cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23826405.v2
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.
DOI: 10.6084/m9.figshare.24190467
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.23826405.v1
title: Lake surface water temperature and oxygen saturation resistance and resilience following extreme storms: Chlorophyll <i>a</i> shapes resistance toward 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 eight 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 when compared to oligotrophic lakes. The lakes tended to be most resistant towards extreme storms when antecedent surface waters were warm and oxygen saturated, but overall resistance was highest in lakes with low concentrations of mean annual chlorophyll <i>a</i> and total phosphorus. Our findings suggest physiochemical responses of lakes to meteorological forcing is shaped by ecological and/or physical feedbacks and processes that determine trophic state, such as the influence of differences in nutrient availability and algal growth.
DOI: 10.6084/m9.figshare.7705784
title: Additional file 10: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S9. AUC, effect and sign of all features when predicting splicing categories switching from iPS to endoderm (tenfold cross-validation). The effect is defined as the absolute effect size weighted by the standard deviation of the feature and the sign is the sign of the effect size. a-j. Prediction of presence/absence of category switching between the two tissue types, for each splicing category, with and without methylation features. (XLSX 314 kb)
DOI: 10.6084/m9.figshare.7705784.v1
title: Additional file 10: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S9. AUC, effect and sign of all features when predicting splicing categories switching from iPS to endoderm (tenfold cross-validation). The effect is defined as the absolute effect size weighted by the standard deviation of the feature and the sign is the sign of the effect size. a-j. Prediction of presence/absence of category switching between the two tissue types, for each splicing category, with and without methylation features. (XLSX 314 kb)
DOI: 10.6084/m9.figshare.7705793
title: Additional file 1: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S1. Sample meta-data and quality control characteristics per cell. a. iPS cells and endoderm, c. mouse ES cells. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.7705793.v1
title: Additional file 1: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S1. Sample meta-data and quality control characteristics per cell. a. iPS cells and endoderm, c. mouse ES cells. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.7705799
title: Additional file 2: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S2. Splicing rates per cell and tissue type. a. iPS cells, b. endoderm, c. mouse ES cells. (XLSX 6381 kb)
DOI: 10.6084/m9.figshare.7705799.v1
title: Additional file 2: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S2. Splicing rates per cell and tissue type. a. iPS cells, b. endoderm, c. mouse ES cells. (XLSX 6381 kb)
DOI: 10.6084/m9.figshare.7705811
title: Additional file 4: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S3. Associations between DNA methylation and splicing as observed in the iPS (a-g) and endoderm (h-n) single cells. Each table contains significant associations per sequence context per tissue. The cassette exon, P value (nominal and after multiple testing correction), effect size and effect direction are shown. a. C1 iPS. b. I1 ‘5 iPS. c. I1 ‘3 iPS. d. A iPS. e. I2 ‘5 iPS. f. I2 ‘3 iPS. g. C2 iPS. h. C1 endoderm. i. I1 ‘5 endoderm. j. I1 ‘3 endoderm. k. A endoderm. l. I2 ‘5 endoderm S. m. I2 ‘3 iPS. n. C2 endoderm. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.7705811.v1
title: Additional file 4: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S3. Associations between DNA methylation and splicing as observed in the iPS (a-g) and endoderm (h-n) single cells. Each table contains significant associations per sequence context per tissue. The cassette exon, P value (nominal and after multiple testing correction), effect size and effect direction are shown. a. C1 iPS. b. I1 ‘5 iPS. c. I1 ‘3 iPS. d. A iPS. e. I2 ‘5 iPS. f. I2 ‘3 iPS. g. C2 iPS. h. C1 endoderm. i. I1 ‘5 endoderm. j. I1 ‘3 endoderm. k. A endoderm. l. I2 ‘5 endoderm S. m. I2 ‘3 iPS. n. C2 endoderm. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.7705817
title: Additional file 5: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S4. Description of features that are used per sequence context to predict splicing, and assignment of these features to the models that include them. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7705817.v1
title: Additional file 5: of Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

description: Table S4. Description of features that are used per sequence context to predict splicing, and assignment of these features to the models that include them. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7705955.v1
title: Additional file 4: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The differential expression genes identified in Prunus mume buds by RNA-Seq. (XLS 391 kb)
DOI: 10.6084/m9.figshare.9277895
title: Additional file 14: of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: Text 4. Synteny gene pairs between rice and Brachypodium distachyon. (TXT 2.59â M) (TXT 2661 kb)
DOI: 10.6084/m9.figshare.9277772.v1
title: Additional file 4: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S2. Analysis and distribution of conserved motifs in Tartary buckwheat GRAS proteins. (XLS 36 kb)
DOI: 10.6084/m9.figshare.9277781.v1
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.12947872.v1
title: Additional file 10 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 10: Table S6. Differentially expressed genes detected in SM vs. HM.
DOI: 10.6084/m9.figshare.12948055.v1
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.12948058
title: Additional file 6 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 6. DMPs between pink and yellow groups.
DOI: 10.6084/m9.figshare.12948058.v1
title: Additional file 6 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 6. DMPs between pink and yellow groups.
DOI: 10.6084/m9.figshare.12948023
title: Additional file 6 of Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab

description: Additional file 6: Table S6. All possible HER2 isoforms from NCBI.
DOI: 10.6084/m9.figshare.12948067.v1
title: Additional file 9 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 9. Gene ontology enrichment analysis in the yellow group.
DOI: 10.6084/m9.figshare.12948023.v1
title: Additional file 6 of Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab

description: Additional file 6: Table S6. All possible HER2 isoforms from NCBI.
DOI: 10.6084/m9.figshare.12948040.v1
title: Additional file 10 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 10. DMPs in the yellow group.
DOI: 10.6084/m9.figshare.12947692
title: Additional file 2 of Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features

description: Additional file 2 Feature importance scores. In Additional File 2, the importance scores for each feature dimension are reported. The feature scores are listed by the position number in all six species.s
DOI: 10.6084/m9.figshare.16617895.v1
title: Special electromagnetic field-treated water and far-infrared radiation alleviates lipopolysaccharide-induced acute respiratory distress syndrome in rats by regulating haptoglobin

description: Special electromagnetic field-treated water (SEW) and far-infrared radiation (FIR) can reduce acute respiratory distress syndrome (ARDS) in rats inflicted by lipopolysaccharides (LPSs). However, little is known about its underlying molecular mechanism. Differentially expressed proteins (DEPs) of SEW and FIR interventions were obtained from a proteomics database. A total of 89 DEPs were identified. Enrichment analysis of DEPs was performed using the Database for Annotation, Visualization, and Integrated Discovery. These DEPs were associated with the responses to LPSs, acute inflammation, extracellular exosomes, glucocorticoids, and electrical stimuli. The protein-protein interaction network was set up using the STRING database. Modular analysis was performed using MCODE in the Cytoscape software. Proteins Haptoglobin, Apolipoprotein B, Transthyretin, and Fatty acid binding protein 1 were among the core networks. A tail vein injection of LPS was used to establish the rat model with ARDS. Parallel reaction monitoring confirmed Hp protein expression. Inflammatory pathway factors were detected using an enzyme-linked immunosorbent assay. This indicates that SEW and FIR can be considered as potential clinical treatment methods for ARDS treatment and that their functional mechanisms are related to the ability of alleviating lung inflammation through Hp protein adjustment.
DOI: 10.6084/m9.figshare.12947692.v1
title: Additional file 2 of Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features

description: Additional file 2 Feature importance scores. In Additional File 2, the importance scores for each feature dimension are reported. The feature scores are listed by the position number in all six species.s
DOI: 10.6084/m9.figshare.12947695.v1
title: Additional file 3 of Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features

description: Additional file 3 Case study results. In Additional File 3, the 4mC-contained DNA sequence and the prediction results of four predictors are reported.
DOI: 10.6084/m9.figshare.12947875.v1
title: Additional file 11 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 11: Table S7. Differentially expressed genes detected in SMD vs. HMD.
DOI: 10.6084/m9.figshare.12947902
title: Additional file 9 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 9: Table S5. Differentially expressed genes detected in S vs. H
DOI: 10.6084/m9.figshare.12948049.v1
title: Additional file 3 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 3. DMPs between blue and yellow groups.
DOI: 10.6084/m9.figshare.7705973
title: Additional file 7: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The differential expressed lncRNAs in this study. (XLS 63 kb)
DOI: 10.6084/m9.figshare.9277886
title: Additional file 12: of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: Text 2. Synteny gene pairs between rice and Brachypodium distachyon. (TXT 1.77â M) (TXT 1818 kb)
DOI: 10.6084/m9.figshare.12947908.v1
title: Additional file 1 of MiR-596 activated by EP300 controls the tumorigenesis in epithelial ovarian cancer by declining BRD4 and KPNA4

description: Additional file 1: Table S1. The sequences of primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.9277901.v1
title: Additional file 1 of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: : Table S1. The chromosome location and physicochemical characteristics of BdGRAS genes. Table S2. The Ka and Ks values and estimated divergence time for tandemly duplicated BdGRAS genes. Table S3. The Ka and Ks values and estimated divergence time for segmentally duplicated BdGRAS genes. Table S4. The chromosome location, Ka and Ks values, and estimated divergence time for orthologous GRAS genes between Brachypodium and rice. Table S5. The chromosome location, Ka and Ks values, and estimated divergence time for orthologous GRAS genes between Brachypodium and sorghum. Table S6. The chromosome location, Ka and Ks values, and estimated divergence time for orthologous GRAS genes between Brachypodium and maize. Table S7. The chromosome location, Ka and Ks values, and estimated divergence time for orthologous GRAS genes between Brachypodium and wheat. Table S8. The primers used in this study. Table S9. GO annotations of BdGRAS proteins. Table S10. GO descriptions for BdGRAS proteins. Table S11. Numbers of known cis-elements in the promoter regions of BdGRAS genes. Table S12. Functions of GRAS genes in other species. (XLSX 163â K) (XLSX 162 kb)
DOI: 10.6084/m9.figshare.7705979
title: Additional file 8: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: The precursor analysis of the new lncRNAs. (XLS 23 kb)
DOI: 10.6084/m9.figshare.9277754
title: Additional file 4: of Depleting PTOV1 sensitizes non-small cell lung cancer cells to chemotherapy through attenuating cancer stem cell traits

description: Figure S3. Depleting PTOV1 activates caspase-3. Representative pictures (A) and quantification (B) of cleaved caspase-3. At least three independent experiments were performed. *, P&lt;0.05; #, P&lt;0.01; $, P&lt;0.001. (CVX 347 kb)
DOI: 10.6084/m9.figshare.12947890
title: Additional file 5 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 5: Table S1. Quality report of 16 RNA samples for RNA sequencing.
DOI: 10.6084/m9.figshare.9277754.v1
title: Additional file 4: of Depleting PTOV1 sensitizes non-small cell lung cancer cells to chemotherapy through attenuating cancer stem cell traits

description: Figure S3. Depleting PTOV1 activates caspase-3. Representative pictures (A) and quantification (B) of cleaved caspase-3. At least three independent experiments were performed. *, P&lt;0.05; #, P&lt;0.01; $, P&lt;0.001. (CVX 347 kb)
DOI: 10.6084/m9.figshare.9277760
title: Additional file 3: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S1. List of the 47 FtGRAS genes identified in this study. (XLS 153 kb)
DOI: 10.6084/m9.figshare.9277772
title: Additional file 4: of Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S2. Analysis and distribution of conserved motifs in Tartary buckwheat GRAS proteins. (XLS 36 kb)
DOI: 10.6084/m9.figshare.9277886.v1
title: Additional file 12: of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: Text 2. Synteny gene pairs between rice and Brachypodium distachyon. (TXT 1.77â M) (TXT 1818 kb)
DOI: 10.6084/m9.figshare.9277898.v1
title: Additional file 15: of Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1

description: Text 5. Protein sequences of GRAS in rice, maize, sorghum, wheat and Brachypodium distachyon. (TXT 270â K) (TXT 270 kb)
DOI: 10.6084/m9.figshare.12947872
title: Additional file 10 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 10: Table S6. Differentially expressed genes detected in SM vs. HM.
DOI: 10.6084/m9.figshare.12947875
title: Additional file 11 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 11: Table S7. Differentially expressed genes detected in SMD vs. HMD.
DOI: 10.6084/m9.figshare.12948011
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.12948020
title: Additional file 5 of Circular HER2 RNA positive triple negative breast cancer is sensitive to Pertuzumab

description: Additional file 5: Table S5. 909 differentially expressed circRNAs derived from 697 host coding genes that were not differentially expressed between 5 paired TNBC samples.
DOI: 10.6084/m9.figshare.12947896.v1
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.12947908
title: Additional file 1 of MiR-596 activated by EP300 controls the tumorigenesis in epithelial ovarian cancer by declining BRD4 and KPNA4

description: Additional file 1: Table S1. The sequences of primers used in qRT-PCR.