25. |
- Dade, M. C., et al.
(författare)
-
Inequalities in the adaptive cycle : reorganizing after disasters in an unequal world
- 2022
-
Ingår i: Ecology and Society. - 1708-3087. ; 27:4
-
Tidskriftsartikel (refereegranskat)abstract
- Natural hazards can trigger disasters that lead to the collapse and reorganization of social-ecological systems. This reorganization can involve systems transitioning to more positive trajectories. The Panarchy framework, which conceptualizes social-ecological systems as dynamic interrelated adaptive cycles, is a common conceptual framework for understanding system reorganization. However, it is unclear how inequalities, social mechanisms known to influence disaster recovery outcomes, shape a system's adaptive cycle post-disaster. Understanding the roles of inequalities can help develop social-ecological models to identify processes that build resilience into disaster recovery. We applied the Panarchy framework to inform propositions describing how inequalities can influence the reorganization of social-ecological systems after disasters triggered by natural hazards. We qualitatively analyzed a selection of case studies that discussed inequalities pre-and post-disasters and related these to adaptive-cycle system characteristics (i.e., potential, connectedness, and resilience). We identified three propositions: 1) The ability of groups to reorganize after a disaster varies across the inequality spectrum; 2) The reorganizing abilities of groups across the inequality spectrum impact one another; and 3) The presence of inequalities affect connectedness within the system. Incorporating these propositions into social-ecological system modeling can improve our understanding of how inequalities impact system reorganization. This information can support disaster recovery plans that strengthen a system's ability to enter a more positive trajectory post-disaster.
|
|
| 26. |
- Downing, Andrea S.
(författare)
-
CLD4SDGs : Integrated assessment of progress and impacts on Sustainable Development Goals using Causal Loop Diagrams
- 2022
-
Ingår i: MethodsX. - : Elsevier BV. - 1258-780X .- 2215-0161. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- The United Nations' 2030 Agenda for sustainable development calls for meeting the global Sustainable Development Goals (SDGs) through local action and integrated approaches. We here describe a method developed to understand how local (un-)sustainable processes in coupled social-ecological systems contribute to or hinder meeting SDGs at the target-level in coupled social-ecological systems (SES). The steps include:The construction of a causal-loop diagram (CLD) of the social-ecological processes that shape system dynamicsCLD simplification for the purpose of the SDG analysis,Steps of the SDG analysis.The methods combine and build on published examples of CLD and SDG analyses and includes instructions for the transparent documentation of the analyses to support review and further development of SDG-target analyses in complex social-ecological systems. A template for the documentation and analysis is provided in the supplementary materials.
|
|
| 27. |
- Downing, Andrea S., et al.
(författare)
-
Effects of resources and mortality on the growth and reproduction of Nile perch in Lake Victoria
- 2013
-
Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 58:4, s. 828-840
-
Tidskriftsartikel (refereegranskat)abstract
- 1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30million people. Furthermore, changes in Nile perch population size-structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over-estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long-term effects of human impact.
|
|
| 28. |
- Downing, Andrea S., et al.
(författare)
-
Learning from generations of sustainability concepts
- 2020
-
Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 15:8
-
Forskningsöversikt (refereegranskat)abstract
- Background: For decades, scientists have attempted to provide a sustainable development framework that integrates goals of environmental protection and human development. The Planetary Boundaries concept (PBc)-a framework to guide sustainable development-juxtaposes a 'safe operating space for humanity' and 'planetary boundaries', to achieve a goal that decades of research have yet to meet. We here investigate if PBc is sufficiently different to previous sustainability concepts to have the intended impact, and map how future sustainability concept developments might make a difference. Design: We build a genealogy of the research that is cited in and informs PBc. We analyze this genealogy with the support of two seminal and a new consumer-resource models, that provide simple and analytically tractable analogies to human-environment relationships. These models bring together environmental limits, minimum requirements for populations and relationships between resource-limited and waste-limited environments. Results: PBc is based on coherent knowledge about sustainability that has been in place in scientific and policy contexts since the 1980s. PBc represents the ultimate framing of limits to the use of the environment, as limits not to single resources, but to Holocene-like Earth system dynamics. Though seldom emphasized, the crux of the limits to sustainable environmental dynamics lies in waste (mis-)management, which sets where boundary values might be. Minimum requirements for populations are under-defined: it is the distribution of resources, opportunities and waste that shape what is a safe space and for whom. Discussion: We suggest that PBc is not different or innovative enough to break 'Cassandra's dilemma' and ensure scientific research effectively guides humanity towards sustainable development. For this, key issues of equality must be addressed, un-sustainability must be framed as a problem of today, rather than projected into the future, and scientific foundations of frameworks such as PBc must be broadened and diversified.
|
|
| 29. |
- Downing, Andrea S., et al.
(författare)
-
Matching scope, purpose and uses of planetary boundaries science
- 2019
-
Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 14:7
-
Forskningsöversikt (refereegranskat)abstract
- Background: The Planetary Boundaries concept (PBc) has emerged as a key global sustainability concept in international sustainable development arenas. Initially presented as an agenda for global sustainability research, it now shows potential for sustainability governance. Weuse the fact that it is widely cited in scientific literature (>3500 citations) and an extensively studied concept to analyse how it has been used and developed since its first publication. Design: From the literature that cites the PBc, we select those articles that have the terms 'planetary boundaries' or 'safe operating space' in either title, abstract or keywords. Weassume that this literature substantively engages with and develops the PBc. Results: Wefind that 6% of the citing literature engages with the concept. Within this fraction of the literature we distinguish commentaries-that discuss the context and challenges to implementing the PBc, articles that develop the core biogeophysical concept and articles that apply the concept by translating to sub-global scales and by adding a human component to it. Applied literature adds to the concept by explicitly including society through perspectives of impacts, needs, aspirations and behaviours. Discussion: Literature applying the concept does not yet include the more complex, diverse, cultural and behavioural facet of humanity that is implied in commentary literature. Wesuggest there is need for a positive framing of sustainability goals-as a Safe Operating Space rather than boundaries. Key scientific challenges include distinguishing generalised from context-specific knowledge, clarifying which processes are generalizable and which are scalable, and explicitly applying complex systems' knowledge in the application and development of the PBc. We envisage that opportunities to address these challenges will arise when more human social dimensions are integrated, as we learn to feed the global sustainability vision with a plurality of bottom-up realisations of sustainability.
|
|
| 30. |
- Downing, Andrea S., et al.
(författare)
-
Unlocking the unsustainable rice-wheat system of Indian Punjab : Assessing alternatives to crop-residue burning from a systems perspective
- 2022
-
Ingår i: Ecological Economics. - : Elsevier BV. - 0921-8009 .- 1873-6106. ; 195
-
Tidskriftsartikel (refereegranskat)abstract
- Crop residue burning in Indian Punjab emits particulate matter with detrimental impacts on health, climate and that threaten agricultural production. Though legal and technological barriers to residue burning exist – and alternatives considered more profitable to farmers – residue burning continues. We review black carbon (BC) emissions from residue burning in Punjab, analyse social-ecological processes driving residue burning, and rice and wheat value-chains. Our aims are to a) understand system feedbacks driving agricultural practices in Punjab; b) identify systemic effects of alternatives to residue burning and c) identify companies and financial actors investing in agricultural production in Punjab. We find feedbacks locking the system into crop residue burning. The Government of India has greatest financial leverage and risk in the current system. Corporate stakeholders have little financial incentive to enact change, but sufficient stakes in the value chains to influence change. Agricultural policy changes are necessary to reduce harmful impacts of current practices, but insufficient to bringing about sustainability. Transformative changes will require crop diversification, circular business models and green financing. Intermediating financial institutions setting sustainability conditions on loans could leverage these changes. Sustainability requires the systems perspective we provide, to reconnect production with demand and with supporting environmental conditions.
|
|
| 31. |
- Downing, Andrea S., et al.
(författare)
-
Was Lates Late? : A Null Model for the Nile Perch Boom in Lake Victoria
- 2013
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:10, s. e76847-
-
Tidskriftsartikel (refereegranskat)abstract
- Nile perch (Lates niloticus) suddenly invaded Lake Victoria between 1979 and 1987, 25 years after its introduction in the Ugandan side of the lake. Nile perch then replaced the native fish diversity and irreversibly altered the ecosystem and its role to lakeshore societies: it is now a prised export product that supports millions of livelihoods. The delay in the Nile perch boom led to a hunt for triggers of the sudden boom and generated several hypotheses regarding its growth at low abundances - all hypotheses having important implications for the management of Nile perch stocks. We use logistic growth as a parsimonious null model to predict when the Nile perch invasion should have been expected, given its growth rate, initial stock size and introduction year. We find the first exponential growth phase can explain the timing of the perch boom at the scale of Lake Victoria, suggesting that complex mechanisms are not necessary to explain the Nile perch invasion or its timing. However, the boom started in Kenya before Uganda, indicating perhaps that Allee effects act at smaller scales than that of the whole Lake. The Nile perch invasion of other lakes indicates that habitat differences may also have an effect on invasion success. Our results suggest there is probably no single management strategy applicable to the whole lake that would lead to both efficient and sustainable exploitation of its resources.
|
|
| 32. |
- Downing, Andrea S., et al.
(författare)
-
When the whole is less than the sum of all parts – Tracking global-level impacts of national sustainability initiatives
- 2021
-
Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 69
-
Tidskriftsartikel (refereegranskat)abstract
- The United Nations' Sustainable Development Goals (SDGs) are described as integrated and indivisible, where sustainability challenges must be addressed across sectors and scales to achieve global-level sustainability. However, SDG monitoring mostly focuses on tracking progress at national-levels, for each goal individually. This approach ignores local and cross-border impacts of national policies and assumes that global-level progress is the sum of national, sector-specific gains. In this study, we investigate effects of reforestation programs in China on countries supplying forest and agricultural commodities to China. Using case studies of rubber and palm oil production in Southeast Asian countries, soy production in Brazil and logging in South Pacific Island states, we investigate cross-sector effects of production for and trade to China in these exporting countries. We use a threestep multi-method approach. 1) We identify distal trade flows and the narratives used to justify them, using a telecoupling framework; 2) we design causal loop diagrams to analyse social-ecological processes of change in our case studies driven by trade to China and 3) we link these processes of change to the SDG framework. We find that sustainability progress in China from reforestation is cancelled out by the deforestation and cross-sectoral impacts supporting this reforestation abroad. Narratives of economic development support commodity production abroad through unrealised aims of benefit distribution and assumptions of substitutability of socioecological forest systems. Across cases, we find the analysed trade supports unambiguous progress on few SDGs only, and we find many mixed effects - where processes that support the achievement of SDGs exist, but are overshadowed by counterproductive processes. Our study represents a useful approach for tracking global-level impacts of national sustainability initiatives and provides cross-scale and cross-sectoral lenses through which to identify drivers of unsustainability that can be addressed in the design of effective sustainability policies.
|
|
| 33. |
- Downing, Andrea S., et al.
(författare)
-
Zooming in on size distribution patterns underlying species coexistence in Baltic Sea phytoplankton
- 2014
-
Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 17:10, s. 1219-1227
-
Tidskriftsartikel (refereegranskat)abstract
- Scale is a key to determining which processes drive community structure. We analyse size distributions of phytoplankton to determine time scales at which we can observe either fixed environmental characteristics underlying communities structure or competition-driven size distributions. Using multiple statistical tests, we characterise size distributions of phytoplankton from 20-year time series in two sites of the Baltic Sea. At large temporal scales (5-20 years), size distributions are unimodal, indicating that fundamental barriers to existence are here subtler than in other systems. Frequency distributions of the average size of the species weighted by biovolume are multimodal over large time scales, although this is the product of often unimodal short-term (<1 year) patterns. Our study represents a much-needed structured, high-resolution analysis of phytoplankton size distributions, revealing that short-term analyses are necessary to determine if, and how, competition shapes them. Our results provide a stepping-stone on which to further investigate the intricacies of competition and coexistence.
|
|
| 34. |
- Downing, Laura J., 1954, et al.
(författare)
-
Against FocusP: Evidence from Durban Zulu
- 2012
-
Ingår i: Contrasts and positions in information structure / edited by Ivona Kučerová, Ad Neeleman.. - Cambridge : Cambridge University Press. - 9781107001985 ; , s. 247-266
-
Bokkapitel (refereegranskat)
|
|
| 35. |
- Downing, Laura J., 1954, et al.
(författare)
-
Clefts in Durban Zulu
- 2013
-
Ingår i: Cleft Structures / edited by Katharina Hartmann, Tonjes Veenstra. - Amsterdam : John Benjamins. - 9789027255914 ; , s. 141-164
-
Bokkapitel (refereegranskat)abstract
- In this paper, we argue that clefts in Zulu have a bipartite structure: a copular sentence with an adjoined DP/clause. This structure accounts for the prosody of clefts. Each constituent is parsed into a separate Intonation Phrase by the independently motivated phrasing algorithm of Zulu. It also accounts for the syntactic properties of Zulu clefts. We further argue that the nature of agreement in Zulu copular sentences support a pronominal predicate analysis.
|
|
| 36. |
- Downing, Laura J., 1954, et al.
(författare)
-
Indefinite subjects in Durban Zulu
- 2014
-
Ingår i: ZAS Papers in Linguistics. - 1435-9588. ; 57, s. 5-25
-
Konferensbidrag (refereegranskat)abstract
- It has long been observed that subjects cross-linguistically have topic properties: they are typically definite, referential and/or generic (Givón 1976). Bantu languages are said to illustrate this generalization: preverbal position for NPs is equated with both subject and topic status and postverbal position with focus (and non-subject). However, there is a growing body of work showing that preverbal subjects are not necessarily syntactically or semantically equivalent to topics. For example, Zerbian’s (2006) careful study of preverbal position in Northern Sotho shows that preverbal subjects meet few of the semantic tests for aboutness topics. The study of restrictions on preverbal subjects in Durban Zulu presented in this paper builds on Zerbian (2006) and Halpert (2012). In particular, we investigate the interpretational properties of preverbal indefinite subjects. These subjects show us that preverbal subjects carry a presupposition of existence. We explore an analysis connecting the “strong reading” of preverbal subjects with how high the verb moves in Zulu (following Tsai’s 2001 work on Mandarin).
|
|
| 37. |
- Downing, Laura J., 1954, et al.
(författare)
-
Where’s the topic in Zulu?
- 2009
-
Ingår i: The Linguistic Review. - : Walter de Gruyter GmbH. - 0167-6318 .- 1613-3676. ; 26:2/3, s. 207-238
-
Tidskriftsartikel (refereegranskat)
|
|
| 38. |
- Downing, Philip A., et al.
(författare)
-
Group formation and the evolutionary pathway to complex sociality in birds
- 2020
-
Ingår i: Nature Ecology and Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 4:3, s. 479-486
-
Tidskriftsartikel (refereegranskat)abstract
- Group-living species show a diversity of social organization, from simple mated pairs to complex communities of interdependent individuals performing specialized tasks. The advantages of living in cooperative groups are well understood, but why some species breed in small aggregations while others evolve large, complex groups with clearly divided roles is unclear. We address this problem by reconstructing the evolutionary pathways to cooperative breeding across 4,730 bird species. We show that differences in the way groups form at the origin of cooperative breeding predicts the level of group complexity that emerges. Groups that originate through the retention of offspring have a clear reproductive divide with distinct breeder and helper roles. This is associated with reproductive specialization, where breeders invest more in fecundity and less in care. In contrast, groups formed through the aggregation of unrelated adults are smaller and lack specialization. These results help explain why some species have not transitioned beyond simple groups while others have taken the pathway to increased group complexity.
|
|
| 39. |
- Downing, Philip A., et al.
(författare)
-
Hard-working helpers contribute to long breeder lifespans in cooperative birds
- 2021
-
Ingår i: Philosophical transactions of the Royal Society of London. Series B, Biological sciences. - : The Royal Society. - 1471-2970. ; 376:1823
-
Tidskriftsartikel (refereegranskat)abstract
- In many species that raise young in cooperative groups, breeders live an exceptionally long time despite high investment in offspring production. How is this possible given the expected trade-off between survival and reproduction? One possibility is that breeders extend their lifespans by outsourcing parental care to non-reproductive group members. Having help lightens breeder workloads and the energy that is saved can be allocated to survival instead. We tested this hypothesis using phylogenetic meta-analysis across 23 cooperatively breeding bird species. We found that breeders with helpers had higher rates of annual survival than those without helpers (8% on average). Increased breeder survival was correlated with reduced investment in feeding offspring, which in turn depended on the proportion of feeding provided by helpers. Helpers had similar effects on female and male breeder survival. Our results indicate that one of the secrets to a long life is reduced investment in parental care. This appears to be a unique feature of cooperative societies with hard-working helpers. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'
|
|
| 40. |
- Downing, Philip A., et al.
(författare)
-
How to make a sterile helper
- 2017
-
Ingår i: BioEssays. - : Wiley. - 0265-9247. ; 39:1
-
Tidskriftsartikel (refereegranskat)abstract
- The sterile worker castes found in the colonies of social insects are often cited as archetypal examples of altruism in nature. The challenge is to explain why losing the ability to mate has evolved as a superior strategy for transmitting genes into future generations. We propose that two conditions are necessary for the evolution of sterility: completely overlapping generations and monogamy. A review of the literature indicates that when these two conditions are met we consistently observe the evolution of sterile helpers. We explain the theory and evidence behind these ideas, and discuss the importance of ecology in predicting whether sterility will evolve using examples from social birds, mammals, and insects. In doing so, we offer an explanation for the extraordinary lifespans of some cooperative species which hint at ways in which we can unlock the secrets of long life.
|
|
| 41. |
- Downing, Philip A., et al.
(författare)
-
Sex differences in helping effort reveal the effect of future reproduction on cooperative behaviour in birds
- 2018
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 285:1885
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of helping behaviour in species that breed cooperatively in family groups is typically attributed to kin selection alone. However, in many species, helpers go on to inherit breeding positions in their natal groups, but the extent to which this contributes to selection for helping is unclear as the future reproductive success of helpers is often unknown. To quantify the role of future reproduction in the evolution of helping, we compared the helping effort of female and male retained offspring across cooperative birds. The kin selected benefits of helping are equivalent between female and male helpers-they are equally related to the younger siblings they help raise-but the future reproductive benefits of helping differ because of sex differences in the likelihood of breeding in the natal group. We found that the sex which is more likely to breed in its natal group invests more in helping, suggesting that in addition to kin selection, helping in family groups is shaped by future reproduction.
|
|
| 42. |
- Downing, Philip A., et al.
(författare)
-
The benefits of help in cooperative birds : Nonexistent or difficult to detect?
- 2020
-
Ingår i: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 195:6, s. 1085-1091
-
Tidskriftsartikel (refereegranskat)abstract
- In birds that breed cooperatively in family groups, adult offspring often delay dispersal to assist the breeding pair in raising their young. Kin selection is thought to play an important role in the evolution of this breeding system. However, evidence supporting the underlying assumption that helpers increase the reproductive success of breeders is inconsistent. In 10 out of 19 species where the effect of helpers on breeder reproductive success has been estimated while controlling for the effects of breeder and territory quality, no benefits of help were detected. Here, we use phylogenetic meta-analysis to show that the inconsistent evidence for helper benefits across species is explained by study design. After accounting for low sample sizes and the different study designs used to control for breeder and territory quality, we found that helpers consistently enhanced the reproductive success of breeders. Therefore, the assumption that helpers increase breeder reproductive success is supported by evidence across cooperatively breeding birds.
|
|
| 43. |
- Downing, Philip, et al.
(författare)
-
Sex, long life and the evolutionary transition to cooperative breeding in birds.
- 2015
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 282:1816
-
Tidskriftsartikel (refereegranskat)abstract
- Long life is a typical feature of individuals living in cooperative societies. One explanation is that group living lowers mortality, which selects for longer life. Alternatively, long life may make the evolution of cooperation more likely by ensuring a long breeding tenure, making helping behaviour and queuing for breeding positions worthwhile. The benefit of queuing will, however, depend on whether individuals gain indirect fitness benefits while helping, which is determined by female promiscuity. Where promiscuity is high and therefore the indirect fitness benefits of helping are low, cooperation can still be favoured by an even longer life span. We present the results of comparative analyses designed to test the likelihood of a causal relationship between longevity and cooperative breeding by reconstructing ancestral states of cooperative breeding across birds, and by examining the effect of female promiscuity on the relationship between these two traits. We found that long life makes the evolution of cooperation more likely and that promiscuous cooperative species are exceptionally long lived. These results make sense of promiscuity in cooperative breeders and clarify the importance of life-history traits in the evolution of cooperative breeding, illustrating that cooperation can evolve via the combination of indirect and direct fitness benefits.
|
|
| 44. |
- Edmonson, MN, et al.
(författare)
-
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
- 2019
-
Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 29:9, s. 1555-1565
-
Tidskriftsartikel (refereegranskat)abstract
- Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.
|
|
| 45. |
- Faber, Zachary J, et al.
(författare)
-
The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
-
Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
|
|
| 46. |
- Goldberg, Rebecca L., et al.
(författare)
-
The costs and benefits of paternal care in fish : a meta-analysis
- 2020
-
Ingår i: Royal Society of London. Proceedings B. Biological Sciences. - : The Royal Society. - 1471-2954. ; 287:1935
-
Tidskriftsartikel (refereegranskat)abstract
- Male-only parental care, while rare in most animals, is a widespread strategy within teleost fish. The costs and benefits to males of acting as sole carer are highly variable among fish species making it challenging to determine the selective pressures driving the evolution of male-only care to such a high prevalence. We conducted a phylogenetic meta-analysis to examine the costs and benefits of paternal care across fish species. We found no evidence that providing care negatively affects male condition. In contrast with other taxa, we also found limited evidence that male care has evolved as a strategy to improve offspring survival. Instead, we found that males already caring for a brood are preferred by females and that this preference is strongest in those species in which males work harder to care for larger broods. Thus, in fish, investment in offspring care does not constrain a male's mating success but rather augments it, suggesting that the relatively high prevalence of male-only care in fish may be in part explained by sexual selection through female preference for caring males.
|
|
| 47. |
- Griffiths, Jennifer R., et al.
(författare)
-
Phytoplankton community interactions and environmental sensitivity in coastal and offshore habitats
- 2016
-
Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 125:8, s. 1134-1143
-
Tidskriftsartikel (refereegranskat)abstract
- Assessing the relative importance of environmental conditions and community interactions is necessary for evaluating the sensitivity of biological communities to anthropogenic change. Phytoplankton communities have a central role in aquatic food webs and biogeochemical cycles, therefore, consequences of differing community sensitivities may have broad ecosystem effects. Using two long-term time series (28 and 20 years) from the Baltic Sea, we evaluated coastal and offshore major phytoplankton taxonomic group biovolume patterns over annual and monthly time-scales and assessed their response to environmental drivers and biotic interactions. Overall, coastal phytoplankton responded more strongly to environmental anomalies than offshore phytoplankton, although the specific environmental driver changed with time scale. A trend indicating a state shift in annual biovolume anomalies occurred at both sites and the shift's timing at the coastal site closely tracked other long-term Baltic Sea ecosystem shifts. Cyanobacteria and the autotrophic ciliate Mesodinium rubrum were more strongly related than other groups to this trend with opposing relationships that were consistent across sites. On a monthly scale, biotic interactions within communities were rare and did not overlap between the coastal and offshore sites. Annual scales may be better able to assess general patterns across habitat types in the Baltic Sea, but monthly community dynamics may differ at relatively small spatial scales and consequently respond differently to future change.
|
|
| 48. |
- Hjerne, Olle, et al.
(författare)
-
Climate Driven Changes in Timing, Composition and Magnitude of the Baltic Sea Phytoplankton Spring Bloom
- 2019
-
Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Spring phytoplankton blooms contribute a substantial part to annual production, support pelagic and benthic secondary production and influence biogeochemical cycles in many temperate aquatic systems. Understanding environmental effects on spring bloom dynamics is important for predicting future climate responses and for managing aquatic systems. We analyzed long-term phytoplankton data from one coastal and one offshore station in the Baltic Sea to uncover trends in timing, composition and size of the spring bloom and its correlations to environmental variables. There was a general trend of earlier phytoplankton blooms by 1-2 weeks over the last 20 years, associated with more sunshine and less windy conditions. High water temperatures were associated with earlier blooms of diatoms and dinoflagellates that dominate the spring bloom, and decreased diatom bloom magnitude. Overall bloom timing, however, was buffered by a temperature and ice related shift in composition from early blooming diatoms to later blooming dinoflagellates and the autotrophic ciliate Mesodinium rubrum. Such counteracting responses to climate change highlight the importance of both general and taxon-specific investigations. We hypothesize that the predicted earlier blooms of diatoms and dinoflagellates as a response to the expected temperature increase in the Baltic Sea might also be counteracted by more clouds and stronger winds. A shift from early blooming and fast sedimenting diatoms to later blooming groups of dinoflagellates and M. rubrum at higher temperatures during the spring period is expected to increase energy transfers to pelagic secondary production and decrease spring bloom inputs to the benthic system, resulting in lower benthic production and reduced oxygen consumption.
|
|
| 49. |
- Holmfeldt, Linda, et al.
(författare)
-
The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
-
Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
|
|
| 50. |
- Janssen, Annette B. G., et al.
(författare)
-
Exploring, exploiting and evolving diversity of aquatic ecosystem models : a community perspective
- 2015
-
Ingår i: Aquatic Ecology. - : Springer Science and Business Media LLC. - 1386-2588 .- 1573-5125. ; 49:4, s. 513-548
-
Tidskriftsartikel (refereegranskat)abstract
- Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
|
|
