cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12948011.v1
title: Additional file 2 of Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab

description: Additional file 2: Table S2. 1200 differentially expressed circRNAs between 5 paired TNBC tissues.
DOI: 10.6084/m9.figshare.12947911
title: Additional file 3 of MiR-596 activated by EP300 controls the tumorigenesis in epithelial ovarian cancer by declining BRD4 and KPNA4

description: Additional file 2: Table S2. The sequences of shRNAs.
DOI: 10.6084/m9.figshare.9277781
title: Additional file 5: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S3. One-to-one orthologous relationships between Tartary buckwheat and other plants. (XLS 82 kb)
DOI: 10.6084/m9.figshare.12948046.v1
title: Additional file 2 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes

description: Additional file 2. DMRs between blue and pink groups.
DOI: 10.6084/m9.figshare.12947896
title: Additional file 7 of Identification of novel molecular markers of mastitis caused by Staphylococcus aureus using gene expression profiling in two consecutive generations of Chinese Holstein dairy cattle

description: Additional file 7: Table S3. Summary of sequence reads aligenment
DOI: 10.6084/m9.figshare.9277880
title: Additional file 11: of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: Text 1. Synteny gene pairs between rice and Brachypodium distachyon. (TXT 904â K) (TXT 903 kb)
DOI: 10.6084/m9.figshare.9277790
title: Additional file 6: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S4. The primer sequences used for RT-qPCR. (XLS 39 kb)
DOI: 10.6084/m9.figshare.9277790.v1
title: Additional file 6: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S4. The primer sequences used for RT-qPCR. (XLS 39 kb)
DOI: 10.6084/m9.figshare.12948055
title: Additional file 5 of Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes

description: Additional file 5. DMPs between pink and yellow groups.
DOI: 10.6084/m9.figshare.12947911.v1
title: Additional file 3 of MiR-596 activated by EP300 controls the tumorigenesis in epithelial ovarian cancer by declining BRD4 and KPNA4

description: Additional file 2: Table S2. The sequences of shRNAs.
DOI: 10.6084/m9.figshare.7705700.v1
title: Additional file 3: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Identification of known genes and new genes in the transcriptome data for eighteen samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7705709
title: Additional file 5: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Significantly enriched GO term analysis of DEGs between ‘SJ’ and ‘SX’ during floral induction. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7705712
title: Additional file 6: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Significantly enriched KEGG pathway analysis of DEGs between ‘SJ’ and ‘SX’ during floral induction. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.24100277
title: Temporal and lake-specific variations in oxygen and hydrogen stable isotopes in a boreal lake-chain during two hydrologically differing years

description: Hydrogen and oxygen stable isotope mass ratios (δ<sup>2</sup>H and δ<sup>18</sup>O) are conservative tracers that reflect hydrological conditions of watersheds and lakes, information that can be used for water budgets, such as estimating nutrient loading from the catchments and direct and indirect effects of climate change on waterbodies. We measured δ<sup>2</sup>H and δ<sup>18</sup>O values and estimated water mass balances over 2 hydrologically differing years in a chain of 10 boreal lakes. During a warm and dry summer, evaporative loss enriched the isotope values at lake surfaces. Thus, in lakes that were thermally stratified during summer, the isotope values differed distinctively between epilimnion and hypolimnion. During the following rainy summer, the within-lake variation of isotope values was much lower with no clear trend, presumably a result of a more unstable water column and faster water throughflow in the lake chain. After autumnal mixing the lake δ<sup>18</sup>O values were strongly correlated with lake area and proportion of inland waters of the catchment area. The interannual within-lake difference was then ∼1‰, indicating differences in evaporation. Isotope mass balance (IMB) calculations and those based on lake temperature and hydrological measurements in the nearby region yielded similar results for the rainy ice-free period. Presumably, prerequisites of steady-state conditions for IMB were better met in the rainy year than during the previous drier year. For some lakes the results suggested remarkable volumes of groundwater inflow, whose role in boreal lake water budgets deserves more attention in future studies.
DOI: 10.6084/m9.figshare.24100277.v2
title: Temporal and lake-specific variations in oxygen and hydrogen stable isotopes in a boreal lake-chain during two hydrologically differing years

description: Hydrogen and oxygen stable isotope mass ratios (δ<sup>2</sup>H and δ<sup>18</sup>O) are conservative tracers that reflect hydrological conditions of watersheds and lakes, information that can be used for water budgets, such as estimating nutrient loading from the catchments and direct and indirect effects of climate change on waterbodies. We measured δ<sup>2</sup>H and δ<sup>18</sup>O values and estimated water mass balances over 2 hydrologically differing years in a chain of 10 boreal lakes. During a warm and dry summer, evaporative loss enriched the isotope values at lake surfaces. Thus, in lakes that were thermally stratified during summer, the isotope values differed distinctively between epilimnion and hypolimnion. During the following rainy summer, the within-lake variation of isotope values was much lower with no clear trend, presumably a result of a more unstable water column and faster water throughflow in the lake chain. After autumnal mixing the lake δ<sup>18</sup>O values were strongly correlated with lake area and proportion of inland waters of the catchment area. The interannual within-lake difference was then ∼1‰, indicating differences in evaporation. Isotope mass balance (IMB) calculations and those based on lake temperature and hydrological measurements in the nearby region yielded similar results for the rainy ice-free period. Presumably, prerequisites of steady-state conditions for IMB were better met in the rainy year than during the previous drier year. For some lakes the results suggested remarkable volumes of groundwater inflow, whose role in boreal lake water budgets deserves more attention in future studies.
DOI: 10.6084/m9.figshare.24118007.v3
title: A national-scale trophic state analysis to prioritize lakes for restoration in Aotearoa New Zealand

description: Pressure on lakes in Aotearoa New Zealand is increasing because of elevated catchment nutrient loads, establishment of non-native species, and climate change. Current government legislation requires that pressures are managed to avoid eutrophication and degradation of lake health. This approach requires information on the state of lakes at regional and national scales, which is challenging because &lt;5% are currently monitored. In this study, we (1) modelled lake trophic status at a national scale using a highly representative dataset and lake characteristics, land use, and environmental parameters as predictor variables; and (2) identified lakes that should be prioritized for protection to prevent further degradation. Six statistical models were evaluated, with extreme boosting producing the highest predictive power and lowest error. This model indicated that for the 3738 lakes in the dataset, 44% were eutrophic or higher trophic state, 22% mesotrophic, and 34% oligotrophic or lower trophic state. These data provide a benchmark to guide management and support the call for more resourcing to restore lakes in Aotearoa New Zealand. To identify lakes to prioritise for protection, we focused on the ∼800 mesotrophic lakes. We used (1) the portion of lake catchment not within conservation estate, and (2) road access as proxies for the likelihood of land-use intensification and the introduction of non-native species, respectively. We identified &gt;170 lakes with limited catchment protection and easy human access. Immediate attention should be given to protecting these waterbodies to prevent the need for costly and resource-intensive remediation in the future.
DOI: 10.6084/m9.figshare.24319220
title: Macrophyte growth forms shift along the trophic gradient of lakes

description: A shift in phototrophic organisms occurs along lake trophic gradients characterized by a change from macrophyte- to phytoplankton-dominated states. Before lakes reach a turbid and phytoplankton-dominated state, shifts from meadow-forming Characeae to canopy-forming macrophyte species can occur where Characea are present, especially in oligotrophic to mesotrophic lakes with sand or gravel substrate. However, eutrophication intensity causing this shift has not previously been examined. We analysed data from 132 lakes located in Mecklenburg-Vorpommern (Germany) with a generalized linear model (GLM) and random forest (RF) models complemented with grid approximation to determine if (1) species richness of macrophytes declines along eutrophication gradients, (2) the chlorophyll <i>a</i> (Chl-<i>a</i>) concentrations above which the abundance of Characeae declines, and (3) the Chl-<i>a</i> concentrations above which the abundance of canopy-forming species declines. The number of macrophyte taxa declined gradually following a log-linear trend and with increasing Chl-<i>a</i> concentrations. Based on the RF models, the abundance of Characeae decreased abruptly at 5–13 µg L<sup>−1</sup> Chl-<i>a</i>, whereas canopy-forming species showed a monotonous and slight unimodal decreasing response at 35–103 µg L<sup>−1</sup> Chl-<i>a</i>. The results support the theory of shifts in growth forms along eutrophication gradients in lakes and provide, for the first time, estimates of Chl-<i>a</i> concentrations required for these shifts. Changes in growth forms are obvious indicators for eutrophication and can serve as an additional incentive to improve lake trophic status.
DOI: 10.6084/m9.figshare.24319220.v1
title: Macrophyte growth forms shift along the trophic gradient of lakes

description: A shift in phototrophic organisms occurs along lake trophic gradients characterized by a change from macrophyte- to phytoplankton-dominated states. Before lakes reach a turbid and phytoplankton-dominated state, shifts from meadow-forming Characeae to canopy-forming macrophyte species can occur where Characea are present, especially in oligotrophic to mesotrophic lakes with sand or gravel substrate. However, eutrophication intensity causing this shift has not previously been examined. We analysed data from 132 lakes located in Mecklenburg-Vorpommern (Germany) with a generalized linear model (GLM) and random forest (RF) models complemented with grid approximation to determine if (1) species richness of macrophytes declines along eutrophication gradients, (2) the chlorophyll <i>a</i> (Chl-<i>a</i>) concentrations above which the abundance of Characeae declines, and (3) the Chl-<i>a</i> concentrations above which the abundance of canopy-forming species declines. The number of macrophyte taxa declined gradually following a log-linear trend and with increasing Chl-<i>a</i> concentrations. Based on the RF models, the abundance of Characeae decreased abruptly at 5–13 µg L<sup>−1</sup> Chl-<i>a</i>, whereas canopy-forming species showed a monotonous and slight unimodal decreasing response at 35–103 µg L<sup>−1</sup> Chl-<i>a</i>. The results support the theory of shifts in growth forms along eutrophication gradients in lakes and provide, for the first time, estimates of Chl-<i>a</i> concentrations required for these shifts. Changes in growth forms are obvious indicators for eutrophication and can serve as an additional incentive to improve lake trophic status.
DOI: 10.6084/m9.figshare.24230425.v2
title: Towards modeling data-poor lakes at the regional scale using parameters from data-rich lakes and relationships to lake characteristics

description: Lakes pivotal for recreation and economically relevant activities are often remote and not well studied, which hinders the application of predictive lake models for their management. Here, we provide an approach to simulate—by means of the process-oriented model MyLake—water temperature, ice cover duration, dissolved oxygen, and light attenuation in 198 data-poor lakes based on parameters obtained for a subgroup of 12 data-rich lakes and morphometric data. Specifically, the model is first calibrated using a genetic algorithm on well-studied lakes. Simple relationships between the fitted parameters and lake-catchment morphometric properties are then derived, and the results of simulations using fitted and derived parameters are compared. The loss in goodness-of-fit, expressed as root mean square error (RMSE) incurred by using estimated rather than calibrated parameters, is 0.17 °C for water temperature and 0.82 mg L<sup>−1</sup> for dissolved oxygen. These general relationships are then used to provide the model parameters for 198 data-poor lakes distributed throughout Sweden and to model these lakes. Overall, this proof of concept allows simulating lakes selected based on their relevance for lake management rather than based on the availability of extensive field datasets.
DOI: 10.6084/m9.figshare.24230431
title: Deepwater dissolved oxygen shows little ecological memory between lake phenological seasons

description: Depletion of deepwater dissolved oxygen (DO) in lakes has become increasingly prevalent and severe because of many external stressors, potentially threatening human-derived ecosystem services ranging from drinking water quality to fisheries. Using year-round, high-frequency DO data from 12 dimictic lakes, we compared 3 measures of deepwater DO depletion during winter and summer: DO depletion rate, DO minimum, and hypoxia duration. Hypoxia (DO &lt; 3 mg L<sup>−1</sup>) occurred in over half of the lakes and persisted an average of 83% longer in summer than in winter. While we found no difference in DO depletion rates between winter versus summer, these rates were significantly related to lake morphology in winter but trophic state in summer. In assessing cross-seasonal linkages, we found limited evidence for significant legacy effects in deepwater DO availability. Only fall mixing efficacy significantly responded to the previous summer’s minimum DO saturation, but it always reached moderate to high DO replenishment levels (&gt;65%) regardless of the previous summer’s DO depletion severity. This lack of ecological memory in deepwater DO depletion across seasons suggests that deepwater DO largely resets during spring and fall mixing periods in most years in these dimictic lakes. Understanding the patterns and drivers in deepwater DO depletion in both winter and summer is a key step forward for predicting future chemical and biological consequences of seasonal DO depletion and managing lake ecosystem health, as well as the effects that climate change may have on these patterns.
DOI: 10.6084/m9.figshare.24230431.v2
title: Deepwater dissolved oxygen shows little ecological memory between lake phenological seasons

description: Depletion of deepwater dissolved oxygen (DO) in lakes has become increasingly prevalent and severe because of many external stressors, potentially threatening human-derived ecosystem services ranging from drinking water quality to fisheries. Using year-round, high-frequency DO data from 12 dimictic lakes, we compared 3 measures of deepwater DO depletion during winter and summer: DO depletion rate, DO minimum, and hypoxia duration. Hypoxia (DO &lt; 3 mg L<sup>−1</sup>) occurred in over half of the lakes and persisted an average of 83% longer in summer than in winter. While we found no difference in DO depletion rates between winter versus summer, these rates were significantly related to lake morphology in winter but trophic state in summer. In assessing cross-seasonal linkages, we found limited evidence for significant legacy effects in deepwater DO availability. Only fall mixing efficacy significantly responded to the previous summer’s minimum DO saturation, but it always reached moderate to high DO replenishment levels (&gt;65%) regardless of the previous summer’s DO depletion severity. This lack of ecological memory in deepwater DO depletion across seasons suggests that deepwater DO largely resets during spring and fall mixing periods in most years in these dimictic lakes. Understanding the patterns and drivers in deepwater DO depletion in both winter and summer is a key step forward for predicting future chemical and biological consequences of seasonal DO depletion and managing lake ecosystem health, as well as the effects that climate change may have on these patterns.
DOI: 10.6084/m9.figshare.24190467.v2
title: High incidence of exotic ostracods in the rice fields of a protected Mediterranean wetland

description: Mediterranean rice fields are human-impacted temporary waterbodies filled during summer, a hot period with scarce rains, that are susceptible to biological invasions. These anthropogenic ecosystems have been previously identified as potential gateways for exotic ostracods to colonize nearby wetlands. In this work, we compared the rice field ostracod composition with a shallow lake in a protected Mediterranean wetland (Albufera N2000 site, Eastern Iberian Peninsula). We found 37 ostracod species, 13 of which were considered exotic. Rice fields harbored the highest number of both native and exotic ostracod taxa (16 and 12 species, respectively). Our hypothesis that exotic species were more abundant during summer while native species dominated the community in winter was confirmed by the analysis of temporal changes along the rice field cycle. Comparing the ostracod composition of rice fields with that of the littoral and central parts of the hypertrophic Lake Albufera showed a clear differentiation according to a spatially constrained cluster analysis, with the richest ostracod community corresponding to the rice fields and the lowest species richness to the center of the lake, where vegetation was scarce. Finally, we suggest some criteria for considering an ostracod species as native or exotic when its origin is unknown and discuss the potential origin of the exotic species found, the pathways they might have used to arrive and establish in new areas, and the biological traits that may facilitate the spread of ostracods over new areas after their arrival.
DOI: 10.6084/m9.figshare.24230425
title: Towards modeling data-poor lakes at the regional scale using parameters from data-rich lakes and relationships to lake characteristics

description: Lakes pivotal for recreation and economically relevant activities are often remote and not well studied, which hinders the application of predictive lake models for their management. Here, we provide an approach to simulate—by means of the process-oriented model MyLake—water temperature, ice cover duration, dissolved oxygen, and light attenuation in 198 data-poor lakes based on parameters obtained for a subgroup of 12 data-rich lakes and morphometric data. Specifically, the model is first calibrated using a genetic algorithm on well-studied lakes. Simple relationships between the fitted parameters and lake-catchment morphometric properties are then derived, and the results of simulations using fitted and derived parameters are compared. The loss in goodness-of-fit, expressed as root mean square error (RMSE) incurred by using estimated rather than calibrated parameters, is 0.17 °C for water temperature and 0.82 mg L<sup>−1</sup> for dissolved oxygen. These general relationships are then used to provide the model parameters for 198 data-poor lakes distributed throughout Sweden and to model these lakes. Overall, this proof of concept allows simulating lakes selected based on their relevance for lake management rather than based on the availability of extensive field datasets.
DOI: 10.6084/m9.figshare.23826405
title: Lake surface water temperature and oxygen saturation resistance and resilience following extreme storms: chlorophyll <i>a</i> shapes resistance to storms

description: Extreme storms are becoming more frequent and intense with climate change. Assessing lake ecosystem responses to extreme storms (resistance) and their capacity to recover (resilience) is critical for predicting the future of lake ecosystems in a stormier world. Here we provide a systematic, standardized, and quantitative approach for identifying critical processes shaping lake ecosystem resistance following extreme storms. We identified 576 extreme wind storms for 8 lakes in Europe and North America. We calculated the resistance and resilience of each lake’s surface water temperature and oxygen saturation following each storm. Sharp decreases and increases in epilimnetic temperature and oxygen saturation caused by extreme storms resulted in unpredictable changes in lake resilience values across lakes, with a tendency not to return to pre-storm conditions. Resistance was primarily shaped by mean annual chlorophyll <i>a</i> concentration and its overall relationship with other physiochemical lake and storm characteristics. We modeled variation in resistance as a function of both lake and storm conditions, and the results suggested that eutrophic lakes were consistently less resistant to extreme storms compared to oligotrophic lakes. The lakes tended to be most resistant to extreme storms when antecedent surface waters were warm and oxygen saturated, but overall resistance was highest in lakes with low mean annual concentrations of chlorophyll <i>a</i> and total phosphorus. Our findings suggest physiochemical responses of lakes to meteorological forcing are shaped by ecological and/or physical feedback and processes that determine trophic state, such as the influence of differences in nutrient availability and algal growth.