cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17059736.v1
title: Unique features of the m<sup>6</sup>A methylome and its response to drought stress in sea buckthorn (<i>Hippophae rhamnoides</i> Linn.)

description: In plants, recent studies have revealed that N6-methyladenosine (m<sup>6</sup>A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m<sup>6</sup>A methyltransferase, m<sup>6</sup>A demethylase and m<sup>6</sup>A-binding proteins can cause differential phenotypes, indicating that m<sup>6</sup>A may have critical roles in the plant. In this study, we depicted the m<sup>6</sup>A map of sea buckthorn (<i>Hippophae rhamnoides</i> Linn.) transcriptome. Similar to <i>A. thaliana</i>, m<sup>6</sup>A sites of sea buckthorn transcriptome is significantly enriched around the stop codon and within 3ʹ-untranslated regions (3ʹUTR). Gene ontology analysis shows that the m<sup>6</sup>A modification genes are associated with metabolic biosynthesis. In addition, we identified 13,287 different m<sup>6</sup>A peaks (DMPs) between leaf under drought (TR) and control (CK) treatment. It reveals that m<sup>6</sup>A has a high level of conservation and has a positive correlation with mRNA abundance in plants. GO and KEGG enrichment results showed that DMP modification DEGs in TR were particularly associated with ABA biosynthesis. Interestingly, our results showed three m<sup>6</sup>A demethylase (<i>HrALKBH10B, HrALKBH10C</i> and <i>HrALKBH10D</i>) genes were significantly increased following drought stress, which indicated that it may contributed the decreased m<sup>6</sup>A levels. This exhaustive m<sup>6</sup>A map provides a basis and resource for the further functional study of mRNA m<sup>6</sup>A modification in abiotic stress.
DOI: 10.6084/m9.figshare.22826862.v1
title: Additional file 2 of Effects of N and P additions on twig traits of wild apple (Malus sieversii) saplings

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.22826857
title: Additional file 4 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 4: Table S1. Genotyping of 98,241 SNPs based on GBS in 159 wild tea accessions.
DOI: 10.6084/m9.figshare.22826845.v1
title: Additional file 1 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 1: Table S1. Information of 159 wild tea accessions used in this study. Table S2. The quality control data of 159 wild tea accessions. Table S3. Statistics of Heterozygosity Rate of 98,241 SNPs in 159 wild tea accessions. Table S4. SNP density. Table S5. Statistics of the number and ratio of the accessions of species, rock classes and geologically suitable area in three inferred populations. Table S6. Statistics of the number and ratio of the accessions of altitude gradient in three inferred populations. Table S7. The soil nutrient content and altitude factor of 159 wild tea accessions.
DOI: 10.6084/m9.figshare.22826845
title: Additional file 1 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 1: Table S1. Information of 159 wild tea accessions used in this study. Table S2. The quality control data of 159 wild tea accessions. Table S3. Statistics of Heterozygosity Rate of 98,241 SNPs in 159 wild tea accessions. Table S4. SNP density. Table S5. Statistics of the number and ratio of the accessions of species, rock classes and geologically suitable area in three inferred populations. Table S6. Statistics of the number and ratio of the accessions of altitude gradient in three inferred populations. Table S7. The soil nutrient content and altitude factor of 159 wild tea accessions.
DOI: 10.6084/m9.figshare.22826854.v1
title: Additional file 3 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 3: Table S1. Sampling localities of 159 wild tea accessions.
DOI: 10.6084/m9.figshare.22826854
title: Additional file 3 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 3: Table S1. Sampling localities of 159 wild tea accessions.
DOI: 10.5281/zenodo.10666383
title: sechiopsis_laciniata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.10666384
title: sechiopsis_laciniata_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22826862
title: Additional file 2 of Effects of N and P additions on twig traits of wild apple (Malus sieversii) saplings

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.11293397
title: MOESM2 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 2. The full microarray data (median centered) is presented in two-way ANOVA analysis. N-6 PUFA adequate and n-6 PUFA deprived diet groups at baseline, day 1, and day 3 following LPS administration.
DOI: 10.6084/m9.figshare.11293397.v1
title: MOESM2 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 2. The full microarray data (median centered) is presented in two-way ANOVA analysis. N-6 PUFA adequate and n-6 PUFA deprived diet groups at baseline, day 1, and day 3 following LPS administration.
DOI: 10.6084/m9.figshare.11293406
title: MOESM3 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 3. The full microarray data (median centered) is presented in one-way ANOVA analysis. N-6 PUFA adequate and n-6 PUFA deprived diet groups at baseline, day 1, and day 3 following LPS administration.
DOI: 10.6084/m9.figshare.11293406.v1
title: MOESM3 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 3. The full microarray data (median centered) is presented in one-way ANOVA analysis. N-6 PUFA adequate and n-6 PUFA deprived diet groups at baseline, day 1, and day 3 following LPS administration.
DOI: 10.6084/m9.figshare.11293418
title: MOESM4 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 4. An exploratory analysis of the candidate genes in response to the n-6 PUFA deprived versus adequate diet using Student’s t-test of microarray data at baseline, day 1, and day 3 following LPS administration.
DOI: 10.6084/m9.figshare.11293418.v1
title: MOESM4 of The effects of n-6 polyunsaturated fatty acid deprivation on the inflammatory gene response to lipopolysaccharide in the mouse hippocampus

description: Additional file 4. An exploratory analysis of the candidate genes in response to the n-6 PUFA deprived versus adequate diet using Student’s t-test of microarray data at baseline, day 1, and day 3 following LPS administration.
DOI: 10.34808/jhn9-5v82
title: Physicochemical studies (Raman, XRD) of poly(lactic acid)-carbon black-nanodiamond composites

description: This dataset contains physico-chemical examination of a new 3D printing-dedicated composites with poly-lactic acid (PLA), carbon black (CB) and nanodiamond fillers. Two types of nanodiamonds were studied: detonation nanodiamonds (DND) and boron-doped carbon nanowalls (BCNW). The investigated techniques include Raman spectroscopy and X-ray diffraction (XRD). The measurements were performed with different range of CB (10-25 wt.%) with or without DND/BCNW additives. 
These results are part of the manuscript published in Microchimica Acta (https://doi.org/10.1007/s00604-023-05940-7). The aim of this research was to optimize the composite composition for its used as electrically-conductive 3D printing filament.
DOI: 10.6084/m9.figshare.7622633
title: Additional file 3: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S3. â The performance of different lengths of input peptides. The table shows the performance measures (Accuracy, Specificity, Sensitivity, AUC, MCC) for different lengths (21, 23, 25, 27, 29, 31, 33, 35) of fragments. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7622666
title: Additional file 7: of A deep learning method to more accurately recall known lysine acetylation sites

description: TableÂ 7. Detailed parameter information about the neural network. The table contains the parameter information of MLP: the number of neurons in each layer, activation function, momentum, loss function, batch size, and learning rate. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.14228027
title: Additional file 6 of Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus

description: Additional file 6: Table S5. Imprinted genes identified in 20 DAP endosperm of reciprocal hybrids.
DOI: 10.6084/m9.figshare.7622666.v1
title: Additional file 7: of A deep learning method to more accurately recall known lysine acetylation sites

description: TableÂ 7. Detailed parameter information about the neural network. The table contains the parameter information of MLP: the number of neurons in each layer, activation function, momentum, loss function, batch size, and learning rate. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.14437202.v3
title: Additional file of Response of swine spleen to Streptococcus suis infection revealed by transcription analysis

description: Additional file of Response of swine spleen to Streptococcus suis infection revealed by transcription analysis
DOI: 10.6084/m9.figshare.22826817
title: Additional file 2 of Magnesium chelatase subunit D is not only required for chlorophyll biosynthesis and photosynthesis, but also affecting starch accumulation in Manihot esculenta Crantz

description: Additional file 2: Table S2. The information of MV, pI and positive/negative charge residues of MeChlD.
DOI: 10.6084/m9.figshare.17059736
title: Unique features of the m<sup>6</sup>A methylome and its response to drought stress in sea buckthorn (<i>Hippophae rhamnoides</i> Linn.)

description: In plants, recent studies have revealed that N6-methyladenosine (m<sup>6</sup>A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m<sup>6</sup>A methyltransferase, m<sup>6</sup>A demethylase and m<sup>6</sup>A-binding proteins can cause differential phenotypes, indicating that m<sup>6</sup>A may have critical roles in the plant. In this study, we depicted the m<sup>6</sup>A map of sea buckthorn (<i>Hippophae rhamnoides</i> Linn.) transcriptome. Similar to <i>A. thaliana</i>, m<sup>6</sup>A sites of sea buckthorn transcriptome is significantly enriched around the stop codon and within 3ʹ-untranslated regions (3ʹUTR). Gene ontology analysis shows that the m<sup>6</sup>A modification genes are associated with metabolic biosynthesis. In addition, we identified 13,287 different m<sup>6</sup>A peaks (DMPs) between leaf under drought (TR) and control (CK) treatment. It reveals that m<sup>6</sup>A has a high level of conservation and has a positive correlation with mRNA abundance in plants. GO and KEGG enrichment results showed that DMP modification DEGs in TR were particularly associated with ABA biosynthesis. Interestingly, our results showed three m<sup>6</sup>A demethylase (<i>HrALKBH10B, HrALKBH10C</i> and <i>HrALKBH10D</i>) genes were significantly increased following drought stress, which indicated that it may contributed the decreased m<sup>6</sup>A levels. This exhaustive m<sup>6</sup>A map provides a basis and resource for the further functional study of mRNA m<sup>6</sup>A modification in abiotic stress.
DOI: 10.6084/m9.figshare.11293574
title: MOESM1 of The expanding pattern of Aedes aegypti in southern Yunnan, China: insights from microsatellite and mitochondrial DNA markers

description: Additional file 1: Table S1. The microsatellite short tandem repeat data.
DOI: 10.6084/m9.figshare.11293574.v1
title: MOESM1 of The expanding pattern of Aedes aegypti in southern Yunnan, China: insights from microsatellite and mitochondrial DNA markers

description: Additional file 1: Table S1. The microsatellite short tandem repeat data.
DOI: 10.6084/m9.figshare.14437202.v2
title: Additional file of Response of swine spleen to Streptococcus suis infection revealed by transcription analysis

description: Additional file of Response of swine spleen to Streptococcus suis infection revealed by transcription analysis
DOI: 10.6084/m9.figshare.8147876
title: Additional file 2: of Genetic relationship between IL-10 gene polymorphisms and the risk of clinical atopic dermatitis

description: Figure S1. Subgroup analysis of the IL-10 -1082 A/G polymorphism according to ethnicity under the allele G vs. A model. Figure S2. Subgroup analysis of the IL-10 -1082 A/G polymorphism according to ethnicity under the AG vs. AA model. Figure S3. Subgroup analysis of the IL-10 -1082 A/G polymorphism according to ethnicity under the AG + GG vs. AA model. Figure S4. Subgroup analysis of the IL-10 -819 T/C polymorphism according to ethnicity under the allele C vs. T model. Figure S5. Subgroup analysis of the IL-10 -819 T/C polymorphism according to ethnicity under the TC vs. TT model. Figure S6. Subgroup analysis of the IL-10 -819 T/C polymorphism according to ethnicity under the TC + CC vs. TT model. Figure S7. Subgroup analysis of IL-10 -592 A/C polymorphism according to ethnicity under the allele C vs. A model. Figure S8. Subgroup analysis of IL-10 -592 A/C polymorphism according to ethnicity under the AC vs. AA model. Figure S9. Subgroup analysis of IL-10 -592 A/C polymorphism according to ethnicity under the AC + CC vs. AA model. (ZIP 2797 kb)
DOI: 10.6084/m9.figshare.7622621.v1
title: Additional file 1: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S1. The performance of six combined features without F-score. The table shows the performance measures (Accuracy, Specificity, Sensitivity, AUC, MCC) for the combination of six encoding methods. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7622633.v1
title: Additional file 3: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S3. â The performance of different lengths of input peptides. The table shows the performance measures (Accuracy, Specificity, Sensitivity, AUC, MCC) for different lengths (21, 23, 25, 27, 29, 31, 33, 35) of fragments. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7622651
title: Additional file 5: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S5. - The independent test set for lysine acetylation. The table shows all independent test sets (positive and negative fragments). (XLSX 314 kb)
DOI: 10.6084/m9.figshare.7622627.v1
title: Additional file 2: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S2. The F-score values of each feature. The table shows the F-score values of the 3972 features obtained by six encoding methods. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.7622645
title: Additional file 4: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S4. The training set for lysine acetylation. The table shows all training sets (positive and negative fragments). (XLSX 1137 kb)
DOI: 10.6084/m9.figshare.22826857.v1
title: Additional file 4 of Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau

description: Additional file 4: Table S1. Genotyping of 98,241 SNPs based on GBS in 159 wild tea accessions.
DOI: 10.6084/m9.figshare.7622645.v1
title: Additional file 4: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S4. The training set for lysine acetylation. The table shows all training sets (positive and negative fragments). (XLSX 1137 kb)
DOI: 10.6084/m9.figshare.7622651.v1
title: Additional file 5: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S5. - The independent test set for lysine acetylation. The table shows all independent test sets (positive and negative fragments). (XLSX 314 kb)
DOI: 10.6084/m9.figshare.14437205.v1
title: Additional file 1 of Response of swine spleen to Streptococcus suis infection revealed by transcription analysis

description: Additional file 1: Spleen transcriptome analysis following S. suis infection using the Affymetrix Porcine Genechip. Data of each probe is from the three piglets of the control group (NC-1P, NC-2P, NC-3P), the WT group (WT-1P, WT-2P, WT-3P) and the △HP0197 group (M97-1P, M97-2P, M97-3P). "P", present; "A", absent; "M", marginal; select while Count (P) ≥ 2 in two groups. Totally, 15,757, 14,992 and 15,487 probesets were detected expression in the control group, the WT group and △HP0197 group respectively. (XLS 8 MB)
DOI: 10.6084/m9.figshare.14437559
title: Additional file of Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

description: Additional file of Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate
DOI: 10.6084/m9.figshare.11293679
title: MOESM2 of Local origin or external input: modern horse origin in East Asia

description: Additional file 2: Table S2. Samples information.
DOI: 10.6084/m9.figshare.11293679.v1
title: MOESM2 of Local origin or external input: modern horse origin in East Asia

description: Additional file 2: Table S2. Samples information.
DOI: 10.6084/m9.figshare.7622621
title: Additional file 1: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S1. The performance of six combined features without F-score. The table shows the performance measures (Accuracy, Specificity, Sensitivity, AUC, MCC) for the combination of six encoding methods. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7622627
title: Additional file 2: of A deep learning method to more accurately recall known lysine acetylation sites

description: Table S2. The F-score values of each feature. The table shows the F-score values of the 3972 features obtained by six encoding methods. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.17059953
title: Genotype I African swine fever viruses emerged in domestic pigs in China and caused chronic infection

description: The Georgia-07-like genotype II African swine fever virus (ASFV) with high virulence has been prevalent in China since 2018. Here, we report that genotype I ASFVs have now also emerged in China. Two non-haemadsorbing genotype I ASFVs, HeN/ZZ-P1/21 and SD/DY-I/21, were isolated from pig farms in Henan and Shandong province, respectively. Phylogenetic analysis of the whole genome sequences suggested that both isolates share high similarity with NH/P68 and OURT88/3, two genotype I ASFVs isolated in Portugal in the last century. Animal challenge testing revealed that SD/DY-I/21 shows low virulence and efficient transmissibility in pigs, and causes mild onset of infection and chronic disease. SD/DY-I/21 was found to cause necrotic skin lesions and joint swelling. The emergence of genotype I ASFVs will present more problems and challenges for the control and prevention of African swine fever in China.
DOI: 10.6084/m9.figshare.25226153
title: 20240216_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.57967/hf/1770
title: ukr_pravda_2y
DOI: 10.57967/hf/1476
title: ukr_pravda_2y
DOI: 10.6084/m9.figshare.7622843.v1
title: MOESM1 of Development of a loop-mediated isothermal amplification coupled lateral flow dipstick targeting erm(41) for detection of Mycobacterium abscessus and Mycobacterium massiliense

description: Additional file 1. MICs of 6 drugs for M. abscessus and M. massiliense.
DOI: 10.5281/zenodo.7774638
title: Autoconfig: Balanced Minimum sum-of-squares clustering case

description: Autoconfig: Balanced Minimum sum-of-squares clustering case
DOI: 10.5281/zenodo.10666512
title: Autoconfig: Balanced Minimum sum-of-squares clustering case

description: Autoconfig: Balanced Minimum Sum-of-Squares Clustering

See https://github.com/rmartinsanta/ac-BMSSC for full details.

 

Authors of the original paper: Alberto (Herrán González)José Manuel (Colmenar Verdugo)Abraham (Duarte Muñoz)
DOI: 10.5281/zenodo.7774637
title: Autoconfig: Balanced Minimum sum-of-squares clustering case

description: Autoconfig: Balanced Minimum Sum-of-Squares Clustering

See https://github.com/rmartinsanta/ac-BMSSC for full details.

 

Authors of the original paper: Alberto (Herrán González)José Manuel (Colmenar Verdugo)Abraham (Duarte Muñoz)
DOI: 10.5281/zenodo.8013540
title: Autoconfig: Balanced Minimum sum-of-squares clustering case

description: Autoconfig: Balanced Minimum sum-of-squares clustering case
DOI: 10.6084/m9.figshare.7622843
title: MOESM1 of Development of a loop-mediated isothermal amplification coupled lateral flow dipstick targeting erm(41) for detection of Mycobacterium abscessus and Mycobacterium massiliense

description: Additional file 1. MICs of 6 drugs for M. abscessus and M. massiliense.
DOI: 10.6084/m9.figshare.19681736
title: Additional file 9 of Transcriptome and metabolome analyses reveal new insights into chlorophyll, photosynthesis, metal ion and phenylpropanoids related pathways during sugarcane ratoon chlorosis

description: Additional file 9: Table S9. The differential expression genes of Phenylpropanoid biosynthesis pathways.
DOI: 10.6084/m9.figshare.12865615.v1
title: Identification of hub genes, miRNAs and regulatory factors relevant for Duchenne muscular dystrophy by bioinformatics analysis

description: Duchenne muscular dystrophy (DMD) is currently the most commonly diagnosed form of muscular dystrophy due to mutations in the dystrophin gene. However, its pathological process remains unknown and there is a lack of specific molecular biomarkers. The aim of our study is to explore key regulatory connections underlying the progression of DMD. The gene expression profile dataset GSE38417 of DMD was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between DMD patients and healthy controls were screened using geo2R, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analyses. Then a protein–protein interaction (PPI) network and sub-network of modules were constructed. To investigate the regulatory network underlying DMD, a global triple network including miRNAs, mRNAs and transcription factors (TFs) was constructed. A total of 1811 DEGs were found between the DMD and control groups, among which HERC5, SKP2 and FBXW5 were defined as hub genes with a degree of connectivity &gt;35 in the PPI network. Furthermore, the five TFs ZNF362, ATAT1, SPI1, TCF12 and ABCF2, as well as the eight miRNAs miR-124a, miR-200b/200c/429, miR-19a/b, miR-23a/b, miR-182, miR-144, miR-498 and miR-18a/b were identified as playing crucial roles in the molecular pathogenesis of DMD. This paper provides a comprehensive perspective on the miRNA–TF–mRNA co-regulatory network underlying DMD, although the bioinformatic findings need further validation in future studies.