cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11375622
title: Table S2 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.11375622.v1
title: Table S2 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.15568285.v1
title: Additional file 4 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 4.
DOI: 10.6084/m9.figshare.7705556
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: 10.5281/zenodo.10683230
title: GPR - AUGMENTED 2
DOI: 10.6084/m9.figshare.7705646
title: Additional file 10: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: KEGG pathways significantly overrepresented in the eight enriched profiles of gene expression versus the reference set in ‘SJ’ and ‘SX’. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.15568270.v1
title: Additional file 2 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 2.
DOI: 10.6084/m9.figshare.7705508.v1
title: Additional file 8: of A role for actomyosin contractility in Notch signaling

description: Raw data file. Data analyzed for the main and supplemental figures. (XLSX 245 kb)
DOI: 10.6084/m9.figshare.7705715
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.7705667
title: Additional file 13: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Flower-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 26 kb)
DOI: 10.6084/m9.figshare.7181060
title: MOESM2 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 2. Phylogenetic analysis of cydC and cydB genomic co-occurrence in bacterial genomes.
DOI: 10.6084/m9.figshare.7181129
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.7181066.v1
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.15568285
title: Additional file 4 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 4.
DOI: 10.6084/m9.figshare.15568297.v1
title: Additional file 5 of Greater morphological and primary metabolic adaptations in roots contribute to phosphate-deficiency tolerance in the bread wheat cultivar Kenong199

description: Additional file 5.
DOI: 10.6084/m9.figshare.7181138
title: Additional file 4: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S3. Annotated SNPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.17141191.v1
title: Additional file 2 of Multi-genotype varieties reduce rice diseases through enhanced genetic diversity and show stability and adaptability in the field

description: Additional file 2: Table S1. Occurrence of three main rice diseases in plot experiments in 2014. Table S2. Yields and agronomic traits of multi-genotype varieties in plot experiments in 2014. Table S3. The genetic diversity index of multi-genotype varieties and their components. Table S4. Occurrence of three main rice diseases in field experiments during 2015–2017. Table S5. Yields and agronomic traits of multi-genotype varieties in field experiments during 2015–2017. Table S6. Parental information of multi-genotype varieties used in this study. Table S7. Grading criteria for evaluation of the severity of rice blast, false smut and bacterial blight.
DOI: 10.6084/m9.figshare.7705415
title: MOESM1 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 1. Fatty acid composition of Graesiella sp. WBG-1 under different acetate feeding strategies and photo of the two types of column reactor.
DOI: 10.6084/m9.figshare.7705415.v1
title: MOESM1 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 1. Fatty acid composition of Graesiella sp. WBG-1 under different acetate feeding strategies and photo of the two types of column reactor.
DOI: 10.6084/m9.figshare.7705445
title: MOESM6 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 6. Calculation of acetate conversion efficiency.
DOI: 10.6084/m9.figshare.7705832.v1
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.11375619.v1
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.20288833
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.7181144
title: Additional file 6: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S5. RNA-seq analyses. (XLSX 4442 kb)
DOI: 10.6084/m9.figshare.7181144.v1
title: Additional file 6: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S5. RNA-seq analyses. (XLSX 4442 kb)
DOI: 10.6084/m9.figshare.7181147
title: Additional file 7: of CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

description: Table S6. Predicted genes regulated by PCa-related K27Ac sites. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7705445.v1
title: MOESM6 of Sequential phototrophicâ mixotrophic cultivation of oleaginous microalga Graesiella sp. WBG-1 in a 1000Â m2 open raceway pond

description: Additional file 6. Calculation of acetate conversion efficiency.
DOI: 10.6084/m9.figshare.7705658.v1
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.7705577
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.7705970.v1
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.7705667.v1
title: Additional file 13: of Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

description: Flower-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 26 kb)
DOI: 10.6084/m9.figshare.7706348
title: <i>Rhodotorula glutinis</i> as a living cell liposome to deliver polypeptide drugs <i>in vivo</i>

description: The potential advantages of recombinant microbes as oral drug carriers for curing diseases have attracted much attention. The use of recombinant oil microbes as living cell liposomes to carry polypeptide drugs may be an ideal polypeptide oral drug delivery system. GM4-ΔTS was constructed by LFH-PCR from <i>Rhodotorula glutinis</i> GM4, which was screened and preserved in our laboratory, and then transferred into choline-phosphate cytidylyltransferase (CCT), which is a rate-limiting enzyme for lecithin synthesis. The results showed that the CCT gene was highly expressed in the GM4-ΔTS strain and could significantly increase fatty acid and lecithin contents in GM4-ΔTS-PGK1-CCT. Moreover, insulin, H22-LP, and α-MSH were successfully introduced into cells <i>in vitro</i>, and the strain no longer proliferated <i>in vivo</i>, for safe and controllable polypeptide drug delivery. <i>In vivo</i>, normal mice were intragastrically administered with recombinant strains carrying insulin and α-MSH, and different levels of polypeptide drugs were detected in serum and tissue, respectively. Then, recombinant strains carrying insulin were administered to type II diabetes mellitus mice. The results showed that the strains could effectively reduce blood glucose levels in mice, which indicated that the recombinant strains could carry insulin into the body, and the drug effect was remarkable. Therefore, recombinant GM4-ΔTS-PGK1-CCT strains were successfully used as living cell liposomes to carry insulin, H22-LP, and α-MSH peptides into the body for the first time; additionally, these strains have enhanced safety, controllability, and efficacy.
DOI: 10.6084/m9.figshare.7706348.v1
title: <i>Rhodotorula glutinis</i> as a living cell liposome to deliver polypeptide drugs <i>in vivo</i>

description: The potential advantages of recombinant microbes as oral drug carriers for curing diseases have attracted much attention. The use of recombinant oil microbes as living cell liposomes to carry polypeptide drugs may be an ideal polypeptide oral drug delivery system. GM4-ΔTS was constructed by LFH-PCR from <i>Rhodotorula glutinis</i> GM4, which was screened and preserved in our laboratory, and then transferred into choline-phosphate cytidylyltransferase (CCT), which is a rate-limiting enzyme for lecithin synthesis. The results showed that the CCT gene was highly expressed in the GM4-ΔTS strain and could significantly increase fatty acid and lecithin contents in GM4-ΔTS-PGK1-CCT. Moreover, insulin, H22-LP, and α-MSH were successfully introduced into cells <i>in vitro</i>, and the strain no longer proliferated <i>in vivo</i>, for safe and controllable polypeptide drug delivery. <i>In vivo</i>, normal mice were intragastrically administered with recombinant strains carrying insulin and α-MSH, and different levels of polypeptide drugs were detected in serum and tissue, respectively. Then, recombinant strains carrying insulin were administered to type II diabetes mellitus mice. The results showed that the strains could effectively reduce blood glucose levels in mice, which indicated that the recombinant strains could carry insulin into the body, and the drug effect was remarkable. Therefore, recombinant GM4-ΔTS-PGK1-CCT strains were successfully used as living cell liposomes to carry insulin, H22-LP, and α-MSH peptides into the body for the first time; additionally, these strains have enhanced safety, controllability, and efficacy.
DOI: 10.6084/m9.figshare.7705991
title: Additional file 7: of Transcriptomic analysis reveals adaptive strategies to chronic low nitrogen in Tibetan wild barley

description: Table S6. DEGs consistently expressed at three time points under low N stress in each genotype (XLSX 13 kb)
DOI: 10.6084/m9.figshare.22385532
title: Jiangzuo_raw data fauna.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.22385526
title: Jiangzuo_matrix-bayes.nex 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.22385532.v1
title: Jiangzuo_raw data fauna.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.