cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4491119.v1
title: Design and characterization of neurodurable gellan-xanthan pH-responsive hydrogels for controlled drug delivery

description: <b>Objectives</b>: The purpose of this study was to develop novel, porous neurodurable interpenetrating networks of gellan-xanthan hydrogel conduits intercalated with pristine polymethyl methacrylate (PMMA) particles for the sustained and concurrent release of two model compounds: bovine serum albumin (BSA) and diclofenac sodium. <b>Methods</b>: Hydrogel conduits were synthesized using a thermal-ionic crosslinking mechanism with direct incorporation of PMMA. The 15 formulations, generated using a Box-Behnken experimental design, were analyzed for drug release, swelling, erosion and textural properties. <b>Results</b>: The 15 formulations provided a near zero-order release of BSA (37–75% fractional release) and diclofenac sodium (14–22% fractional release) over 20 and 30 days, respectively, modulated via a combination of pH-responsive (pH 7.4) dissolution of the intercalated pristine polymer particles and the unique gelling and erosion properties imparted by the graded addition of xanthan gum to the hydrogel blend. The concentration-dependent intercalation of PMMA extended drug release rates and enhanced matrix resilience from 31% to 56%. <b>Conclusions</b>: The gellan-xanthan ratio variability and the pore-inducing effects of intercalated PMMA yielded a means for fine tuning the mechanical attributes of the hydrogel matrices, particularly matrix rigidity and flexibility, offering an appealing strategy for the design and development of synthetic bioactive-releasing peripheral nerve repair conduits.
DOI: 10.5281/zenodo.10669196
title: Tabular data and analyses of Fura-2 Ca2+ experiment from Kilfeather et al., 2024
DOI: 10.5281/zenodo.10669197
title: Tabular data and analyses of Fura-2 Ca2+ experiment from Kilfeather et al., 2024
DOI: 10.6084/m9.figshare.20219736
title: Additional file 2 of N6-methyladenosine-related lncRNAs identified as potential biomarkers for predicting the overall survival of Asian gastric cancer patients

description: Additional file 2: Supplementary Table S1.
DOI: 10.6084/m9.figshare.20219736.v1
title: Additional file 2 of N6-methyladenosine-related lncRNAs identified as potential biomarkers for predicting the overall survival of Asian gastric cancer patients

description: Additional file 2: Supplementary Table S1.
DOI: 10.6084/m9.figshare.11306930
title: Effect of high mobility group box 1 on Toll-like receptor 9 in B cells in myeloperoxidase-ANCA-associated vasculitis

description: High mobility group box 1 (HMGB1) played pathogenic role in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Recent findings demonstrated that Toll-like receptor 9 (TLR9) was involved in B cell tolerance breaking of autoimmune disease, including AAV. Here, we investigated the effect of HMGB1 on TLR9 in B cells of AAV. In the present work, patients with myeloperoxidase (MPO)-AAV in active stage were recruited. Intracellular TLR9 expression in various B cell subpopulations of the whole blood was detected by flow cytometry and the correlation with clinical data was analysed. Our results showed that intracellular TLR9 expression in B cells, memory B cells and plasmablasts correlated with erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). In particular, TLR9 expression in plasma cells correlated with ESR, CRP, serum creatinine, eGFR, and Birmingham Vasculitis Activity Score. To further explore the effect of HMGB1 on B cell, peripheral blood mononuclear cells (PBMCs) from AAV patients were isolated. After stimulated with HMGB1, TLR9 expression in various B cell subpopulations and proliferation ratio of live B cells were analysed by flow cytometry. We found that TLR9 expression in plasma cells and the proliferation ratio of live B cells by HMGB1 stimulation were significantly upregulated compared with the control group. Therefore, TLR9 expression in plasma cells was associated with disease activity of MPO-AAV. HMGB1 could enhance TLR9 expression in plasma cells and B cell proliferation. These indicated a role of HMGB1 on TLR9 in B cells in MPO-AAV, which would provide potential clues for intervention strategies.
DOI: 10.6084/m9.figshare.11306930.v1
title: Effect of high mobility group box 1 on Toll-like receptor 9 in B cells in myeloperoxidase-ANCA-associated vasculitis

description: High mobility group box 1 (HMGB1) played pathogenic role in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Recent findings demonstrated that Toll-like receptor 9 (TLR9) was involved in B cell tolerance breaking of autoimmune disease, including AAV. Here, we investigated the effect of HMGB1 on TLR9 in B cells of AAV. In the present work, patients with myeloperoxidase (MPO)-AAV in active stage were recruited. Intracellular TLR9 expression in various B cell subpopulations of the whole blood was detected by flow cytometry and the correlation with clinical data was analysed. Our results showed that intracellular TLR9 expression in B cells, memory B cells and plasmablasts correlated with erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). In particular, TLR9 expression in plasma cells correlated with ESR, CRP, serum creatinine, eGFR, and Birmingham Vasculitis Activity Score. To further explore the effect of HMGB1 on B cell, peripheral blood mononuclear cells (PBMCs) from AAV patients were isolated. After stimulated with HMGB1, TLR9 expression in various B cell subpopulations and proliferation ratio of live B cells were analysed by flow cytometry. We found that TLR9 expression in plasma cells and the proliferation ratio of live B cells by HMGB1 stimulation were significantly upregulated compared with the control group. Therefore, TLR9 expression in plasma cells was associated with disease activity of MPO-AAV. HMGB1 could enhance TLR9 expression in plasma cells and B cell proliferation. These indicated a role of HMGB1 on TLR9 in B cells in MPO-AAV, which would provide potential clues for intervention strategies.
DOI: 10.6084/m9.figshare.7636946
title: Ubiquitination of UVRAG by SMURF1 promotes autophagosome maturation and inhibits hepatocellular carcinoma growth

description: UVRAG (UV radiation resistance associated) is an important regulator of mammalian macroautophagy/autophagy by interacting with BECN1, PIK3C3, and RUBCN. Phosphorylation of UVRAG by MTORC1 negatively regulates autophagosome maturation under nutrient-enriched conditions. However, how UVRAG ubiquitination is regulated is still unknown. Here we report that UVRAG is ubiquitinated by SMURF1 at lysine residues 517 and 559, which decreases the association of UVRAG with RUBCN and promotes autophagosome maturation. However, the deubiquitinase ZRANB1 specifically cleaves SMURF1-induced K29 and K33-linked polyubiquitin chains from UVRAG, thereby increasing the binding of UVRAG to RUBCN and inhibiting autophagy flux. We also demonstrate that CSNK1A1-mediated UVRAG phosphorylation at Ser522 disrupts the binding of SMURF1 to UVRAG through PPxY motif and blocks UVRAG ubiquitination-mediated autophagosome maturation. Interestingly, ZRANB1 is phosphorylated at Thr35, and Ser209 residues by CSNK1A1, and this phosphorylation activates its deubiquitinating activity. Importantly, we provide <i>in vitro</i> and <i>in vivo</i> evidence that UVRAG ubiquitination at lysine residues 517 and 559 or prevention of Ser522 phosphorylation by D4476, a CSNK1A1 inhibitor, enhances the lysosomal degradation of EGFR, which significantly inhibits hepatocellular carcinoma (HCC) growth. Furthermore, UVRAG S522 phosphorylation levels correlate with ZRANB1 T35/S209 phosphorylation levels and poor prognosis in HCC patients. These findings identify a novel molecular mechanism by which ubiquitination and phosphorylation of UVRAG regulate its function in autophagosome maturation and HCC growth, encouraging further study of their potential therapeutic implications. <b>Abbreviations:</b> ATG: autophagy related; BafA<sub>1</sub>: bafilomycin A<sub>1</sub>; BECN1: beclin 1; CHX: cycloheximide; CSNK1A1/CK1α: casein kinase 1 alpha 1; CQ: chloroquine; DUB: deubiquitinase; EBSS: Earle’s balanced salt solution; EGF: epidermal growth factor; GFP: green fluorescent protein; GST: glutathione S-transferase; HBSS: Hanks balanced salts solution; HCC: hepatocellular carcinoma; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MEFs: mouse embryo fibroblasts; mRFP: monomeric red fluorescent protein; PIK3C3<i>/</i>VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PTMs: post-translational modifications; RUBCN: rubicon autophagy regulator; siRNA: small interfering RNA; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; Ub-AMC: ubiquitin-7-amido-4-methylcoumarin: a fluorogenic substrate; UVRAG: UV radiation resistance associated; ZRANB1/TRABID: zinc finger RANBP2-type containing 1
DOI: 10.6084/m9.figshare.21268435
title: Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing

description: Primary congenital glaucoma (PCG) is characterized by developmental abnormalities of the anterior chamber angle. Although several genes have been associated with PCG, pathogenic mutations could only be detected in about 20% of Chinese patients. GLC3B (1p36.2–36.1) and GLC3C (14q24.3) loci were previously identified in PCG pedigrees via linkage analysis. However, no causative genes were reported in these loci. This study was designed to search for novel PCG-related genes in these genetic regions. DNA samples from 100 PCG patients and 200 normal controls were pooled and sequenced using a customized panel of 133 positional candidate genes located around GLC3B and GLC3C loci (±1Mb). PCG-related genes were prioritized by the distribution of variants between patients and controls. Confirmation of selected variants and co-segregation analysis were performed using Sanger sequencing. Patient and control group contained 116 and 147 rare variants respectively after screening. Three genes (ZC2HC1C, VPS13D, and PGF) were prioritized according to the distribution of variants between the two groups. Rare variants of PGF were only identified in PCG patients. To the best of our knowledge, this is the first study aiming at exploring novel PCG-related genes at GLC3B and GLC3C loci. Our preliminary results suggest that there are potential associations between ZC2HC1C, VPS13D, PGF, and PCG. However, larger cohort studies and functional assays are required to provide further evidence for the proposed genotype-phenotype association.
DOI: 10.6084/m9.figshare.21268435.v1
title: Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing

description: Primary congenital glaucoma (PCG) is characterized by developmental abnormalities of the anterior chamber angle. Although several genes have been associated with PCG, pathogenic mutations could only be detected in about 20% of Chinese patients. GLC3B (1p36.2–36.1) and GLC3C (14q24.3) loci were previously identified in PCG pedigrees via linkage analysis. However, no causative genes were reported in these loci. This study was designed to search for novel PCG-related genes in these genetic regions. DNA samples from 100 PCG patients and 200 normal controls were pooled and sequenced using a customized panel of 133 positional candidate genes located around GLC3B and GLC3C loci (±1Mb). PCG-related genes were prioritized by the distribution of variants between patients and controls. Confirmation of selected variants and co-segregation analysis were performed using Sanger sequencing. Patient and control group contained 116 and 147 rare variants respectively after screening. Three genes (ZC2HC1C, VPS13D, and PGF) were prioritized according to the distribution of variants between the two groups. Rare variants of PGF were only identified in PCG patients. To the best of our knowledge, this is the first study aiming at exploring novel PCG-related genes at GLC3B and GLC3C loci. Our preliminary results suggest that there are potential associations between ZC2HC1C, VPS13D, PGF, and PCG. However, larger cohort studies and functional assays are required to provide further evidence for the proposed genotype-phenotype association.
DOI: 10.6084/m9.figshare.10258394
title: A NOVEL RAISIN SEGMENTATION ALGORITHM BASED ON DEEP LEARNING AND MORPHOLOGICAL ANALYSIS

description: ABSTRACT We propose a segmentation algorithm for raisin extraction. The proposed approach consists of the following aspects. Deep learning is used to predict the number of raisins in each connected region, and the shape features such as the roundness, area, X-axis value for the centroid, Y-axis value for the centroid, axis length and perimeter of each region will be used to establish the prediction model. Morphological analysis, based on edge parameters including the polar axis, polar angle and angular velocity, is applied to search for the suitable break points that are useful for identifying the dividing lines between two adjacent raisins. To make our segmentation more accurate, some machine-learning algorithms such as the random forest (RF), support vector machine (SVM) and deep learning (deep neural network, DNN) are applied to predict the number of raisins and to decide whether the raisins need more segmentation. The performance of the three models is compared, and the DNN is the most accurate.
DOI: 10.6084/m9.figshare.10258394.v1
title: A NOVEL RAISIN SEGMENTATION ALGORITHM BASED ON DEEP LEARNING AND MORPHOLOGICAL ANALYSIS

description: ABSTRACT We propose a segmentation algorithm for raisin extraction. The proposed approach consists of the following aspects. Deep learning is used to predict the number of raisins in each connected region, and the shape features such as the roundness, area, X-axis value for the centroid, Y-axis value for the centroid, axis length and perimeter of each region will be used to establish the prediction model. Morphological analysis, based on edge parameters including the polar axis, polar angle and angular velocity, is applied to search for the suitable break points that are useful for identifying the dividing lines between two adjacent raisins. To make our segmentation more accurate, some machine-learning algorithms such as the random forest (RF), support vector machine (SVM) and deep learning (deep neural network, DNN) are applied to predict the number of raisins and to decide whether the raisins need more segmentation. The performance of the three models is compared, and the DNN is the most accurate.
DOI: 10.6084/m9.figshare.17598431
title: Additional file 3 of Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1–Cyc8 complex in Penicillium oxalicum and Trichoderma reesei

description: Additional file 3: Spreadsheet S1. Proteins interacting with T. reesei TrCRE1, P. oxalicum PoCreA, and PoCyc8 identified through TAP-MS. The peptide counts (PepCount) of each biological replicate, the sum of PepCount of three biological replicates, the number of observable peptides, and Exponentially Modified Protein Abundance Index (emPAI) were listed. The proteins are arranged according to the value of emPAI.
DOI: 10.6084/m9.figshare.17598431.v1
title: Additional file 3 of Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1–Cyc8 complex in Penicillium oxalicum and Trichoderma reesei

description: Additional file 3: Spreadsheet S1. Proteins interacting with T. reesei TrCRE1, P. oxalicum PoCreA, and PoCyc8 identified through TAP-MS. The peptide counts (PepCount) of each biological replicate, the sum of PepCount of three biological replicates, the number of observable peptides, and Exponentially Modified Protein Abundance Index (emPAI) were listed. The proteins are arranged according to the value of emPAI.
DOI: 10.6084/m9.figshare.10258421
title: Oblique penetration of tungsten alloy rod to finite-thickness metal plate

description: Abstract In order to study the critical ricochet velocity and critical penetration velocity of tungsten alloy rod obliquely penetrating a finite-thickness metal plate, experiment and numerical calculation of tungsten alloy rod impacting on homogeneous armor steel plate with a thickness of 30mm at an angle of 60° were carried out. Compared the experimental and numerical results with the results using models, it is found that, the results of the ricochet models proposed by Tate, Rosenberg and Steven B for semi-infinite thick plate are quite different from those of experiment and numerical calculation, so they can not be applied to the ricochet situation of finite-thickness plate. The critical penetration velocity model proposed by De Marre and Zhao are in good agreement with the numerical and experimental results, which can predict critical penetration velocity of tungsten alloy rod obliquely penetrating a finite-thickness metal plate with large impact angle. The penetration depth of the projectile under the critical ricochet velocity is about 1/3 of the thickness of the target plate, and the angle between the ejection trajectory of the fragments produced by projectile and target plate and projectile penetration trajectory is exactly 90° in the first penetration stage.
DOI: 10.6084/m9.figshare.10258421.v1
title: Oblique penetration of tungsten alloy rod to finite-thickness metal plate

description: Abstract In order to study the critical ricochet velocity and critical penetration velocity of tungsten alloy rod obliquely penetrating a finite-thickness metal plate, experiment and numerical calculation of tungsten alloy rod impacting on homogeneous armor steel plate with a thickness of 30mm at an angle of 60° were carried out. Compared the experimental and numerical results with the results using models, it is found that, the results of the ricochet models proposed by Tate, Rosenberg and Steven B for semi-infinite thick plate are quite different from those of experiment and numerical calculation, so they can not be applied to the ricochet situation of finite-thickness plate. The critical penetration velocity model proposed by De Marre and Zhao are in good agreement with the numerical and experimental results, which can predict critical penetration velocity of tungsten alloy rod obliquely penetrating a finite-thickness metal plate with large impact angle. The penetration depth of the projectile under the critical ricochet velocity is about 1/3 of the thickness of the target plate, and the angle between the ejection trajectory of the fragments produced by projectile and target plate and projectile penetration trajectory is exactly 90° in the first penetration stage.
DOI: 10.6084/m9.figshare.21995069
title: Files for Main Figure 4

description: GSVA scores with DNA/RNA sensing genesDNA_RNA_gene_TE_cor_GSVA_telescope: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by TelescopeDNA_RNA_gene_TE_cor_GSVA_LocusMasterTE: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by LocusMasterTECorrelation with intergenic TEs and nearby Genescorrelation_intergenic_TEs_Gene: Spearman correlation between intergenic TEs and nearby GenesLocusMasterTE_cor: correlation score between intergenic TEs quantified by LocusMasterTEs and GenesTelescope_cor: correlation score between intergenic TEs quantified by Telescope and GenesSurvival AnalysisTCGA_COAD_log2TPM_Gene: log2TPM values of GenesTCGA_COAD_log2TPM_TE: log2TPM values of TEs quantified by LocusMasterTETEs_catpured_only_by_LocusMasterTE: A list of TEs captured exclusively by LocusMasterTETCGA_COAD_four_endpoint_survival: TCGA-COAD four endpoint survival informationInverted SINE mutational Signaturemutational_profile_TCGA-COAD: mutational profiles of TCGA-COAD tumor samples and inverted SINE sample<br>
DOI: 10.6084/m9.figshare.21995069.v7
title: Files for Main Figure 4

description: GSVA scores with DNA/RNA sensing genesDNA_RNA_gene_TE_cor_GSVA_telescope: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by TelescopeDNA_RNA_gene_TE_cor_GSVA_LocusMasterTE: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by LocusMasterTECorrelation with intergenic TEs and nearby Genescorrelation_intergenic_TEs_Gene: Spearman correlation between intergenic TEs and nearby GenesLocusMasterTE_cor: correlation score between intergenic TEs quantified by LocusMasterTEs and GenesTelescope_cor: correlation score between intergenic TEs quantified by Telescope and GenesSurvival AnalysisTCGA_COAD_log2TPM_Gene: log2TPM values of GenesTCGA_COAD_log2TPM_TE: log2TPM values of TEs quantified by LocusMasterTETEs_catpured_only_by_LocusMasterTE: A list of TEs captured exclusively by LocusMasterTETCGA_COAD_four_endpoint_survival: TCGA-COAD four endpoint survival informationInverted SINE mutational Signaturemutational_profile_TCGA-COAD: mutational profiles of TCGA-COAD tumor samples and inverted SINE sample<br>
DOI: 10.6084/m9.figshare.21995069.v6
title: Files for Main Figure 4

description: GSVA scores with DNA/RNA sensing genesDNA_RNA_gene_TE_cor_GSVA_telescope: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by TelescopeDNA_RNA_gene_TE_cor_GSVA_LocusMasterTE: Correlation between GSVA score of DNA/RNA sensing genes with TEs quantified by LocusMasterTECorrelation with intergenic TEs and nearby Genescorrelation_intergenic_TEs_Gene: Spearman correlation between intergenic TEs and nearby GenesLocusMasterTE_cor: correlation score between intergenic TEs quantified by LocusMasterTEs and GenesTelescope_cor: correlation score between intergenic TEs quantified by Telescope and GenesSurvival AnalysisTCGA_COAD_log2TPM_Gene: log2TPM values of GenesTCGA_COAD_log2TPM_TE: log2TPM values of TEs quantified by LocusMasterTETEs_catpured_only_by_LocusMasterTE: A list of TEs captured exclusively by LocusMasterTETCGA_COAD_four_endpoint_survival: TCGA-COAD four endpoint survival informationInverted SINE mutational Signaturemutational_profile_TCGA-COAD: mutational profiles of TCGA-COAD tumor samples and inverted SINE sample<br>
DOI: 10.6084/m9.figshare.19695614
title: Additional file 2 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 2.
DOI: 10.6084/m9.figshare.19695614.v1
title: Additional file 2 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 2.
DOI: 10.6084/m9.figshare.19695617
title: Additional file 3 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 3.
DOI: 10.6084/m9.figshare.19695617.v1
title: Additional file 3 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 3.
DOI: 10.6084/m9.figshare.19695620
title: Additional file 4 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 4.
DOI: 10.6084/m9.figshare.19695620.v1
title: Additional file 4 of Functional annotation of creeping bentgrass protein sequences based on convolutional neural network

description: Additional file 4.
DOI: 10.6084/m9.figshare.9734153
title: Source Data.xlsx

description: Nitrogen uptake by the forest canopy enhances carbon sequestration
DOI: 10.6084/m9.figshare.17598471
title: Additional file 1 of Integrated genomic and DNA methylation analysis of patients with advanced non-small cell lung cancer with brain metastases

description: Additional file 1: Data S1. Raw methylation values for 363 blocks.
DOI: 10.6084/m9.figshare.17598471.v1
title: Additional file 1 of Integrated genomic and DNA methylation analysis of patients with advanced non-small cell lung cancer with brain metastases

description: Additional file 1: Data S1. Raw methylation values for 363 blocks.