cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7081478.v1
title: Additional file 3: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâ s disease

description: Table S2. The overlapping positions for 106 identified candidate regions with QTLs related to MD disease. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7081535
title: Additional file 6: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâ s disease

description: Table S5. Unique and shared homozygous segments across all chickens included RCS lines and line 63 chickens were compared with the line 72. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7081733
title: MOESM2 of Phosphotyrosine profiling of human cerebrospinal fluid

description: Additional file 2: Table S2. A summary of tyrosine phosphorylated proteins identified in CSF.
DOI: 10.6084/m9.figshare.7081571
title: Additional file 1: of Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment

description: List of DEGs produced by edgeR for all contrasts presented in this study. (XLS 173 kb)
DOI: 10.6084/m9.figshare.7081571.v1
title: Additional file 1: of Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment

description: List of DEGs produced by edgeR for all contrasts presented in this study. (XLS 173 kb)
DOI: 10.6084/m9.figshare.7081733.v1
title: MOESM2 of Phosphotyrosine profiling of human cerebrospinal fluid

description: Additional file 2: Table S2. A summary of tyrosine phosphorylated proteins identified in CSF.
DOI: 10.6084/m9.figshare.7081463.v1
title: Additional file 2: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâ s disease

description: Table S1. GO analysis for 51 genes in 106 identified candidate regions. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7081763.v1
title: Additional file 10: of Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

description: Table S8. Conserved domains of the predicted protein-coding products. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.9179138.v2
title: ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway

description: Macroautophagy (autophagy) is a key catabolic pathway for the maintenance of proteostasis through constant digestion of selective cargoes. The selectivity of autophagy is mediated by autophagy receptors that recognize and recruit cargoes to autophagosomes. SQSTM1/p62 is a prototype autophagy receptor, which is commonly found in protein aggregates associated with major neurodegenerative diseases. While accumulation of SQSTM1 implicates a disturbance of selective autophagy pathway, the pathogenic mechanism that contributes to impaired autophagy degradation remains poorly characterized. Herein we show that amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD)-linked mutations of <i>TBK1</i> and <i>SQSTM1</i> disrupt selective autophagy and cause neurotoxicity. Our data demonstrates that proteotoxic stress activates serine/threonine kinase TBK1, which coordinates with autophagy kinase ULK1 to promote concerted phosphorylation of autophagy receptor SQSTM1 at the UBA domain and activation of selective autophagy. In contrast, ALS-FTLD-linked mutations of <i>TBK1</i> or <i>SQSTM1</i> reduce SQSTM1 phosphorylation and compromise ubiquitinated cargo binding and clearance. Moreover, disease mutation SQSTM1<sup>G427R</sup> abolishes phosphorylation of Ser351 and impairs KEAP1-SQSTM1 interaction, thus diminishing NFE2L2/Nrf2-targeted gene expression and increasing TARDBP/TDP-43 associated stress granule formation under oxidative stress. Furthermore, expression of SQSTM1<sup>G427R</sup> in neurons impairs dendrite morphology and KEAP1-NFE2L2 signaling. Therefore, our results reveal a mechanism whereby pathogenic SQSTM1 mutants inhibit selective autophagy and disrupt NFE2L2 anti-oxidative stress response underlying the neurotoxicity in ALS-FTLD. <b>Abbreviations:</b> ALS: amyotrophic lateral sclerosis; FTLD: frontotemporal lobar degeneration; G3BP1: GTPase-activating protein (SH3 domain) binding protein 1; GSTM1: glutathione S-transferase, mu 1; HMOX/HO-1: Heme oxygenase 1; IP: immunoprecipitation; KEAP1: kelch-like ECH associated protein 1; KI: kinase inactive; KIR: KEAP1 interaction region; KO: knockout; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MBP: maltose binding protein; NBR1: NBR1, autophagy cargo receptor; NFE2L2/Nrf2: nuclear factor, erythroid derived 2, like 2; NQO1: NAD(P)H quinone dehydrogenase 1; SQSTM1/p62: sequestosome 1; SOD1: superoxide dismutase 1, soluble; S.S.: serum starvation; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; UBA: <i>ub</i>iquitin <i>a</i>ssociation; ULK1: unc-51 like autophagy activating kinase 1; WT: wild type.
DOI: 10.6084/m9.figshare.12324644
title: Additional file 1 of Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds

description: Additional file 1: Table S1. Phenotypic traits of two B. rapa accessions. Table S2. Overview of transcriptomic data and mapping efficiency. Table S3. Classification and overview of DEGs. Table S4. Identification of classification of all TF, TR and kinase genes in B. rapa. Table S5. GO enrichment analysis of DEGs obtained by comparison two accessions at the seven stages. Table S6. GO enrichment analysis of DEGs obtained by comparison the adjacent stages in each one accession. Table S7. Homologous cell cycle genes in Arabidopsis and B. rapa. Table S8. GO enrichment analysis of color modules in WGCNA. Table S9. Expression values of flavonoid pathway genes in two B. rapa accessions at seven seed developmental stages. Table S10. Expression values of genes involved in fatty acid metabolism in two B. rapa accessions at seven seed developmental stages. Table S11. Primers used in qRT-PCR.
DOI: 10.6084/m9.figshare.7081991.v1
title: Additional file 3: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S2. InterPro annotation for 190 putative disease resistance/susceptibility-related protein-encoding transcripts (119 groups) encoded by the rice genes under the control of PIPs. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.7082006.v1
title: Additional file 8: of Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

description: All DEGs with exonic SNPs. (XLSX 504 kb)
DOI: 10.6084/m9.figshare.11276318
title: Identifying potential entry inhibitors for emerging Nipah virus by molecular docking and chemical-protein interaction network

description: Nipah Virus (NiV) is a newly emergent paramyxovirus that has caused various outbreaks in Asian countries. Despite its acute pathogenicity and lack of approved therapeutics for human use, there is an urgent need to determine inhibitors against NiV. Hence, this work includes prospection of potential entry inhibitors by implementing an integrative structure- and network-based drug discovery approach. FDA-approved drugs were screened against attachment glycoprotein (NiV-G, PDB: 2VSM), one of the prime targets to inhibit viral entry, using a molecular docking approach that was benchmarked both on CCDC/ASTEX and known NIV-G inhibitor set. The predicted small molecules were prioritized on the basis of topological analysis of the chemical-protein interaction network, which was inferred by integrating the drug-target network, NiV-human interaction network, and human protein-protein interaction network. A total of 17 drugs were predicted to be NiV-G inhibitors using molecular docking studies that were further prioritized to 3 novel leads − Nilotinib, Deslanoside and Acetyldigitoxin − on the basis of topological analysis of inferred chemical-protein interaction network. While Deslanoside and Acetyldigitoxin belong to an already known class of anti-NiV inhibitors, Nilotinib belongs to Benzenoids chemical class that has not been reported hitherto for developing anti-NiV inhibitors. These identified drugs are expected to be successful in further experimental evaluation and therefore could be used for anti-Nipah drug discovery. Apart, we also obtained various insights into the underlying chemical-protein interaction network, based on which several important network nodes were predicted. The applicability of our proposed approach was also demonstrated by prospecting for anti-NiV phytochemicals on an independent dataset. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11276318.v2
title: Identifying potential entry inhibitors for emerging Nipah virus by molecular docking and chemical-protein interaction network

description: Nipah Virus (NiV) is a newly emergent paramyxovirus that has caused various outbreaks in Asian countries. Despite its acute pathogenicity and lack of approved therapeutics for human use, there is an urgent need to determine inhibitors against NiV. Hence, this work includes prospection of potential entry inhibitors by implementing an integrative structure- and network-based drug discovery approach. FDA-approved drugs were screened against attachment glycoprotein (NiV-G, PDB: 2VSM), one of the prime targets to inhibit viral entry, using a molecular docking approach that was benchmarked both on CCDC/ASTEX and known NIV-G inhibitor set. The predicted small molecules were prioritized on the basis of topological analysis of the chemical-protein interaction network, which was inferred by integrating the drug-target network, NiV-human interaction network, and human protein-protein interaction network. A total of 17 drugs were predicted to be NiV-G inhibitors using molecular docking studies that were further prioritized to 3 novel leads − Nilotinib, Deslanoside and Acetyldigitoxin − on the basis of topological analysis of inferred chemical-protein interaction network. While Deslanoside and Acetyldigitoxin belong to an already known class of anti-NiV inhibitors, Nilotinib belongs to Benzenoids chemical class that has not been reported hitherto for developing anti-NiV inhibitors. These identified drugs are expected to be successful in further experimental evaluation and therefore could be used for anti-Nipah drug discovery. Apart, we also obtained various insights into the underlying chemical-protein interaction network, based on which several important network nodes were predicted. The applicability of our proposed approach was also demonstrated by prospecting for anti-NiV phytochemicals on an independent dataset. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7082042
title: Additional file 6: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S5. Differentially expressed transcripts driven by PIPs with the PICEs identified from the rice microarray data analysis. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7082051.v1
title: Additional file 1: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S1. Sample information: The clinical and sequencing information of the sample. (XLS 71 kb)
DOI: 10.6084/m9.figshare.7082063
title: Additional file 2: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S2. Factors influence the gut microbiome: Test the factors influence the gut microbiome with PERMANOVA. (XLS 7 kb)
DOI: 10.6084/m9.figshare.7082084
title: Additional file 10: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S3. Univariate analysis of factors associated with prognosis in the HGG group. (XLS 13 kb)
DOI: 10.5517/ccdc.csd.cc25lwrf
title: CCDC 2014155: Experimental Crystal Structure Determination

description: Related Article: Wei Jiang, Shanshan Liang, Xiaoye Jiang, Yuan Ma, Yonggang Wu|2022|J.Cluster Sci.|33|1773|doi:10.1007/s10876-021-02105-5
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc25lwsg
title: CCDC 2014156: Experimental Crystal Structure Determination

description: Related Article: Wei Jiang, Shanshan Liang, Xiaoye Jiang, Yuan Ma, Yonggang Wu|2022|J.Cluster Sci.|33|1773|doi:10.1007/s10876-021-02105-5
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc25m8nr
title: CCDC 2014524: Experimental Crystal Structure Determination

description: Related Article: Ting Yin, Ruirui Wang, Shaozhe Yang |2022|J.Cluster Sci.|33|2763|doi:10.1007/s10876-021-02192-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc260c9x
title: CCDC 2026138: Experimental Crystal Structure Determination

description: Related Article: Ying Zhou|2022|Inorg.Nano-Metal Chem.|52|144|doi:10.1080/24701556.2020.1862230
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc260cby
title: CCDC 2026139: Experimental Crystal Structure Determination

description: Related Article: Ying Zhou|2022|Inorg.Nano-Metal Chem.|52|144|doi:10.1080/24701556.2020.1862230
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc265vdn
title: CCDC 2031411: Experimental Crystal Structure Determination

description: Related Article: Jin-Dou Hao, Ji-Ying Ma, Guo-Sheng Liu, Jie Huang, Xin-Zhu Lin|2022|J.Cluster Sci.|33|1961|doi:10.1007/s10876-021-02118-0
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc265vfp
title: CCDC 2031412: Experimental Crystal Structure Determination

description: Related Article: Jin-Dou Hao, Ji-Ying Ma, Guo-Sheng Liu, Jie Huang, Xin-Zhu Lin|2022|J.Cluster Sci.|33|1961|doi:10.1007/s10876-021-02118-0
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc28sv20
title: CCDC 2109242: Experimental Crystal Structure Determination

description: Related Article: Hao Liu, Liying Wu, Jiji Cui, Dan Wang|2023|J.Cluster Sci.|34|1195|doi:10.1007/s10876-021-02201-6
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.7082147
title: Additional file 8: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S5. MGSs from the cohort: The relative abundance and statistical test of the MGSs. (XLS 1648 kb)
DOI: 10.6084/m9.figshare.23918603
title: Male diversity matters: genetic structuring of insular male date palm (<i>Phoenix dactylifera</i> L.) revealed valuable breeding and conservation resources

description: Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favourable fruit production is related to the quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterisation of the male progenitors should be the first step to establish a selection programme to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. The highest mean number of alleles per locus was obtained for Tozeur group. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of <i>Phoenix dactylifera</i> L. breeding programmes and the protection and conservation of valuable resources.
DOI: 10.6084/m9.figshare.23918603.v1
title: Male diversity matters: genetic structuring of insular male date palm (<i>Phoenix dactylifera</i> L.) revealed valuable breeding and conservation resources

description: Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favourable fruit production is related to the quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterisation of the male progenitors should be the first step to establish a selection programme to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. The highest mean number of alleles per locus was obtained for Tozeur group. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of <i>Phoenix dactylifera</i> L. breeding programmes and the protection and conservation of valuable resources.
DOI: 10.6084/m9.figshare.7081796
title: Additional file 2: of Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection

description: Table S2. The detail information of identified peptides pertinent to detected proteins. (XLSX 8119 kb)
DOI: 10.6084/m9.figshare.7081796.v1
title: Additional file 2: of Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection

description: Table S2. The detail information of identified peptides pertinent to detected proteins. (XLSX 8119 kb)
DOI: 10.6084/m9.figshare.4985195
title: Genetic polymorphism of 29 STR loci in the Hunan Han population from China

description: Genetic polymorphism of 29 STR loci in the Hunan Han population from China
DOI: 10.6084/m9.figshare.7081799
title: Additional file 3: of Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

description: Table S3. The homologous circRNAs identified in this study vs. previous study of Zhao et al. (XLSX 3455 kb)
DOI: 10.6084/m9.figshare.12849620
title: Large-Dimensional Factor Analysis Without Moment Constraints

description: Large-dimensional factor model has drawn much attention in the big-data era, to reduce the dimensionality and extract underlying features using a few latent common factors. Conventional methods for estimating the factor model typically requires finite fourth moment of the data, which ignores the effect of heavy-tailedness and thus may result in unrobust or even inconsistent estimation of the factor space and common components. In this article, we propose to recover the factor space by performing principal component analysis to the spatial Kendall’s tau matrix instead of the sample covariance matrix. In a second step, we estimate the factor scores by the ordinary least square regression. Theoretically, we show that under the elliptical distribution framework the factor loadings and scores as well as the common components can be estimated consistently without any moment constraint. The convergence rates of the estimated factor loadings, scores, and common components are provided. The finite sample performance of the proposed procedure is assessed through thorough simulations. An analysis of a financial dataset of asset returns shows the superiority of the proposed method over the classical principle component analysis method.
DOI: 10.6084/m9.figshare.21762545
title: Experiment data

description: Data on ADAM17 protein levels and inflammatory factor levels in COPD