cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13145/bacdive101640.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101641.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101642.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101643.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101644.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101645.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101646.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101647.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive101648.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive102482.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive102483.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive102484.20170829.2
title: Arthrobacter sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.6084/m9.figshare.23797287.v1
title: Additional file 1 of The role of NPY2R/NFATc1/DYRK1A regulatory axis in sebaceous glands for sebum synthesis

description: Additional file 1: Table S1. Gene information of DEGs compared between PND-25 and PND-35. DEGs are defined as log2 fold change &gt; 1 or &lt; − 1, and p &lt; 0.05. MS: mammary skin; VS: volar skin; AS: abdominal skin.
DOI: 10.6084/m9.figshare.16456851
title: Additional file 4 of Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation

description: Additional file 4: Table S2. EPIC CpGs significantly associated with child’s sex
DOI: 10.6084/m9.figshare.23797319.v1
title: Additional file 3 of Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

description: Additional file 3: Table S1. Soil background information. Table S2. RNA-Seq data summary for "XH2008" and "Lanshan" under different calcium treatments. Table S3. Primer sequences of six pairs of genes to be validated using qRT-PCR. Table S4. The module-trait correlation analysis showing pearson correlation value and p-value. Table S5. The KEGG pathways enriched for 61 differentially expressed genes (DEGs) in "XH2008". Table S6. The KEGG pathways enriched for 58 differentially expressed genes (DEGs) in "Lanshan". Table S7. The topological results and  annotationinformation for hub-gene sets in the blue module of "XH2008" cultivar. Table S8. The topological results and  annotation information for hub-gene sets in the green module of "Lanshan" cultivar. Table S9. The gene expression modes for the genes annotated to secondary metabolites.
DOI: 10.6084/m9.figshare.13311001.v1
title: Additional file 1 of Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast

description: Additional file 2: Table S1. Outline of differentially expressed genes in the strains BY4742/IrrE and BY4742/I24 relative to the control strain with or without FAP. log2foldchange &gt; 1.0 and p value &lt; 0.05.
DOI: 10.6084/m9.figshare.16456815.v1
title: Additional file 11 of Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation

description: Additional file 11: Table S8. Biological function GO terms which are significantly enriched for genes from the turquoise module at FDR-level of 5%
DOI: 10.6084/m9.figshare.14885412.v1
title: rspa20210337supp1.txt from Optimization of a type of elastic metamaterial for broadband wave suppression

description: Data for optimization result and corresponding numerical validation-transmissibility versus frequency in Figure 7 from “Optimization of a type of elastic metamaterial for broadband wave suppression”.
DOI: 10.6084/m9.figshare.23274248.v1
title: Analysis of the complete plastomes of <i>Bidens pilosa</i> L. 1753 (Asteraceae, Coreopsideae) from Beijing, China reveals high genetic diversity and possible misidentifications

description: <i>Bidens pilosa</i> L. 1753 is a perennial herbaceous flowering plant, traditionally used in foods and medicines. In this study, we sequenced, assembled, and characterized the complete plastome of <i>B. pilosa</i> from Beijing, China. The plastome (MN385242) is circularized with a conservative quadripartite structure. Its length is 150,524 bp, including a large single-copy region (83,535 bp), a small single-copy region (17,627 bp), and a pair of inverted repeat regions (each 24,681 bp). The plastome consists of 128 genes, including 78 unique protein-coding, 28 unique tRNA, and 4 unique rRNA genes. Phylogenetic analyses showed all five <i>B. pilosa</i> plants couldn’t form a monophyletic clade and were separated into three clades. The results of K2P distance and molecular markers were all consistent with those of phylogenetic analysis, revealing high genetic diversity and even possible misidentifications of the <i>B. pilosa</i>. Our results highlighted the importance of correct species identification of materials in medicinal products.
DOI: 10.6084/m9.figshare.16456815
title: Additional file 11 of Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation

description: Additional file 11: Table S8. Biological function GO terms which are significantly enriched for genes from the turquoise module at FDR-level of 5%
DOI: 10.6084/m9.figshare.13310977
title: Additional file 4 of Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions

description: Additional file 4: Supplementary Table S3. Genotypes of the 102 InDel markers for 1,251 Malus accessions.
DOI: 10.5281/zenodo.7554234
title: Dataset related to: Sirtuin 3 Deficiency Aggravates Kidney Disease in Response to High-Fat Diet through Lipotoxicity-Induced Mitochondrial Damage

description: The files contain all the dataset included in the manuscript divided by figures.

 

Abstract: Sirtuin 3 (SIRT3) is the primary mitochondrial deacetylase that controls the antioxidantpathway and energy metabolism. We previously found that renal Sirt3 expression and activity werereduced in mice with type 2 diabetic nephropathy associated with oxidative stress and mitochondrialabnormalities and that a specific SIRT3 activator improved renal damage. SIRT3 is modulated bydiet, and to assess whether Sirt3 deficiency aggravates mitochondrial damage and accelerates kidneydisease in response to nutrient overloads, wild-type (WT) and Sirt3-/- mice were fed a high-fat-diet(HFD) or standard diet for 8 months. Sirt3-/- mice on HFD exhibited earlier and more severealbuminuria compared to WT mice, accompanied by podocyte dysfunction and glomerular capillaryrarefaction. Mesangial matrix expansion, tubular vacuolization and inflammation, associated withenhanced lipid accumulation, were more evident in Sirt3-/- mice. After HFD, kidneys from Sirt3-/-mice showed more oxidative stress than WT mice, mitochondria ultrastructural damage in tubularcells, and a reduction in mitochondrial mass and energy production. Our data demonstrate that Sirt3deficiency renders mice more prone to developing oxidative stress and mitochondrial abnormalitiesin response to HFD, resulting in more severe kidney diseases, and this suggests that mitochondriaprotection may be a method to prevent HFD-induced renal injury.
description: The study was partially supported by Fondazione Cariplo.
DOI: 10.5281/zenodo.7554235
title: Dataset related to: Sirtuin 3 Deficiency Aggravates Kidney Disease in Response to High-Fat Diet through Lipotoxicity-Induced Mitochondrial Damage

description: The files contain all the dataset included in the manuscript divided by figures.

 

Abstract: Sirtuin 3 (SIRT3) is the primary mitochondrial deacetylase that controls the antioxidantpathway and energy metabolism. We previously found that renal Sirt3 expression and activity werereduced in mice with type 2 diabetic nephropathy associated with oxidative stress and mitochondrialabnormalities and that a specific SIRT3 activator improved renal damage. SIRT3 is modulated bydiet, and to assess whether Sirt3 deficiency aggravates mitochondrial damage and accelerates kidneydisease in response to nutrient overloads, wild-type (WT) and Sirt3-/- mice were fed a high-fat-diet(HFD) or standard diet for 8 months. Sirt3-/- mice on HFD exhibited earlier and more severealbuminuria compared to WT mice, accompanied by podocyte dysfunction and glomerular capillaryrarefaction. Mesangial matrix expansion, tubular vacuolization and inflammation, associated withenhanced lipid accumulation, were more evident in Sirt3-/- mice. After HFD, kidneys from Sirt3-/-mice showed more oxidative stress than WT mice, mitochondria ultrastructural damage in tubularcells, and a reduction in mitochondrial mass and energy production. Our data demonstrate that Sirt3deficiency renders mice more prone to developing oxidative stress and mitochondrial abnormalitiesin response to HFD, resulting in more severe kidney diseases, and this suggests that mitochondriaprotection may be a method to prevent HFD-induced renal injury.
description: The study was partially supported by Fondazione Cariplo.
DOI: 10.6084/m9.figshare.12262595
title: Additional file 4 of Differences in airway microbiome and metabolome of single lung transplant recipients

description: Additional file 4.
DOI: 10.6084/m9.figshare.12262604
title: Additional file 5 of Differences in airway microbiome and metabolome of single lung transplant recipients

description: Additional file 5.
DOI: 10.6084/m9.figshare.12788530.v1
title: Additional file 2 of Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

description: Additional file 2: Table S1. An overview of the QTL-seq results. Table S2. SNPs results between two parents and two mixed pools. Table S3. Annotated genes within the interval detected by QTL-seq. Table S4. Phenotypic variation of parents and F2:3 lines. Table S5. Summary of Illumina transcriptome reads mapped to the reference genome. Table S6. Statistics of transcriptome sequencing results. Table S7. RNA-seq data of the genes in candidate region. Table S8. The KASP genotyping results. Table S9. ANOVA results of three genotypes. Table S10. The Arabidopsis homologous genes of Os07g0569700. Table S11. The genotype of 1 bp Indel in 66 diverse rice accessions. Table S12. Primers of 25 KASP markers. Table S13. The KASP reaction system. Table S14. Primers for qRT-PCR in this study.
DOI: 10.6084/m9.figshare.23274249
title: The complete chloroplast genome of <i>Primula vialii</i> (Primulaceae), an ornamental plant

description: <i>Primula vialii</i> Delavay ex Franch. (1905) is an alpine species with an ornamental value. In this study, we sequenced, assembled, and annotated the chloroplast genome of <i>P. vialii.</i> The results showed that it was a double-stranded, closed circular DNA with 154,897 bp in length, comprising a small single-copy (SSC) region of 17,766 bp, a large single-copy (LSC) region of 85,379 bp and a pair of inverted repeat (IR) regions of 25,876 bp. A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that <i>P. vialii</i> is closely related to <i>Primula flaccida.</i> The cp genomic data will be useful for systematics and evolutionary studies of <i>Primula</i>.
DOI: 10.6084/m9.figshare.16456809
title: Additional file 10 of Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation

description: Additional file 10: Table S7. Genes from turquoise module overlapping with differential expressed genes in Uitert et al.
DOI: 10.6084/m9.figshare.12262628.v1
title: Additional file 8 of Differences in airway microbiome and metabolome of single lung transplant recipients

description: Additional file 8.
DOI: 10.6084/m9.figshare.13311211
title: Additional file 7 of Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

description: Additional file 7. List of genes in female and male network.
DOI: 10.6084/m9.figshare.13312624.v1
title: Functional analysis of a novel <i>cryptochrome</i> gene (<i>GbCRY1</i>) from <i>Ginkgo biloba</i>

description: Cryptochrome (CRY) is a blue light receptor that is widely distributed in animals, plants, and microorganisms. <i>CRY</i> as a coding gene of cryptochrome that regulates the organism gene expression and plays an important role in organism growth and development. In this study, we identified four photolyase/cryptochrome (PHR/CRY) members from the genome of <i>Ginkgo biloba</i>. Phylogenetic tree analysis showed that the Ginkgo PHR/CRY family members were closely related to <i>Arabidopsis thaliana</i> and <i>Solanum lycopersicum</i>. We isolated a cryptochrome gene, <i>GbCRY1</i>, from <i>G. biloba</i> and analyzed its structure and function. <i>GbCRY1</i> shared high similarity with <i>AtCRY1</i> from <i>A. thaliana. GbCRY1</i> expression level was higher in stems and leaves and lower in roots, male strobili, female strobili. <i>GbCRY1</i> expression level fluctuated periodically within 24 h, gradually increased in the dark, and decreased under blue light. The newly germinated ginkgo seedlings were cultured under dark, white light, and blue light conditions. The blue light normally induced photomorphogenesis of ginkgo seedlings, which included hypocotyl elongation inhibition, leaf expansion inhibition, and chlorophyll formation. Treating dark-adapted ginkgo leaves with blue light could induce stomatal opening. At the same time, blue light reduced the expression level of <i>GbCRY1</i> in the process of inducing photomorphogenesis and stoma opening. Our results provide evidence that <i>GbCRY1</i> expression is affected by space, circadian cycle and light, and also proves that <i>GbCRY1</i> is related to ginkgo circadian clock, photomorphogenesis and stoma opening process.
DOI: 10.6084/m9.figshare.9118373.v1
title: Estimating Time-Varying Graphical Models

description: In this paper, we study time-varying graphical models based on data measured over a temporal grid. Such models are motivated by the needs to describe and understand evolving interacting relationships among a set of random variables in many real applications, for instance the study of how stock prices interact with each other and how such interactions change over time. We propose a new model, <i>LOcal Group Graphical Lasso Estimation</i> (loggle), under the assumption that the graph topology changes gradually over time. Specifically, loggle uses a novel local group-lasso type penalty to efficiently incorporate information from neighboring time points and to impose structural smoothness of the graphs. We implement an ADMM based algorithm to fit the loggle model. This algorithm utilizes blockwise fast computation and pseudo-likelihood approximation to improve computational efficiency. An R package loggle has also been developed and is available on https://cran.r-project.org/. We evaluate the performance of loggle by simulation experiments. We also apply loggle to S&P 500 stock price data and demonstrate that loggle is able to reveal the interacting relationships among stock prices and among industrial sectors in a time period that covers the recent global financial crisis. The supplemental materials for this paper are also available online.
DOI: 10.6084/m9.figshare.23797308
title: Additional file 1 of Diagnostic yield and novel candidate genes for neurodevelopmental disorders by exome sequencing in an unselected cohort with microcephaly

description: Additional file 1: Supplementary Table S1. Detailed phenotypic and genotypic data of 55 cases with a monogenic cause.
DOI: 10.6084/m9.figshare.13311231
title: Additional file 1 of Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

description: Additional file 1. Supplementary Information which contains Extended results note 1, Figure S1 and Supplementary Table 1.
DOI: 10.6084/m9.figshare.21175666
title: Additional file 3 of Incorporating kernelized multi-omics data improves the accuracy of genomic prediction

description: Additional file 3: Table S1. The details of 25 Pearson’s correlation coefficients of GBLUP, mssBLUP, and wmssBLUP for LDM, HWC, SF, and pH.
DOI: 10.6084/m9.figshare.8073650
title: Additional file 5: of Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells

description: Down_KEGG_pathway_iden. (XLS 13 kb)
DOI: 10.6084/m9.figshare.8073659
title: Additional file 6: of Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells

description: Up_KEGG_pathway_iden. (XLS 33 kb)
DOI: 10.6084/m9.figshare.12788439.v1
title: Additional file 4 of Prognostic value of a five-lncRNA signature in esophageal squamous cell carcinoma

description: Additional file 4: Table S3. The 1023 signatures comprising lncRNAs in the GSE53624 dataset (n = 119)
DOI: 10.6084/m9.figshare.12788430
title: Additional file 1 of Prognostic value of a five-lncRNA signature in esophageal squamous cell carcinoma

description: Additional file 1: Table S1. The detail of lncRNAs and GAPDH primers in this study.
DOI: 10.6084/m9.figshare.12788436
title: Additional file 3 of Prognostic value of a five-lncRNA signature in esophageal squamous cell carcinoma

description: Additional file 3: Table S2. Ten out of the 19 prognostic-related lncRNAs showed a consistent risk trend in the high throughput sequencing data.
DOI: 10.6084/m9.figshare.23274248
title: Analysis of the complete plastomes of <i>Bidens pilosa</i> L. 1753 (Asteraceae, Coreopsideae) from Beijing, China reveals high genetic diversity and possible misidentifications

description: <i>Bidens pilosa</i> L. 1753 is a perennial herbaceous flowering plant, traditionally used in foods and medicines. In this study, we sequenced, assembled, and characterized the complete plastome of <i>B. pilosa</i> from Beijing, China. The plastome (MN385242) is circularized with a conservative quadripartite structure. Its length is 150,524 bp, including a large single-copy region (83,535 bp), a small single-copy region (17,627 bp), and a pair of inverted repeat regions (each 24,681 bp). The plastome consists of 128 genes, including 78 unique protein-coding, 28 unique tRNA, and 4 unique rRNA genes. Phylogenetic analyses showed all five <i>B. pilosa</i> plants couldn’t form a monophyletic clade and were separated into three clades. The results of K2P distance and molecular markers were all consistent with those of phylogenetic analysis, revealing high genetic diversity and even possible misidentifications of the <i>B. pilosa</i>. Our results highlighted the importance of correct species identification of materials in medicinal products.
DOI: 10.6084/m9.figshare.12788490.v1
title: Additional file 4 of Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

description: Additional file 4: Supplementary Table S11. Sample correlation analysis of three biological replicates in RNA-seq. Supplementary Table S12. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR &lt; 0.05, log2FC &gt; 1 or log2FC &lt; − 1,verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of salt. Supplementary Table S13. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR &lt; 0.05, log2FC &gt; 1 or log2FC &lt; − 1, verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of alkali. Supplementary Table S14. Differentially expressed genes (DEGs) detected by DESeq2 methods (FDR &lt; 0.05, log2FC &gt; 1 or log2FC &lt; − 1,verticals represent normal genes. Up and down arrows represent up and down) in RNA-seq of salt-alkali. Supplementary Table S15. Co-expression network identified by AppleMDO analysis tools in hybrids tolerant or sensitive to salt, alkali, and salt-alkali treatments in hybrids from Malus robusta Rehd. ‘Baleng Crab’ × M. pumila Mill. ‘M9’. Supplementary Table S16. Data for allelic variations of markers using for KASP assay in hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S17. Estimates of marker genotype effects on salt, alkali, and salt-alkali injury indices in hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S18. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of alkali injury index in 299 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila) . Supplementary Table S19. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of salt injury index in 285 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila). Supplementary Table S20. The marker genotypes, genomics predicted values (GPV), and observed phenotype values (OPV) of saline-alkali injury index in 194 F1 hybrids from ‘Baleng Crab’ (Malus robusta) × ‘M9’ (M. pumila)
DOI: 10.6084/m9.figshare.8073704.v1
title: Additional file 3: of Photoperiod sensitivity of Canadian flax cultivars and 5-azacytidine treated early flowering derivative lines

description: CDC Sorrel x (Royal orÂ RE1/2/3) field data. Start of flowering time, start of full flowering, days to maturity and plantÂ height for F2, F3 and bulk F3Â CDC Sorrel x RE1/2/3 or Royal populations. (XLS 81 kb)
DOI: 10.6084/m9.figshare.12262937
title: Additional file 2 of Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)

description: Additional file 2: Table S2. Statistical data of the RNA-Seq reads for four samples.
DOI: 10.6084/m9.figshare.12262946
title: Additional file 3 of Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)

description: Additional file 3: Table S3. All lncRNAs in peanut.
DOI: 10.6084/m9.figshare.12262958.v1
title: Additional file 5 of Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)

description: Additional file 5: Table S5. Target genes prediction of differentially expressed lncRNAs. (S5–1) Target genes prediction of differentially expressed lncRNAs in T1 vs C1. (S5–2) Target genes prediction of differentially expressed lncRNAs in T2 vs C2.