cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19634972.v1
title: Additional file 3 of Developing long-term conservation priority planning for medicinal plants in China by combining conservation status with diversity hotspot analyses and climate change prediction

description: Additional file 3: Table S3.1. The threatened species used for the predication of potential suitable habitat areas and their Areas under the Operating Characteristic Curve (AUC) in MaxEnt. Table S3.2. The list of total, endemic (China), threatened, CITES listed and national protected species of medicinal plants. Table S3.3. The species richness of each grid cell and the integrated hotspots of the top 5% richness algorithm. Table S3.4. The species number of each grid cell under complementary algorithm and the integrated hotspots of the complementary algorithm. Table S3.5. The diversity hotspot grids obtained from the integrated hotspots of both “top 5% richness algorithm” and “complementary algorithm”. Table S3.6. Correlation analysis of the distribution pattern of top 5% richness algorithm(R) and complementary algorithm(C) of all medicinal plants (All), endemic medicinal plants (EN), threatened medicinal plants (TH), CITES listed medicinal plants (CI) and national protected medicinal plants (NP). Table S3.7. The seven bioclimatic variables marked in red out of nineteen ones were employed in prediction of suitable habitat areas.
DOI: 10.6084/m9.figshare.19634972
title: Additional file 3 of Developing long-term conservation priority planning for medicinal plants in China by combining conservation status with diversity hotspot analyses and climate change prediction

description: Additional file 3: Table S3.1. The threatened species used for the predication of potential suitable habitat areas and their Areas under the Operating Characteristic Curve (AUC) in MaxEnt. Table S3.2. The list of total, endemic (China), threatened, CITES listed and national protected species of medicinal plants. Table S3.3. The species richness of each grid cell and the integrated hotspots of the top 5% richness algorithm. Table S3.4. The species number of each grid cell under complementary algorithm and the integrated hotspots of the complementary algorithm. Table S3.5. The diversity hotspot grids obtained from the integrated hotspots of both “top 5% richness algorithm” and “complementary algorithm”. Table S3.6. Correlation analysis of the distribution pattern of top 5% richness algorithm(R) and complementary algorithm(C) of all medicinal plants (All), endemic medicinal plants (EN), threatened medicinal plants (TH), CITES listed medicinal plants (CI) and national protected medicinal plants (NP). Table S3.7. The seven bioclimatic variables marked in red out of nineteen ones were employed in prediction of suitable habitat areas.
DOI: 10.6084/m9.figshare.19634640
title: Supplementary Material for: Desidustat in Anemia due to Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-D)

description: <b><i>Background:</i></b> A phase 3 study to assess the efficacy and safety of the desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, against the epoetin alfa for the treatment of anemia in patients with chronic kidney disease (CKD) with dialysis dependency. <b><i>Methods:</i></b> DREAM-D was a phase 3, multicenter, open-label, randomized, active-controlled clinical study conducted across 38 centers in India. A total of 392 patients with clinical diagnosis of anemia due to CKD with dialysis need (Erythrocyte Stimulating Agent [ESA] naïve or prior ESA users) and with baseline hemoglobin levels of 8.0–11.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat oral tablets (thrice a week) or epoetin alfa subcutaneous injection for 24 weeks to maintain a hemoglobin level of 10–12 g/dL. The primary endpoint was to assess the change in the hemoglobin level between the desidustat and the epoetin alfa groups from the baseline to evaluation period week 16–24. The key secondary efficacy endpoint was the number of patients with hemoglobin response. <b><i>Results:</i></b> The least square mean (standard error) change in hemoglobin from the baseline to week 16–24 was 0.95 (0.09) g/dL in the desidustat group and 0.80 (0.09) g/dL in the epoetin alfa group (difference: 0.14 [0.14] g/dL; 95% confidence interval: −0.1304, 0.4202), which met the prespecified noninferiority margin. The number of hemoglobin responders was significantly higher in the desidustat group (106 [59.22%]) when compared to the epoetin alfa group (89 [48.37%]) (<i>p</i> = 0.0382). The safety profile of the desidustat oral tablet was comparable with the epoetin alfa injection. There were no new risks or no increased risks seen with the use of desidustat compared to epoetin alfa. <b><i>Conclusion:</i></b> In this study, desidustat was found to be noninferior to epoetin in the treatment of anemia in CKD patients on dialysis and it was well-tolerated. <b><i>Clinical Trial Registry Identifier:</i></b> CTRI/2019/12/022312 (India).
DOI: 10.6084/m9.figshare.19634640.v1
title: Supplementary Material for: Desidustat in Anemia due to Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-D)

description: <b><i>Background:</i></b> A phase 3 study to assess the efficacy and safety of the desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, against the epoetin alfa for the treatment of anemia in patients with chronic kidney disease (CKD) with dialysis dependency. <b><i>Methods:</i></b> DREAM-D was a phase 3, multicenter, open-label, randomized, active-controlled clinical study conducted across 38 centers in India. A total of 392 patients with clinical diagnosis of anemia due to CKD with dialysis need (Erythrocyte Stimulating Agent [ESA] naïve or prior ESA users) and with baseline hemoglobin levels of 8.0–11.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat oral tablets (thrice a week) or epoetin alfa subcutaneous injection for 24 weeks to maintain a hemoglobin level of 10–12 g/dL. The primary endpoint was to assess the change in the hemoglobin level between the desidustat and the epoetin alfa groups from the baseline to evaluation period week 16–24. The key secondary efficacy endpoint was the number of patients with hemoglobin response. <b><i>Results:</i></b> The least square mean (standard error) change in hemoglobin from the baseline to week 16–24 was 0.95 (0.09) g/dL in the desidustat group and 0.80 (0.09) g/dL in the epoetin alfa group (difference: 0.14 [0.14] g/dL; 95% confidence interval: −0.1304, 0.4202), which met the prespecified noninferiority margin. The number of hemoglobin responders was significantly higher in the desidustat group (106 [59.22%]) when compared to the epoetin alfa group (89 [48.37%]) (<i>p</i> = 0.0382). The safety profile of the desidustat oral tablet was comparable with the epoetin alfa injection. There were no new risks or no increased risks seen with the use of desidustat compared to epoetin alfa. <b><i>Conclusion:</i></b> In this study, desidustat was found to be noninferior to epoetin in the treatment of anemia in CKD patients on dialysis and it was well-tolerated. <b><i>Clinical Trial Registry Identifier:</i></b> CTRI/2019/12/022312 (India).
DOI: 10.6084/m9.figshare.19635053
title: Additional file 2 of Predicting RNA splicing from DNA sequence using Pangolin

description: Additional file 2 Table S1: Mapping statistics for RNA-seq datasets from Cardoso-Moreira et al., 2019 used for Pangolin training and testing. Table S2: Mapping statistics for RNA-seq datasets from Kanton et al., 2019 used in the chimp-human splice site divergence analysis.
DOI: 10.6084/m9.figshare.19635053.v1
title: Additional file 2 of Predicting RNA splicing from DNA sequence using Pangolin

description: Additional file 2 Table S1: Mapping statistics for RNA-seq datasets from Cardoso-Moreira et al., 2019 used for Pangolin training and testing. Table S2: Mapping statistics for RNA-seq datasets from Kanton et al., 2019 used in the chimp-human splice site divergence analysis.
DOI: 10.6084/m9.figshare.19634634
title: Supplementary Material for: Desidustat in Anemia due to Non-Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-ND)

description: <b><i>Background:</i></b> Desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, is being developed to treat anemia in patients with chronic kidney disease (CKD) without dialysis dependency. <b><i>Methods:</i></b> In total, 588 patients with a clinical diagnosis of anemia due to CKD without dialysis need and with baseline hemoglobin of 7.0–10.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat 100 mg oral tablets thrice a week for 24 weeks or biosimilar darbepoetin subcutaneous injection 0.75 μg/kg once in 2 weeks for 24 weeks. The primary outcome was the change from baseline in hemoglobin to evaluation period of Weeks 16–24. Key secondary outcomes included the number of patients with hemoglobin response, changes in the hepcidin levels, changes in the vascular endothelial growth factor (VEGF) levels, and changes in the lipid and lipoprotein profiles. <b><i>Results:</i></b> Hemoglobin change from baseline to Weeks 16–24 was 1.95 g/dL in the desidustat group and 1.83 g/dL in the darbepoetin group (difference: 0.11 g/dL; 95% CI: −0.12, 0.34), which met prespecified non-inferiority margin (−0.75 g/dL). The hemoglobin responders were significantly higher (<i>p</i> = 0.0181) in the desidustat group (196 [77.78%]) compared to the darbepoetin group (176 [68.48%]). The difference of change in hepcidin from baseline to Week 12 and Week 24 (<i>p</i> = 0.0032 at Week 12, <i>p</i> = 0.0016 at Week 24) and the difference of change in low-density lipoprotein from baseline to Week 24 (<i>p</i> value = 0.0269) between the two groups was statistically significant. The difference of change from baseline in VEGF to Weeks 12 and 24 between the two groups was not statistically significant. <b><i>Conclusion:</i></b> Desidustat is non-inferior to darbepoetin in the treatment of anemia due to non-dialysis dependent CKD and it is well-tolerated.
DOI: 10.6084/m9.figshare.19634634.v1
title: Supplementary Material for: Desidustat in Anemia due to Non-Dialysis-Dependent Chronic Kidney Disease: A Phase 3 Study (DREAM-ND)

description: <b><i>Background:</i></b> Desidustat, an oral hypoxia-inducible factor prolyl hydroxylase inhibitor, is being developed to treat anemia in patients with chronic kidney disease (CKD) without dialysis dependency. <b><i>Methods:</i></b> In total, 588 patients with a clinical diagnosis of anemia due to CKD without dialysis need and with baseline hemoglobin of 7.0–10.0 g/dL (inclusive) were randomized in a 1:1 ratio to receive either desidustat 100 mg oral tablets thrice a week for 24 weeks or biosimilar darbepoetin subcutaneous injection 0.75 μg/kg once in 2 weeks for 24 weeks. The primary outcome was the change from baseline in hemoglobin to evaluation period of Weeks 16–24. Key secondary outcomes included the number of patients with hemoglobin response, changes in the hepcidin levels, changes in the vascular endothelial growth factor (VEGF) levels, and changes in the lipid and lipoprotein profiles. <b><i>Results:</i></b> Hemoglobin change from baseline to Weeks 16–24 was 1.95 g/dL in the desidustat group and 1.83 g/dL in the darbepoetin group (difference: 0.11 g/dL; 95% CI: −0.12, 0.34), which met prespecified non-inferiority margin (−0.75 g/dL). The hemoglobin responders were significantly higher (<i>p</i> = 0.0181) in the desidustat group (196 [77.78%]) compared to the darbepoetin group (176 [68.48%]). The difference of change in hepcidin from baseline to Week 12 and Week 24 (<i>p</i> = 0.0032 at Week 12, <i>p</i> = 0.0016 at Week 24) and the difference of change in low-density lipoprotein from baseline to Week 24 (<i>p</i> value = 0.0269) between the two groups was statistically significant. The difference of change from baseline in VEGF to Weeks 12 and 24 between the two groups was not statistically significant. <b><i>Conclusion:</i></b> Desidustat is non-inferior to darbepoetin in the treatment of anemia due to non-dialysis dependent CKD and it is well-tolerated.
DOI: 10.6084/m9.figshare.19635073
title: Supplementary data tables from Convergent copy number increase of genes associated with freshwater colonization in fishes

description: Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB81) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
DOI: 10.6084/m9.figshare.19635073.v1
title: Supplementary data tables from Convergent copy number increase of genes associated with freshwater colonization in fishes

description: Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB81) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
DOI: 10.15151/esrf-es-686690552
title: Cryo-electron microscopy EPN BAG

description: At the EPN campus level structural biology work is carried out in all the 4 institutes (IBS, ESRF, ILL and EMBL). Today all structural biology groups are turning to cryo-EM. The EM demand is therefore extremely high and present in the 4 Institutes. In a nutshell, there are 42 PIs that could benefit from Krios time on the EPN campus (more than 90 different samples). Around 20 % of the sample are ready for high resolution data collection with already prepared grids that have been pre-screened on Glacios microscopes. Whereas some work could be carried out on Glacios microscopes, for difficult samples the use of a krios is indispensable (heterogeneous sample or limited concentration requiring a large number of images; small protein etc). Only these samples will be selected for Krios time at the BAG level.
DOI: 10.5281/zenodo.6477062
title: Dual purpose: Predatory hoverflies pollinate strawberry crops and protect them against the strawberry aphid, Chaetospihon fragaefolii

description: BACKGROUND: Predatory syrphids are an important functional group due to their potential for providing multiple ecosystem services. Adults feed on nectar and pollen and can be effective pollinators, while larvae are voracious predators that can reduce aphid pressure. Still, little research has addressed their potential dual function in agroecosystems. In this study, we assessed the potential of two predatory hoverflies, Eupeodes corollae and Sphaerophoria rueppellii, for delivering concurrent pollination and biological control of Chaetospihon fragaefolii in greenhouse strawberries. RESULTS: Both hoverfly species effectively pollinated strawberry flowers of two different varieties (‘Elsanta’ and ‘Sonsation’), resulting in an increase in high quality marketable fruits, a reduction of fruit deformities, and higher number of seeds per fruit compared to pollinator-excluded fruits. S. ruepellii had a significantly longer flower handling time than E. corollae, which translated to a more efficient pollination expressed as higher seed numbers per fruit after a single flower visit. By contrast, flowers that were open to multiple visits were more effectively pollinated by E. corollae, suggesting that E. corollae is potentially a better cross-pollinator than S. rueppellii. In addition, both hoverfly species suppressed aphid populations in strawberry (var. ‘Sonata’), with S. rueppellii and E. corollae reducing aphid populations by 49% and 62%, respectively. CONCLUSION: Predatory syrphids can concurrently contribute to pollination and biological control in strawberry in a greenhouse setting.
description: Data sets used for the results presented in the research article "Dual purpose: Predatory hoverflies pollinate strawberry crops and protect them against the strawberry aphid, Chaetospihon fragaefolii", published in Pest Management Science 2022. Data set "aphid_hoverfly.txt" contains data on aphid populations over time. Data set "durationvisitR.csv" contains data on strawberry flower visitation time (var. Elsanta) of the two hoverfly species S. rueppellii and E. corollae. Data set "FINALfruitquality.csv" contains data on pollination of var. Sonsation whereby hoverflies were not limited in the number of flower visits (unlimited visits vs no visits as a control). All assessed fruit quality parameters are included in this file. Data set "fruits_singlevisitR.csv" contains data on pollination of var. Elsanta whereby hoverflies either visited flowers a single time, unlimited times or no visits as a control. All assessed fruit quality parameters are included in this file. Data set "singlevisit_achenes.csv" contains data on pollination of var. Elsanta whereby hoverflies either visited flowers a single time, unlimited times or no visits as a control. This data set contains information on the number of achenes counted in fruits belonging to the different treatments.
DOI: 10.5281/zenodo.6477061
title: Dual purpose: Predatory hoverflies pollinate strawberry crops and protect them against the strawberry aphid, Chaetospihon fragaefolii

description: BACKGROUND: Predatory syrphids are an important functional group due to their potential for providing multiple ecosystem services. Adults feed on nectar and pollen and can be effective pollinators, while larvae are voracious predators that can reduce aphid pressure. Still, little research has addressed their potential dual function in agroecosystems. In this study, we assessed the potential of two predatory hoverflies, Eupeodes corollae and Sphaerophoria rueppellii, for delivering concurrent pollination and biological control of Chaetospihon fragaefolii in greenhouse strawberries. RESULTS: Both hoverfly species effectively pollinated strawberry flowers of two different varieties (‘Elsanta’ and ‘Sonsation’), resulting in an increase in high quality marketable fruits, a reduction of fruit deformities, and higher number of seeds per fruit compared to pollinator-excluded fruits. S. ruepellii had a significantly longer flower handling time than E. corollae, which translated to a more efficient pollination expressed as higher seed numbers per fruit after a single flower visit. By contrast, flowers that were open to multiple visits were more effectively pollinated by E. corollae, suggesting that E. corollae is potentially a better cross-pollinator than S. rueppellii. In addition, both hoverfly species suppressed aphid populations in strawberry (var. ‘Sonata’), with S. rueppellii and E. corollae reducing aphid populations by 49% and 62%, respectively. CONCLUSION: Predatory syrphids can concurrently contribute to pollination and biological control in strawberry in a greenhouse setting.
description: Data sets used for the results presented in the research article "Dual purpose: Predatory hoverflies pollinate strawberry crops and protect them against the strawberry aphid, Chaetospihon fragaefolii", published in Pest Management Science 2022. Data set "aphid_hoverfly.txt" contains data on aphid populations over time. Data set "durationvisitR.csv" contains data on strawberry flower visitation time (var. Elsanta) of the two hoverfly species S. rueppellii and E. corollae. Data set "FINALfruitquality.csv" contains data on pollination of var. Sonsation whereby hoverflies were not limited in the number of flower visits (unlimited visits vs no visits as a control). All assessed fruit quality parameters are included in this file. Data set "fruits_singlevisitR.csv" contains data on pollination of var. Elsanta whereby hoverflies either visited flowers a single time, unlimited times or no visits as a control. All assessed fruit quality parameters are included in this file. Data set "singlevisit_achenes.csv" contains data on pollination of var. Elsanta whereby hoverflies either visited flowers a single time, unlimited times or no visits as a control. This data set contains information on the number of achenes counted in fruits belonging to the different treatments.
DOI: 10.6084/m9.figshare.19533082
title: Data on occurrence of perfluoroalkyl substances in influents and effluents collected from different wastewater treatment plants in Latvia

description: The data set contains occurrence data of 17 perfluoroalkyl substances (PFAS) (including 10 perfluorinated carboxylic acids and 7 perfluorinated sulfonic acids) in influent and effluent samples collected from 43 wastewater treatment plants (WWTPs) located in different cities in Latvia.
DOI: 10.6084/m9.figshare.19533082.v3
title: Data on occurrence of perfluoroalkyl substances in influents and effluents collected from different wastewater treatment plants in Latvia

description: The data set contains occurrence data of 17 perfluoroalkyl substances (PFAS) (including 10 perfluorinated carboxylic acids and 7 perfluorinated sulfonic acids) in influent and effluent samples collected from 43 wastewater treatment plants (WWTPs) located in different cities in Latvia.
DOI: 10.6084/m9.figshare.19533082.v2
title: Data on occurrence of perfluoroalkyl substances in influents and effluents collected from different wastewater treatment plants in Latvia

description: The data set contains occurrence data of 17 perfluoroalkyl substances (PFAS) (including 10 perfluorinated carboxylic acids and 7 perfluorinated sulfonic acids) in influent and effluent samples collected from 43 wastewater treatment plants (WWTPs) located in different cities in Latvia.
DOI: 10.6084/m9.figshare.19612110.v1
title: surface data during autumn of Bohai and Yellow Sea in 2020.xlsx

description: surface data during autumn of Bohai and Yellow Sea in 2020