cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1144803.09fu
title: SH1144803.09FU

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/sh1144804.09fu
title: SH1144804.09FU

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/sh1144805.09fu
title: SH1144805.09FU

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/sh1144806.09fu
title: SH1144806.09FU

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/sh1144807.09fu
title: SH1144807.09FU

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: 10.6084/m9.figshare.22623253
title: Additional file 1 of MicroRNA-Transcription factor regulatory networks in the early strobilar development of Echinococcus granulosus protoscoleces

description: Additional file 1: Table S1. List of Echinococcus granulosus Transcription factors with differentially expressed genes in early stages of strobilar development. Table S2. List of predicted targets derived from miRanda, PITA, and RNA22 and their comparison with 818 differentially expresssed genes and 41 differentially expressed transcription factors. Table S3. The summary of gene enrichment data obtained from KEGG database for predicted targets of selected differentially expressed miRNAs. Table S4. Prediction of protein?protein interaction network for six differentially expressed TFs by using the Search Tool for Recurring Instances of Neighboring Genes (STRING). Table S5. Comparison of the in vivo, in vitro and the RNA-seq data of the selected differentially expressed TFs and their related miRNAs. Table S6. Calculation of the Betweenness, Degree and Closeness centrality of the predicted network by using the cytoHubba (version 0.1). Table S7. List of Echinococcus granulosus differentially expressed genes in early stages of strobilar development according to Debarba et. al 2020. Table S8. List of Echinococcus granulosus miRNAs with differentially expressed genes in early stages of strobilar development according to Bai et. al 2020. Table S9. List of 396 Echinococcus granulosus Transcription factors and related DNA-binding domains/transcription factors families according to AnimalTFDB 3.0 database (394 unique TFs). Table S10. Sequences of forward and reverse primers of eight differentially expressed transcription factors and references genes used in qPCR validation.
DOI: 10.6084/m9.figshare.22623253.v1
title: Additional file 1 of MicroRNA-Transcription factor regulatory networks in the early strobilar development of Echinococcus granulosus protoscoleces

description: Additional file 1: Table S1. List of Echinococcus granulosus Transcription factors with differentially expressed genes in early stages of strobilar development. Table S2. List of predicted targets derived from miRanda, PITA, and RNA22 and their comparison with 818 differentially expresssed genes and 41 differentially expressed transcription factors. Table S3. The summary of gene enrichment data obtained from KEGG database for predicted targets of selected differentially expressed miRNAs. Table S4. Prediction of protein?protein interaction network for six differentially expressed TFs by using the Search Tool for Recurring Instances of Neighboring Genes (STRING). Table S5. Comparison of the in vivo, in vitro and the RNA-seq data of the selected differentially expressed TFs and their related miRNAs. Table S6. Calculation of the Betweenness, Degree and Closeness centrality of the predicted network by using the cytoHubba (version 0.1). Table S7. List of Echinococcus granulosus differentially expressed genes in early stages of strobilar development according to Debarba et. al 2020. Table S8. List of Echinococcus granulosus miRNAs with differentially expressed genes in early stages of strobilar development according to Bai et. al 2020. Table S9. List of 396 Echinococcus granulosus Transcription factors and related DNA-binding domains/transcription factors families according to AnimalTFDB 3.0 database (394 unique TFs). Table S10. Sequences of forward and reverse primers of eight differentially expressed transcription factors and references genes used in qPCR validation.
DOI: 10.6084/m9.figshare.19028945
title: Additional file 6 of Genome-wide annotation of protein-coding genes in pig

description: Additional file 6. Includes a list of a subset of orthologs with one parsimonious high confidence ortholog used in human-pig comparison analyses, a table of specificity classification for human and pig, indicating overlap in classification, and the inputs for hypergeometric test for assessing the classification overlap between pig and human tissues.
DOI: 10.6084/m9.figshare.20078596
title: Circular RNA hsa_circ_0057452 facilitates keloid progression by targeting the microRNA-1225-3p/AF4/FMR2 family member 4 axis

description: The circular RNA, hsa_circ_0057452, is highly expressed in keloids, but its specific mechanism of action remains unknown. The levels of hsa_circ_0057452, microRNA (miR)-1225-3p, and AF4/FMR2 family member 4 (AFF4) in keloid tissues and keloid fibroblasts (KFs) were determined using quantitative reverse transcription-polymerase chain reaction. Changes in KFs viability, proliferation, apoptosis, and migration were investigated using the cell counting kit-8, bromodeoxyuridine, flow cytometry, and Transwell assays. Luciferase, RNA immunoprecipitation, and RNA pull-down assays were performed to identify the binding relationship among hsa_circ_0057452, miR-1225-3p, and AFF4. We found that hsa_circ_0057452 and AFF4 expression levels were upregulated, whereas miR-1225-3p expression levels were downregulated in keloids. Knockdown of hsa_circ_0057452 or AFF4 suppressed the viability, proliferation, and migration of KFs and induced apoptosis, whereas hsa_circ_0057452 overexpression and miR-1225-3p knockdown showed the opposite trend. Furthermore, hsa_circ_0057452 affected the biological behavior of KFs by releasing AFF4 via sponging of miR-1225-3p. Therefore, our results show that hsa_circ_0057452 promotes keloid progression by targeting miR-1225-3p and regulating AFF4 levels.
DOI: 10.6084/m9.figshare.20078597.v1
title: Shikonin inhibited glycolysis and sensitized cisplatin treatment in non-small cell lung cancer cells via the exosomal pyruvate kinase M2 pathway

description: The active ingredient of the traditional Chinese medicine comfrey is shikonin, a naphthoquinone compound. The focus of this study was to investigate the effect of shikonin on the proliferation, invasion, migration, and chemoresistance of non-small cell lung cancer (NSCLC) cells, and to explore its underlying molecular biological mechanisms. The results show that shikonin inhibited the viability, proliferation, invasion, and migration of NSCLC cells A549 and PC9, and induced apoptosis. As the inhibitor of pyruvate kinase M2 (PKM2), a key enzyme in glycolysis, shikonin inhibited glucose uptake and the production of lactate, the final metabolite of aerobic glycolysis. <i>In vivo</i> chemotherapeutic assay showed that shikonin reduced the tumor volume and weight in NSCLC mice model and increased the sensitivity to cisplatin chemotherapy. Histoimmunology experiments showed the combination of shikonin and cisplatin downregulated the expression of PKM2 and its transcriptionally regulated downstream gene glucose transporter 1 (Glut1) in tumor tissue. In an assessment of glucose metabolism, micro-PET/CT data showed a combination of shikonin and cisplatin inhibited the fluorodeoxy glucose (<sup>18</sup>F-FDG) uptake into tumor. Since exosomal PKM2 affected the sensitivity to cisplatin in NSCLC cells, we also demonstrated shikonin could inhibit exosome secretion and exosomal PKM2 through the administration of exosomal inhibitor GW4869. Furthermore, shikonin sensitized cisplatin treatment by reducing the extracellular secretion of exosomal PKM2. In conclusion, we suggest that shikonin not only inhibits PKM2 intracellularly but also reduces glycolytic flux and increases cisplatin sensitivity through the exosomal pathway.
DOI: 10.6084/m9.figshare.20078596.v1
title: Circular RNA hsa_circ_0057452 facilitates keloid progression by targeting the microRNA-1225-3p/AF4/FMR2 family member 4 axis

description: The circular RNA, hsa_circ_0057452, is highly expressed in keloids, but its specific mechanism of action remains unknown. The levels of hsa_circ_0057452, microRNA (miR)-1225-3p, and AF4/FMR2 family member 4 (AFF4) in keloid tissues and keloid fibroblasts (KFs) were determined using quantitative reverse transcription-polymerase chain reaction. Changes in KFs viability, proliferation, apoptosis, and migration were investigated using the cell counting kit-8, bromodeoxyuridine, flow cytometry, and Transwell assays. Luciferase, RNA immunoprecipitation, and RNA pull-down assays were performed to identify the binding relationship among hsa_circ_0057452, miR-1225-3p, and AFF4. We found that hsa_circ_0057452 and AFF4 expression levels were upregulated, whereas miR-1225-3p expression levels were downregulated in keloids. Knockdown of hsa_circ_0057452 or AFF4 suppressed the viability, proliferation, and migration of KFs and induced apoptosis, whereas hsa_circ_0057452 overexpression and miR-1225-3p knockdown showed the opposite trend. Furthermore, hsa_circ_0057452 affected the biological behavior of KFs by releasing AFF4 via sponging of miR-1225-3p. Therefore, our results show that hsa_circ_0057452 promotes keloid progression by targeting miR-1225-3p and regulating AFF4 levels.
DOI: 10.6084/m9.figshare.25206755
title: Supplementary Information Raw Data File

description: We hypothesise that antimicrobial resistance (AMR) cannot be overcome by simply 'drugging' a single biological target, therefore, our focus is developing broad-spectrum therapeutics.Herein we present the synthesis of two novel spacer-linked, anthraquinone-triphenylphosphonium (AQ-TPP) conjugates (4) and (5) as early lead compounds in a new class of agent designed to penetrate the lipophilic barriers of the membranes of a diverse family of species; and establish bacterial growth inhibitory properties against methicillin-resistant <i>Staphylococcus aureus</i> (NCTC 13616) and Mycobacterium smegmatis [mc2155] (as a surrogate for <i>Mycobacterium tuberculosis</i>).The MIC and MBC values of (4) and (5) were determined against MRSA and found to be equipotent [MIC for each: 1 µg/mL (1.2 µM)]. Whereas the amide-linked conjugate (5) was determined to have 2-fold greater bactericidal potency [MBC 1 µg/mL (1.2 µM] than ester-linked (4).The anthraquinone-TPP conjugates (4) and (5) were active in vitro against <i>Mycobacterium smegmatis</i> and were equipotent as determined by their MIC values; in contrast to MRSA, the less hydrophobic (4) had 2-fold greater bactericidal potency than (5) as measured by their MBC values. Notably, both conjugates showed potent intracellular growth inhibitory activity in infected THP-1 macrophages. The conjugates are promising leads for the development of new antibacterial drugs.
DOI: 10.6084/m9.figshare.25206755.v1
title: Supplementary Information Raw Data File

description: We hypothesise that antimicrobial resistance (AMR) cannot be overcome by simply 'drugging' a single biological target, therefore, our focus is developing broad-spectrum therapeutics.Herein we present the synthesis of two novel spacer-linked, anthraquinone-triphenylphosphonium (AQ-TPP) conjugates (4) and (5) as early lead compounds in a new class of agent designed to penetrate the lipophilic barriers of the membranes of a diverse family of species; and establish bacterial growth inhibitory properties against methicillin-resistant <i>Staphylococcus aureus</i> (NCTC 13616) and Mycobacterium smegmatis [mc2155] (as a surrogate for <i>Mycobacterium tuberculosis</i>).The MIC and MBC values of (4) and (5) were determined against MRSA and found to be equipotent [MIC for each: 1 µg/mL (1.2 µM)]. Whereas the amide-linked conjugate (5) was determined to have 2-fold greater bactericidal potency [MBC 1 µg/mL (1.2 µM] than ester-linked (4).The anthraquinone-TPP conjugates (4) and (5) were active in vitro against <i>Mycobacterium smegmatis</i> and were equipotent as determined by their MIC values; in contrast to MRSA, the less hydrophobic (4) had 2-fold greater bactericidal potency than (5) as measured by their MBC values. Notably, both conjugates showed potent intracellular growth inhibitory activity in infected THP-1 macrophages. The conjugates are promising leads for the development of new antibacterial drugs.
DOI: 10.6084/m9.figshare.5398558.v1
title: Geochronology, geochemistry, Sr–Nd–Hf isotopic compositions, and petrogenetic and tectonic implications of Early Cretaceous intrusions associated with the Duolong porphyry–epithermal Cu–Au deposit, central Tibet

description: This article reports new zircon laser ablation-multicollector-inductively coupled plasma-mass spectrometry U–Pb and Hf isotope, whole-rock major and trace element, and Sr–Nd isotope data for mineralized and barren intrusions associated with the Duolong porphyry–epithermal copper–(gold) deposit (DPCD, a mining camp containing several individual deposits) in the western Qiangtang Terrane (QT), central Tibet. These data are used to further our understanding of the geological evolution of this region. The mineralized and barren DPCD intrusions are typical I-type granitoids that were synchronously emplaced at ca. 112.6–125.9 Ma. These igneous rocks show arc affinities that are characterized by enrichments in the light rare earth elements (La<sub>N</sub>/Yb<sub>N</sub> = 4.08–15.23) and the light ion lithophile elements (Rb, Th, U, K, and Pb), and depletions in the high field strength elements (Nb, Ta, and Ti). They have <sup>87</sup>Sr/<sup>86</sup>Sr<sub>(i)</sub> values of 0.7046–0.7079, <sub>Nd</sub>(<i>t</i>) values of –6.0 to +1.1, and two-stage Nd model ages of ca. 823–1410 Ma. Zircons from these intrusive rocks have variable but generally positive <i>ε</i><sub>Hf</sub>(<i>t</i>) values (–2.7 to +13.7) and relatively young zircon Hf crustal model ages of 335–1351 Ma. Combining these data with geochemical data reported in recent studies, we infer that the mineralized and barren DPCD intrusions formed in a continental marginal arc setting and likely originated from a common parental magma that was result of magma mixing of juvenile crust-derived basaltic melts and old lower crust-derived melts. The formation of the DPCD intrusions indicates that the Bangongco–Nujiang oceanic lithosphere was still undergoing northward subduction beneath the western QT at ca. 112.6–125.9 Ma, suggesting in turn that the oceanic basin have not closed completely during the Early Cretaceous. These new data also indicate that the processes that occur during the subduction of oceanic crust in continental marginal arc settings produce and preserve juvenile crustal material, leading to net continental crust vertical growth and thickening.
DOI: 10.6084/m9.figshare.20078597
title: Shikonin inhibited glycolysis and sensitized cisplatin treatment in non-small cell lung cancer cells via the exosomal pyruvate kinase M2 pathway

description: The active ingredient of the traditional Chinese medicine comfrey is shikonin, a naphthoquinone compound. The focus of this study was to investigate the effect of shikonin on the proliferation, invasion, migration, and chemoresistance of non-small cell lung cancer (NSCLC) cells, and to explore its underlying molecular biological mechanisms. The results show that shikonin inhibited the viability, proliferation, invasion, and migration of NSCLC cells A549 and PC9, and induced apoptosis. As the inhibitor of pyruvate kinase M2 (PKM2), a key enzyme in glycolysis, shikonin inhibited glucose uptake and the production of lactate, the final metabolite of aerobic glycolysis. <i>In vivo</i> chemotherapeutic assay showed that shikonin reduced the tumor volume and weight in NSCLC mice model and increased the sensitivity to cisplatin chemotherapy. Histoimmunology experiments showed the combination of shikonin and cisplatin downregulated the expression of PKM2 and its transcriptionally regulated downstream gene glucose transporter 1 (Glut1) in tumor tissue. In an assessment of glucose metabolism, micro-PET/CT data showed a combination of shikonin and cisplatin inhibited the fluorodeoxy glucose (<sup>18</sup>F-FDG) uptake into tumor. Since exosomal PKM2 affected the sensitivity to cisplatin in NSCLC cells, we also demonstrated shikonin could inhibit exosome secretion and exosomal PKM2 through the administration of exosomal inhibitor GW4869. Furthermore, shikonin sensitized cisplatin treatment by reducing the extracellular secretion of exosomal PKM2. In conclusion, we suggest that shikonin not only inhibits PKM2 intracellularly but also reduces glycolytic flux and increases cisplatin sensitivity through the exosomal pathway.
DOI: 10.6084/m9.figshare.20078605
title: Omentin-1 alleviate interleukin-1β(IL-1β)-induced nucleus pulposus cells senescence

description: One of the main causes of low back pain (LBP) and degenerative musculoskeletal disorders is intervertebral disc degeneration (IVDD). Inflammation-associated senescence of Human nucleus pulposus cells (HNPCs) plays an essential function in the disease progression of IVDD. Omentin-1 is an adipokine that has been recently reported to have anti-inflammatory potential. In our research, IL-1β was used to simulate the inflammatory environment in the IVDD. We investigated in vitro the effects of Omentin-1 on HNPCs, including the components of senescence, cell cycle and extracellular matrix (ECM) synthesis. The results showed that the addition of Omentin-1 improved IL-1β-induced senescence in HNPCs. G1 phase cell cycle arrest and reduced ECM synthesis in HNPCs. Furthermore, we demonstrated that the effect of Omentin-1 in reducing senescence of HNPCs is dependent on SIRT1. These findings suggest that Omentin-1 plays an important function in protecting HNPCs against senescence and has the potential for IVDD gene target therapy.
DOI: 10.6084/m9.figshare.20078605.v1
title: Omentin-1 alleviate interleukin-1β(IL-1β)-induced nucleus pulposus cells senescence

description: One of the main causes of low back pain (LBP) and degenerative musculoskeletal disorders is intervertebral disc degeneration (IVDD). Inflammation-associated senescence of Human nucleus pulposus cells (HNPCs) plays an essential function in the disease progression of IVDD. Omentin-1 is an adipokine that has been recently reported to have anti-inflammatory potential. In our research, IL-1β was used to simulate the inflammatory environment in the IVDD. We investigated in vitro the effects of Omentin-1 on HNPCs, including the components of senescence, cell cycle and extracellular matrix (ECM) synthesis. The results showed that the addition of Omentin-1 improved IL-1β-induced senescence in HNPCs. G1 phase cell cycle arrest and reduced ECM synthesis in HNPCs. Furthermore, we demonstrated that the effect of Omentin-1 in reducing senescence of HNPCs is dependent on SIRT1. These findings suggest that Omentin-1 plays an important function in protecting HNPCs against senescence and has the potential for IVDD gene target therapy.