| 1. |
- 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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| 2. |
- Soranno, Patricia A., et al.
(författare)
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LAGOS-NE : A multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. lakes
- 2017
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 6:12, s. 1-22
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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
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| 3. |
- Kraemer, Benjamin M., et al.
(författare)
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Climate change drives widespread shifts in lake thermal habitat
- 2021
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 11:6, s. 521-529
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Tidskriftsartikel (refereegranskat)abstract
- Lake surfaces are warming worldwide, raising concerns about lake organism responses to thermal habitat changes. Species may cope with temperature increases by shifting their seasonality or their depth to track suitable thermal habitats, but these responses may be constrained by ecological interactions, life histories or limiting resources. Here we use 32 million temperature measurements from 139 lakes to quantify thermal habitat change (percentage of non-overlap) and assess how this change is exacerbated by potential habitat constraints. Long-term temperature change resulted in an average 6.2% non-overlap between thermal habitats in baseline (1978-1995) and recent (1996-2013) time periods, with non-overlap increasing to 19.4% on average when habitats were restricted by season and depth. Tropical lakes exhibited substantially higher thermal non-overlap compared with lakes at other latitudes. Lakes with high thermal habitat change coincided with those having numerous endemic species, suggesting that conservation actions should consider thermal habitat change to preserve lake biodiversity. Using measurements from 139 global lakes, the authors demonstrate how long-term thermal habitat change in lakes is exacerbated by species' seasonal and depth-related constraints. They further reveal higher change in tropical lakes, and those with high biodiversity and endemism.
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| 4. |
- Ayala, Ana I., et al.
(författare)
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Analysis of summer heat budget of lakes under a changing climate across a geographic gradient
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Warming surface water temperature is the most direct consequence of climate change in lakes and therefore, predicting the heat exchange at the air-water interface is important to understand how atmospheric forcing will affect lake temperature and thermal structure. Here, we forced a one-dimensional hydrodynamic lake model with outputs from four different climate models under three future greenhouse gas emission scenarios from 1976 to 2099. To investigate the changes in summer (June to August or December to February in the northern or southern hemisphere, respectively) net surface heat flux and the individual flux components for 47 lakes with varying in size and geographic location were analysed. The results show that in the most extreme case (RCP 8.5) summer lake surface temperature is projected to increase by 4.72±0.70 °C by the end of the 21st century, due to increasing absorption of solar radiation (17.40±8.81 W m-2) and of long-wave radiation (33.01±5.44 W m-2). The increased lake surface temperature, also lead to higher heat losses to the atmosphere by outgoing long-wave radiation (27.54±4.07 W m-2) and by latent heat flux (25.10±7.37 W m-2), while a lower heat loss by sensible heat flux is projected (-3.20±1.94 W m-2). Altogether, the net heat balance and thus the accumulation of heat in the lakes over summer remains almost unchanged. However, a shift in the contributions of the individuals heat fluxes is projected, with the latent heat flux gaining relative importance.
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| 5. |
- Ayala, Ana I., et al.
(författare)
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Climate Change Impacts on Surface Heat Fluxes in a Deep Monomictic Lake
- 2023
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Ingår i: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 128:11
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Tidskriftsartikel (refereegranskat)abstract
- Turbulent and radiative energy exchanges between lakes and the atmosphere play an importantrole in determining the process of lake-mixing and stratification, including how lakes respond to climate andto climate change. Here we used a one-dimensional hydrodynamic lake model to assess seasonal impacts ofclimate change on individual surface heat flux components in Lough Feeagh, Ireland, a deep, monomictic lake.We drove the lake model with an ensemble of outputs from four climate models under three future greenhousegas scenarios from 1976 to 2099. In these experiments, the results showed significant increases in the radiativebudget that were largely counteracted by significant increases in the turbulent fluxes. The combined change inthe individual surface heat fluxes led to a change in the total surface heat flux that was small, but sufficient tolead to significant changes in the volume-weighted average lake temperature. The largest projected changes intotal surface heat fluxes were in spring and autumn. Both spring heating and autumnal cooling significantlydecreased under future climate conditions, while changes to total surface heat fluxes in winter and summerwere an order of magnitude lower. This led to counter-intuitive results that, in a warming world, there wouldbe less heat not more entering Lough Feeagh during the springtime, and little change in net heating over thesummer or winter compared to natural climate conditions, projected increases in the volume-weighted averagelake temperature were found to be largely due to reduced heat loss during autumn.
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| 6. |
- Ayala, Ana I.
(författare)
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Modelling impact climate-related change on the thermal responses of lakes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In response to climate-related changes, lakes worldwide have experienced warmer surface water temperatures, shorter ice cover periods and changes in lake stratification. As these aspects of lake dynamics exert substantial control over nutrient availability, oxygenation and biogeochemical cycling, predicting changes in lake water temperature and stratification dynamics can improve our understanding of the consequences of warming on lake ecosystems. This thesis investigates the long-term and short-term (extreme event) effects of climate change on lake thermal dynamics using 1D hydrodynamic lake models.Long-term lake water temperature simulations showed that water temperatures and thermal stratification metrics were projected to clearly shift toward lake thermal conditions that are consistent with a warmer climate at the end of the 21st century, i.e. warmer surface and bottom temperatures and a stronger and longer duration of summer thermal stratification as a result of an earlier onset of stratification and later fall overturn. The simulated lake thermal structure was controlled by energy exchange between the lake surface and the atmosphere (surface heat fluxes) and wind stress. The individual surface heat flux components were projected to change substantially under future climate scenarios. However, the combined changes showed compensating effects, leading to a small overall change in total surface heat flux, that was still sufficient to lead to important changes in whole-lake temperature. On a seasonal scale, spring heating and autumnal cooling were projected to decrease, while only small changes were projected in winter and summer. An extended analysis during summer using 47 lakes showed that while all lakes gained heat during summer under all scenarios, differences in the amount of heat gained during historical and future conditions were small. Additionally, hydrodynamic lake models performed well in reproducing the magnitude and direction of changes in lake temperature and stratification metrics during storms and heatwaves. However, the lake model performance decreased in accuracy compared to non-extreme condition, which should be taken into account. 1D hydrodynamic lake models have been shown to be powerful tools to predict long-term and short-term climate-related changes in lake thermal dynamics, making an in-depth analysis of the surface heat fluxes possible.
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| 7. |
- Ayala, Ana I., et al.
(författare)
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Simulations of future changes in thermal structure of Lake Erken : proof of concept for ISIMIP2b lake sector local simulation strategy
- 2020
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Ingår i: Hydrology and Earth System Sciences. - : Copernicus GmbH. - 1027-5606 .- 1607-7938. ; 24:6, s. 3311-3330
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Tidskriftsartikel (refereegranskat)abstract
- This paper, as a part of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP2b), assesses the impacts of different levels of global warming on the thermal structure of Lake Erken (Sweden). The General Ocean Turbulence Model (GOTM) one-dimensional hydrodynamic model was used to simulate water temperature when using ISIMIP2b bias-corrected climate model projections as input. These projections have a daily time step, while lake model simulations are often forced at hourly or shorter time steps. Therefore, it was necessary to first test the ability of GOTM to simulate Lake Erken water temperature using daily vs hourly meteorological forcing data. In order to do this, three data sets were used to force the model as follows: (1) hourly measured data, (2) daily average data derived from the first data set, and (3) synthetic hourly data created from the daily data set using generalised regression artificial neural network methods. This last data set is developed using a method that could also be applied to the daily time step ISIMIP scenarios to obtain hourly model input if needed. The lake model was shown to accurately simulate Lake Erken water temperature when forced with either daily or synthetic hourly data. Long-term simulations forced with daily or synthetic hourly meteorological data suggest that by the late 21st century the lake will undergo clear changes in thermal structure. For the representative concentration pathway (RCP) scenario, namely RCP2.6, surface water temperature was projected to increase by 1.79 and 1.36 ∘C when the lake model was forced at daily and hourly resolutions respectively, and for RCP6.0 these increases were projected to be 3.08 and 2.31 ∘C. Changes in lake stability were projected to increase, and the stratification duration was projected to be longer by 13 and 11 d under RCP2.6 scenario and 22 and 18 d under RCP6.0 scenario for daily and hourly resolutions. Model changes in thermal indices were very similar when using either the daily or synthetic hourly forcing, suggesting that the original ISIMIP climate model projections at a daily time step can be sufficient for the purpose of simulating lake water temperature.
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| 8. |
- Jennings, Eleanor, et al.
(författare)
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From Highs to Lows : Changes in Dissolved Organic Carbon in a Peatland Catchment and Lake Following Extreme Flow Events
- 2020
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Ingår i: Water. - : MDPI AG. - 2073-4441. ; 12:10
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Tidskriftsartikel (refereegranskat)abstract
- The concentration of dissolved organic carbon (DOC) in freshwater catchments has implications for carbon availability in downstream lakes and for water supplies. The links between catchment hydrology and stream and lake DOC concentrations are, however, still not fully understood. Much of the literature has been from catchments with organo-mineral soils, with fewer studies from upland peat sites. We used high-frequency fluorescence data, a proxy for DOC, to investigate 1. the relationship between stream discharge and concentration in a blanket peat catchment during extreme high flows and 2. the relationship between inflow and in-lake estimated DOC concentrations. We found that for approximately two thirds of extreme events, there was a decrease in stream DOC concentration (i.e., a dilution) on the rising limb rather than an increase (i.e., a flushing out of DOC from terrestrial stores). Flushing events dominated only in summer when concentrations in the stream were also increasing. In comparison to the stream, concentrations in the downstream lake were less variable, and peaks and troughs were damped and lagged. Replicating these patterns and processes in DOC models would be critical in order to provide appropriate simulations in response to shorter- and longer-term changes in climate, and thus inform future catchment and lake management.
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| 9. |
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| 10. |
- Kutser, Tiit, et al.
(författare)
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Variations in colored dissolved organic matter between boreal lakes studied by satellite remote sensing
- 2009
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Ingår i: Journal of Applied Remote Sensing. - : SPIE-Intl Soc Optical Eng. - 1931-3195. ; 3, s. 033538-
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Tidskriftsartikel (refereegranskat)abstract
- Therehave been major improvements in our understanding of the roleof lakes and impoundments in global carbon cycle. Estimating thetrue role of lakes as sentinels, regulators and integrators ofclimate change requires analyzing carbon content of vast number oflakes. This is not realistic without using remote sensing methods.There are no satellite sensors at the moment that providefull global coverage and at the same time have spatialand radiometric resolutions suitable for lake color dissolved organic matter(CDOM) mapping. Therefore, the global study has to be performedusing more sensitive sensors to create regional lake CDOM statisticsfor as many sites as possible and extrapolating the resultson global lake map that can be created from lesssensitive sensor data with full global coverage (Landsat). As afirst step towards the global lake carbon mapping we showthat the Advanced Land Imager (ALI) allows to study regionalvariations in lake CDOM content and consequently estimate closely correlatedDOC (dissolved organic carbon) and CO2 saturation values. The resultsshow also that there may be regional differences in lakeCDOM content even if the study sites are geographically relativelyclose to each other and occupying zones with similar landcover and annual runoff. In one occasion the difference canbe explained with human impact that has caused acidification oflakes but the other occasion needs further studies.
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