cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22557706.v2
title: Supplemental Data for "Quantifying uncertainty in sustainable biomass and production of biotic carbon in Enceladus' notional methanogenic biosphere"

description: This is simulation data for results presented in "Quantifying uncertainty in sustainable biomass and production of biotic carbon in Enceladus' notional methanogenic biosphere"; <i>JGR:Planets</i>. To exactly replicate or extend analysis of these data, these archives can be extracted and placed in the 'data' directory of NutMEG-Implementations/Enceladus2024_BiomassBiosignatures/ (exact version for this work archived on zenodo: https://doi.org/10.5281/zenodo.10647803)<b>biomass.zip</b> contains results from the individual Monte Carlo simulations to estimate steady state biomass and turnover on Enceladus per mole of H2 consumed by hypothetical methanogens per second.<b>BMTO_means_CIs.zip</b> contains means and confidence intervals extracted from the Monte Carlo simulations above, which are presented in Supplemental Tables S4-S27 in Higgins et al. 2024, <i>JGR: Planets</i>.<b>speciation.zip </b>contains raw data output from the chemical speciation calculations across temperature and bulk ocean pH-space for Enceladus seawater. See methods and supplement of Higgins et al. 2024, <i>JGR: Planets</i> for further information and limitations in this chemcal speciation model.
DOI: 10.6084/m9.figshare.16946357
title: Additional file 7 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 7. GO annotation of DEGs in RD cell
DOI: 10.6084/m9.figshare.22557706.v1
title: Supplemental Data for "Quantifying uncertainty in sustainable biomass and production of biotic carbon in Enceladus' notional methanogenic biosphere"

description: This is simulation data for results presented in "Quantifying uncertainty in sustainable biomass and production of biotic carbon in Enceladus' notional methanogenic biosphere"; <i>JGR:Planets</i>. To exactly replicate or extend analysis of these data, these archives can be extracted and placed in the 'data' directory of NutMEG-Implementations/Enceladus2024_BiomassBiosignatures/ (exact version for this work archived on zenodo: https://doi.org/10.5281/zenodo.10647803)<b>biomass.zip</b> contains results from the individual Monte Carlo simulations to estimate steady state biomass and turnover on Enceladus per mole of H2 consumed by hypothetical methanogens per second.<b>BMTO_means_CIs.zip</b> contains means and confidence intervals extracted from the Monte Carlo simulations above, which are presented in Supplemental Tables S4-S27 in Higgins et al. 2024, <i>JGR: Planets</i>.<b>speciation.zip </b>contains raw data output from the chemical speciation calculations across temperature and bulk ocean pH-space for Enceladus seawater. See methods and supplement of Higgins et al. 2024, <i>JGR: Planets</i> for further information and limitations in this chemcal speciation model.
DOI: 10.6084/m9.figshare.16946345
title: Additional file 3 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 3. The whole of differentially expression genes of mRNAs
DOI: 10.6084/m9.figshare.16946348
title: Additional file 4 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 4. The whole of differentially expression genes of miRNAs
DOI: 10.6084/m9.figshare.16946351.v1
title: Additional file 5 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 5. The whole of differentially expression genes of lncRNAs
DOI: 10.6084/m9.figshare.16946348.v1
title: Additional file 4 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 4. The whole of differentially expression genes of miRNAs
DOI: 10.6084/m9.figshare.16946351
title: Additional file 5 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 5. The whole of differentially expression genes of lncRNAs
DOI: 10.6084/m9.figshare.12752159.v1
title: Additional file 11 of Comparative transcriptome analysis reveals ecological adaption of cold tolerance in northward invasion of Alternanthera philoxeroides

description: Additional file 11: Table S9. KEGG pathway annotation analysis for the total number of DEGs.
DOI: 10.6084/m9.figshare.10130129
title: Metadata record for: Global sea-surface iodide observations, 1967-2018

description: This dataset contains key characteristics about the data described in the Data Descriptor Global sea-surface iodide observations, 1967-2018. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.16946360
title: Additional file 8 of High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

description: Additional file 8. KEGG enrichment of DEGs in RD cell
DOI: 10.6084/m9.figshare.12752165
title: Additional file 13 of Comparative transcriptome analysis reveals ecological adaption of cold tolerance in northward invasion of Alternanthera philoxeroides

description: Additional file 13: Table S11. KEGG enrichment analysis for DEGs during the two cold treatment time points in HK and JN populations.
DOI: 10.6084/m9.figshare.16946392
title: Additional file 12 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 12: Table S6. Genome-wide significant association signals of SL using the single-population GWAS and meta-GWAS.
DOI: 10.6084/m9.figshare.11703033.v2
title: Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy

description: Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (<i>Atg5</i> or <i>Ulk1/Ulk2</i>) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of <i>CALCOCO1</i> disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. <b>Abbreviations:</b> ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
DOI: 10.6084/m9.figshare.12752195
title: Additional file 5 of Comparative transcriptome analysis reveals ecological adaption of cold tolerance in northward invasion of Alternanthera philoxeroides

description: Additional file 5: Table S3. BUSCO analysis for quality assessment of assembled transcripts.
DOI: 10.17028/rd.lboro.22189279
title: Supplementary information files for The effect of COVID rehabilitation for ongoing symptoms post hospitalisation with COVID-19 (PHOSP-R): protocol for a randomised parallel group controlled trial on behalf of the PHOSP consortium

description: Supplementary files for article The effect of COVID rehabilitation for ongoing symptoms post hospitalisation with COVID-19 (PHOSP-R): protocol for a randomised parallel group controlled trial on behalf of the PHOSP consortium
 
<strong>Introduction:</strong> Many adults hospitalised with COVID-19 have persistent symptoms such as fatigue, breathlessness and brain fog that limit day-to-day activities. These symptoms can last over 2 years. Whilst there is limited controlled studies on interventions that can support those with ongoing symptoms, there has been some promise in rehabilitation interventions in improving function and symptoms either using face-to-face or digital methods, but evidence remains limited and these studies often lack a control group.
<br>
<strong>Methods and analysis:</strong> This is a nested single-blind, parallel group, randomised control trial with embedded qualitative evaluation comparing rehabilitation (face-to-face or digital) to usual care and conducted within the PHOSP-COVID study. The aim of this study is to determine the effectiveness of rehabilitation interventions on exercise capacity, quality of life and symptoms such as breathlessness and fatigue. The primary outcome is the Incremental Shuttle Walking Test following the eight week intervention phase. Secondary outcomes include measures of function, strength and subjective assessment of symptoms. Blood inflammatory markers and muscle biopsies are an exploratory outcome. The interventions last eight weeks and combine symptom-titrated exercise therapy, symptom management and education delivered either in a face-to-face setting or through a digital platform (www.yourcovidrecovery.nhs.uk). The proposed sample size is 159 participants, and data will be intention-to-treat analyses comparing rehabilitation (face-to-face or digital) to usual care.
<br>
<strong>Ethics and dissemination:</strong> Ethical approval was gained as part of the PHOSP-COVID study by Yorkshire and the Humber Leeds West Research NHS Ethics Committee, and the study was prospectively registered on the ISRCTN trial registry (ISRCTN13293865). Results will be disseminated to stakeholders, including patients and members of the public, and published in appropriate journals.
 
<strong>Article summary</strong>
Strengths and limitations of this study
• This protocol utilises two interventions to support those with ongoing symptoms of COVID-19
• This is a two-centre parallel-group randomised controlled trial
• The protocol has been supported by patient and public involvement groups who identified treatments of symptoms and activity limitation as a top priority
DOI: 10.6084/m9.figshare.12752195.v1
title: Additional file 5 of Comparative transcriptome analysis reveals ecological adaption of cold tolerance in northward invasion of Alternanthera philoxeroides

description: Additional file 5: Table S3. BUSCO analysis for quality assessment of assembled transcripts.
DOI: 10.6084/m9.figshare.14324494
title: Theory of Weightless Sagging Elasto-Flexible Cables

description: Abstract In this Paper, a theory of single sagging planer weightless elasto-flexible cables is proposed. In reference to the instantaneous natural state, hypoelastic rate- type constitutive equations and third-order nonlinear differential equations of planer motion for massless cables with nodal masses are derived. New concepts like configurational complementary potential and contra-gradient principles are proposed. Typical dynamic response of these elastic cables with different sustained loads, axial rigidity and sag/span ratios is determined. Modal, subharmonic and internal resonances, jump and beat phenomena, etc., a re predicted. A new mode of damping of 'free' vibration of the system perturbed from its equilibrium state is identified. Significance of the proposed theory of weightless sagging elasto-flexible cables is discussed.
DOI: 10.6084/m9.figshare.12752207.v1
title: Additional file 9 of Comparative transcriptome analysis reveals ecological adaption of cold tolerance in northward invasion of Alternanthera philoxeroides

description: Additional file 9: Table S7. GO annotation analysis for the total number of DEGs.
DOI: 10.6084/m9.figshare.16946407.v1
title: Additional file 17 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 17: Table S8. GO enrichments of modules.
DOI: 10.17028/rd.lboro.22189279.v1
title: Supplementary information files for The effect of COVID rehabilitation for ongoing symptoms post hospitalisation with COVID-19 (PHOSP-R): protocol for a randomised parallel group controlled trial on behalf of the PHOSP consortium

description: Supplementary files for article The effect of COVID rehabilitation for ongoing symptoms post hospitalisation with COVID-19 (PHOSP-R): protocol for a randomised parallel group controlled trial on behalf of the PHOSP consortium
 
<strong>Introduction:</strong> Many adults hospitalised with COVID-19 have persistent symptoms such as fatigue, breathlessness and brain fog that limit day-to-day activities. These symptoms can last over 2 years. Whilst there is limited controlled studies on interventions that can support those with ongoing symptoms, there has been some promise in rehabilitation interventions in improving function and symptoms either using face-to-face or digital methods, but evidence remains limited and these studies often lack a control group.
<br>
<strong>Methods and analysis:</strong> This is a nested single-blind, parallel group, randomised control trial with embedded qualitative evaluation comparing rehabilitation (face-to-face or digital) to usual care and conducted within the PHOSP-COVID study. The aim of this study is to determine the effectiveness of rehabilitation interventions on exercise capacity, quality of life and symptoms such as breathlessness and fatigue. The primary outcome is the Incremental Shuttle Walking Test following the eight week intervention phase. Secondary outcomes include measures of function, strength and subjective assessment of symptoms. Blood inflammatory markers and muscle biopsies are an exploratory outcome. The interventions last eight weeks and combine symptom-titrated exercise therapy, symptom management and education delivered either in a face-to-face setting or through a digital platform (www.yourcovidrecovery.nhs.uk). The proposed sample size is 159 participants, and data will be intention-to-treat analyses comparing rehabilitation (face-to-face or digital) to usual care.
<br>
<strong>Ethics and dissemination:</strong> Ethical approval was gained as part of the PHOSP-COVID study by Yorkshire and the Humber Leeds West Research NHS Ethics Committee, and the study was prospectively registered on the ISRCTN trial registry (ISRCTN13293865). Results will be disseminated to stakeholders, including patients and members of the public, and published in appropriate journals.
 
<strong>Article summary</strong>
Strengths and limitations of this study
• This protocol utilises two interventions to support those with ongoing symptoms of COVID-19
• This is a two-centre parallel-group randomised controlled trial
• The protocol has been supported by patient and public involvement groups who identified treatments of symptoms and activity limitation as a top priority
DOI: 10.6084/m9.figshare.16946374.v1
title: Additional file 6 of Contextual reprogramming of CAR-T cells for treatment of HER2+ cancers

description: Additional file 6: Table S1. P values related to Fig. 2. Table S2. P values related to Fig. 3. Table S3. P values related to Fig. 4. Table S4. P values related to Fig. 5. Table S5. P values related to Fig. 6. Table S6. P values related to Fig. 7.
DOI: 10.6084/m9.figshare.8032937
title: Additional file 2: of Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant

description: Data S1. The sequences of pGWB2-BpCCR1. (TXT 16 kb)
DOI: 10.6084/m9.figshare.6985049
title: Data of the climbing velocity from Contributions of lunate cells and wax crystals to the surface anisotropy of <i>Nepenthes</i> slippery zone.

description: Data of Figure 5
DOI: 10.6084/m9.figshare.16946428
title: Additional file 5 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 5: Table S3. Statistical table of sequence alignment results between sample sequencing data and selected reference genome.
DOI: 10.6084/m9.figshare.10130129.v2
title: Metadata record for: Global sea-surface iodide observations, 1967-2018

description: This dataset contains key characteristics about the data described in the Data Descriptor Global sea-surface iodide observations, 1967-2018. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.16946428.v1
title: Additional file 5 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 5: Table S3. Statistical table of sequence alignment results between sample sequencing data and selected reference genome.
DOI: 10.6084/m9.figshare.6985058
title: Data of Figure7 (AFM Scanning) 800-3000nN from Contributions of lunate cells and wax crystals to the surface anisotropy of <i>Nepenthes</i> slippery zone.

description: <i>Nepenthes</i> slippery zone presents surface anisotropy depending on its specialized structures. Herein, <i>via</i> macro–micro–nano scaled experiments, we analysed the contributions of lunate cells and wax crystals to this anisotropy. Macroscopic climbing of insects showed large displacements (triple body length within 3 s) and high velocities (6.16–20.47 mm s<sup>−1</sup>) in the inverted-fixed (towards digestive zone) slippery zone, but failed to climb forward in the normal-fixed (towards peristome) one. Friction force of insect claws sliding across inverted-fixed lunate cells was about 2.4 times of that sliding across the normal-fixed ones, whereas showed unobvious differences (1.06–1.11 times) between the inverted- and normal-fixed wax crystals. Innovative results from atomic force microscope scanning and microstructure examination demonstrated the upper layer of wax crystals causes the cantilever tip to generate rather small differences in friction data (1.92–2.72%), and the beneath layer provides slightly higher differences (4.96–7.91%). The study confirms the anisotropic configuration of lunate cells produces most of the anisotropy, whereas both surface topography and structural features of the wax crystals generate a slight contribution. These results are helpful for understanding the surface anisotropy of <i>Nepenthes</i> slippery zone, and guide the design of bioinspired surface with anisotropic properties.
DOI: 10.6084/m9.figshare.16946425.v1
title: Additional file 4 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 4: Table S2. Quality of sequencing data.
DOI: 10.6084/m9.figshare.19728536.v1
title: Additional file 1 of A novel tRNA-derived fragment AS-tDR-007333 promotes the malignancy of NSCLC via the HSPB1/MED29 and ELK4/MED29 axes

description: Additional file 1: Table S1. Characteristics of NSCLC patients recruited for tRF and tiRNA sequencing. Table S2. Sequences of primers, inhibitor, and probes used in this study. Table S3. Expression levels of cytoplasmic AS-tDR-007333 between NSCLC tumor and adjacent tissues. Table S4. Expression levels of nucleus AS-tDR-007333 between NSCLC tumor and adjacent tissues. Table S5. Cox regression analysis on the association of AS-tDR-007333 with NSCLC prognosis. Table S6. Genes significantly regulated by AS-tDR-007333 over expression. Table S7. Gene ontology enrichment analysis of up-regulated genes by AS-tDR-007333. Table S8. Gene set enrichment analysis in AS-tDR-007333-overexpression cells vs. control cells.
DOI: 10.6084/m9.figshare.19728539
title: Additional file 2 of A novel tRNA-derived fragment AS-tDR-007333 promotes the malignancy of NSCLC via the HSPB1/MED29 and ELK4/MED29 axes

description: Additional file 2: Figure S1. Characteristics of AS-tDR-007333. Figure S2. The transfection efficiencies of mimics, plasmids, and si-RNAs in NSCLC cells. Figure S3. AS-tDR-007333 did not affect apoptosis phenotypes in NSCLC cells. Figure S4. Gene set enrichment analysis (GSEA) of AS-tDR-007333-treated cells. Figure S5. In silico analysis of MED29 in NSCLC based on TCGA database. Figure S6. AS-tDR-007333 regulates MED29 expression and functionally interacts with MED29 in NSCLC cells. Figure S7. HSPB1 is up-regulated in NSCLC (in silico analysis based on TCGA database). Figure S8. CHX-chase assay results suggested that AS-tDR-007333 may not affect HSPB1 protein degradation. Figure S9. ELK4 was up-regulated in NSCLC based on TCGA database. Figure S10. ELK4 was up-regulated in NSCLC cells. Figure S11. Schematic diagram of genomic organization and chromatin state of the human MED29 gene locus. Figure S12. Overview of AS-tDR-007333 staining in tissue microarrays (TMAs) spots. Figure S13. AS-tDR-007333 inhibitor did not affect the body weight different subgroups of rats during the period of experiments. Figure S14. Correlations between AS-tDR-007333 and HSPB1, ELK4, and MED29 in NSCLC tumor tissues.
DOI: 10.6084/m9.figshare.6985076
title: Data for the riction force of insect claws from Contributions of lunate cells and wax crystals to the surface anisotropy of <i>Nepenthes</i> slippery zone.

description: Data of Figure 6
DOI: 10.6084/m9.figshare.6985073.v2
title: absorption from High-sensitive and fast response to 255 nm deep-UV light of CH<sub>3</sub>NH<sub>3</sub>PbX<sub>3</sub> (X = Cl, Br, I) bulk crystals.

description: Original data of the absorption spectra of the sample
DOI: 10.6084/m9.figshare.6985082.v2
title: photoluminescence from High-sensitive and fast response to 255 nm deep-UV light of CH<sub>3</sub>NH<sub>3</sub>PbX<sub>3</sub> (X = Cl, Br, I) bulk crystals.

description: Original data of the photoluminescence spectra of the sample
DOI: 10.6084/m9.figshare.16946374
title: Additional file 6 of Contextual reprogramming of CAR-T cells for treatment of HER2+ cancers

description: Additional file 6: Table S1. P values related to Fig. 2. Table S2. P values related to Fig. 3. Table S3. P values related to Fig. 4. Table S4. P values related to Fig. 5. Table S5. P values related to Fig. 6. Table S6. P values related to Fig. 7.
DOI: 10.6084/m9.figshare.16946440.v1
title: Additional file 9 of Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

description: Additional file 9: Table S5. QTL for silique length detected in the RILs across five environments, BLUE, and BLUP.