cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24849200.v1
title: CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair

description: Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 putative miR-7-binding sites, as an enhancer of miRISC condensation and DNA repair. Both <i>in vivo</i> and <i>in vitro</i> experiments confirmed the condensation of TNRC6B and AGO2, two core protein components of human miRISC. Moreover, overexpressing ciRS-7 largely increased the condensate number of TNRC6B and AGO2 in cells, while silencing ciRS-7 reduced it. Additionally, miR-7 overexpression also promoted miRISC condensation. Consistent with the previous report that AGO2 participated in RAD51-mediated DNA damage repair, the overexpression of ciRS-7 significantly promoted irradiation-induced DNA damage repair by enhancing RAD51 recruitment. Our results uncover a new role of circRNA in liquid-liquid phase separation and provide new insight into the regulatory mechanism of ciRS-7 on miRISC function and DNA repair.
DOI: 10.6084/m9.figshare.14363466
title: 4DNvestigator: time series genomic data analysis toolbox

description: Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.
DOI: 10.6084/m9.figshare.7547726.v1
title: MOESM4 of Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

description: Additional file 4: Dataset S3. Quantification of the total proteome from A. fumigatus Z5 in different treatments.
DOI: 10.6084/m9.figshare.7547735.v1
title: MOESM7 of Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

description: Additional file 7: Dataset S6. KEGG and GO analysis results of the total proteome from A. fumigatus Z5 in different treatments.
DOI: 10.6084/m9.figshare.7547738
title: MOESM8 of Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

description: Additional file 8: Dataset S7. KEGG and GO analysis results of the transcriptome of A. fumigatus Z5 in different treatments.
DOI: 10.6084/m9.figshare.11742072
title: Additional file 1 of Analysis of the relationship between the mutation site of the SLC39A4 gene and acrodermatitis enteropathica by reporting a rare Chinese twin: a case report and review of the literature

description: Additional file 1: Table S1. Details of clinical features of AE patients in 27 cases.
DOI: 10.6084/m9.figshare.11742072.v1
title: Additional file 1 of Analysis of the relationship between the mutation site of the SLC39A4 gene and acrodermatitis enteropathica by reporting a rare Chinese twin: a case report and review of the literature

description: Additional file 1: Table S1. Details of clinical features of AE patients in 27 cases.
DOI: 10.6084/m9.figshare.24849303
title: 1.3M gene-related novel SNPs from the pan-genome 3K-RGP study.

description: This file includes 1.3M gene-related novel SNPs that is out of ~2.3 M genome-wide novel SNPs, which were identified relative to the IRGSP RefSeq using analysis of a 16-genome rice reference panel.More details could be identified from the manuscript titled: "A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset." (https://www.biorxiv.org/content/biorxiv/early/2023/06/26/2023.06.25.546420.full.pdf)
DOI: 10.6084/m9.figshare.7856774
title: Greater cumulative benefits from ixekizumab versus ustekinumab treatment over 52 weeks for patients with moderate-to-severe psoriasis in a randomized, double-blinded phase 3b clinical trial

description: <b>Background</b>: Ixekizumab (IXE), a high-affinity monoclonal antibody that selectively targets interleukin-17A, has shown superiority to ustekinumab (UST) and etanercept in skin clearance from randomized clinical trials in patients with moderate-to-severe psoriasis. <b>Objective:</b> To compare cumulative benefits of IXE versus UST over 52 weeks of treatment. <b>Methods:</b> Cumulative clinical benefit of IXE and UST was assessed by evaluating the area under the curve (AUC) for responders of Psoriasis Area and Severity Index (PASI), itch numeric rating scale (Itch NRS), and Dermatology Life Quality Index (DLQI) outcomes over 52 weeks using data from IXORA-S trial comparing IXE (<i>N</i> = 136) and UST (<i>N</i> = 166). Normalized cumulative benefit was calculated to obtain the percentage of the maximum AUC for each outcome measure. Missing values were imputed using non-responder imputation. <b>Results:</b> Significantly greater cumulative benefits were obtained for IXE compared with UST. Normalized cumulative benefit with IXE versus UST for PASI 75/90/100, Itch NRS (0), and DLQI (0,1) were 83.1% and 67.6%; 68.9% and 46.5%; 41.1% and 23.4%; 40.4% and 30.9%; and 62.2% and 46.6%, respectively. Cumulative clinical benefit ratios for IXE:UST were 1.23 for PASI 75, 1.48 for PASI 90, and 1.76 for PASI 100, indicating an increase in the cumulative clinical benefit for IXE versus UST as the clearance levels increased. <b>Conclusions:</b> IXE showed greater cumulative clinical benefit than UST.
DOI: 10.6084/m9.figshare.7856774.v2
title: Greater cumulative benefits from ixekizumab versus ustekinumab treatment over 52 weeks for patients with moderate-to-severe psoriasis in a randomized, double-blinded phase 3b clinical trial

description: <b>Background</b>: Ixekizumab (IXE), a high-affinity monoclonal antibody that selectively targets interleukin-17A, has shown superiority to ustekinumab (UST) and etanercept in skin clearance from randomized clinical trials in patients with moderate-to-severe psoriasis. <b>Objective:</b> To compare cumulative benefits of IXE versus UST over 52 weeks of treatment. <b>Methods:</b> Cumulative clinical benefit of IXE and UST was assessed by evaluating the area under the curve (AUC) for responders of Psoriasis Area and Severity Index (PASI), itch numeric rating scale (Itch NRS), and Dermatology Life Quality Index (DLQI) outcomes over 52 weeks using data from IXORA-S trial comparing IXE (<i>N</i> = 136) and UST (<i>N</i> = 166). Normalized cumulative benefit was calculated to obtain the percentage of the maximum AUC for each outcome measure. Missing values were imputed using non-responder imputation. <b>Results:</b> Significantly greater cumulative benefits were obtained for IXE compared with UST. Normalized cumulative benefit with IXE versus UST for PASI 75/90/100, Itch NRS (0), and DLQI (0,1) were 83.1% and 67.6%; 68.9% and 46.5%; 41.1% and 23.4%; 40.4% and 30.9%; and 62.2% and 46.6%, respectively. Cumulative clinical benefit ratios for IXE:UST were 1.23 for PASI 75, 1.48 for PASI 90, and 1.76 for PASI 100, indicating an increase in the cumulative clinical benefit for IXE versus UST as the clearance levels increased. <b>Conclusions:</b> IXE showed greater cumulative clinical benefit than UST.
DOI: 10.6084/m9.figshare.7856774.v1
title: Greater cumulative benefits from ixekizumab versus ustekinumab treatment over 52 weeks for patients with moderate-to-severe psoriasis in a randomized, double-blinded phase 3b clinical trial

description: <b>Background</b>: Ixekizumab (IXE), a high-affinity monoclonal antibody that selectively targets interleukin-17A, has shown superiority to ustekinumab (UST) and etanercept in skin clearance from randomized clinical trials in patients with moderate-to-severe psoriasis. <b>Objective:</b> To compare cumulative benefits of IXE versus UST over 52 weeks of treatment. <b>Methods:</b> Cumulative clinical benefit of IXE and UST was assessed by evaluating the area under the curve (AUC) for responders of Psoriasis Area and Severity Index (PASI), itch numeric rating scale (Itch NRS), and Dermatology Life Quality Index (DLQI) outcomes over 52 weeks using data from IXORA-S trial comparing IXE (<i>N</i> = 136) and UST (<i>N</i> = 166). Normalized cumulative benefit was calculated to obtain the percentage of the maximum AUC for each outcome measure. Missing values were imputed using non-responder imputation. <b>Results:</b> Significantly greater cumulative benefits were obtained for IXE compared with UST. Normalized cumulative benefit with IXE versus UST for PASI 75/90/100, Itch NRS (0), and DLQI (0,1) were 83.1% and 67.6%; 68.9% and 46.5%; 41.1% and 23.4%; 40.4% and 30.9%; and 62.2% and 46.6%, respectively. Cumulative clinical benefit ratios for IXE:UST were 1.23 for PASI 75, 1.48 for PASI 90, and 1.76 for PASI 100, indicating an increase in the cumulative clinical benefit for IXE versus UST as the clearance levels increased. <b>Conclusions:</b> IXE showed greater cumulative clinical benefit than UST.
DOI: 10.6084/m9.figshare.10693559.v1
title: Quality control and other metadata of British dataset.

description: Metadata and quality control information associated with the British Salmonella Typhimurium dataset collected to develop WGS-based source attribution methods.
DOI: 10.6084/m9.figshare.7020725.v1
title: MOESM1 of Tumor-associated macrophages derived CCL18 promotes metastasis in squamous cell carcinoma of the head and neck

description: Additional file 1.Â  Differentially expressed genes (DEGs) of Tu686 cells stimulated by rhCCL18
DOI: 10.6084/m9.figshare.7020734.v1
title: MOESM2 of Tumor-associated macrophages derived CCL18 promotes metastasis in squamous cell carcinoma of the head and neck

description: Additional file 2. Â GO Biological Process, Molecular Function, and Cellular Component for the DEGs
DOI: 10.6084/m9.figshare.11742162
title: Additional file 10 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 10: Table S6. Complete list of proteins identified in whole cell LFQ MS analysis to compare WT to TRAP1 KO HEK293T and HCT116 cells.
DOI: 10.6084/m9.figshare.11742162.v1
title: Additional file 10 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 10: Table S6. Complete list of proteins identified in whole cell LFQ MS analysis to compare WT to TRAP1 KO HEK293T and HCT116 cells.
DOI: 10.6084/m9.figshare.11742165
title: Additional file 11 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 11: Table S7. List of high confidence proteins identified in whole cell LFQ analysis to compare WT to TRAP1 KO HEK293T and HCT116 cells. The 4578 proteins from Additional file 10: Table S6 were reduced to 3679 by selecting only those with at least 4 identified unique peptides in the LFQ analysis.
DOI: 10.6084/m9.figshare.11742165.v1
title: Additional file 11 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 11: Table S7. List of high confidence proteins identified in whole cell LFQ analysis to compare WT to TRAP1 KO HEK293T and HCT116 cells. The 4578 proteins from Additional file 10: Table S6 were reduced to 3679 by selecting only those with at least 4 identified unique peptides in the LFQ analysis.
DOI: 10.6084/m9.figshare.7020737
title: Additional file 1: of Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel NGS panel testing

description: Table S1. Clinical characteristics of enrolled NSCLC patients. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.22227935
title: Colourful 3D anti-counterfeiting label using nanoscale additive manufacturing

description: Microprinting is changing anti-counterfeit technology by producing complex micro-/nano-scale labels to increase the security level. However, the current microprinted anti-counterfeiting labels only contain 2D features, thought of as single coding (e.g. mostly in texts or graphs), unable to satisfy the high-end anti-counterfeiting demands of producing multi-coding, high-storage-density labels. Here, we introduce an approach for fluorescence printing to produce a 3D colourful, sophisticated anti-counterfeiting label. In the method, pre-synthetic QDs are printed with photoresists based on two-photon polymerisation, allowing for accurate regulation of fluorescence in both 2D and 3D. The fabricated photoresists exhibit immediate and postprocessing-free colour emissions under UV light. We demonstrated the ultra-high free design and accurate manufacturing capability of the approach by fabricating multi-colour, multi-layer patterns containing both texts and graphs on a 50μm × 50μm × 30μm portable label. The approach can also be applied to multi-dimensional optical data storage and colourful microdisplays.
DOI: 10.6084/m9.figshare.22227935.v1
title: Colourful 3D anti-counterfeiting label using nanoscale additive manufacturing

description: Microprinting is changing anti-counterfeit technology by producing complex micro-/nano-scale labels to increase the security level. However, the current microprinted anti-counterfeiting labels only contain 2D features, thought of as single coding (e.g. mostly in texts or graphs), unable to satisfy the high-end anti-counterfeiting demands of producing multi-coding, high-storage-density labels. Here, we introduce an approach for fluorescence printing to produce a 3D colourful, sophisticated anti-counterfeiting label. In the method, pre-synthetic QDs are printed with photoresists based on two-photon polymerisation, allowing for accurate regulation of fluorescence in both 2D and 3D. The fabricated photoresists exhibit immediate and postprocessing-free colour emissions under UV light. We demonstrated the ultra-high free design and accurate manufacturing capability of the approach by fabricating multi-colour, multi-layer patterns containing both texts and graphs on a 50μm × 50μm × 30μm portable label. The approach can also be applied to multi-dimensional optical data storage and colourful microdisplays.
DOI: 10.6084/m9.figshare.11742183
title: Additional file 13 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 13: Table S8. TRAP1 complex MS analysis.
DOI: 10.6084/m9.figshare.11742183.v1
title: Additional file 13 of The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis

description: Additional file 13: Table S8. TRAP1 complex MS analysis.
DOI: 10.6084/m9.figshare.19603654
title: Additional file 3 of Comparative study on molecular epidemiology of measles H1 outbreak and sporadic cases in Shandong Province, 2013–2019

description: Additional file 3. The KML file generated for the spatiotemporal analysis of measles viruses in this study.
DOI: 10.6084/m9.figshare.13312212
title: Silencing long non-coding RNA NEAT1 attenuates rheumatoid arthritis via the MAPK/ERK signalling pathway by downregulating microRNA-129 and microRNA-204

description: The participation of long noncoding RNAs (lncRNAs) and microRNAs (miRs) in the progression of rheumatoid arthritis (RA) is a key area of investigation. The current study aimed to investigate the action of lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in fibroblast-like synoviocyte (FLS) proliferation and synovitis in RA. A rat model of RA was established. LncRNA NEAT1 expression in the synovial tissues of patients with RA and FLSs from the RA rat model was determined using RT-qPCR. Next, dual luciferase reporter gene assay was applied to investigate the relationship between miR-129/204 and mitogen-activated protein kinase (MAPK)/extracellular regulated protein kinase (ERK). A putative binding relationship between miR-204 and lncRNA NEAT1 was evaluated by RIP assay, and miR-129 promoter methylation was determined using MSP. After the expression of lncRNA NEAT1, miR-129 or miR-204 was altered in FLSs, the extent of ERK1/2 phosphorylation was assessed. In addition, FLS synovitis and proliferation were determined by ELISA and EdU assay, respectively. In RA rats, lncRNA NEAT1 was silenced and miR-129/miR-204 was overexpressed to explore their roles <i>in vivo</i>. LncRNA NEAT1 was upregulated, while miR-129 and miR-204 were downregulated in RA synovial tissues and FLSs. MAPK1 was target gene of both miR-129 and miR-204. LncRNA NEAT1 bound to miR-204 and promoted miR-129 promoter methylation. Silencing lncRNA NEAT1 or overexpressing miR-129/miR-204 enhanced miR-129/miR-204 expression, but reduced the extent of ERK1/2 phosphorylation, proliferation of FLSs, and synovitis in RA. Collectively, silencing lncRNA NEAT1 promoted miR-129 and miR-204 to inhibit the MAPK/ERK signalling pathway, reducing FLS synovitis in RA. <b>Abbreviations:</b> ACR: American College of Rheumatology; ELISA: Enzyme-linked immunosorbent assay; ERK: extracellular signal-regulated kinase; FLS: fibroblast-like synoviocyte; GADPH: glyceraldehyde-3-phosphate dehydrogenase; HRP: horseradish peroxidase; IFA: Incomplete Freund’s Adjuvant; lncRNAs: long noncoding RNAs; MSP: Methylation-specific PCR; NC: negative control; NEAT1: nuclear paraspeckle assembly transcript 1; OD: optical density; RA: rheumatoid arthritis; RIPA: Radio Immunoprecipitation Assay; RLU: relative light units; RT-qPCR: reverse transcription quantitative polymerase chain reaction; UTR: untranslated region.
DOI: 10.6084/m9.figshare.19603648
title: Additional file 1 of Comparative study on molecular epidemiology of measles H1 outbreak and sporadic cases in Shandong Province, 2013–2019

description: Additional file 1. The XML file generated for the phylogenetic analysis with BEAST software.
DOI: 10.6084/m9.figshare.19603648.v1
title: Additional file 1 of Comparative study on molecular epidemiology of measles H1 outbreak and sporadic cases in Shandong Province, 2013–2019

description: Additional file 1. The XML file generated for the phylogenetic analysis with BEAST software.
DOI: 10.6084/m9.figshare.13312212.v1
title: Silencing Long Non-Coding RNA NEAT1 Attenuates Rheumatoid Arthritis via the MAPK/ERK Signaling Pathway by Downregulating microRNA-129 and microRNA-204

description: The participation of long noncoding RNAs (lncRNAs) and microRNAs (miRs) in the progression of rheumatoid arthritis (RA) is a key area of investigation. The current study aimed to investigate the action of lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in fibroblast-like synoviocyte (FLS) proliferation and synovitis in RA. A rat model of RA was established. LncRNA NEAT1 expression in the synovial tissues of patients with RA and FLSs from the RA rat model was determined using RT-qPCR. Next, dual luciferase reporter gene assay was applied to investigate the relationship between miR-129/204 and mitogen-activated protein kinase (MAPK)/extracellular regulated protein kinase (ERK). A putative binding relationship between miR-204 and lncRNA NEAT1 was evaluated by RIP assay, and miR-129 promoter methylation was determined using MSP. After the expression of lncRNA NEAT1, miR-129 or miR-204 were altered in FLSs, the extent of ERK1/2 phosphorylation was assessed. In addition, FLS synovitis and proliferation were determined by ELISA and EdU assay, respectively. In RA rats, lncRNA NEAT1 was silenced and miR-129/miR-204 was overexpressed to explore their roles <i>in vivo</i>. LncRNA NEAT1 was upregulated, while miR-129 and miR-204 were downregulated in RA synovial tissues and FLSs. MAPK1 was target gene of both miR-129 and miR-204. LncRNA NEAT1 bound to miR-204 and promoted miR-129 promoter methylation. Silencing lncRNA NEAT1 or overexpressing miR-129/miR-204 enhanced miR-129/miR-204 expression, but reduced the extent of ERK1/2 phosphorylation, proliferation of FLSs, and synovitis in RA. Collectively, silencing lncRNA NEAT1 promoted miR-129 and miR-204 to inhibit the MAPK/ERK signaling pathway, reducing FLS synovitis in RA.
DOI: 10.6084/m9.figshare.19603654.v1
title: Additional file 3 of Comparative study on molecular epidemiology of measles H1 outbreak and sporadic cases in Shandong Province, 2013–2019

description: Additional file 3. The KML file generated for the spatiotemporal analysis of measles viruses in this study.
DOI: 10.6084/m9.figshare.20455213
title: Germination and vigor of soybean genotypes seeds under saline stress

description: ABSTRACT Soybean stands out among the crops with the greatest application of transgenics, mainly for tolerance to herbicides, pests, and diseases; however, studies on salt stress in genetically modified plants are scarce. This study aimed to evaluate the tolerance of both traditional and genetically modified soybean genotypes to saline stress during the germination and seedling phases. Seeds of 13 soybean genotypes were selected (five traditional (BRS Carnaúba, BRS Pérola, BRS Tracajá, BRS Sambaíba, and FTR-4389) and eight transgenic (BRS Sambaíba RR, BRS-333-RR, BRS-9820- RR, PAS-13565-74-RR, PAS-11711-007-RR, BRS-918-IPRO, AS-3810-IPRO, and M-8210-IPRO)), subjected to four osmotic potentials (0.0, 0.1, -0.2, and -0.3 MPa). The seed quality was evaluated using the following variables: the germination percentage, germination speed index, shoot length, root length, dry mass accumulation, and salinity tolerance index. All variables were found to be affected by salt stress. However, the conventional genotypes, BRS Carnaúba, BRS Pérola, BRS Tracajá, and BRS Sambaíba, and the RR group PAS-13565-74-RR, and PAS-11711-007-RR were tolerant to salinity, whereas the genotypes FTR-4389 (conventional) and BRS Sambaíba RR (RR) were less tolerant to salt stress, and all genotypes in the IPRO group were moderately tolerant to salt stress.
DOI: 10.6084/m9.figshare.20455213.v1
title: Germination and vigor of soybean genotypes seeds under saline stress

description: ABSTRACT Soybean stands out among the crops with the greatest application of transgenics, mainly for tolerance to herbicides, pests, and diseases; however, studies on salt stress in genetically modified plants are scarce. This study aimed to evaluate the tolerance of both traditional and genetically modified soybean genotypes to saline stress during the germination and seedling phases. Seeds of 13 soybean genotypes were selected (five traditional (BRS Carnaúba, BRS Pérola, BRS Tracajá, BRS Sambaíba, and FTR-4389) and eight transgenic (BRS Sambaíba RR, BRS-333-RR, BRS-9820- RR, PAS-13565-74-RR, PAS-11711-007-RR, BRS-918-IPRO, AS-3810-IPRO, and M-8210-IPRO)), subjected to four osmotic potentials (0.0, 0.1, -0.2, and -0.3 MPa). The seed quality was evaluated using the following variables: the germination percentage, germination speed index, shoot length, root length, dry mass accumulation, and salinity tolerance index. All variables were found to be affected by salt stress. However, the conventional genotypes, BRS Carnaúba, BRS Pérola, BRS Tracajá, and BRS Sambaíba, and the RR group PAS-13565-74-RR, and PAS-11711-007-RR were tolerant to salinity, whereas the genotypes FTR-4389 (conventional) and BRS Sambaíba RR (RR) were less tolerant to salt stress, and all genotypes in the IPRO group were moderately tolerant to salt stress.