cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3qbqgp
title: Occurrence Download

description: A dataset containing 1287 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Israel",
 "TaxonKey is Bufotes viridis (Laurenti, 1768)"
 ]
}

 The dataset includes 1287 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0319136-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trwxem
title: Occurrence Download

description: A dataset containing 1472048 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Cunninghamia R.Br., Taiwania Hayata, Dipteris Reinw., Cheiropleuria C.Presl, Equisetum L., Dipteris Reinw., Cheiropleuria C.Presl, Eupodium J.Sm., Ptisana Murdock, Marattia Kaulf., Osmunda L., Osmundastrum C.Presl, Todea Willd. ex Bernh., Leptopteris C.Presl)"
 ]
}

 The dataset includes 1472048 records from 1690 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067158-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.14724658
title: Supplementary Figure This file contains Figure S1. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.13265063.v1
title: LncRNA <i>GAS5</i> alleviates rheumatoid arthritis through regulating miR-222-3p/Sirt1 signalling axis

description: Rheumatoid arthritis (RA) is an autoimmune disease that affects millions of people. Fibroblast-like synoviocytes (FLSs) located in rheumatoid panni play a pivotal role in the formation of RA. The long noncoding RNA (lncRNA) <i>GAS5</i> is reportedly downregulated in rheumatoid arthritis. However, its detailed mechanism in RA remains to be explored. This study investigated the roles and related mechanisms of <i>GAS5</i> in RA. The expression levels of <i>GAS5</i>, miR-222-3p, and sirtuin 1 (Sirt1) were evaluated by quantitative PCR (qPCR). Cell proliferation was analyzed by CCK-8 and BrdU assays. Cell apoptosis was assessed by flow cytometry and western blotting. Enzyme-linked immunosorbent assay (ELISA) was utilized to evaluate the levels of TNF-α, IL-1β, and IL-6. The interaction between <i>GAS5</i> or Sirt1 and miR-222-3p was predicted by starBase and validated by dual-luciferase reporter assay. <i>GAS5</i> expression was found to be downregulated in the serum samples of RA patients and in RA-FLSs. <i>GAS5</i> overexpression or the inhibition of miR-222-3p impeded the activity of RA-FLSs by repressing their proliferation and inflammation and by promoting apoptosis. Mechanistically, <i>GAS5</i> indirectly regulates Sirt1 expression by binding miR-222-3p. Further experiments confirmed that Sirt1 overexpression restored the anti-RA activity of <i>GAS5</i> under miR-222-3p mimic. The miR-222-3p/Sirt1 axis was found to be critical for the function of <i>GAS5</i> in regulating the proliferation, inflammation, and apoptosis of RA-FLSs. These data indicate <i>GAS5</i> activation as a potential therapeutic strategy for RA progression.
DOI: 10.2909/a6b1526a-3906-4178-a1be-d75d0c260f18
title: Emerald Network data (vector) - the Pan-European network of protected sites version 2023, Feb 2024

description: This is the metadata that refer to the spatial data covering the Emerald Network which is an ecological network made up of Areas of Special Conservation Interest. The objective of the Emerald Network is the long-term survival of the species and habitats. This version covers the reporting in 2023.

The Emerald Network consists of the Areas of Special Conservation Interest (ASCI) designated under Recommendation No. 16 (1989) and Resolution No. 3 (1996) of the Standing Committee to the Bern Convention.

The Network is to be set up in each Contracting Party or observer State to the Convention. It thus involves all the European Union member States, some non-Community States and a number of African States. As a Contracting Party, the European Union contributes to the Emerald Network with its Natura 2000 sites.

The Emerald Network aggregated database is updated annually.

Besides the web service link provided in the metadata, the following services provide information on species and habitat types inside the Emerald sites:
https://bio.discomap.eea.europa.eu/arcgis/rest/services/ProtectedSites/EmeraldSpecies/MapServer
https://bio.discomap.eea.europa.eu/arcgis/rest/services/ProtectedSites/EmeraldHabitats/MapServer
DOI: 10.2909/0f6948c3-24fb-41af-ad88-45fbadcc1848
title: Emerald Network data (tabular) - the Pan-European network of protected sites version 2023, Feb 2024

description: This is the metadata that refer to the tabular data covering the Emerald Network which is an ecological network made up of Areas of Special Conservation Interest. The objective of the Emerald Network is the long-term survival of the species and habitats. This version covers the reporting in 2023.

The Emerald Network consists of the Areas of Special Conservation Interest (ASCI) designated under Recommendation No. 16 (1989) and Resolution No. 3 (1996) of the Standing Committee to the Bern Convention.

The Network is to be set up in each Contracting Party or observer State to the Convention. It thus involves all the European Union member States, some non-Community States and a number of African States. As a Contracting Party, the European Union contributes to the Emerald Network with its Natura 2000 sites.

The Emerald Network aggregated database is updated annually.
DOI: 10.6084/m9.figshare.6973523
title: Additional file 4: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a Differential analysis results for all intronic joint peaks. b Differential analysis results for all intronic joint peaks. (XLSX 14058 kb)
DOI: 10.6084/m9.figshare.6449258
title: Additional file 6: of RNA sequencing-based longitudinal transcriptomic profiling gives novel insights into the disease mechanism of generalized pustular psoriasis

description: Table S4. List of DEGs enriched in canonical pathways by IPA analysis. (XLS 198Â kb)
DOI: 10.6084/m9.figshare.6973547.v1
title: Additional file 6: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a List of alternative last exons differentially utilized in MNs vs WSC. b List of alternative last exons differentially utilized in wild-type vs Nova2 knockout mouse brain. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.6973550.v1
title: Additional file 7: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: List of RNA linkers and DNA primers used in CLIP. (XLSX 70 kb)
DOI: 10.5281/zenodo.10642251
title: IODP Expedition 390C ICP-AES elemental analysis (interstitial water)

description: Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.
DOI: 10.5281/zenodo.10642250
title: IODP Expedition 390C Hole summary

description: Report lists hole data: location, water depth, drilling, coring system, and core recovery.
DOI: 10.5281/zenodo.10642252
title: IODP Expedition 390C ICP-AES elemental analysis (interstitial water)

description: Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.
DOI: 10.5281/zenodo.10642249
title: IODP Expedition 390C Hole summary

description: Report lists hole data: location, water depth, drilling, coring system, and core recovery.
DOI: 10.6084/m9.figshare.10120673.v1
title: Manipulation of Mitophagy by “All-in-One” Nanosensitizer Augments Sonodynamic Glioma Therapy

description: Limited penetration of chemotherapeutic drugs through the blood brain barrier (BBB), and the increased chemo-resistance of glioma cells due to macroautophagy/autophagy, result in high tumor recurrence and extremely limited survival of glioma patients. Ultrasound-targeted microbubble destruction (UTMD) is a technique of transient and reversible BBB disruption, which greatly facilitates intracerebral drug delivery. In addition, sonodynamic therapy (SDT) based on ultrasound stimulation and a sonosensitizer, can be a safe and non-invasive strategy for treating glioma. We innovatively designed a smart “all-in-one” nanosensitizer platform by incorporating the sonoactive chlorin e6 (Ce6) and an autophagy inhibitor-hydroxychloroquine (HCQ) into angiopep-2 peptide-modified liposomes (designated as ACHL), which integrates multiple diagnostic and therapeutic functions. ACHL selectively accumulated in the brain tumors during the optimal time-window of transient UTMD-mediated BBB opening. The nanosensitizer then responded to a second ultrasonic stimulation, and simultaneously unloaded HCQ and generated ROS in the glioma cells. The sonotherapy triggered apoptosis as well as MAPK/p38-PINK1-PRKN-dependent mitophagy, in which the antioxidant relieved the sonotoxicity and MAPK/p38 activation, while the inhibition of MAPK/p38 attenuated the progression toward mitophagy by compromising redistribution of PRKN. Moreover, HCQ blocking autophagosome degradation, augmented intracellular ROS production and resulted in an oxidative-damage regenerative loop. ACHL-SDT treatment using this construct significantly inhibited the xenograft-tumor growth and prolonged the survival time of tumor-bearing mice, exhibiting an improved therapeutic efficiency. All together, we demonstrated a precision sonotherapy with simultaneous apoptosis induction and mitophagy inhibition, which served as an intelligently strategic sense of working alongside, providing new insights into the theranostics of brain tumors.
DOI: 10.6084/m9.figshare.14839672
title: The diagnostic value of CEA for lung cancer-related malignant pleural effusion in China: a meta-analysis

description: To accurately evaluate the diagnostic value of carcinoembryonic antigen (CEA) for malignant pleural effusion associated with lung cancer in the Chinese population. Three English databases, PubMed, Embase and Web of Science, and two Chinese databases, China National Knowledge Infrastructure (CNKI) and Wanfang Data, up to 5 November 2020, were searched. The literature on the diagnosis of lung cancer-related malignant pleural effusion by CEA in the Chinese population were collected. The data was analyzed by Stata15.0 software. A total of 15 studies were included in the meta-analysis. The combined sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio were 0.80 (95% CI: 0.74–0.84), 0.92 (95% CI: 0.89–0.95), 10.46 (95% CI: 7.29–15.00), 0.22 (95% CI: 0.17–0.28), 47.26 (95% CI: 28.84–77.44), respectively . The area under the receiver operating characteristic curve was 0.93 (95% CI: 0.91–0.95). No significant publication bias was found (<i>P</i> &gt; 0.05) CEA has anexcellent diagnostic value for patients with lung cancer-related malignant pleural effusion in the Chinese population.
DOI: 10.6084/m9.figshare.24277133
title: Additional file 1 of Phytosulfokine contributes to suspension culture of Cunninghamia lanceolata through its impact on redox homeostasis

description: Additional file 1. Table S1. Data statistics of RNA-seq data. Table S2. Length distribution of assembled transcripts and unigenes. Table S3. BUSCO assessment for transcript assembly completeness.
DOI: 10.6084/m9.figshare.24277133.v1
title: Additional file 1 of Phytosulfokine contributes to suspension culture of Cunninghamia lanceolata through its impact on redox homeostasis

description: Additional file 1. Table S1. Data statistics of RNA-seq data. Table S2. Length distribution of assembled transcripts and unigenes. Table S3. BUSCO assessment for transcript assembly completeness.
DOI: 10.6084/m9.figshare.6973514
title: Additional file 3: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: a Sequencing and mapping statistics of MN and WSC NOVA CLIP. b Sequencing and mapping statistics of MN and WSC NOVA CLIP. c mm9 coordinates and genomic annotation of WSC NOVA CLIP peaks. d List of known NOVA targets harboring WSC NOVA CLIP peaks. e List of known NOVA targets harboring MN NOVA CLIP peaks. f GO enrichment of known MN versus WSC NOVA targets. g Transcripts with enriched NOVA CLIP signals in MNs compared to WSC. h Transcripts with depleted NOVA CLIP signals in MNs compared to WSC. (XLSX 13044 kb)
DOI: 10.5281/zenodo.10642227
title: IODP Expedition 390C Core composite images

description: A digital composite image (PNG) is made for each core comprising core sections scanned using a line-scan camera. The composite layout is equivalent to traditional core table photos. Top left is top of core; color and meter rule references are included.
DOI: 10.5281/zenodo.10642228
title: IODP Expedition 390C Core composite images

description: A digital composite image (PNG) is made for each core comprising core sections scanned using a line-scan camera. The composite layout is equivalent to traditional core table photos. Top left is top of core; color and meter rule references are included.
DOI: 10.6084/m9.figshare.6973550
title: Additional file 7: of Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

description: List of RNA linkers and DNA primers used in CLIP. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.13265063
title: LncRNA <i>GAS5</i> alleviates rheumatoid arthritis through regulating miR-222-3p/Sirt1 signalling axis

description: Rheumatoid arthritis (RA) is an autoimmune disease that affects millions of people. Fibroblast-like synoviocytes (FLSs) located in rheumatoid panni play a pivotal role in the formation of RA. The long noncoding RNA (lncRNA) <i>GAS5</i> is reportedly downregulated in rheumatoid arthritis. However, its detailed mechanism in RA remains to be explored. This study investigated the roles and related mechanisms of <i>GAS5</i> in RA. The expression levels of <i>GAS5</i>, miR-222-3p, and sirtuin 1 (Sirt1) were evaluated by quantitative PCR (qPCR). Cell proliferation was analyzed by CCK-8 and BrdU assays. Cell apoptosis was assessed by flow cytometry and western blotting. Enzyme-linked immunosorbent assay (ELISA) was utilized to evaluate the levels of TNF-α, IL-1β, and IL-6. The interaction between <i>GAS5</i> or Sirt1 and miR-222-3p was predicted by starBase and validated by dual-luciferase reporter assay. <i>GAS5</i> expression was found to be downregulated in the serum samples of RA patients and in RA-FLSs. <i>GAS5</i> overexpression or the inhibition of miR-222-3p impeded the activity of RA-FLSs by repressing their proliferation and inflammation and by promoting apoptosis. Mechanistically, <i>GAS5</i> indirectly regulates Sirt1 expression by binding miR-222-3p. Further experiments confirmed that Sirt1 overexpression restored the anti-RA activity of <i>GAS5</i> under miR-222-3p mimic. The miR-222-3p/Sirt1 axis was found to be critical for the function of <i>GAS5</i> in regulating the proliferation, inflammation, and apoptosis of RA-FLSs. These data indicate <i>GAS5</i> activation as a potential therapeutic strategy for RA progression.
DOI: 10.6084/m9.figshare.13265080
title: Investigating stable and dynamic aspects of student motivation using generalizability theory

description: The Academic Motivation Scale (AMS) is a commonly used 28‐item measure of motivation orientation. However, the scale has not been examined using methods to distinguish between state and trait aspects of motivation. We applied Generalizability Theory to appraise the psychometric properties of the AMS and to differentiate items measuring state or trait motivation within the AMS. One hundred and thirty medical students completed the 28‐item AMS at three time points. Generalizability Theory was applied to examine the generalizability of the AMS (total and sub‐scales) and to estimate state and trait aspects of student motivation. The overall AMS showed high generalizability (<i>G</i> = .93) in assessing student motivation across student populations and occasions, whereas the AMS subscales demonstrated low levels of generalizability. The majority of the AMS items scored high for the state component index suggesting movement between motivational priorities while maintaining the overall stability of the individual motivation levels. The total AMS is suitable as a reliable measurement of motivation among student populations with high generalizability of scores across students and assessment occasions. Measuring trait motivation using the total AMS score instead of subscale scores reduces measurement error and optimises instrument reliability.
DOI: 10.6084/m9.figshare.13265080.v1
title: Investigating stable and dynamic aspects of student motivation using generalizability theory

description: The Academic Motivation Scale (AMS) is a commonly used 28‐item measure of motivation orientation. However, the scale has not been examined using methods to distinguish between state and trait aspects of motivation. We applied Generalizability Theory to appraise the psychometric properties of the AMS and to differentiate items measuring state or trait motivation within the AMS. One hundred and thirty medical students completed the 28‐item AMS at three time points. Generalizability Theory was applied to examine the generalizability of the AMS (total and sub‐scales) and to estimate state and trait aspects of student motivation. The overall AMS showed high generalizability (<i>G</i> = .93) in assessing student motivation across student populations and occasions, whereas the AMS subscales demonstrated low levels of generalizability. The majority of the AMS items scored high for the state component index suggesting movement between motivational priorities while maintaining the overall stability of the individual motivation levels. The total AMS is suitable as a reliable measurement of motivation among student populations with high generalizability of scores across students and assessment occasions. Measuring trait motivation using the total AMS score instead of subscale scores reduces measurement error and optimises instrument reliability.
DOI: 10.6084/m9.figshare.22177989.v1
title: Characterization of the mitochondrial genome of the lawn cutworm <i>Spodoptera depravata</i> (Lepidoptera: Noctuidae)

description: The lawn cutworm, <i>Spodoptera depravata</i>, is one of the most important pests that causes economic damage to grass crops. This study reports the complete mitochondrial genome of an <i>S. depravata</i> sample collected in China. The genome is a circular molecule 15,460 bp in length with an overall A + T content of 81.6%. It contains 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The gene content and organization of the mitogenome of <i>S. depravata</i> are identical to those of other <i>Spodoptera</i> species. Maximum-likelihood phylogenetic analysis based on mitogenomes showed a close evolutionary relationship between <i>S. depravata</i> and <i>S. exempta</i>. This study provides new molecular data for the identification and further phylogenetic analyses of <i>Spodoptera</i> species.
DOI: 10.5281/zenodo.10642322
title: IODP Expedition 390C X-ray fluorescence (XRF)

description: Elemental peak intensities in section halves were measured by an Avaatech X-ray fluorescence (XRF) Core Scanner post-expedition. Each measurement position may be measured at multiple XRF conditions in order to excite and measure specific ranges of elements (e.g., 10 kV and no filter for light elements). Peak intensity changes (concentrations not provided) are then used to help recognize and define major chemostratigraphic units without the need for destructive sampling. Data are presented in comma-delimited (CSV) files by section and by energy/instrumental conditions.
DOI: 10.5281/zenodo.10642323
title: IODP Expedition 390C X-ray fluorescence (XRF)

description: Elemental peak intensities in section halves were measured by an Avaatech X-ray fluorescence (XRF) Core Scanner post-expedition. Each measurement position may be measured at multiple XRF conditions in order to excite and measure specific ranges of elements (e.g., 10 kV and no filter for light elements). Peak intensity changes (concentrations not provided) are then used to help recognize and define major chemostratigraphic units without the need for destructive sampling. Data are presented in comma-delimited (CSV) files by section and by energy/instrumental conditions.
DOI: 10.6084/m9.figshare.24277276
title: The activation of SIRT1 by resveratrol reduces breast cancer metastasis to lung through inhibiting neutrophil extracellular traps

description: Neutrophil extracellular traps (NETs) play a crucial role in breast cancer metastasis. However, the therapeutic target of NETs in breast cancer metastasis is still unknown. Using a natural metabolite library and single-cell sequencing data analysis, we identified resveratrol (RES), a polyphenolic natural phytoalexin, and agonist of silent information regulator-1 (SIRT1) that suppressed NETs formation after cathepsin C (CTSC) treatment. <i>In vivo</i>, RES significantly hindered breast cancer metastasis in a murine orthotopic 4T1 breast cancer model. Serum levels of myeloperoxidase-DNA and neutrophil elastase-DNA in mouse breast cancer model were significantly lower after RES treatment. Correspondingly, the tumour infiltrated CD8<sup>+</sup>T cells in the lungs increased after the treatment. Mechanistically, RES targets SIRT1 in neutrophils and significantly inhibits the citrullination of histones H3, which is essential for chromatin decondensation and NETs formation. Furthermore, we identified that the NETs were suppressed by RES in bone marrow neutrophils after CTSC treatment, while specific deficiency of SIRT1 in neutrophils promoted NETs formation and breast cancer to lung metastasis. Thus, our results revealed that RES could be potentially identified as a viable therapeutic drug to prevent neutrophil cell death and breast cancer metastasis.