cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22385535.v1
title: Jiangzuo_character_description.xlsx from Origin of adaptations to open environments and social behaviour in sabertoothed cats from the northeastern border of the Tibetan Plateau

description: The iconic sabertooth <i>Homotherium</i> is thought to hunt cooperatively, but the origin of this behaviour and correlated morphological adaptations are largely unexplored. Here we report the most primitive species of <i>Amphimachairodus</i> (<i>Amphimachairodus hezhengensis</i> sp. nov.), a member of Machairodontini basal to <i>Homotherium</i>, from the Linxia Basin, northeastern border of the Tibetan Plateau (9.8–8.7 Ma). The long snout, laterally oriented and posteriorly located orbit of <i>Amphimachairodus</i> suggest a better ability to observe the surrounding environment, rather than targeting single prey, pointing to an adaptation to the open environment/social behaviour. A pathological forepaw of <i>Amphimachairodus</i> provides direct evidence of partner care. Our analyses of trait evolutionary rates support that traits correlated with killing behaviour and open environment adaptation evolved prior to other traits, suggesting that changes in hunting behaviour may be the major evolutionary driver in the early evolution of the lineage. <i>A. hezhengensis</i> represents one of the most important transitions in the evolution of Machairodontini, leading to adaptation in open environments and contributing to their further dispersal and radiation worldwide. This rapid morphological change is likely to be correlated with increasingly arid environments caused by the rise of the Tibetan Plateau, and competition from abundant large carnivores in this area.
DOI: 10.6084/m9.figshare.12947822
title: Additional file 3 of Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study

description: Additional file 3 Supplemental Table 2. List 3480 DEGs between HLC_SM and HLC_GF (FC &gt; 2.0 and p &lt; 0.05).
DOI: 10.6084/m9.figshare.22385535
title: Jiangzuo_character_description.xlsx from Origin of adaptations to open environments and social behaviour in sabertoothed cats from the northeastern border of the Tibetan Plateau

description: The iconic sabertooth <i>Homotherium</i> is thought to hunt cooperatively, but the origin of this behaviour and correlated morphological adaptations are largely unexplored. Here we report the most primitive species of <i>Amphimachairodus</i> (<i>Amphimachairodus hezhengensis</i> sp. nov.), a member of Machairodontini basal to <i>Homotherium</i>, from the Linxia Basin, northeastern border of the Tibetan Plateau (9.8–8.7 Ma). The long snout, laterally oriented and posteriorly located orbit of <i>Amphimachairodus</i> suggest a better ability to observe the surrounding environment, rather than targeting single prey, pointing to an adaptation to the open environment/social behaviour. A pathological forepaw of <i>Amphimachairodus</i> provides direct evidence of partner care. Our analyses of trait evolutionary rates support that traits correlated with killing behaviour and open environment adaptation evolved prior to other traits, suggesting that changes in hunting behaviour may be the major evolutionary driver in the early evolution of the lineage. <i>A. hezhengensis</i> represents one of the most important transitions in the evolution of Machairodontini, leading to adaptation in open environments and contributing to their further dispersal and radiation worldwide. This rapid morphological change is likely to be correlated with increasingly arid environments caused by the rise of the Tibetan Plateau, and competition from abundant large carnivores in this area.
DOI: 10.6084/m9.figshare.7705712.v1
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.7705997
title: Additional file 9: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S7. Enzymes and sequences in one KEGG pathway (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7705658
title: Additional file 12: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Hormone-related DEGs in two longan cultivars during the floral induction process. Red indicates genes that showed upregulated expression; blue indicates genes that showed downregulated expression. (XLSX 107 kb)
DOI: 10.6084/m9.figshare.7705715.v1
title: Additional file 7: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: DEGs in â SJâ during floral induction. (XLS 7620 kb)
DOI: 10.6084/m9.figshare.7181063
title: MOESM3 of Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC

description: Additional file 3. Shotgun proteomics raw data for cydC-D86G and control strains.
DOI: 10.6084/m9.figshare.7181066
title: MOESM4 of Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC

description: Additional file 4. Targeted MRM proteomics raw data for cydC-D86G and control strains.
DOI: 10.6084/m9.figshare.7705541.v1
title: Additional file 1: of Transcriptome and metabolome analyses of two contrasting sesame genotypes reveal the crucial biological pathways involved in rapid adaptive response to salt stress

description: Table S1. Summary of RNA-Seq data. Table S2. Significantly enriched KEGG pathways of the DEGs in ST and SS in response to salt stress (P-Valueâ &lt;â 0.05). Table S3. List of genes that were exclusively up-regulated in ST genotype at all salt stress time points. Table S4. List of the core gene set involved in sesame response to salt stress. Table S5. GO terms enriched amongst the core salt-responsive genes in sesame (top 30 terms only). Table S6. The core metabolites involved in sesame response to salt stress. Table S7. The metabolites increased significantly and exclusively in ST genotype in response to salt stress. Table S8. Primers used in qRT-PCR analysis. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.7705670
title: Additional file 14: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: GARS, NAC, MADs, MYB TFs in two longan cultivars during the floral induction process. Red indicates genes that showed upregulated expression; blue indicates genes that showed downregulated expression. (XLSX 125 kb)
DOI: 10.6084/m9.figshare.7705670.v1
title: Additional file 14: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: GARS, NAC, MADs, MYB TFs in two longan cultivars during the floral induction process. Red indicates genes that showed upregulated expression; blue indicates genes that showed downregulated expression. (XLSX 125 kb)
DOI: 10.6084/m9.figshare.7705556.v1
title: Additional file 1: of circKIF4A acts as a prognostic factor and mediator to regulate the progression of triple-negative breast cancer

description: Table S1. The sequences of siRNAs and primer sequences for qRT-PCR used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.12947825.v1
title: Additional file 4 of Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study

description: Additional file 4. Supplemental Table 3. List of 43 KEGG pathways enriched by the DEGs between HLC_SM and HLC_GF.
DOI: 10.6084/m9.figshare.12947840.v1
title: Additional file 9 of Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study

description: Additional file 9. Supplemental Table 8. List of 480 transcription regulators identified for the 10,053 DEGs between HLC_SM and PHHs.
DOI: 10.6084/m9.figshare.7705370.v1
title: Additional file 2: of The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau

description: Table S5. Genotype and phenotype information. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.7705577.v1
title: Additional file 1: of Prevalence of human papillomavirus infection of 65,613 women in East China

description: Table S1. The estimated percentage of women who will be protected by the vaccines targeting different HR-HPV types (XLSX 56â kb)
DOI: 10.6084/m9.figshare.7705706
title: Additional file 4: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: DEGs between ‘SJ’ and ‘SX’ during floral induction. (XLS 11846 kb)
DOI: 10.6084/m9.figshare.7705832
title: Additional file 1: of Identification of potential blood biomarkers for Parkinsonâ s disease by gene expression and DNA methylation data integration analysis

description: Table S1. Differentially Expressed Gene List. Table S2. Previous differential probes and our analysis results. Table S3. Differentially expressed gene functional enrichment results. Table S4. Differentially methylated intergenic CpG sites. Table S5. Differentially methylated gene list. Table S6. Gene set enrichment analysis results (GO-BP). Table S7. Hypo-up genes in different regions. Table S8. Differentially methylated gene list based on all region CpGs. Table S9. Gene enrichment analysis results. Table S10. Hypo-up gene-associated differentially methylated CpGs. Table S11. Dominant methylation-altered regions for hypo-up genes. Table S12. Correlation Coefficient between gene expression and region-specific methylation level. Table S13. The importance of each hypo-up gene in gene expression classifier. Table S14. Union of best predictors of the three classifiers. (ZIP 1455 kb)
DOI: 10.6084/m9.figshare.7705709.v1
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.11375616.v1
title: Table S3 from Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3

description: Gata3 is a DNA-binding transcription factor involved in cellular differentiation in a variety of tissues including inner ear, hair follicle, kidney, mammary gland and T-cells. In a previous study in 2009, Maeda <i>et al</i>. (<i>Dev. Dyn.</i> <b>238</b>, 2280–2291; doi:10.1002/dvdy.22035) found that Gata3 mutants could be rescued from midgestational lethality by the expression of a Gata3 transgene in sympathoadrenal neuroendocrine cells. The rescued embryos clearly showed multiple defects in lens fibre cell differentiation. To determine whether these defects were truly due to the loss of Gata3 expression in the lens, we generated a lens-specific Gata3 loss-of-function model. Analogous to the previous findings, our Gata3 null embryos showed abnormal regulation of cell cycle exit during lens fibre cell differentiation, marked by reduction in the expression of the cyclin-dependent kinase inhibitors Cdkn1b/p27 and Cdkn1c/p57, and the retention of nuclei accompanied by downregulation of Dnase IIβ. Comparisons of transcriptomes between control and mutated lenses by RNA-Seq revealed dysregulation of lens-specific crystallin genes and intermediate filament protein Bfsp2. Both Cdkn1b/p27 and Cdkn1c/p57 loci are occupied <i>in vivo</i> by Gata3, as well as Prox1 and c-Jun, in lens chromatin. Collectively, our studies suggest that Gata3 regulates lens differentiation through the direct regulation of the Cdkn1b/p27and Cdkn1c/p57 expression, and the direct/or indirect transcriptional control of Bfsp2 and Dnase IIβ.
DOI: 10.6084/m9.figshare.11375619
title: Table S1 from Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3

description: Gata3 is a DNA-binding transcription factor involved in cellular differentiation in a variety of tissues including inner ear, hair follicle, kidney, mammary gland and T-cells. In a previous study in 2009, Maeda <i>et al</i>. (<i>Dev. Dyn.</i> <b>238</b>, 2280–2291; doi:10.1002/dvdy.22035) found that Gata3 mutants could be rescued from midgestational lethality by the expression of a Gata3 transgene in sympathoadrenal neuroendocrine cells. The rescued embryos clearly showed multiple defects in lens fibre cell differentiation. To determine whether these defects were truly due to the loss of Gata3 expression in the lens, we generated a lens-specific Gata3 loss-of-function model. Analogous to the previous findings, our Gata3 null embryos showed abnormal regulation of cell cycle exit during lens fibre cell differentiation, marked by reduction in the expression of the cyclin-dependent kinase inhibitors Cdkn1b/p27 and Cdkn1c/p57, and the retention of nuclei accompanied by downregulation of Dnase IIβ. Comparisons of transcriptomes between control and mutated lenses by RNA-Seq revealed dysregulation of lens-specific crystallin genes and intermediate filament protein Bfsp2. Both Cdkn1b/p27 and Cdkn1c/p57 loci are occupied <i>in vivo</i> by Gata3, as well as Prox1 and c-Jun, in lens chromatin. Collectively, our studies suggest that Gata3 regulates lens differentiation through the direct regulation of the Cdkn1b/p27and Cdkn1c/p57 expression, and the direct/or indirect transcriptional control of Bfsp2 and Dnase IIβ.
DOI: 10.6084/m9.figshare.7181120.v1
title: Additional file 2: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S1. List of ChIP-seq and RNA-seq datasets. 18Â KB (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7705694
title: Additional file 2: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: The sequencing and mapped results obtained from each sample. (XLS 22 kb)
DOI: 10.6084/m9.figshare.7705730.v1
title: Additional file 9: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: GO terms significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘SJ’ and ‘SX’. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.24118007.v2
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.7181129.v1
title: Additional file 3: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S2. ChIP-seq peaks. (XLSB 21665 kb)
DOI: 10.6084/m9.figshare.7705964
title: Additional file 2: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S2. Summary of mapping reads of the RNA-Seq (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7705970
title: Additional file 3: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S3. The FPKM value of 520 DEGs in XZ149 and XZ56 (XLSX 113 kb)
DOI: 10.6084/m9.figshare.7705985
title: Additional file 9: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Target miRNAs of the DEKLs and DENLs. (XLS 46 kb)
DOI: 10.6084/m9.figshare.7181141
title: Additional file 5: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S4. Sequences of guide RNAs and primers. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7705706.v1
title: Additional file 4: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: DEGs between ‘SJ’ and ‘SX’ during floral induction. (XLS 11846 kb)
DOI: 10.6084/m9.figshare.7706057
title: Additional file 2: of Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm

description: Supplementary tables. (ZIP 3966 kb)
DOI: 10.6084/m9.figshare.7181141.v1
title: Additional file 5: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S4. Sequences of guide RNAs and primers. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7705649
title: Additional file 11: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Sugar-related DEGs in two longan cultivars during the floral induction process. Red indicates the genes that showed upregulated expression; blue indicates the genes that showed downregulated expression. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7705730
title: Additional file 9: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: GO terms significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘SJ’ and ‘SX’. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.11899983.v2
title: Constrained Varying-Coefficient Model for Time-Course Experiments in Soft Tissue Fabrication

description: In the fabrication of artificial soft tissues, novel biomaterials with the required properties are obtained by appropriately adjusting process parameters during material synthesis. One key step in finding the desired material is understanding the relationship between the process parameters and the material properties, and time-course experiments are typically conducted for this purpose. This article proposes a constrained varying-coefficient modeling method for such data in which expert knowledge is properly accommodated in the model estimation to make the modeling practically meaningful. The proposed model has a semiparametric structure and incorporates expert knowledge in the form of constraints on model coefficients. Estimation algorithms based on a smoothing spline and a weighted smoothing spline are also provided. Finally, the proposed method is compared with existing methods in a case study and a numerical study.
DOI: 10.6084/m9.figshare.11900472.v1
title: Preoperative serum total cholesterol is a predictor of prognosis in patients with renal cell carcinoma: a meta-analysis of observational studies

description: ABSTRACT Purpose Several studies have demonstrated the strong correlation between the levels of preoperative serum total cholesterol (TC) and the survival of patients with surgically treated renal cell carcinoma (RCC). However, this association remains controversial. We performed a meta-analysis of published reports to evaluate the prognostic significance of the preoperative serum TC levels for patients with surgically treated RCC. Material and Methods The databases from MEDLINE (via PubMed), Embase, Web of Science and Cochrane Library were systematically searched to identify the eligible studies published before August 2019. Multivariate adjusted hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated through inverse variance by using random-effects models. Results Nine cohort studies comprising 15.609 patients were identified. Low preoperative serum TC levels were associated with poor cancer-specific survival (CSS; HR=0.98, 95% CI: 0.97-0.99; P=0.005; I2=74.2%) and progression-free survival (PFS; HR=0.69, 95% CI: 0.49-0.98; P=0.036; I2=80%) in patients with surgically treated RCC. However, no significant association was observed between low preoperative serum TC levels and shorter overall survival (HR=0.93, 95% CI: 0.87-1.00; P=0.057; I2=86.2%). Sensitivity analyses validated the reliability and rationality of the results. Conclusions Preoperative serum TC level is an independent poor prognostic factor for patients with surgically treated RCC, with lower levels associated with worse CSS and PFS. Hence, this parameter may provide additional guidance in the selection of therapeutic strategies to improve prognosis, considering that cholesterol is a broadly applied routine marker in clinical practice.
DOI: 10.6084/m9.figshare.7705685
title: Additional file 1: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: List of primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.20288833.v1
title: Analysis of groups’ multi-day leisure travel behaviors

description: The purpose of this paper is to study the behavior characteristics and spatiotemporal distribution of groups’ multi-day leisure travel, and to quantify the impact of the elderly and children on group travel choices. Based on questionnaire and social media data, three choice models and an agent-based simulation model were established to explore the micro-choice behavior characteristics and the macro-spatiotemporal distribution of groups’ multi-day leisure travel by arranging the travel rules and by simulating the route of travel groups. The results of data analysis and simulation indicate that: (1) Travel groups with the elderly or children are less affected by the high-speed railway network and prefer self-driving traveling. (2) Groups with the elderly or children tend to travel for more days and visit more cities, while groups without the elderly or children pursue high-quality tourism resources. (3) High-quality tourist attractions bring more tourists to nearby tourist attractions, promoting regional tourism cooperation.
DOI: 10.6084/m9.figshare.7705922
title: Additional file 10: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Differential expression lncRNAs cis- and trans-target genes. (XLS 100 kb)
DOI: 10.6084/m9.figshare.7705934
title: Additional file 1: of Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

description: Statistical data of the mapped reads. (XLS 11 kb)
DOI: 10.6084/m9.figshare.15568282.v1
title: Additional file 3 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 3.