cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11952990.v1
title: Additional file 12 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 12: Table S7. Primers for dual luciferase assay.
DOI: 10.6084/m9.figshare.11952996
title: Additional file 1 of Intestinal flora imbalance affects bile acid metabolism and is associated with gallstone formation

description: Additional file 1. Sequencing data quality assessment.
DOI: 10.6084/m9.figshare.11952996.v1
title: Additional file 1 of Intestinal flora imbalance affects bile acid metabolism and is associated with gallstone formation

description: Additional file 1. Sequencing data quality assessment.
DOI: 10.6084/m9.figshare.11953023
title: Additional file 6 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 6: Table S1. Stages of peaches and strawberries selected for transcriptome sequencing.
DOI: 10.6084/m9.figshare.11953023.v1
title: Additional file 6 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 6: Table S1. Stages of peaches and strawberries selected for transcriptome sequencing.
DOI: 10.6084/m9.figshare.11953026
title: Additional file 7 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 7: Table S2. Overlap of differential expressed genes with QTL regions related to fruit size.
DOI: 10.6084/m9.figshare.11953026.v1
title: Additional file 7 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 7: Table S2. Overlap of differential expressed genes with QTL regions related to fruit size.
DOI: 10.6084/m9.figshare.11953029
title: Additional file 8 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 8: Table S3. Candidate genes involved into fruit enlargement in Model I.
DOI: 10.6084/m9.figshare.11953029.v1
title: Additional file 8 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 8: Table S3. Candidate genes involved into fruit enlargement in Model I.
DOI: 10.6084/m9.figshare.11953032
title: Additional file 9 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 9: Table S4. Candidate genes involved into fruit enlargement in Model II.
DOI: 10.6084/m9.figshare.11953032.v1
title: Additional file 9 of Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns

description: Additional file 9: Table S4. Candidate genes involved into fruit enlargement in Model II.
DOI: 10.6084/m9.figshare.11953047
title: Additional file 10 of The genome evolution and domestication of tropical fruit mango

description: Additional file 10: Table S8. Plant genomes used for comparative genomics investigation.
DOI: 10.6084/m9.figshare.11953053
title: Additional file 11 of The genome evolution and domestication of tropical fruit mango

description: Additional file 11: Table S9. Statistics of collinear genes among the blocks within mango genome.
DOI: 10.6084/m9.figshare.11953053.v1
title: Additional file 11 of The genome evolution and domestication of tropical fruit mango

description: Additional file 11: Table S9. Statistics of collinear genes among the blocks within mango genome.
DOI: 10.6084/m9.figshare.11953062
title: Additional file 12 of The genome evolution and domestication of tropical fruit mango

description: Additional file 12: Table S10. Statistics of collinear blocks among chromosomes resulting from mango-specific WGD events.
DOI: 10.6084/m9.figshare.11953062.v1
title: Additional file 12 of The genome evolution and domestication of tropical fruit mango

description: Additional file 12: Table S10. Statistics of collinear blocks among chromosomes resulting from mango-specific WGD events.
DOI: 10.6084/m9.figshare.11953065
title: Additional file 13 of The genome evolution and domestication of tropical fruit mango

description: Additional file 13: Table S11. Gene Ontology enrichment analysis of Retained Genes post-WGD.
DOI: 10.6084/m9.figshare.11953065.v1
title: Additional file 13 of The genome evolution and domestication of tropical fruit mango

description: Additional file 13: Table S11. Gene Ontology enrichment analysis of Retained Genes post-WGD.
DOI: 10.6084/m9.figshare.11953068
title: Additional file 14 of The genome evolution and domestication of tropical fruit mango

description: Additional file 14: Table S12. Sample summary for RNA-Seq library construction.
DOI: 10.6084/m9.figshare.11953068.v1
title: Additional file 14 of The genome evolution and domestication of tropical fruit mango

description: Additional file 14: Table S12. Sample summary for RNA-Seq library construction.
DOI: 10.6084/m9.figshare.11953071
title: Additional file 15 of The genome evolution and domestication of tropical fruit mango

description: Additional file 15: Table S13. Statistics of photosynthesis-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953071.v1
title: Additional file 15 of The genome evolution and domestication of tropical fruit mango

description: Additional file 15: Table S13. Statistics of photosynthesis-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953074
title: Additional file 16 of The genome evolution and domestication of tropical fruit mango

description: Additional file 16: Table S14. Statistics of sugar metabolism-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953074.v1
title: Additional file 16 of The genome evolution and domestication of tropical fruit mango

description: Additional file 16: Table S14. Statistics of sugar metabolism-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953077
title: Additional file 17 of The genome evolution and domestication of tropical fruit mango

description: Additional file 17: Table S15. Statistics of lipid metabolism-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953077.v1
title: Additional file 17 of The genome evolution and domestication of tropical fruit mango

description: Additional file 17: Table S15. Statistics of lipid metabolism-related duplicated genes in mango genome.
DOI: 10.6084/m9.figshare.11953080
title: Additional file 18 of The genome evolution and domestication of tropical fruit mango

description: Additional file 18: Table S16. Statistics of duplicated genes related to biosynthesis of isopentenyl diphosphate in mango genome.
DOI: 10.6084/m9.figshare.11953080.v1
title: Additional file 18 of The genome evolution and domestication of tropical fruit mango

description: Additional file 18: Table S16. Statistics of duplicated genes related to biosynthesis of isopentenyl diphosphate in mango genome.
DOI: 10.6084/m9.figshare.11953083
title: Additional file 19 of The genome evolution and domestication of tropical fruit mango

description: Additional file 19: Table S17. Significant variation mango gene familes within 12 plant genomes.
DOI: 10.6084/m9.figshare.11953083.v1
title: Additional file 19 of The genome evolution and domestication of tropical fruit mango

description: Additional file 19: Table S17. Significant variation mango gene familes within 12 plant genomes.
DOI: 10.6084/m9.figshare.11953092
title: Additional file 20 of The genome evolution and domestication of tropical fruit mango

description: Additional file 20: Table S18. Gene Ontology enrichment analysis of genes in significant expanded gene families.
DOI: 10.6084/m9.figshare.11953092.v1
title: Additional file 20 of The genome evolution and domestication of tropical fruit mango

description: Additional file 20: Table S18. Gene Ontology enrichment analysis of genes in significant expanded gene families.
DOI: 10.6084/m9.figshare.11953101
title: Additional file 21 of The genome evolution and domestication of tropical fruit mango

description: Additional file 21: Table S19. Comparative analysis of disease resistance-related genes in mango and other taxonomically closely related species.
DOI: 10.6084/m9.figshare.11953101.v1
title: Additional file 21 of The genome evolution and domestication of tropical fruit mango

description: Additional file 21: Table S19. Comparative analysis of disease resistance-related genes in mango and other taxonomically closely related species.
DOI: 10.6084/m9.figshare.11953107
title: Additional file 2 of Gamevar.f90: a software package for calculating individual gametic diversity

description: Additional file 2. Source code of Gamevar.f90. An Fortran source code file for gamevar.f90.
DOI: 10.6084/m9.figshare.11953107.v1
title: Additional file 2 of Gamevar.f90: a software package for calculating individual gametic diversity

description: Additional file 2. Source code of Gamevar.f90. An Fortran source code file for gamevar.f90.
DOI: 10.6084/m9.figshare.11953110
title: Additional file 22 of The genome evolution and domestication of tropical fruit mango

description: Additional file 22: Table S20. Publically available transcriptomic data for retrieval of CHS homologs.
DOI: 10.6084/m9.figshare.11953110.v1
title: Additional file 22 of The genome evolution and domestication of tropical fruit mango

description: Additional file 22: Table S20. Publically available transcriptomic data for retrieval of CHS homologs.
DOI: 10.6084/m9.figshare.11953113
title: Additional file 3 of Gamevar.f90: a software package for calculating individual gametic diversity

description: Additional file 3. Executable file of Gamevar.f90. An executable file for linux system.
DOI: 10.6084/m9.figshare.11953113.v1
title: Additional file 3 of Gamevar.f90: a software package for calculating individual gametic diversity

description: Additional file 3. Executable file of Gamevar.f90. An executable file for linux system.
DOI: 10.6084/m9.figshare.20341715
title: Additional file 1 of Nurses’ perceptions of barriers and supportive behaviors in end-of-life care in the intensive care unit: a cross-sectional study

description: Additional file 1.
DOI: 10.6084/m9.figshare.20341715.v1
title: Additional file 1 of Nurses’ perceptions of barriers and supportive behaviors in end-of-life care in the intensive care unit: a cross-sectional study

description: Additional file 1.
DOI: 10.6084/m9.figshare.11953119
title: Additional file 23 of The genome evolution and domestication of tropical fruit mango

description: Additional file 23: Table S21. Ks values calculated among CHS genes in mango genome.
DOI: 10.6084/m9.figshare.11953119.v1
title: Additional file 23 of The genome evolution and domestication of tropical fruit mango

description: Additional file 23: Table S21. Ks values calculated among CHS genes in mango genome.
DOI: 10.6084/m9.figshare.11953125
title: Additional file 24 of The genome evolution and domestication of tropical fruit mango

description: Additional file 24: Table S22. Identity values of sweet orange and mango CHS peptides.
DOI: 10.6084/m9.figshare.11953125.v1
title: Additional file 24 of The genome evolution and domestication of tropical fruit mango

description: Additional file 24: Table S22. Identity values of sweet orange and mango CHS peptides.
DOI: 10.6084/m9.figshare.11953128
title: Additional file 25 of The genome evolution and domestication of tropical fruit mango

description: Additional file 25: Table S23. Frequency distribution of SNPs and Stopgain SNPs in each MAF.
DOI: 10.6084/m9.figshare.11953128.v1
title: Additional file 25 of The genome evolution and domestication of tropical fruit mango

description: Additional file 25: Table S23. Frequency distribution of SNPs and Stopgain SNPs in each MAF.
DOI: 10.6084/m9.figshare.11953131
title: Additional file 26 of The genome evolution and domestication of tropical fruit mango

description: Additional file 26: Table S24. Statistics of heterozygous rate and ROH (length &gt;50kb) in mango genome.
DOI: 10.6084/m9.figshare.11953131.v1
title: Additional file 26 of The genome evolution and domestication of tropical fruit mango

description: Additional file 26: Table S24. Statistics of heterozygous rate and ROH (length &gt;50kb) in mango genome.
DOI: 10.6084/m9.figshare.11953152
title: Additional file 3 of The genome evolution and domestication of tropical fruit mango

description: Additional file 3: Table S1. Genome survey sequencing of mango cultivates and wild relatives.
DOI: 10.6084/m9.figshare.11953152.v1
title: Additional file 3 of The genome evolution and domestication of tropical fruit mango

description: Additional file 3: Table S1. Genome survey sequencing of mango cultivates and wild relatives.
DOI: 10.6084/m9.figshare.11953158
title: Additional file 4 of The genome evolution and domestication of tropical fruit mango

description: Additional file 4: Table S2. Summary of data used for Genome Sequencing.
DOI: 10.6084/m9.figshare.11953158.v1
title: Additional file 4 of The genome evolution and domestication of tropical fruit mango

description: Additional file 4: Table S2. Summary of data used for Genome Sequencing.
DOI: 10.6084/m9.figshare.11953164
title: Additional file 5 of The genome evolution and domestication of tropical fruit mango

description: Additional file 5: Table S3. Summary of mango genome assembly.
DOI: 10.6084/m9.figshare.11953164.v1
title: Additional file 5 of The genome evolution and domestication of tropical fruit mango

description: Additional file 5: Table S3. Summary of mango genome assembly.
DOI: 10.6084/m9.figshare.11953170
title: Additional file 6 of The genome evolution and domestication of tropical fruit mango

description: Additional file 6: Table S4. Assessment of gene coverage in mango Genome Using Trinity assembled transcripts.
DOI: 10.6084/m9.figshare.11953170.v1
title: Additional file 6 of The genome evolution and domestication of tropical fruit mango

description: Additional file 6: Table S4. Assessment of gene coverage in mango Genome Using Trinity assembled transcripts.
DOI: 10.6084/m9.figshare.11953173
title: Additional file 7 of The genome evolution and domestication of tropical fruit mango

description: Additional file 7: Table S5. Summary of transposable elements in mango genome.
DOI: 10.6084/m9.figshare.11953179
title: Additional file 8 of The genome evolution and domestication of tropical fruit mango

description: Additional file 8: Table S6. The Summary of Mango Protein-coding Genes.
DOI: 10.6084/m9.figshare.11953185
title: Additional file 9 of The genome evolution and domestication of tropical fruit mango

description: Additional file 9: Table S7. Annotation statistics of predicted proteins encoded in mango genome.
DOI: 10.6084/m9.figshare.11953185.v1
title: Additional file 9 of The genome evolution and domestication of tropical fruit mango

description: Additional file 9: Table S7. Annotation statistics of predicted proteins encoded in mango genome.
DOI: 10.6084/m9.figshare.8283191
title: WDR45 contributes to neurodegeneration through regulation of ER homeostasis and neuronal death

description: Mutations in the macroautophagy/autophagy gene <i>WDR45</i> cause β-propeller protein-associated neurodegeneration (BPAN); however the molecular and cellular mechanism of the disease process is largely unknown. Here we generated constitutive <i>wdr45</i> knockout (KO) mice that displayed cognitive impairments, abnormal synaptic transmission and lesions in several brain regions. Immunohistochemistry analysis showed loss of neurons in prefrontal cortex and basal ganglion in aged mice, and increased apoptosis in prefrontal cortex, recapitulating a hallmark of neurodegeneration. Quantitative proteomic analysis showed accumulation of endoplasmic reticulum (ER) proteins in KO mouse. At the cellular level, accumulation of ER proteins due to WDR45 deficiency resulted in increased ER stress and impaired ER quality control. The unfolded protein response (UPR) was elevated through ERN1/IRE1 or EIF2AK3/PERK pathway, and eventually led to neuronal apoptosis. Suppression of ER stress or activation of autophagy through MTOR inhibition alleviated cell death. Thus, the loss of WDR45 cripples macroautophagy machinery in neurons and leads to impairment in organelle autophagy, which provides a mechanistic understanding of cause of BPAN and a potential therapeutic strategy to treat this genetic disorder. 7-ADD: 7-aminoactinomycin D; ASD: autistic spectrum disorder; ATF6: activating transcription factor 6; ATG: autophagy-related; BafA1: bafilomycin A<sub>1</sub>; BCAP31: B cell receptor associated protein 31; BPAN: β-propeller protein-associated neurodegeneration; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CDIPT: CDP-diacylglycerol–inositol 3-phosphatidyltransferase (phosphatidylinositol synthase); DDIT3/CHOP: DNA-damage inducible transcript 3; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; GFP: green fluorescent protein; HIP: hippocampus; HSPA5/GRP78: heat shock protein family A (HSP70) member 5; KO: knockout; LAMP1: lysosomal-associated membrane 1; mEPSCs: miniature excitatory postsynaptic currents; MG132: N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal; MIB: mid-brain; MTOR: mechanistic target of rapamycin kinase; PCR: polymerase chain reaction; PFA: paraformaldehyde; PFC: prefrontal cortex; PRM: parallel reaction monitoring; RBFOX3/NEUN: RNA binding protein, fox-1 homolog [C. elegans] 3; RTN3: reticulon 3; SEC22B: SEC22 homolog B, vesicle trafficking protein; SEC61B: SEC61 translocon beta subunit; SEM: standard error of the mean; SNR: substantia nigra; SQSTM1/p62: sequestosome 1; TH: tyrosine hydroxylase; Tm: tunicamycin; TMT: tandem mass tag; TUDCA: tauroursodeoxycholic acid; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UPR: unfolded protein response; WDR45: WD repeat domain 45; WT: wild type; XBP1: X-box binding protein 1.
DOI: 10.6084/m9.figshare.8283191.v1
title: WDR45 contributes to neurodegeneration through regulation of ER homeostasis and neuronal death

description: Mutations in the macroautophagy/autophagy gene <i>WDR45</i> cause β-propeller protein-associated neurodegeneration (BPAN); however the molecular and cellular mechanism of the disease process is largely unknown. Here we generated constitutive <i>wdr45</i> knockout (KO) mice that displayed cognitive impairments, abnormal synaptic transmission and lesions in several brain regions. Immunohistochemistry analysis showed loss of neurons in prefrontal cortex and basal ganglion in aged mice, and increased apoptosis in prefrontal cortex, recapitulating a hallmark of neurodegeneration. Quantitative proteomic analysis showed accumulation of endoplasmic reticulum (ER) proteins in KO mouse. At the cellular level, accumulation of ER proteins due to WDR45 deficiency resulted in increased ER stress and impaired ER quality control. The unfolded protein response (UPR) was elevated through ERN1/IRE1 or EIF2AK3/PERK pathway, and eventually led to neuronal apoptosis. Suppression of ER stress or activation of autophagy through MTOR inhibition alleviated cell death. Thus, the loss of WDR45 cripples macroautophagy machinery in neurons and leads to impairment in organelle autophagy, which provides a mechanistic understanding of cause of BPAN and a potential therapeutic strategy to treat this genetic disorder. <b>Abbreviations:</b> 7-ADD: 7-aminoactinomycin D; ASD: autistic spectrum disorder; ATF6: activating transcription factor 6; ATG: autophagy-related; BafA1: bafilomycin A<sub>1</sub>; BCAP31: B cell receptor associated protein 31; BPAN: β-propeller protein-associated neurodegeneration; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CDIPT: CDP-diacylglycerol–inositol 3-phosphatidyltransferase (phosphatidylinositol synthase); DDIT3/CHOP: DNA-damage inducible transcript 3; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; GFP: green fluorescent protein; HIP: hippocampus; HSPA5/GRP78: heat shock protein family A (HSP70) member 5; KO: knockout; LAMP1: lysosomal-associated membrane 1; mEPSCs: miniature excitatory postsynaptic currents; MG132: N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal; MIB: mid-brain; MTOR: mechanistic target of rapamycin kinase; PCR: polymerase chain reaction; PFA: paraformaldehyde; PFC: prefrontal cortex; PRM: parallel reaction monitoring; RBFOX3/NEUN: RNA binding protein, fox-1 homolog [C. elegans] 3; RTN3: reticulon 3; SEC22B: SEC22 homolog B, vesicle trafficking protein; SEC61B: SEC61 translocon beta subunit; SEM: standard error of the mean; SNR: substantia nigra; SQSTM1/p62: sequestosome 1; TH: tyrosine hydroxylase; Tm: tunicamycin; TMT: tandem mass tag; TUDCA: tauroursodeoxycholic acid; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UPR: unfolded protein response; WDR45: WD repeat domain 45; WT: wild type; XBP1: X-box binding protein 1.