cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20035790
title: Additional file 2 of Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus

description: Additional file 2: Table S1. Phenotypic data of T1 are expressed as mean ± SD, T1 refers to 21 DAS. The data represents the results of three biological repetitions. Table S2. Phenotypic data of T2 are expressed as mean ± SD, T2 refers to 24 DAS. The data represents the results of three biological repetitions. Table S3. Quality evaluation of RNA-seq reads and mapped to reference genome. Table S4. Information on upregulated and downregulated DEGs of 21 DAS hybrid F1 (AM, CM, HM, HW) and their parents (A, C, H, M, W). Table S5. Information on upregulated and downregulated DEGs of 24 DAS hybrid F1 (AM, CM, HM, HW) and their parents (A, C, H, M, W). Table S6. Specific gene information for the classification of expression patterns of 12 types of ELD genes at 21 DAS. Table S7. Specific gene information for the classification of expression patterns of 12 types of ELD genes at 24 DAS. Table S8. Results of significant GO enrichment of F1 relative to the parent of the parental-ELD gene at 21 DAS. Table S9. Results of significant GO enrichment of F1 relative to the parent of the parental-ELD gene at 24 DAS. Table S10. Information on DEGs of strong hybrids and weak hybrids at 21 DAS. Table S11. The results of the significantly enriched GO terms of the DEGs shared by the two pairs of strong and weak hybrids at 21 DAS. Table S12. The results of the significantly enriched KEGG pathways of the DEGs shared by the two pairs of strong and weak hybrids at 21 DAS. Table S13. Information on DEGs of strong hybrids and weak hybrids at 24 DAS. Table S14. The results of the significantly enriched GO terms of the DEGs shared by the two pairs of strong and weak hybrids at 24 DAS. Table S15. The results of the significantly enriched KEGG pathways of the DEGs shared by the two pairs of strong and weak hybrids at 24 DAS. Table S16. Total genes in the yellow module. Table S17. KEGG results of significant enrichment of genes in the yellow module. Table S18. Hub genes in the yellow module. Table S19. GO terms that were significantly enriched with respect to hub genes in the yellow module. Table S20. Specific information about the sequence of the quantitative primers of randomly selected genes.
DOI: 10.6084/m9.figshare.20035820
title: Additional file 8 of Comprehensive analysis of the MYB transcription factor gene family in Morus alba

description: Additional file 8: Table S6. Relative expression matrix for 20 differentially expressed R2R3-MaMYBs during fruit ripening.
DOI: 10.6084/m9.figshare.24160872
title: Functional trait dataset of European groundwater Amphipoda: Niphargidae and Typhlogammaridae V1

description: The dataset contains morphological functional trait data for over 1100 individuals from 180 species and over 300 MOTUs of two groundwater Amphipoda families, Niphargidae and Typhlogammaridae. Measurements of 27 morphological traits are included in the dataset and accompanied by extensive metadata.
DOI: 10.6084/m9.figshare.24160875
title: Niphargidae phylogeny

description: The latest available phylogeny for Niphargidae. Currently published as a preprint: https://www.biorxiv.org/content/10.1101/2023.09.13.557531v1
DOI: 10.6084/m9.figshare.24160875.v1
title: Niphargidae phylogeny

description: The latest available phylogeny for Niphargidae. Currently published as a preprint: https://www.biorxiv.org/content/10.1101/2023.09.13.557531v1
DOI: 10.6084/m9.figshare.25102775
title: Data records summary and plots R code

description: The R code used for summarization of the dataset contents and production of the figures presented in the Data Descriptor.
DOI: 10.6084/m9.figshare.25102775.v1
title: Data records summary and plots R code

description: The R code used for summarization of the dataset contents and production of the figures presented in the Data Descriptor.
DOI: 10.6084/m9.figshare.25102781
title: List of Niphargidae Dinaric MOTUs

description: List of Niphargidae MOTUs distributed in the region of the Dinarides, Western Balkans.
DOI: 10.6084/m9.figshare.25102781.v1
title: List of Niphargidae Dinaric MOTUs

description: List of Niphargidae MOTUs distributed in the region of the Dinarides, Western Balkans.
DOI: 10.6084/m9.figshare.13226417.v1
title: Additional file 8 of Loss of PLK2 induces acquired resistance to temozolomide in GBM via activation of notch signaling

description: Additional file 8: Supplementary Table 3. The differentially expressed kinases in TCGA GBM.
DOI: 10.6084/m9.figshare.13226411
title: Additional file 6 of Loss of PLK2 induces acquired resistance to temozolomide in GBM via activation of notch signaling

description: Additional file 6: Supplementary Table 1. The differentially expressed kinases in GSE68029.
DOI: 10.6084/m9.figshare.13226414.v1
title: Additional file 7 of Loss of PLK2 induces acquired resistance to temozolomide in GBM via activation of notch signaling

description: Additional file 7: Supplementary Table 2. The differentially expressed kinases in GSE16011.
DOI: 10.5281/zenodo.10630628
title: Benchmarking in silico dataset for mammalian cell cultures

description: Dataset used for benchmarking in the publication "Calibration design for pharmaceutical bioprocesses: A novelapproach for knowledge transfer in Design of Experiments".

 

The dataset contain the same data in three formats: .csv as plain data format, .xlsx with additional metadata as required for DataHowLab, as well as plots in .pdf. Data marked with "fixed" is simulated without measurement noise, "noisy" indicates data corruption as explained in the paper. More details can be found in the main manuscript.
DOI: 10.24403/jp.1330382
title: Über die Verbreitung von Orobanche caryophyllacea SM. (Nelken-Sommerwurz) und Orobanche lutea BAUMG. (Gelbe Sommerwurz) in den östlichen Bundesländern Deutschlands / Jürgen Pusch, Klaus-Jörg Barthel, Ralph Schäfter
DOI: 10.24403/jp.1330383
title: Kleine lichenologische Mitteilungen III. / Ludwig Meinunger
DOI: 10.6084/m9.figshare.13226414
title: Additional file 7 of Loss of PLK2 induces acquired resistance to temozolomide in GBM via activation of notch signaling

description: Additional file 7: Supplementary Table 2. The differentially expressed kinases in GSE16011.
DOI: 10.6084/m9.figshare.13226426.v1
title: Additional file 1 of Identification of biomarkers and pathways in hypertensive nephropathy based on the ceRNA regulatory network

description: Additional file 1.
DOI: 10.6084/m9.figshare.20035799
title: Additional file 1 of Comprehensive analysis of the MYB transcription factor gene family in Morus alba

description: Additional file 1: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.20035808.v1
title: Additional file 4 of Comprehensive analysis of the MYB transcription factor gene family in Morus alba

description: Additional file 4: Table S3. Predicted cis-elements in promoter regions of MaMYBs.
DOI: 10.6084/m9.figshare.20035811
title: Additional file 5 of Comprehensive analysis of the MYB transcription factor gene family in Morus alba

description: Additional file 5: Table S4. Gene duplication in Morus alba.
DOI: 10.6084/m9.figshare.12177900.v1
title: Additional file 8 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 8: Supplementary Figure 6. The quality distribution maps of the clean tag base in each sample. The X-axis is the position of base in read, and the Y-axis represents the base mass value.
DOI: 10.24403/jp.1330384
title: Three new species of Passiflora from Ecuador / Michael Schwerdtfeger
DOI: 10.6084/m9.figshare.12177861
title: Additional file 2 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 2: Supplementary Table 2. RNA quality of six DPC samples. Supplementary Fig. 2. RNA quality (a) Agarose electrophoresis of RNA in DPCs; (b) Quality test results of total RNA by Agilent 2100.
DOI: 10.24403/jp.1330385
title: Bibliographie der Verbreitungskarten cubanischer Gefäßpflanzen / Hermann Manitz
DOI: 10.6084/m9.figshare.12177897
title: Additional file 7 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 7: Supplementary Figure 5. The quantity distribution maps of clean tag base in each sample. The X-axis is the position of the base in read, and the Y-axis represents the proportion of the base.
DOI: 10.6084/m9.figshare.12177855
title: Additional file 1 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 1: Supplementary Figure 1. Skin crosscutting HE staining of Rex rabbits with different hair density (100 magnification)(a) Low hair density (b) High hair density. Supplementary Table 1. Statistics of hair follicle numbers of Rex rabbits with different hair density. Note: Data shown are mean values ± s. d., and n = 3 per group. In the same row, values with with different letter superscripts mean significant difference(P &lt; 0.05).
DOI: 10.6084/m9.figshare.12177900
title: Additional file 8 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 8: Supplementary Figure 6. The quality distribution maps of the clean tag base in each sample. The X-axis is the position of base in read, and the Y-axis represents the base mass value.
DOI: 10.6084/m9.figshare.12177906
title: Additional file 9 of The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits

description: Additional file 9: Supplementary Table 5. LD-vs-HD_DEGseq. diffexpfilter.
DOI: 10.6084/m9.figshare.7459718.v1
title: Additional file 10: of Transmembrane protein GRINA modulates aerobic glycolysis and promotes tumor progression in gastric cancer

description: Table S7. Transcription factors predicted from JASPAR database that probably regulate GRINA expression. (XLS 169 kb)
DOI: 10.6084/m9.figshare.19518372
title: Additional file 5 of Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

description: Additional file 5: Table S2. Gene list of the 5 modules (midnight blue, skyblue2, brown2, navajowhite1, and lightpink3).
DOI: 10.6084/m9.figshare.7459718
title: Additional file 10: of Transmembrane protein GRINA modulates aerobic glycolysis and promotes tumor progression in gastric cancer

description: Table S7. Transcription factors predicted from JASPAR database that probably regulate GRINA expression. (XLS 169 kb)
DOI: 10.5281/zenodo.10529646
title: CEX Project - GROBID annotation aligned Gold Standard

description: The files here published represent the Gold Standard files mentioned below aligned to the GROBID guidelines for the creatin of a valid custom training dataset and has been used for training the citation model of the tool.

 

This publication is part of my Thesis research for the Digital Humanities and Digital Knowledge Master's Course at University of Bologna.

The gold standard can be found here, Pagnotta, O. (2024). CEX Project - Dataset and Gold Standard [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10535653.

The code can be found here Olga Pagnotta. (2024). olgagolgan/CEX-Project: CEX Project Code (software). Zenodo. https://doi.org/10.5281/zenodo.10638757.

The output dataset of Anystyle, Grobid, Outcite can be found here  Pagnotta, O. (2024). CEX Project - Output Dataset (Anystyle, GROBID, OUTCITE) (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10524898.

The trained GROBID citation models can be found here Pagnotta, O. (2024). CEX Project - trained GROBID citation models. Zenodo. https://doi.org/10.5281/zenodo.10529709.

Some results can be found here Pagnotta, O. (2023). Investigating the performance of GROBID and OUTCITE (Version v1). Zenodo. https://doi.org/10.5281/zenodo.10036455.

The final service can be found here Pagnotta, O. and Paolini, L. (2024). opencitations/cec: alpha version (service). Zenodo. https://doi.org/10.5281/zenodo.10635630.
DOI: 10.6084/m9.figshare.19518378.v1
title: Additional file 7 of Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

description: Additional file 7: Table S4. List of differentially expressed genes in breast muscle of Gushi chickens among 6, 14, 22, and 30 weeks.
DOI: 10.6084/m9.figshare.7459748
title: Additional file 2: of Subject level clustering using a negative binomial model for small transcriptomic studies

description: Table S1. Summary Statistics of ARI for G = 1000 and Non-zero Shift in Dispersion. Table S2. Summary Statistics of ARI for G = 5000 and Non-zero Shift in Dispersion. Table S3. Summary Statistics of ARI for G = 1000 and Zero Shift in Dispersion. Table S4. Summary Statistics of ARI for G = 5000 and Zero Shift in Dispersion (XLSX 129 kb)
DOI: 10.6084/m9.figshare.19518375
title: Additional file 6 of Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

description: Additional file 6: Table S3. List of hub genes indicated in the manuscript with midnight blue module.
DOI: 10.6084/m9.figshare.19518375.v1
title: Additional file 6 of Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

description: Additional file 6: Table S3. List of hub genes indicated in the manuscript with midnight blue module.
DOI: 10.6084/m9.figshare.22664111.v1
title: Complete mitochondrial genomes reveal the phylogenetic relationships of Duoma with eight representative sheep breeds and two ovis species

description: The <i>Ovis aries</i> Duoma breed is one of the most important alpine grassland-type sheep breeds in China. In this current study, we first reported the complete mitochondrial genome of Duoma sheep. Mitochondrial genome is 16,618 bp in length and exhibits the same typical structure as the other published sheep breeds. The genome contains 37 genes (22 tRNA, two rRNA, and 13 protein-coding genes (PCGs)) and a control region (D-loop region). Phylogenetic analysis shows that the Duoma sheep breed is closer to Ganjia sheep. Our findings will help the further evolution and conservation studies of Duoma sheep.
DOI: 10.6084/m9.figshare.16896971.v1
title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development

description: Preimplantation development is critical for reproductive successes in mammals. Thus, it is important to understand how preimplantation embryogenesis is regulated. As a key event of preimplantation development, epigenetic reprogramming has been widely studied, yet how epigenetic complexes regulate preimplantation development remains largely unknown. Retinoblastoma binding protein 4 (RBBP4) and 7 (RBBP7) are integral components of epigenetic complexes including SIN3A, NuRD, and CoREST. Here, we demonstrate that double knockdown of <i>Rbbp4</i> and <i>7</i>, but not individually, causes embryonic lethality during the morula-to-blastocyst transition. Mechanistically, depletion of RBBP4 and 7 results in dysregulation of genes related to cell cycle, lineage development, and regulation of transcription, which is accompanied by cell cycle block, disrupted lineage specification and chromatin structure. Interestingly, RBBP4/7 depletion leads to a dramatic increase in H3.3 and H3K27ac abundance during morula-to-blastocyst transition. ChIP-seq analysis in early embryos and embryonic stem cells reveals enrichment of H3.3 at the promoter regions of RBBP4/7 target genes. In summary, our studies demonstrate the compensatory role of RBBP4/7 and reveal its potential mechanisms in preimplantation development. <b>Summary sentence</b>: RBBP4 and RBBP7 play a compensatory role in regulating cell proliferation, apoptosis, and histone H3.3 deposition during preimplantation development.
DOI: 10.6084/m9.figshare.20035802.v1
title: Additional file 2 of Comprehensive analysis of the MYB transcription factor gene family in Morus alba

description: Additional file 2: Table S2. MYBs in Morus alba.
DOI: 10.6084/m9.figshare.7459835
title: MOESM2 of Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

description: Additional file 2. Gene expression data. The complete gene expression data.
DOI: 10.6084/m9.figshare.7459835.v1
title: MOESM2 of Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

description: Additional file 2. Gene expression data. The complete gene expression data.
DOI: 10.24403/jp.1330386
title: Adler, W., Oswald, K. & Fischer, R.: Exkursionsflora von Österreich. - Stuttgart ; Wien : Verlag Eugen Ulmer, 1994 / [rezensiert von] H. Manitz
DOI: 10.24403/jp.1330387
title: Augustin, H.: Die Waldgesellschaften des Oberpfalzer Waldes. - Hoppea 51: 5-314, 1991. / [rezensiert von] H.-J. Zündorf
DOI: 10.6084/m9.figshare.19518347
title: Additional file 1 of Identification of severe fever with thrombocytopenia syndrome virus genotypes in patients and ticks in Liaoning Province, China

description: Additional file 1: 16S.mas. The alignment of the 16S rRNA sequences of 59 tick samples.
DOI: 10.6084/m9.figshare.16896971
title: Overlapping functions of RBBP4 and RBBP7 in regulating cell proliferation and histone H3.3 deposition during mouse preimplantation development

description: Preimplantation development is critical for reproductive successes in mammals. Thus, it is important to understand how preimplantation embryogenesis is regulated. As a key event of preimplantation development, epigenetic reprogramming has been widely studied, yet how epigenetic complexes regulate preimplantation development remains largely unknown. Retinoblastoma binding protein 4 (RBBP4) and 7 (RBBP7) are integral components of epigenetic complexes including SIN3A, NuRD, and CoREST. Here, we demonstrate that double knockdown of <i>Rbbp4</i> and <i>7</i>, but not individually, causes embryonic lethality during the morula-to-blastocyst transition. Mechanistically, depletion of RBBP4 and 7 results in dysregulation of genes related to cell cycle, lineage development, and regulation of transcription, which is accompanied by cell cycle block, disrupted lineage specification and chromatin structure. Interestingly, RBBP4/7 depletion leads to a dramatic increase in H3.3 and H3K27ac abundance during morula-to-blastocyst transition. ChIP-seq analysis in early embryos and embryonic stem cells reveals enrichment of H3.3 at the promoter regions of RBBP4/7 target genes. In summary, our studies demonstrate the compensatory role of RBBP4/7 and reveal its potential mechanisms in preimplantation development. <b>Summary sentence</b>: RBBP4 and RBBP7 play a compensatory role in regulating cell proliferation, apoptosis, and histone H3.3 deposition during preimplantation development.
DOI: 10.6084/m9.figshare.7459859.v1
title: MOESM5 of Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

description: Additional file 5. Regulators of differentially expressed genes. Full list of regulators of differentially expressed genes.
DOI: 10.6084/m9.figshare.19518347.v1
title: Additional file 1 of Identification of severe fever with thrombocytopenia syndrome virus genotypes in patients and ticks in Liaoning Province, China

description: Additional file 1: 16S.mas. The alignment of the 16S rRNA sequences of 59 tick samples.
DOI: 10.6084/m9.figshare.19518470.v1
title: Additional file 4 of Dynamic contrast-enhanced MRI radiomics nomogram for predicting axillary lymph node metastasis in breast cancer

description: Additional file 4.
DOI: 10.6084/m9.figshare.19518473
title: Additional file 5 of Dynamic contrast-enhanced MRI radiomics nomogram for predicting axillary lymph node metastasis in breast cancer

description: Additional file 5.
DOI: 10.6084/m9.figshare.19518369
title: Additional file 4 of Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

description: Additional file 4: Table S1. Gene list analyzed by WGCNA.
DOI: 10.6084/m9.figshare.19518461
title: Additional file 1 of Dynamic contrast-enhanced MRI radiomics nomogram for predicting axillary lymph node metastasis in breast cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.19518473.v1
title: Additional file 5 of Dynamic contrast-enhanced MRI radiomics nomogram for predicting axillary lymph node metastasis in breast cancer

description: Additional file 5.
DOI: 10.7270/q2g73gc7
title: BindingDB Entry 50044892: Synthesis and analysis of potentiala1,3-fucosyltransferase inhibitors.

description: Small molecule binding data for protein Alpha-(1,3)-fucosyltransferase 9, Uniprot Q9Y231
DOI: 10.7270/q2gm88rc
title: BindingDB Entry 50043247: Synthesis of novel diarylamino-1,3,5-triazine derivatives as FAK inhibitors with anti-angiogenic activity.

description: Small molecule binding data for protein Focal adhesion kinase 1/vascular endothelial growth factor receptor 3, Uniprot Q05397
DOI: 10.7270/q2jm2bz7
title: BindingDB Entry 50042245: Synthesis and structure-activity relationships of suramin-derived P2Y11 receptor antagonists with nanomolar potency.

description: Small molecule binding data for protein P2X purinoceptor 1, P2X purinoceptor 3, P2X purinoceptor 4, P2X2/P2X3 receptor, Purinergic receptor P2Y1, Purinergic receptor P2Y11, Purinergic receptor P2Y2, and Purinergic, P2X2, Uniprot P41231, P47900, P49653, P49654, P51575, P51577, P56373, and Q96G91
DOI: 10.7270/q2kp83p1
title: BindingDB Entry 50044355: Discovery of structurally novel, potent and orally efficacious GPR119 agonists.

description: Small molecule binding data for protein G-protein coupled receptor 119 (GPR119) and Glucose-dependent insulinotropic receptor, Uniprot Q7TQP3 and Q8TDV5
DOI: 10.7270/q2ks6sw8
title: BindingDB Entry 50042774: Design, synthesis, and pharmacological characterization of novel endomorphin-1 analogues as extremely potentµ-opioid agonists.

description: Small molecule binding data for protein Delta-type opioid receptor, Kappa-type opioid receptor, Mu-type opioid receptor, and mu/kappa opioid receptor, Uniprot P35372, P41143, P41145, P42866, and P97266
DOI: 10.7270/q2m0472h
title: BindingDB Entry 50044891: Inhibition of myeloperoxidase: evaluation of 2H-indazoles and 1H-indazolones.

description: Small molecule binding data for protein Myeloperoxidase (MPO), Uniprot P05164
DOI: 10.7270/q2mc91fn
title: BindingDB Entry 50043246: Optimization of N-benzoylindazole derivatives as inhibitors of human neutrophil elastase.

description: Small molecule binding data for protein Beta-chymotrypsin and Leukocyte elastase, Uniprot P08246
DOI: 10.7270/q2p270m7
title: BindingDB Entry 50043857: Structure-activity relationships of diamine inhibitors of cytochrome P450 (CYP) 3A as novel pharmacoenhancers. Part II: P2/P3 region and discovery of cobicistat (GS-9350).

description: Small molecule binding data for protein Cytochrome P450 1A, Cytochrome P450 2C19, Cytochrome P450 2C9, and Cytochrome P450 2D6 (2D6), Uniprot P05177, P10635, P11712, and P33261
DOI: 10.7270/q2qj7jnf
title: BindingDB Entry 50042773: Pyrimidoaminotropanes as potent, selective, and efficacious small molecule kinase inhibitors of the mammalian target of rapamycin (mTOR).

description: Small molecule binding data for protein Cytochrome P450 3A and Serine/threonine-protein kinase mTOR, Uniprot P08684 and P42345