| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 4. |
- Gladstone-Gallagher, Rebecca V., et al.
(författare)
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Social-ecological connections across land, water, and sea demand a reprioritization of environmental management
- 2022
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Ingår i: Elementa. - : University of California Press. - 2325-1026. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Despite many sectors of society striving for sustainability in environmental management, humans often fail to identify and act on the connections and processes responsible for social–ecological tipping points. Part of the problem is the fracturing of environmental management and social–ecological research into ecosystem domains (land, freshwater, and sea), each with different scales and resolution of data acquisition and distinct management approaches. We present a perspective on the social–ecological connections across ecosystem domains that emphasize the need for management reprioritization to effectively connect these domains. We identify critical nexus points related to the drivers of tipping points, scales of governance, and the spatial and temporal dimensions of social–ecological processes. We combine real-world examples and a simple dynamic model to illustrate the implications of slow management responses to environmental impacts that traverse ecosystem domains. We end with guidance on management and research opportunities that arise from this cross-domain lens to foster greater opportunity to achieve environmental and sustainability goals.
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| 5. |
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| 6. |
- Thrush, S. F., et al.
(författare)
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beta-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat, Distance and Productivity on Ecological Connectivity
- 2010
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 5:7
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Tidskriftsartikel (refereegranskat)abstract
- High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in beta-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and beta-diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on beta-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.
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| 7. |
- Cheung, Henry Lok Shan, et al.
(författare)
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Denitrification, anammox, and DNRA in oligotrophic continental shelf sediments
- 2024
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Ingår i: Limnology and Oceanography. - 1939-5590 .- 0024-3590.
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Tidskriftsartikel (refereegranskat)abstract
- Continental shelf sediments are considered hotspots for nitrogen (N) removal. While most investigations have quantified denitrification in shelves receiving large amounts of anthropogenic nutrient supply, we lack insight into the key drivers of N removal on oligotrophic shelves. Here, we measured rates of N removal through denitrification and anammox by the revised-isotope pairing technique (r-IPT) along the Northeastern New Zealand shelf. Denitrification dominated total N2 production at depths between 30 and 128 m with average rates (± SE) ranging from 65 ± 28 to 284 ± 72 μmol N m−2 d−1. N2 production by anammox ranged from 3 ± 1 to 28 ± 11 μmol N m−2 d−1 and accounted for 2–19% of total N2 production. DNRA was negligible in these oligotrophic settings. Parallel microbial community analysis showed that both Proteobacteria and Planctomycetota were key taxa driving denitrification. Denitrification displayed a negative correlation with oxygen penetration depth, and a positive correlation with macrofauna abundance. Our denitrification rates were comparable to oligotrophic shelves from the Arctic, but were lower than those from nutrient-rich Pacific and Atlantic shelves. Based on our results and existing IPT measurements, the global shelf denitrification rate was reassessed to be 53.5 ± 8.1 Tg N yr−1, equivalent to 20 ± 2% of marine N removal. We suggest that previous estimates of global shelf N loss might have been overestimated due to sampling bias toward areas with high N loads in the Northern Hemisphere.
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| 8. |
- Cummings, Vonda J., et al.
(författare)
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Linking Ross Sea Coastal Benthic Communities to Environmental Conditions : Documenting Baselines in a Spatially Variable and Changing World
- 2018
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the functionality of marine benthic ecosystems, and how they are influenced by their physical environment, is fundamental to realistically predicting effects of future environmental change. The Antarctic faces multiple environmental pressures associated with greenhouse gas emissions, emphasizing the need for baseline information on biodiversity and the bio-physical processes that influence biodiversity. We describe a survey of shallow water benthic communities at eight Ross Sea locations with a range of environmental characteristics. Our analyses link coastal benthic community composition to seafloor habitat and sedimentary parameters and broader scale features, at locations encompassing considerable spatial extent and variation in environmental characteristics (e.g., seafloor habitat, sea ice conditions, hydrodynamic regime, light). Our aims were to: (i) document existing benthic communities, habitats and environmental conditions against which to assess future change, (ii) investigate the relationships between environmental and habitat characteristics and benthic community structure and function, and (iii) determine whether these relationships were dependent on spatial extent. A very high percentage (>95%) of the between-location variability in macro- or epifaunal community composition was explainable using multi-scale environmental variables. The explanatory power varied depending on the scale of influence of the environmental variables measured (fine and medium-scale habitat, broad scale), and with community type. However, the inclusion of parameters at all scales produced the most powerful model for both communities. Ice duration, ice thickness and snow cover were important broad scale variables identified that directly relate to climate change. Even when using only habitat-scale variables, extending the spatial scale of the study from three locations covering 32 km to eight locations covering ~340 km increased the degree of explanatory power from 18–32 to 64–78%. The increase in explanatory power with spatial extent lends weight to the possibility of using an indirect “space for time” substitution approach for future predictions of the effects of change on these coastal marine ecosystems. Given the multiple and interacting drivers of change in Antarctic coastal ecosystems a multidisciplinary, long term, repeated observation approach will be vital to both improve and test predictions of how coastal communities will respond to environmental change.
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