cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16960508.v1
title: Additional file 12 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 12: Supplementary file 12. The differentially m6A methylated and expressed genes (DMEGs) identified in this study.
DOI: 10.6084/m9.figshare.16960529.v1
title: Additional file 6 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 6: Supplementary file 6. High-confidence m6A peaks identified for control samples and CGMMV-infected samples.
DOI: 10.6084/m9.figshare.16960511
title: Additional file 13 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 13: Supplementary file 13. Primers used for m6A-immunoprecipitation(IP)-qPCR (m6A -IP-qPCR) and Real-time quantitative PCR (qPCR).
DOI: 10.6084/m9.figshare.12644466
title: Additional file 1 of Next-generation sequencing analysis of endometrial screening liquid-based cytology specimens: a comparative study to tissue specimens

description: Additional file 1: Table S1. Somatic mutation prolife detected in endometrial cancers.
DOI: 10.6084/m9.figshare.21972917.v1
title: Table_Nephropathies_Lifetime risk_Raw data included variants.xlsx

description: Raw data to the paper " Lifetime risk of autosomal recessive kidney diseases calculated from genetic databases". All (likely) pathogenic included variants, their allele frequencies as listed in our in-house and gnomAD database.
DOI: 10.6084/m9.figshare.16960535
title: Additional file 8 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 8: Supplementary file 8. Characteristics of differentially methylated peaks (DMPs) in CGMMV-infected and control samples.
DOI: 10.6084/m9.figshare.16960538.v1
title: Additional file 9 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 9: Supplementary file 9. The m6A modification level of DEGs involved in immune responses and the production of siRNA involved in RNA interference in this study.
DOI: 10.57745/0anmo5
title: telomeres-eG1.tgz

description: Telomeres, early G1 phase
DOI: 10.57745/on5mlu
title: telomeres-siCTRL-S.tgz

description: Telomeres, siCTRL, S-phase
DOI: 10.57745/w36fl5
title: centromeres-G2.tgz

description: Centromeres, G2-phase
DOI: 10.6084/m9.figshare.16960477.v1
title: Additional file 2 of Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

description: Additional file 2.
DOI: 10.6084/m9.figshare.22723027.v1
title: Additional file 1 of Finerenone attenuates myocardial apoptosis, metabolic disturbance and myocardial fibrosis in type 2 diabetes mellitus

description: Additional file 1. Western blot.
DOI: 10.6084/m9.figshare.16960483.v1
title: Additional file 4 of Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

description: Additional file 4.
DOI: 10.5281/zenodo.10362041
title: Dataset: Environmental benchmarks for European Cement Industry

description: This dataset contains the information relative to the article "Environemntal benchmarks for European cement industry".

Reference paper

ResearchGate link
DOI: 10.5281/zenodo.10362042
title: Dataset: Environmental benchmarks for European Cement Industry

description: This dataset contains the information relative to the article "Environemntal benchmarks for European cement industry".

Reference paper

ResearchGate link
DOI: 10.6084/m9.figshare.16960499
title: Additional file 9 of Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

description: Additional file 9: Supplementary Table 8. The primers sequences used in this study.
DOI: 10.6084/m9.figshare.16960532.v1
title: Additional file 7 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 7: Supplementary file 7. Gene ontology (GO) analysis of the biological process, molecular function, and cellular component for the m6A -containing transcripts identified in m6A -seq in watermelon.
DOI: 10.6084/m9.figshare.6999176.v1
title: Additional file 2: of Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

description: Table S2. The count matrix for each sample. (XLSX 440 kb)
DOI: 10.6084/m9.figshare.16960478
title: Additional file 2 of Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

description: Additional file 2: Supplementary Table 1. Physicochemical characterization analysis of poplar XTH protein.
DOI: 10.6084/m9.figshare.16960492.v1
title: Additional file 7 of Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

description: Additional file 7.
DOI: 10.6084/m9.figshare.16960478.v1
title: Additional file 2 of Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

description: Additional file 2: Supplementary Table 1. Physicochemical characterization analysis of poplar XTH protein.
DOI: 10.6084/m9.figshare.16960495
title: Additional file 8 of Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

description: Additional file 8.
DOI: 10.6084/m9.figshare.16960495.v1
title: Additional file 8 of Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

description: Additional file 8.
DOI: 10.6084/m9.figshare.21679097.v1
title: AIM2 inflammasome activation may mediate high mobility group box 1 release in murine allergic rhinitis

description: Abstract Introduction: High mobility group box 1 protein participates in the pathogenesis of allergic rhinitis. Activation of the inflammasome can mediate the release of high mobility group box 1. The role of the absent in melanoma 2 inflammasome in allergic rhinitis remains unclear. Objective: This study aimed to investigate the function of absent in melanoma 2 inflammasome in murine allergic rhinitis and the interaction between high mobility group box 1 and the absent in melanoma 2 inflammasome. Methods: A murine allergic rhinitis model was established using twenty Balb/c mice. Expression of the components of the absent in melanoma 2 inflammasome: absent in melanoma 2, apoptosis-associated speck-like protein containing a CARD (Asc), caspase-1 p20, and additional nod-like receptor family pyrin domain containing 3 (Nlrp3) were detected by western blotting during allergic rhinitis. Alterations of absent in melanoma 2, caspase-1, and high mobility group box 1 after ovalbumin challenge were demonstrated by immunohistochemistry. TdT-mediated dUTP Nick end labeling, TUNEL assay, and cleavage of caspase-3 and PARP-1 were used for the observation of pyroptosis. Results: Eosinophilia and goblet cell infiltration were observed in the nasal mucosa of mice in the allergic rhinitis group. Absent in melanoma 2, Asc, and caspase-1 p20 increased after ovalbumin exposure while Nlrp3 did not. High mobility group box 1 was released in the nasal mucosa of allergic rhinitis mice. TUNEL-positive cells increased in the epithelium and laminae propria, whereas cleavage of caspase-3 and PARP-1 was not observed. Conclusions: The absent in melanoma 2 inflammasome was activated and pyroptosis may occur in the nasal mucosa after ovalbumin treatment. These may contribute to the translocation of high mobility group box 1 and the development of allergic rhinitis.
DOI: 10.6084/m9.figshare.16960496.v1
title: Additional file 8 of Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

description: Additional file 8: Supplementary Table 7. The fold-changes of differentially expressed PtrXTH genes under salt stress.
DOI: 10.6084/m9.figshare.4910039
title: Gene Function Expression Profile of Faba bean (Vicia faba) Seeds

description: <strong>These were Faba bean (Vicia faba L) genome assembly data</strong>.<strong>Total All-Unique genes number = 47621, Max length = 6656, Total length = 27605508, Average
length = 579, Number&gt;1000bp = 7092, Number&gt;2000bp = 1350.</strong> 

<br>
DOI: 10.6084/m9.figshare.7007228.v1
title: Genome-wide profiling of sRNAs in the <i>Verticillium dahliae</i>-infected <i>Arabidopsis</i> roots

description: Small RNAs (sRNAs, including small interfering RNAs [siRNAs] and micro RNAs [miRNAs]) are key mediators of RNA silencing (or RNA interference), which play important roles in plant development and response to biotic and abiotic stimulation. Verticillium wilt is a plant vascular disease caused by the soil-borne fungal pathogens, such as <i>Verticillium dahliae</i>. We previously reported that <i>V. dahliae</i> infection increased two plant endogenous miRNAs that were exported to fungal cell to silence virulence genes. To investigate plant sRNAs in genome-wide response to <i>V. dahliae</i> infection, in this study, we constructed two sRNA libraries from <i>Arabidopsis</i> roots with and without <i>V. dahliae</i> infection, respectively. In total, 31 conserved miRNAs were found to be differentially expressed during the early stage of infection with <i>V. dahliae</i> using sRNA sequencing. Among these, the expression levels of miR160, miR164, miR166, miR167, miR390 and miR156h were confirmed by northern blot. Reverse transcription quantitative real time polymerase chain reaction results showed that the induction of miRNAs (miR160, miR164, miR166 and miR167) upon <i>V. dahliae</i> infection downregulated the expression of their targeted genes (<i>ARF10, NAC1, PHV</i> and <i>ARF6</i>), respectively. In addition, we identified specific phased siRNAs generated from distinct regions of two libraries. Profiling of these miRNAs and sRNAs lay the foundation for further understanding and utilising the host-induced gene silencing strategy to control plant vascular pathogens.
DOI: 10.6084/m9.figshare.7007231
title: Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

description: Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.
DOI: 10.6084/m9.figshare.8047742
title: Supplementary Material

description: Supplementary Material to the paper 'Non-invasive coronary CT angiography-derived fractional flow reserve (FFR): A benchmark study comparing the diagnostic performance of four different computational methodologies'. <br>The data includes clinical data and 1D, 3D meshes for computational purposes.
DOI: 10.6084/m9.figshare.6999161
title: Additional file 1: of Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

description: Table S1. The RNA quality for each sample. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.21163030
title: Bipolar database with data including current PTSD diagnosis

description: Dataset of 79 patients with BD-I and BD-II with a history of psychological trauma.
DOI: 10.6084/m9.figshare.15041284
title: Additional file 3 of Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

description: Additional file 3. Table S2. Oligonucleotides used in this study.
DOI: 10.6084/m9.figshare.16960615.v1
title: Additional file 1 of Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

description: Additional file 1: Figure S1. Pearson correlation coefficients among 3 biological replications from chrysanthemum flowers under the soil system (Flower-CK-1, Flower-CK-2 and Flower-CK-3) and hydroponic system (Flower-SP-1, Flower-SP-2 and Flower-SP-3). The numbers in the scale bar stand for correlation coefficients. Figure S2. Principal component analysis among 3 biological replications from flowers under soil and hydroponic system. Figure S3. Difference of total nitrogen content in chrysanthemum flower under soil and hydroponic system. *P &lt; 0.05, **P &lt; 0.01.
DOI: 10.6084/m9.figshare.16960618
title: Additional file 2 of Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

description: Additional file 2: Table S1. GO enrichment of chrysanthemum flowers. Table S2. KEGG pathways enriched in the chrysanthemum flowers. Table S3. List of flavonoid biosynthesis-related DEGs. Table S4. List of Phenylpropanoid biosynthesis-related DEGs. Table S5. List of fatty acid and unsaturated fatty acid biosynthesis-related DEGs. Table S6. List of cell wall metabolism-related DEGs. Table S7. List of TF-related DEGs. Table S8. List of the quantitative primers for qRT-PCR in this study. Table S9. List of hormone-related DEGs. Table S10. List of photosynthesis-related DEGs.
DOI: 10.5258/soton/d2918
title: Dataset supporting the study of 'Exploring experiences of autistic children in participatory design through digital stories'

description: This dataset is from the second of two studies undertaken in support of the University of Southampton Doctoral Thesis entitled 'Reimagining co-production as playful learning: A new perspective on autistic students’ experiences of participatory design and Digital Storytelling'.

The study examined the students' experiences of using participatory design to create a computer game, which they named "Birds with Guns".

The dataset consists of co-created digital stories, session transcripts, demographic information about participants, a video of the game students created, and transcripts from evaluation interviews. Participant information sheets are also included for those needing them. All data has been pseudo-anonymised, though the school name is genuine.

Data to be available only to UK researchers from HE settings, who have sought ethical approval from their own institutions.
DOI: 10.6084/m9.figshare.11726025
title: Additional file 3 of Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production

description: Additional file 3: Table S2. Cell growth, glucose consumption, ethanol and byproduct of Z. mobilis recombinant strain ZMQ3-A4 for isobutanol production using different concentrations of tetracycline induction in flask with different medium volume 20, 50, 80%, respectively. ND: no determined.
DOI: 10.6084/m9.figshare.11726025.v1
title: Additional file 3 of Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production

description: Additional file 3: Table S2. Cell growth, glucose consumption, ethanol and byproduct of Z. mobilis recombinant strain ZMQ3-A4 for isobutanol production using different concentrations of tetracycline induction in flask with different medium volume 20, 50, 80%, respectively. ND: no determined.
DOI: 10.6084/m9.figshare.6999176
title: Additional file 2: of Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

description: Table S2. The count matrix for each sample. (XLSX 440 kb)
DOI: 10.6084/m9.figshare.20626424
title: Additional file 1 of Proteomics-based evaluation of the mechanism underlying vascular injury via DNA interstrand crosslinks, glutathione perturbation, mitogen-activated protein kinase, and Wnt and ErbB signaling pathways induced by crotonaldehyde

description: Additional file 1: Table S1. Quantitative analysis of total proteins by TMT-based proteomics analysis.
DOI: 10.57745/xslc6n
title: telomeres-S.tgz

description: Telomeres, S-phase
DOI: 10.6084/m9.figshare.16960532
title: Additional file 7 of Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

description: Additional file 7: Supplementary file 7. Gene ontology (GO) analysis of the biological process, molecular function, and cellular component for the m6A -containing transcripts identified in m6A -seq in watermelon.
DOI: 10.6084/m9.figshare.12774689
title: Dissolved black carbon: unlikely a significant refractory dissolved organic carbon pool cycling in rivers and oceans

description: This data set provides details for concentrations and carbon isotopic (δ<sup>13</sup>C and Δ<sup>14</sup>C) compositions of DOC, SPE-DOC and DBC in rivers and ocean.
DOI: 10.6084/m9.figshare.21687692
title: datasets

description: datasets
DOI: 10.23641/asha.24309193
title: Potential treatments and interventions of HHL (Lu et al., 2023)

description: <b>Purpose: </b>The purpose of this study was to systematically review the research literature with regards to treatments and intervention methods for hereditary hearing loss. Our goal was to provide reference guidelines for the rational use of medication and gene-targeted therapy for patients with hereditary hearing loss and discuss the future development of research in this area.<b>Method:</b> We searched two core databases, PubMed and Web of Science, for relevant literature relating to potential treatments and interventional methods for hereditary hearing loss. Then, we used Microsoft Excel to perform basic statistical analysis of the data, the R language to perform bibliometric analyses, and VOSviewer and CiteSpace to visualize data. In addition, we clustered and descriptively analyzed the data and identified the relative importance of each approach with regard to precise patient outcomes.<b>Results:</b> In this study, we followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standardized screening process and identified a total of 103 research articles. The average annual growth rate of publications in this area was 12.73%. The country with the highest number of publications and citations was the United States; 80 of these publications (associated with 76.92% of funding) were supported by grants from 16 countries. Potential treatments and interventions were clustered according to the stage of research and showed that 8.74% remain in the research design stage, 59.22% are in the clinical validation stage, and 32.04% are being applied in the clinic. The main research focus in this field is cochlear implants and gene therapy.<b>Conclusions:</b> Hereditary hearing loss is in a critical period of transition from preventive to therapeutic research. Gene-targeted interventions represent one of the most promising and effective treatments.<b>Supplemental Material S1.</b> Search formulas and search time frames for each database.<b>Supplemental Material S2.</b> Ranking of authors with &gt; 4 publications and articles fractionalized.<b>Supplemental Material S3.</b> Top 10 countries with average articles cited.Lu, Y., Hu, Y., Wang, S., Pan, S., An, K., Wang, T., He, Y., Tian, C., & Lei, J. (2023). Hereditary hearing loss: A systematic review of potential treatments and interventions. <i>American Journal of Audiology</i>. Advance online publication. https://doi.org/10.1044/2023_AJA-23-00069
DOI: 10.23641/asha.24309193.v1
title: Potential treatments and interventions of HHL (Lu et al., 2023)

description: <b>Purpose: </b>The purpose of this study was to systematically review the research literature with regards to treatments and intervention methods for hereditary hearing loss. Our goal was to provide reference guidelines for the rational use of medication and gene-targeted therapy for patients with hereditary hearing loss and discuss the future development of research in this area.<b>Method:</b> We searched two core databases, PubMed and Web of Science, for relevant literature relating to potential treatments and interventional methods for hereditary hearing loss. Then, we used Microsoft Excel to perform basic statistical analysis of the data, the R language to perform bibliometric analyses, and VOSviewer and CiteSpace to visualize data. In addition, we clustered and descriptively analyzed the data and identified the relative importance of each approach with regard to precise patient outcomes.<b>Results:</b> In this study, we followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standardized screening process and identified a total of 103 research articles. The average annual growth rate of publications in this area was 12.73%. The country with the highest number of publications and citations was the United States; 80 of these publications (associated with 76.92% of funding) were supported by grants from 16 countries. Potential treatments and interventions were clustered according to the stage of research and showed that 8.74% remain in the research design stage, 59.22% are in the clinical validation stage, and 32.04% are being applied in the clinic. The main research focus in this field is cochlear implants and gene therapy.<b>Conclusions:</b> Hereditary hearing loss is in a critical period of transition from preventive to therapeutic research. Gene-targeted interventions represent one of the most promising and effective treatments.<b>Supplemental Material S1.</b> Search formulas and search time frames for each database.<b>Supplemental Material S2.</b> Ranking of authors with &gt; 4 publications and articles fractionalized.<b>Supplemental Material S3.</b> Top 10 countries with average articles cited.Lu, Y., Hu, Y., Wang, S., Pan, S., An, K., Wang, T., He, Y., Tian, C., & Lei, J. (2023). Hereditary hearing loss: A systematic review of potential treatments and interventions. <i>American Journal of Audiology</i>. Advance online publication. https://doi.org/10.1044/2023_AJA-23-00069
DOI: 10.6084/m9.figshare.16960615
title: Additional file 1 of Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

description: Additional file 1: Figure S1. Pearson correlation coefficients among 3 biological replications from chrysanthemum flowers under the soil system (Flower-CK-1, Flower-CK-2 and Flower-CK-3) and hydroponic system (Flower-SP-1, Flower-SP-2 and Flower-SP-3). The numbers in the scale bar stand for correlation coefficients. Figure S2. Principal component analysis among 3 biological replications from flowers under soil and hydroponic system. Figure S3. Difference of total nitrogen content in chrysanthemum flower under soil and hydroponic system. *P &lt; 0.05, **P &lt; 0.01.