cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15074520
title: Tight focusing of laser light using microlens array combined with radially polarised light converter

description: A facile method to prepare a liquid crystal polarisation conversion microlens array (LCPC MLA) is reported. One-step photolithography was used to form a microhole array patterned fluoropolymer poly (butenyl vinyl ether) (CYTOP) layer on the front and back side of a thin glass substrate. On the front side, LC droplets are radially aligned in the microholes, and a twisted radial arrangement texture is formed by the integration of another glass substrate coated with a parallel alignment layer to create the LCPC array. The MLA is located at the rear side of the thin glass substrate and each microlens centre is completely aligned with the centres of the LC droplets in the LCPC array. The LCPC array can convert linearly polarised light to radially polarised light and the MLA can focus the radially polarised light to a spot array. This tightly focused array has a high intensity and at each focused spot, a large component of the electric field is in the longitudinal direction. The LCPC MLA has a compact structure, good stability, and highly uniformity, and it shows potential for applications such as material processing, phase modulation, polarisation compensation, and polarisation imaging.
DOI: 10.5281/zenodo.10695468
title: Patient sex and origin influence distribution of driver genes and clinical presentation of paraganglioma - Supplement 2

description: Supplement 2 : Clinical data collected for patients with pheochromocytoma and paraganglioma and known pathogenic driver mutation.
DOI: 10.5281/zenodo.10695469
title: Patient sex and origin influence distribution of driver genes and clinical presentation of paraganglioma - Supplement 2

description: Supplement 2 : Clinical data collected for patients with pheochromocytoma and paraganglioma and known pathogenic driver mutation.
DOI: 10.6084/m9.figshare.24208719.v3
title: <b>Chromosome-level genome assembly of the common chiton, </b><b>Liolophura japonica </b><b>(Lischke, 1873)</b>

description: Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ~609 Mb with a scaffold N50 length of 37.34 Mb (96.4% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.
DOI: 10.6084/m9.figshare.21365999
title: Additional file 1 of A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome

description: Additional file 1: Table S1. Summary of TF ChIP-seq datasets of mouse cell/tissue types. Table S2. Unique motifs (UMs) matching known motifs of TFs in the Hocomoco and JASPAR databases.
DOI: 10.6084/m9.figshare.21365999.v1
title: Additional file 1 of A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome

description: Additional file 1: Table S1. Summary of TF ChIP-seq datasets of mouse cell/tissue types. Table S2. Unique motifs (UMs) matching known motifs of TFs in the Hocomoco and JASPAR databases.
DOI: 10.6084/m9.figshare.21366018
title: Additional file 2 of Mitochondrial phylogenomics of Acanthocephala: nucleotide alignments produce long-branch attraction artefacts

description: Additional file 2: Dataset S1. Comparative overall mitogenomic architecture features of the Acanthocephala. Dataset S2. Comparative features of individual genes in mitogenomes of the Acanthocephala.
DOI: 10.6084/m9.figshare.21366018.v1
title: Additional file 2 of Mitochondrial phylogenomics of Acanthocephala: nucleotide alignments produce long-branch attraction artefacts

description: Additional file 2: Dataset S1. Comparative overall mitogenomic architecture features of the Acanthocephala. Dataset S2. Comparative features of individual genes in mitogenomes of the Acanthocephala.
DOI: 10.6084/m9.figshare.19793300
title: Additional file 1 of RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection

description: Additional file 1: Information of differentially expressed genes at 12 hpi after DTMUV infection.
DOI: 10.6084/m9.figshare.19793300.v1
title: Additional file 1 of RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection

description: Additional file 1: Information of differentially expressed genes at 12 hpi after DTMUV infection.
DOI: 10.6084/m9.figshare.19793306
title: Additional file 3 of RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection

description: Additional file 3: Information of differentially expressed genes at 36 hpi after DTMUV infection.
DOI: 10.6084/m9.figshare.19793306.v1
title: Additional file 3 of RNA-Seq analysis of duck embryo fibroblast cells gene expression during duck Tembusu virus infection

description: Additional file 3: Information of differentially expressed genes at 36 hpi after DTMUV infection.
DOI: 10.6084/m9.figshare.7734755
title: Histone acetyltransferase MoHat1 acetylates autophagy-related proteins MoAtg3 and MoAtg9 to orchestrate functional appressorium formation and pathogenicity in <i>Magnaporthe oryzae</i>

description: Macroautophagy/autophagy is critical for normal appressorium formation and pathogenicity of the rice blast fungus <i>Magnaporthe oryzae</i>, but the molecular base of autophagy linked to pathogenicity remains elusive in this or other pathogenic fungi. We found that MoHat1, a histone acetyltransferase (HAT) homolog, had a role in the regulation of autophagy through the acetylation of autophagy related proteins MoAtg3 and MoAtg9. We also found that MoHat1 was subject to regulation by the protein kinase MoGsk1 that modulated the translocation of MoHat1 from the nucleus to the cytoplasm with the assistance of MoSsb1, a protein chaperone. The alternation of intracellular location affected MoHat1 in the modification of cytosolic autophagy proteins that maintained normal autophagy. Furthermore, we provided evidence linking acetylation of MoAtg3 and MoAtg9 by MoHat1 to functional appressorium development and pathogenicity. Together with the first report of MoAtg9 being subject to acetylation regulation by MoHat1, our studies depicted how MoHat1 regulated autophagy in conjunction with MoGsk1 and how normal autophagy was linked to appressorium formation and function and pathogenicity of <i>M. oryzae</i>. <b>Abbreviations</b>: A/Ala: alanine; AP: autophagosome; Atg genes/proteins: autophagy-related genes/proteins; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; DAPI: 4ʹ, 6-diamidino-2-phenylindole; D/Asp: aspartic acid; GFP: green fluorescent protein; GSK3: glycogen synthase kinase 3; HAT: histone acetyltransferase; Hsp70: heat-shock protein 70; IH: invasive hyphae; K/Lys: lysine; MMS: methyl methanesulfonate; Mo: <i>Magnaporthe oryzae</i>; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; R/Arg: arginine; S/Ser: serine; T/Thr: threonine; TOR: target of rapamycin; WT: wild type; YFP: yellow fluorescent protein
DOI: 10.6084/m9.figshare.7734755.v1
title: Histone acetyltransferase MoHat1 acetylates autophagy-related proteins MoAtg3 and MoAtg9 to orchestrate functional appressorium formation and pathogenicity in <i>Magnaporthe oryzae</i>

description: Macroautophagy/autophagy is critical for normal appressorium formation and pathogenicity of the rice blast fungus <i>Magnaporthe oryzae</i>, but the molecular base of autophagy linked to pathogenicity remains elusive in this or other pathogenic fungi. We found that MoHat1, a histone acetyltransferase (HAT) homolog, had a role in the regulation of autophagy through the acetylation of autophagy related proteins MoAtg3 and MoAtg9. We also found that MoHat1 was subject to regulation by the protein kinase MoGsk1 that modulated the translocation of MoHat1 from the nucleus to the cytoplasm with the assistance of MoSsb1, a protein chaperone. The alternation of intracellular location affected MoHat1 in the modification of cytosolic autophagy proteins that maintained normal autophagy. Furthermore, we provided evidence linking acetylation of MoAtg3 and MoAtg9 by MoHat1 to functional appressorium development and pathogenicity. Together with the first report of MoAtg9 being subject to acetylation regulation by MoHat1, our studies depicted how MoHat1 regulated autophagy in conjunction with MoGsk1 and how normal autophagy was linked to appressorium formation and function and pathogenicity of <i>M. oryzae</i>. <b>Abbreviations</b>: A/Ala: alanine; AP: autophagosome; Atg genes/proteins: autophagy-related genes/proteins; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; DAPI: 4ʹ, 6-diamidino-2-phenylindole; D/Asp: aspartic acid; GFP: green fluorescent protein; GSK3: glycogen synthase kinase 3; HAT: histone acetyltransferase; Hsp70: heat-shock protein 70; IH: invasive hyphae; K/Lys: lysine; MMS: methyl methanesulfonate; Mo: <i>Magnaporthe oryzae</i>; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; R/Arg: arginine; S/Ser: serine; T/Thr: threonine; TOR: target of rapamycin; WT: wild type; YFP: yellow fluorescent protein
DOI: 10.6084/m9.figshare.19793391
title: Additional file 3 of Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum

description: Additional files 3: Table S1. The fold change and P-value of DEGs.
DOI: 10.6084/m9.figshare.19793400
title: Additional file 6 of Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum

description: Additional files 6: Table S4. The total metabolites from the leaf of C. longepaniculatum.
DOI: 10.6084/m9.figshare.19793391.v1
title: Additional file 3 of Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum

description: Additional files 3: Table S1. The fold change and P-value of DEGs.
DOI: 10.6084/m9.figshare.17696251
title: Additional file 5 of Down-regulation of OsMYB103L distinctively alters beta-1,4-glucan polymerization and cellulose microfibers assembly for enhanced biomass enzymatic saccharification in rice

description: Additional file 5: Table S4. 149 overlapped genes related to OsMYB103L regulation by using multi-omics analysis.
DOI: 10.6084/m9.figshare.17696251.v1
title: Additional file 5 of Down-regulation of OsMYB103L distinctively alters beta-1,4-glucan polymerization and cellulose microfibers assembly for enhanced biomass enzymatic saccharification in rice

description: Additional file 5: Table S4. 149 overlapped genes related to OsMYB103L regulation by using multi-omics analysis.
DOI: 10.6084/m9.figshare.19793400.v1
title: Additional file 6 of Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum

description: Additional files 6: Table S4. The total metabolites from the leaf of C. longepaniculatum.
DOI: 10.6084/m9.figshare.9831986
title: SuppMaterial_OrigamiContactSimulator from An efficient numerical approach for simulating contact in origami assemblages.

description: This file includes all the source code of the contact simulator and the several examples presented in the paper.
DOI: 10.5281/zenodo.10680250
title: Supporting data for manuscript "Quantitative Insights on Impurities in Ice Cores at the Micro-scale from Calibrated LA-ICP-MS Imaging"

description: The datasets are supporting information for the manuscript "Quantitative Insights on Impurities in Ice Cores at the Micro-scale from Calibrated LA-ICP-MS Imaging" submitted for consideration at Geochemistry, Geophysics, Geosystems. Measurements using ice core LA-ICP-MS imaging were performed at the Ca’Foscari University of Venice, for 23Na, 24Mg, 27Al, 56Fe and 88Sr. Impurity maps are acquired as a pattern of lines, without overlap in the direction perpendicular to that of the scan, and without any further spatial interpolation. If denoted as "_calibrated" the files contain concentration values as parts per billion (ppb) after matrix-matched calibration by method B described in the manuscript, using a 40 micron spot. Datasets denoted as "MethodC_" refer to the basic grain growth experiment described in the manuscript (Figure 4). Here uncalibrated intensities are recorded as counts for a 20 micron spot.
DOI: 10.6084/m9.figshare.9831986.v2
title: SuppMaterial_OrigamiContactSimulator from An efficient numerical approach for simulating contact in origami assemblages.

description: This file includes all the source code of the contact simulator and the several examples presented in the paper.
DOI: 10.4121/18ef279f-b771-466e-bc7c-04b365c7e7c8
title: Fast-breaking MCBJ data underlying the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions"

description: Zipped files containing room-temperature fast-breaking mechanically controlled break junction measurements at low temperature of the 2-OS and Sme-2OS di-radicals and 2-CS and Sme-2CS precursors for chapter 3 of the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions". The two folders in Data/ corresponds to the two setups used for the experiments. In the setup folder, the subfolder contain experiment for each molecule measured with a folder for each samples. The Gold/ subfolders contain reference measurements and Molecule/ contain breaking traces after molecule deposition.The Clustering/ folder contain all the code to produce the figures of the chapter, the result of analysis is stored in each data experiment folder. The scan* files correspond to breaking traces data. More extensive description can be found in the headers of the files.
DOI: 10.6084/m9.figshare.9831986.v1
title: SuppMaterial_OrigamiContactSimulator from An efficient numerical approach for simulating contact in origami assemblages

description: This file includes all the source code of the contact simulator and the several examples presented in the paper.
DOI: 10.4121/18ef279f-b771-466e-bc7c-04b365c7e7c8.v1
title: Fast-breaking MCBJ data underlying the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions"

description: Zipped files containing room-temperature fast-breaking mechanically controlled break junction measurements at low temperature of the 2-OS and Sme-2OS di-radicals and 2-CS and Sme-2CS precursors for chapter 3 of the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions". The two folders in Data/ corresponds to the two setups used for the experiments. In the setup folder, the subfolder contain experiment for each molecule measured with a folder for each samples. The Gold/ subfolders contain reference measurements and Molecule/ contain breaking traces after molecule deposition.The Clustering/ folder contain all the code to produce the figures of the chapter, the result of analysis is stored in each data experiment folder. The scan* files correspond to breaking traces data. More extensive description can be found in the headers of the files.
DOI: 10.6084/m9.figshare.20317747
title: Additional file 2 of Gestational heat stress alters skeletal muscle gene expression profiles and vascularity in fetal pigs in a sexually dimorphic manner

description: Additional file 2: Table S2. Full list of significantly enriched gene ontology terms.
DOI: 10.6084/m9.figshare.20317747.v1
title: Additional file 2 of Gestational heat stress alters skeletal muscle gene expression profiles and vascularity in fetal pigs in a sexually dimorphic manner

description: Additional file 2: Table S2. Full list of significantly enriched gene ontology terms.
DOI: 10.6084/m9.figshare.20317785
title: Additional file 14 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 14: Table S14. KEGG enrichment of targets of DE mRNA.
DOI: 10.6084/m9.figshare.20317776
title: Additional file 11 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 11: Table S11. GO enrichment of trans-regulatory targets of DE lncRNA.
DOI: 10.6084/m9.figshare.20317776.v1
title: Additional file 11 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 11: Table S11. GO enrichment of trans-regulatory targets of DE lncRNA.
DOI: 10.6084/m9.figshare.20317785.v1
title: Additional file 14 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 14: Table S14. KEGG enrichment of targets of DE mRNA.
DOI: 10.4121/2442b619-8ecd-4a11-9495-ec959f3366fe
title: EMBJ data underlying the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions"

description: Zipped files containing low-temperature electromigration break junctions measurements at low temperature of the 2-OS and Sme-2OS di-radicals for the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions". The analysis code and figures are contained in each device folder. The Data/ subfolder contain the raw data of the experiment in txt format. More extensive description of the data can be found in the headers of the files. The Scripts/ folder contain the Matlab code to explore, analyze and compare EMBJ and MCBJ data.
DOI: 10.4121/2442b619-8ecd-4a11-9495-ec959f3366fe.v1
title: EMBJ data underlying the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions"

description: Zipped files containing low-temperature electromigration break junctions measurements at low temperature of the 2-OS and Sme-2OS di-radicals for the thesis: "Electronic transport signatures of two-electron interactions in all-organic single-molecule junctions". The analysis code and figures are contained in each device folder. The Data/ subfolder contain the raw data of the experiment in txt format. More extensive description of the data can be found in the headers of the files. The Scripts/ folder contain the Matlab code to explore, analyze and compare EMBJ and MCBJ data.
DOI: 10.6084/m9.figshare.20317815
title: Additional file 5 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 5: Table S5. Summary of differentially expressed lncRNA in DPV infected DEF cells.
DOI: 10.6084/m9.figshare.20317815.v1
title: Additional file 5 of Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

description: Additional file 5: Table S5. Summary of differentially expressed lncRNA in DPV infected DEF cells.
DOI: 10.6084/m9.figshare.20317831
title: Additional file 6 of Clinical research capability enhanced for medical undergraduates: an innovative simulation-based clinical research curriculum development

description: Additional file 6. Data.
DOI: 10.15156/bio/sh2800826.08fu
title: SH2800826.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh532617.07fu
title: SH532617.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh532618.07fu
title: SH532618.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.