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- Aebersold, Ruedi, et al.
(author)
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How many human proteoforms are there?
- 2018
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In: Nature Chemical Biology. - : NATURE PUBLISHING GROUP. - 1552-4450 .- 1552-4469. ; 14:3, s. 206-214
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Journal article (peer-reviewed)abstract
- Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA-and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.
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- Haider, L. Jamila, 1987-
(author)
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Development and Resilience : Re-thinking poverty and intervention in biocultural landscapes
- 2017
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Doctoral thesis (other academic/artistic)abstract
- The practices related to the growing, harvesting, preparation, and celebration of food over millennia have given rise to diverse biocultural landscapes the world over. These landscapes – rich in biological and cultural diversity – are often characterised by persistent poverty, and, as such, are often the target of development interventions. Yet a lack of understanding of the interdependencies between human well-being, nature, and culture in these landscapes means that such interventions are often unsuccessful - and can even have adverse effects, exacerbating the poverty they were designed to address. This thesis investigates different conceptualisations of persistent poverty in rural biocultural landscapes, the consequences of these conceptualisations, and the ways in which development interventions can benefit from, rather than erode, biocultural diversity.The thesis first reviews conceptualisations of persistent poverty and specifically, the notion of a poverty trap (Paper I), and examines the consequences of different conceptualisations of traps for efforts to alleviate poverty (Paper II). Paper I argues that the trap concept can be usefully broadened beyond a dominant development economics perspective to incorporate critical interdependencies between humans and nature. Paper II uses multi-dimensional dynamical systems models to show how nature and culture can be impacted by different development interventions, and, in turn, how the degradation of both can undermine the effectiveness of conventional poverty alleviation strategies in certain contexts.In the second section, the thesis focuses on the effects of, and responses to, trap-like situations and development interventions in a specific context of high biocultural diversity: the Pamir Mountains of Tajikistan. Paper III advances a typology of responses to traps based around the mismatch of desires, abilities and opportunities. Observing daily practice provides a way to study social-ecological relationships as a dynamic process, as practices can embody traditional and tacit knowledge in a holistic way. Paper IV examines the diverse effects of a development intervention on the coevolution of biocultural landscapes and the ways in which everyday practice – particularly around food – can be a source of both innovation and resilience.Papers I-IV together combine insights from diverse disciplines and methodologies, from systematic review to dynamic systems thinking and participant observation. Paper V provides a critical analysis of the opportunities and challenges involved in pursuing such an approach in sustainability science, underscoring the need to balance methodological groundedness with epistemological agility.Overall, the thesis contributes to understanding resilience and development, highlighting the value of viewing their interrelation as a dynamic, coevolving process. From this perspective, development should not be regarded as a normative endpoint to be achieved, but rather as a coevolving process between constantly changing ecological and social contexts. The thesis proposes that resilience can be interpreted as the active and passive filtering of practices via the constant discarding and retention of old and new, social and ecological, and endogenous and exogenous factors. This interpretation deepens understanding of resilience as the capacity to persist, adapt and transform, and ultimately shape new development pathways. The thesis also illustrates how daily practices, such as the growing, harvesting, and preparation of food, offer a powerful heuristic device for understanding this filtering process, and therefore the on-going impact of development interventions in rural landscapes across the world.
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- Lago, M., et al.
(author)
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Introducing the H2020 AQUACROSS project : Knowledge, Assessment, and Management for AQUAtic Biodiversity and Ecosystem Services aCROSS EU policies
- 2019
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 652, s. 320-329
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Journal article (peer-reviewed)abstract
- The AQUACROSS project was an unprecedented effort to unify policy concepts, knowledge, and management of freshwater, coastal, and marine ecosystems to support the cost-effective achievement of the targets set by the EU Biodiversity Strategy to 2020. AQUACROSS aimed to support EU efforts to enhance the resilience and stop the loss of biodiversity of aquatic ecosystems as well as to ensure the ongoing and future provision of aquatic ecosystem services. The project focused on advancing the knowledge base and application of Ecosystem-Based Management. Through elaboration of eight diverse case studies in freshwater and marine and estuarine aquatic ecosystem across Europe covering a range of environmental management problems including, eutrophication, sustainable fisheries as well as invasive alien species AQUACROSS demonstrated the application of a common framework to establish cost-effective measures and integrated Ecosystem-Based Management practices. AQUACROSS analysed the EU policy framework (i.e. goals, concepts, time frames) for aquatic ecosystems and built on knowledge stemming from different sources (i.e. WISE, BISE, Member State reporting within different policy processes, modelling) to develop innovative management tools, concepts, and business models (i.e. indicators, maps, ecosystem assessments, participatory approaches, mechanisms for promoting the delivery of ecosystem services) for aquatic ecosystems at various scales of space and time and relevant to different ecosystem types.
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- Meyfroid, P., et al.
(author)
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Middle-range theories of land system change
- 2018
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In: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 53, s. 52-67
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Journal article (peer-reviewed)abstract
- Changes in land systems generate many sustainability challenges. Identifying more sustainable land-use alternatives requires solid theoretical foundations on the causes of land-use/cover changes. Land system science is a maturing field that has produced a wealth of methodological innovations and empirical observations on land cover and land-use change, from patterns and processes to causes. We take stock of this knowledge by reviewing and synthesizing the theories that explain the causal mechanisms of land-use change, including systemic linkages between distant land-use changes, with a focus on agriculture and forestry processes. We first review theories explaining changes in land-use extent, such as agricultural expansion, deforestation, frontier development, and land abandonment, and changes in land-use intensity, such as agricultural intensification and disintensification. We then synthesize theories of higher-level land system change processes, focusing on: (i) land-use spillovers, including land sparing and rebound effects with intensification, leakage, indirect land-use change, and land-use displacement, and (ii) land-use transitions, defined as structural non-linear changes in land systems, including forest transitions. Theories focusing on the causes of land system changes span theoretically and epistemologically disparate knowledge domains and build from deductive, abductive, and inductive approaches. A grand, integrated theory of land system change remains elusive. Yet, we show that middle-range theories - defined here as contextual generalizations that describe chains of causal mechanisms explaining a well-bounded range of phenomena, as well as the conditions that trigger, enable, or prevent these causal chains -, provide a path towards generalized knowledge of land systems. This knowledge can support progress towards sustainable social-ecological systems.
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- Schill, Caroline, et al.
(author)
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A more dynamic understanding of human behaviour for the Anthropocene
- 2019
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In: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2:12, s. 1075-1082
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Research review (peer-reviewed)abstract
- Human behaviour is of profound significance in shaping pathways towards sustainability. Yet, the approach to understanding human behaviour in many fields remains reliant on overly simplistic models. For a better understanding of the interface between human behaviour and sustainability, we take work in behavioural economics and cognitive psychology as a starting point, but argue for an expansion of this work by adopting a more dynamic and systemic understanding of human behaviour, that is, as part of complex adaptive systems. A complex adaptive systems approach allows us to capture behaviour as ''enculturated' and 'enearthed', co-evolving with socio-cultural and biophysical contexts. Connecting human behaviour and context through a complex adaptive systems lens is critical to inform environmental governance and management for sustainability, and ultimately to better understand the dynamics of the Anthropocene itself.
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- Silberzahn, Raphael, et al.
(author)
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Many analysts, one dataset : Making transparent how variations in analytical choices affect results
- 2018
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In: Advances in Methods and Practices in Psychological Science. - : Sage Publications. - 2515-2459 .- 2515-2467. ; 1:3, s. 337-356
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Journal article (peer-reviewed)abstract
- Twenty-nine teams involving 61 analysts used the same dataset to address the same research question: whether soccer referees are more likely to give red cards to dark skin toned players than light skin toned players. Analytic approaches varied widely across teams, and estimated effect sizes ranged from 0.89 to 2.93 in odds ratio units, with a median of 1.31. Twenty teams (69%) found a statistically significant positive effect and nine teams (31%) observed a non-significant relationship. Overall 29 differentanalyses used 21 unique combinations of covariates. We found that neither analysts' prior beliefs about the effect, nor their level of expertise, nor peer-reviewed quality of analysis readily explained variation in analysis outcomes. This suggests that significant variation in the results of analyses of complex data may be difficult to avoid, even by experts with honest intentions. Crowdsourcing data analysis, a strategy by which numerous research teams are recruited to simultaneously investigate the same research question, makes transparent how defensible, yet subjective analytic choices influence research results.
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