cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9744962
title: Spectral library from Fusion instrument for inputing to Skyline Software

description: Spectral library from Fusion instrument for inputing to Skyline Software Part 1.
The original file is too big and exceeds Skyline limits. Thus it was divided into two parts.
DOI: 10.6084/m9.figshare.12366467
title: Tracing <i>Brucella</i> evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes

description: The host range of <i>Brucella</i> organisms has expanded from terrestrial and marine mammals to fish and amphibians. The high homology genomes of different <i>Brucella</i> organisms promote us to investigate evolutionary patterns for nucleotide, codon and amino acid usage patterns at gene levels among <i>Brucella</i> species. Although the similar patterns for nucleotide and synonymous codon usages exist in gene population, GC composition at the first codon position has significant correlations to that of the second and third codon positions, respectively, suggesting that nucleotide usages surrounding one codon influence synonymous codon usage patterns. Evolutionary patterns represented by synonymous codon and amino acid usages reflect host factor impacting <i>Brucella</i> speciation. As for genetic variations of important virulent factors involved with different biological functions, genes encoding lipoplysaccharides (LPSs) display more distinctive codon adaptation to <i>Brucella</i> than those of the BvrR/BvrS system and type IV secretion system. By Bayesian analysis, the polygenetic constructions for these genes of virulent factors shared by <i>Brucella</i> species display the purifying/positive selections and partially host factor in mediating genetic variations of these genes. The systemic analyses for nucleotide, synonymous codon and amino acid usages at gene level and genetic variations of important virulent factor genes display that host limitation influences either genetic characterizations at gene level or a particular gene involved in virulent factors of <i>Brucella</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14988096
title: Data_File_2.csv

description: Values underlying Fig. 4b for ECO-BB sensor
DOI: 10.6084/m9.figshare.8172317
title: Additional file 2: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S2. The change fold of genes listed in the manuscript. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12890699
title: figure 3 from The adsorption and mechanism of the nitrification inhibitor nitrapyrin in different types of soils

description: Fig. 3 The contribution of partitioning and surface adsorption
DOI: 10.6084/m9.figshare.8172356
title: Additional file 7: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S7. The homologous genes between M. bovis BCG and M. tuberculosis H37Rv. (XLS 1840 kb)
DOI: 10.6084/m9.figshare.12890699.v1
title: figure 3 from The adsorption and mechanism of the nitrification inhibitor nitrapyrin in different types of soils

description: Fig. 3 The contribution of partitioning and surface adsorption
DOI: 10.6084/m9.figshare.12890702
title: figure 1 from The adsorption and mechanism of the nitrification inhibitor nitrapyrin in different types of soils

description: Fig. 1 Adsorption kinetics curve (the initial concentration was 50 mg/L)
DOI: 10.6084/m9.figshare.8172317.v1
title: Additional file 2: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S2. The change fold of genes listed in the manuscript. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8172335.v1
title: Additional file 4: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S4. The complete list of differentially produced metabolites in control and VB1-treated samples. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.12890693
title: figure 2 from The adsorption and mechanism of the nitrification inhibitor nitrapyrin in different types of soils

description: Fig. 2 Adsorption isotherm curves
DOI: 10.6084/m9.figshare.8172374.v1
title: Additional file 5: of Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family

description: Table S4 A. Oxidative related genes from the Rhodospirillaceae members; Table S4 B. Iron related genes from the Rhodospirillaceae members; Table S4 C DNA repair related genes from the Rhodospirillaceae members (XLSX 459 kb)
DOI: 10.6084/m9.figshare.12366467.v2
title: Tracing <i>Brucella</i> evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes

description: The host range of <i>Brucella</i> organisms has expanded from terrestrial and marine mammals to fish and amphibians. The high homology genomes of different <i>Brucella</i> organisms promote us to investigate evolutionary patterns for nucleotide, codon and amino acid usage patterns at gene levels among <i>Brucella</i> species. Although the similar patterns for nucleotide and synonymous codon usages exist in gene population, GC composition at the first codon position has significant correlations to that of the second and third codon positions, respectively, suggesting that nucleotide usages surrounding one codon influence synonymous codon usage patterns. Evolutionary patterns represented by synonymous codon and amino acid usages reflect host factor impacting <i>Brucella</i> speciation. As for genetic variations of important virulent factors involved with different biological functions, genes encoding lipoplysaccharides (LPSs) display more distinctive codon adaptation to <i>Brucella</i> than those of the BvrR/BvrS system and type IV secretion system. By Bayesian analysis, the polygenetic constructions for these genes of virulent factors shared by <i>Brucella</i> species display the purifying/positive selections and partially host factor in mediating genetic variations of these genes. The systemic analyses for nucleotide, synonymous codon and amino acid usages at gene level and genetic variations of important virulent factor genes display that host limitation influences either genetic characterizations at gene level or a particular gene involved in virulent factors of <i>Brucella</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22328160.v1
title: Histone demethylase KDM4B contributes to advanced clear cell renal carcinoma and association with copy number variations and cell cycle progression

description: Advanced renal cell carcinoma (RCC) poses a threat to patient survival. Epigenetic remodelling is the pathogenesis of renal cancer. Histone demethylase 4B (KDM4B) is overexpressed in many cancers through various pathways. However, the role of KDM4B in clear cell renal carcinoma has not yet been elucidated. The differential expression of KDM4B was first verified by analysing public databases. The expression of KDM4B in fresh tissues and pathology slides was further analysed by western blotting and immunohistochemical staining. KDM4B overexpression and knockdown cell lines were also established. Cell Counting Kit-8 (CCK-8) assay was used to detect cell growth. Transwell assays were performed to assess cell migration. Xenografts were used to evaluate tumour growth and metastasis <i>in vivo</i>. Finally, KDM4B expression levels associated with copy number variation (CNV) and cell cycle stage were evaluated based on single-cell RNA sequencing data. KDM4B was expressed at higher levels in tumour tissues than in the adjacent normal tissues. High levels of KDM4B are associated with worse pathological features and poorer prognosis. KDM4B also promotes cell proliferation and migration <i>in vitro</i>, as well as tumour growth and metastasis <i>in vivo</i>. Tumour cells with high KDM4B expression exhibited higher CNV levels and a greater proportion of cells in the G1/S transition phase. Our results confirm that KDM4B promotes the progression of clear cell renal carcinoma, is correlated with poor prognosis, and may be related to high levels of CNV and cell cycle progression.
DOI: 10.6084/m9.figshare.8172341.v1
title: Additional file 5: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S5. The complete list of detected amino acids in control and VB1-treated samples. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8172350
title: Additional file 6: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S6. The associated KEGG analysis of transcriptomics and metabolomics in control and VB1-treated samples. (XLS 44 kb)
DOI: 10.6084/m9.figshare.8172350.v1
title: Additional file 6: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S6. The associated KEGG analysis of transcriptomics and metabolomics in control and VB1-treated samples. (XLS 44 kb)
DOI: 10.6084/m9.figshare.11317895
title: Population Grid for China SSP2RCP4.5

description: Population Grid for China under SSP2RCP4.5 from 2010 to 2100
DOI: 10.6084/m9.figshare.8172266
title: Additional file 1: of Relationship between burnout and career choice regret among Chinese neurology postgraduates

description: The initial and final logistic models of binary logistic regression analysis of burnout. (XLS 41 kb)
DOI: 10.6084/m9.figshare.22328160
title: Histone demethylase KDM4B contributes to advanced clear cell renal carcinoma and association with copy number variations and cell cycle progression

description: Advanced renal cell carcinoma (RCC) poses a threat to patient survival. Epigenetic remodelling is the pathogenesis of renal cancer. Histone demethylase 4B (KDM4B) is overexpressed in many cancers through various pathways. However, the role of KDM4B in clear cell renal carcinoma has not yet been elucidated. The differential expression of KDM4B was first verified by analysing public databases. The expression of KDM4B in fresh tissues and pathology slides was further analysed by western blotting and immunohistochemical staining. KDM4B overexpression and knockdown cell lines were also established. Cell Counting Kit-8 (CCK-8) assay was used to detect cell growth. Transwell assays were performed to assess cell migration. Xenografts were used to evaluate tumour growth and metastasis <i>in vivo</i>. Finally, KDM4B expression levels associated with copy number variation (CNV) and cell cycle stage were evaluated based on single-cell RNA sequencing data. KDM4B was expressed at higher levels in tumour tissues than in the adjacent normal tissues. High levels of KDM4B are associated with worse pathological features and poorer prognosis. KDM4B also promotes cell proliferation and migration <i>in vitro</i>, as well as tumour growth and metastasis <i>in vivo</i>. Tumour cells with high KDM4B expression exhibited higher CNV levels and a greater proportion of cells in the G1/S transition phase. Our results confirm that KDM4B promotes the progression of clear cell renal carcinoma, is correlated with poor prognosis, and may be related to high levels of CNV and cell cycle progression.
DOI: 10.6084/m9.figshare.8172428.v1
title: MOESM1 of Development of large-scale mosquito densovirus production by in vivo methods

description: Additional file 1: Table S1. Primers and amplification conditions for PCR and qPCR assays.
DOI: 10.6084/m9.figshare.8172266.v1
title: Additional file 1: of Relationship between burnout and career choice regret among Chinese neurology postgraduates

description: The initial and final logistic models of binary logistic regression analysis of burnout. (XLS 41 kb)
DOI: 10.6084/m9.figshare.8172461.v1
title: Additional file 2: of New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes

description: Table S1. Sequenced libraries of O. felineus. Table S2. Functionally annotated genes of O. felineus. Table S3. F. hepatica transposable elements and their classification. 3.2. O. felineus transposable elements and their classification. 3.3. O. viverrini transposable elements and their classification. 3.4. C. sinensis transposable elements and their classification. Table S4. Genome-wide synteny between O. felineus, O. viverrini and ĐĄ. sinensis. Table S5. Summary statistics of the gene annotations produced by a number of prediction approaches used for the annotation of O. felineus genome assembly. Table S6. Differential gene expression in O. felineus metacercariae and adult stage. Data are presented as FPKM values (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) with p-value adjusted &lt;â 0.05. Table S7. Orthologous genes detected by ProteinOrtho software with the aid of syntenic information. Table S8. Differentially expressed genes in adult O. felineus and O. viverrini (expression values differing more than fourfold). Table S9. Differentially expressed genes in adult O. felineus and C. sinensis (expression values differing more than fourfold). Table S10. Statistics on completeness of genome annotations, as reported by BUSCO software using Eukaryota (EU) & Metazoa (MZ) sets of orthologs. Table S11. Evaluation report of O. felineus genome assembly produced by REAPR software. (XLSX 4591 kb)
DOI: 10.6084/m9.figshare.8172374
title: Additional file 5: of Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family

description: Table S4 A. Oxidative related genes from the Rhodospirillaceae members; Table S4 B. Iron related genes from the Rhodospirillaceae members; Table S4 C DNA repair related genes from the Rhodospirillaceae members (XLSX 459 kb)
DOI: 10.6084/m9.figshare.8172488.v1
title: Additional file 2: of A new chicken 55K SNP genotyping array

description: The second group of SNPs which related to the economic traits. The locus and the p-value of SNPs which related to 15 economic traits were provided. (XLSX 998 kb)
DOI: 10.6084/m9.figshare.8172494
title: Additional file 3: of A new chicken 55K SNP genotyping array

description: The third group of SNPs which related to 861 candidate genes. The information of 861 candidate genes and 118.4â K SNPs selected were provided. (XLSX 6645 kb)
DOI: 10.6084/m9.figshare.8172512.v1
title: Additional file 5: of A new chicken 55K SNP genotyping array

description: The loci information for the 55K array. The loci, allele information, SNPs frequencies in each breed/line, and overlap information were provided. (XLSX 7761 kb)
DOI: 10.6084/m9.figshare.8172467
title: Additional file 3: of Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors

description: Table S1. Targeted deep sequencing results. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7648259
title: Additional file 1: of Expression profile of microRNAs in porcine alveolar macrophages after Toxoplasma gondii infection

description: Table S1. Detailed miRNA data for the different groups (M12, M24, R12, and R24). (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8172356.v1
title: Additional file 7: of The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1

description: Table S7. The homologous genes between M. bovis BCG and M. tuberculosis H37Rv. (XLS 1840 kb)
DOI: 10.6084/m9.figshare.8172461
title: Additional file 2: of New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes

description: Table S1. Sequenced libraries of O. felineus. Table S2. Functionally annotated genes of O. felineus. Table S3. F. hepatica transposable elements and their classification. 3.2. O. felineus transposable elements and their classification. 3.3. O. viverrini transposable elements and their classification. 3.4. C. sinensis transposable elements and their classification. Table S4. Genome-wide synteny between O. felineus, O. viverrini and ĐĄ. sinensis. Table S5. Summary statistics of the gene annotations produced by a number of prediction approaches used for the annotation of O. felineus genome assembly. Table S6. Differential gene expression in O. felineus metacercariae and adult stage. Data are presented as FPKM values (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) with p-value adjusted &lt;â 0.05. Table S7. Orthologous genes detected by ProteinOrtho software with the aid of syntenic information. Table S8. Differentially expressed genes in adult O. felineus and O. viverrini (expression values differing more than fourfold). Table S9. Differentially expressed genes in adult O. felineus and C. sinensis (expression values differing more than fourfold). Table S10. Statistics on completeness of genome annotations, as reported by BUSCO software using Eukaryota (EU) & Metazoa (MZ) sets of orthologs. Table S11. Evaluation report of O. felineus genome assembly produced by REAPR software. (XLSX 4591 kb)
DOI: 10.6084/m9.figshare.8172473
title: Additional file 4: of Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors

description: Table S2. Single-cell sequencing results. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.8172476.v1
title: Additional file 5: of Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors

description: Table S3. Primers used in the study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.18134025
title: Caffeine prevents restenosis and inhibits vascular smooth muscle cell proliferation through the induction of autophagy

description: Caffeine is among the most highly consumed substances worldwide, and it has been associated with decreased cardiovascular risk. Although caffeine has been shown to inhibit the proliferation of vascular smooth muscle cells (VSMCs), the mechanism underlying this effect is unknown. Here, we demonstrated that caffeine decreased VSMC proliferation and induced macroautophagy/autophagy in an <i>in vivo</i> vascular injury model of restenosis. Furthermore, we studied the effects of caffeine in primary human and mouse aortic VSMCs and immortalized mouse aortic VSMCs. Caffeine decreased cell proliferation, and induced autophagy flux via inhibition of MTOR signaling in these cells. Genetic deletion of the key autophagy gene <i>Atg5</i>, and the <i>Sqstm1</i>/<i>p62</i> gene encoding a receptor protein, showed that the anti-proliferative effect by caffeine was dependent upon autophagy. Interestingly, caffeine also decreased WNT-signaling and the expression of two WNT target genes, <i>Axin2</i> and <i>Ccnd1</i> (cyclin D1). This effect was mediated by autophagic degradation of a key member of the WNT signaling cascade, DVL2, by caffeine to decrease WNT signaling and cell proliferation. SQSTM1/p62, MAP1LC3B-II and DVL2 were also shown to interact with each other, and the overexpression of DVL2 counteracted the inhibition of cell proliferation by caffeine. Taken together, our <i>in vivo</i> and <i>in vitro</i> findings demonstrated that caffeine reduced VSMC proliferation by inhibiting WNT signaling via stimulation of autophagy, thus reducing the vascular restenosis. Our findings suggest that caffeine and other autophagy-inducing drugs may represent novel cardiovascular therapeutic tools to protect against restenosis after angioplasty and/or stent placement.
DOI: 10.6084/m9.figshare.8172482
title: Additional file 1: of A new chicken 55K SNP genotyping array

description: The summary of each sequencing pools. The raw reads number, clean reads number, sequencing depth, Q30 percentage, and coverage et al. for each sequencing library were provided. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8172560
title: Additional file 2: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S2. The differentially expressed genes in three tissues between ad libitum and restricted feeding group. (XLSX 3189 kb)
DOI: 10.6084/m9.figshare.8172476
title: Additional file 5: of Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors

description: Table S3. Primers used in the study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8172440
title: Additional file 1: of Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing

description: Table S1. Total RNA-Seq summary statistics. Table S2. List of differentially expressed genes in CF vs HC. Table S3. List of differentially expressed genes in Severe vs Mild CF. Table S4. List of differentially expressed transcripts in CF vs HC. Table S5. List of differentially expressed transcripts in Severe vs Mild CF. Table S6. List of differentially expressed miRNAs in CF vs HC. Table S7. List of differentially expressed miRNAs in Severe vs Mild CF. Table S8. Sample information. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.8172440.v1
title: Additional file 1: of Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing

description: Table S1. Total RNA-Seq summary statistics. Table S2. List of differentially expressed genes in CF vs HC. Table S3. List of differentially expressed genes in Severe vs Mild CF. Table S4. List of differentially expressed transcripts in CF vs HC. Table S5. List of differentially expressed transcripts in Severe vs Mild CF. Table S6. List of differentially expressed miRNAs in CF vs HC. Table S7. List of differentially expressed miRNAs in Severe vs Mild CF. Table S8. Sample information. (XLSX 151 kb)
DOI: 10.5281/zenodo.10669666
title: Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia

description: This repository contains all the PSI values, predictions, and RBP binding profiles needed to reproduce the figures and train your own models. 

The code to reproduce the figures, train your logistic regression or deep learning models models can be found on GitHub: https://github.com/lcmmichielsen/PSI_pred.
DOI: 10.5281/zenodo.10669667
title: Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia

description: This repository contains all the PSI values, predictions, and RBP binding profiles needed to reproduce the figures and train your own models. 

The code to reproduce the figures, train your logistic regression or deep learning models models can be found on GitHub: https://github.com/lcmmichielsen/PSI_pred.
DOI: 10.6084/m9.figshare.8172482.v1
title: Additional file 1: of A new chicken 55K SNP genotyping array

description: The summary of each sequencing pools. The raw reads number, clean reads number, sequencing depth, Q30 percentage, and coverage et al. for each sequencing library were provided. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8172512
title: Additional file 5: of A new chicken 55K SNP genotyping array

description: The loci information for the 55K array. The loci, allele information, SNPs frequencies in each breed/line, and overlap information were provided. (XLSX 7761 kb)
DOI: 10.6084/m9.figshare.7648274
title: Additional file 2: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S2. Amino acid sequences of 205 SWEET proteins from 14 plant species. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.7648274.v1
title: Additional file 2: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S2. Amino acid sequences of 205 SWEET proteins from 14 plant species. (XLSX 35 kb)