cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48370/ofd/bqh4ba/jh9stc
title: HMW_Hieracium_caespitosum_Dumort._H_5408.jpg

description: :unav
DOI: 10.48370/ofd/bqh4ba
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 5408

description: Herbarium
DOI: 10.48370/ofd/wnmant/g9koty
title: HMW_Hieracium_caespitosum_Dumort._H_5442.jpg

description: :unav
DOI: 10.48370/ofd/wnmant
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 5442

description: Herbarium
DOI: 10.48370/ofd/zl71mz/c444lb
title: HMW_Hieracium_caespitosum_Dumort._H_5443.jpg

description: :unav
DOI: 10.48370/ofd/zl71mz
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 5443

description: Herbarium
DOI: 10.5281/zenodo.5355659
title: Large eddy simulation input data for publication "Pressure fields in the airflow over wind-generated surface waves" by Funke et al.

description: Input files allow for the simulation of a turbulent flow over a sinusoidal surface using the PALM LES model, version 6.0, revision 4901.
DOI: 10.5281/zenodo.5355658
title: Large eddy simulation input data for publication "Pressure fields in the airflow over wind-generated surface waves" by Funke et al.

description: Input files allow for the simulation of a turbulent flow over a sinusoidal surface using the PALM LES model, version 6.0, revision 4901.
DOI: 10.48370/ofd/rn7g1i/x3o5pr
title: HMW_Hieracium_caespitosum_Dumort._H_5881.jpg

description: :unav
DOI: 10.48370/ofd/rn7g1i
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 5881

description: Herbarium
DOI: 10.48370/ofd/bxonhk/kkdwzx
title: HMW_Hieracium_caespitosum_Dumort._H_5909.jpg

description: :unav
DOI: 10.48370/ofd/bxonhk
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 5909

description: Herbarium
DOI: 10.48370/ofd/x28ro6/jjhofr
title: HMW_Hieracium_caespitosum_Dumort._H_6053.jpg

description: :unav
DOI: 10.48370/ofd/x28ro6
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6053

description: Herbarium
DOI: 10.48370/ofd/diifpr/fko1gx
title: HMW_Hieracium_caespitosum_Dumort._H_6081.jpg

description: :unav
DOI: 10.48370/ofd/diifpr
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6081

description: Herbarium
DOI: 10.48370/ofd/mkapuw/g834np
title: HMW_Hieracium_caespitosum_Dumort._H_6450.jpg

description: :unav
DOI: 10.48370/ofd/mkapuw
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6450

description: Herbarium
DOI: 10.48370/ofd/07xixl/d1aahj
title: HMW_Hieracium_caespitosum_Dumort._H_6451.jpg

description: :unav
DOI: 10.48370/ofd/07xixl
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6451

description: Herbarium
DOI: 10.48370/ofd/rtqmmr/832fdi
title: HMW_Hieracium_caespitosum_Dumort._H_6453.jpg

description: :unav
DOI: 10.48370/ofd/rtqmmr
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6453

description: Herbarium
DOI: 10.48370/ofd/0sqlfe/y39v6w
title: HMW_Hieracium_caespitosum_Dumort._H_6454.jpg

description: :unav
DOI: 10.48370/ofd/0sqlfe
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6454

description: Herbarium
DOI: 10.48370/ofd/ndn5xr/bsigjr
title: HMW_Hieracium_caespitosum_Dumort._H_6455.jpg

description: :unav
DOI: 10.48370/ofd/ndn5xr
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6455

description: Herbarium
DOI: 10.48370/ofd/17mqtj/cl4nzu
title: HMW_Hieracium_caespitosum_Dumort._H_0066.jpg

description: :unav
DOI: 10.48370/ofd/17mqtj
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 66

description: Herbarium
DOI: 10.48370/ofd/gezofj/lfzgnd
title: HMW_Hieracium_caespitosum_Dumort._H_6976.jpg

description: :unav
DOI: 10.48370/ofd/gezofj
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 6976

description: Herbarium
DOI: 10.48370/ofd/2eh5bk/5woqbc
title: HMW_Hieracium_caespitosum_Dumort._H_7258.jpg

description: :unav
DOI: 10.48370/ofd/2eh5bk
title: Jastrzębiec łąkowy (Hieracium caespitosum Dumort.), 7258

description: Herbarium
DOI: 10.6084/m9.figshare.22611046.v1
title: Additional file 5 of High proportion of circulating CD8 + CD28- senescent T cells is an independent predictor of distant metastasis in nasopharyngeal carcinoma after radiotherapy

description: Additional file 5. Multivariate Cox regression analysis results.
DOI: 10.6084/m9.figshare.22611040
title: Additional file 3 of High proportion of circulating CD8 + CD28- senescent T cells is an independent predictor of distant metastasis in nasopharyngeal carcinoma after radiotherapy

description: Additional file 3. NPC patients characteristics.
DOI: 10.6084/m9.figshare.5833821
title: Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

description: Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call ‘homeostatic tolerance,’ is involved in amino acid signaling in <i>Arabidopsis</i>. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in <i>atg5</i>, <i>atg7</i>, and <i>gcn2</i> single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in <i>atg5 gcn2</i> and <i>atg7 gcn2</i> double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced <i>TOR</i> RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.
DOI: 10.25549/usctheses-ouc11256078
title: FULL TITLE HERE IN ALL CAPS IN A FORMAT
DOI: 10.6084/m9.figshare.21562446.v1
title: Additional file 4 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

description: Additional file 4: Table S8. The differential expressed genes identified inwillow barks.
DOI: 10.6084/m9.figshare.13698155
title: Additional file 3 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 3. Table S2. Enrichment analysis on GO and KEGG gene sets among DEGs.
DOI: 10.6084/m9.figshare.13698155.v1
title: Additional file 3 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 3. Table S2. Enrichment analysis on GO and KEGG gene sets among DEGs.
DOI: 10.6084/m9.figshare.13698164.v1
title: Additional file 6 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 6. Table S5. Enrichment analysis on GO and KEGG gene sets among DEGs in the turquoise module.
DOI: 10.6084/m9.figshare.22611052.v1
title: Additional file 7 of High proportion of circulating CD8 + CD28- senescent T cells is an independent predictor of distant metastasis in nasopharyngeal carcinoma after radiotherapy

description: Additional file 7. Raw data of cytokine detection.
DOI: 10.6084/m9.figshare.13698158.v1
title: Additional file 4 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 4. Table S3. Summary of the 2D-PCA among all genes and DEGs.
DOI: 10.6084/m9.figshare.25164521
title: 20240208_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.13698152.v1
title: Additional file 2 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 2. Table S1. Differentially expressed genes (DEGs) in TAA compared to normal condition.
DOI: 10.6084/m9.figshare.13698161
title: Additional file 5 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 5. Table S4. List of genes in the four modules.
DOI: 10.6084/m9.figshare.13698161.v1
title: Additional file 5 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 5. Table S4. List of genes in the four modules.
DOI: 10.6084/m9.figshare.13698152
title: Additional file 2 of The potential role of chemotaxis and the complement system in the formation and progression of thoracic aortic aneurysms inferred from the weighted gene coexpression network analysis

description: Additional file 2. Table S1. Differentially expressed genes (DEGs) in TAA compared to normal condition.
DOI: 10.5281/zenodo.10578475
title: Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes

description: Data presented in the manuscript "Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes", authored by Catalán, N., Peter H. et al. 2024 published in Nature Communications. 

There are these Annex:

Annex1. Contains the data set on dissolved organic matter (DOM) compositions of samples from two lakes where the effect of treeline advancement was experimentally tested.  Samples correspond to the two lakes with amendments of soils extracts from below and above the treeline and incubated in-situ during 72h. Compositional metrics were derived from Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to evaluate differences in DOM composition between the treatments. There are three files in this Annex:



Catalan_et_al_2024_TREELINE_Crosstab_singletons_removed.txt: containing the data on FT-ICR-MS

Catalan_et_al_2024_TREELINE_samples.txt: containing the list of samples analyzed by FT-ICR-MS

Catalan_et_al_2024_TREELINE_ancilary.txt: Data on other variables measured, such as DOC degradation and concentrations, fluorescence spectroscopy indices or nutrients. File


Annex2. Code to produce figures 1, 2 and 3 of the main text. The language used was R 4.3.1., using RStudio. The files in Annex 1 and 2 are used here. 



Catalan_et_al_2024_TREELINE_Fig1_Enrichment

Catalan_et_al_2024_TREELINE_Fig2_Chemodiversity

Catalan_et_al_2024_TREELINE_Fig3_DOM_decay


Annex3. PARAFAC model components for DOM excitation-emission fluorcescence matrices. Also available in OpenFluor, with accession number 18555



Catalan_et_al_2024_TREELINE_PARAFAC_model.xlsx
DOI: 10.5281/zenodo.10578476
title: Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes

description: Data presented in the manuscript "Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes", authored by Catalán, N., Peter H. et al. 2024 published in Nature Communications. 

There are these Annex:

Annex1. Contains the data set on dissolved organic matter (DOM) compositions of samples from two lakes where the effect of treeline advancement was experimentally tested.  Samples correspond to the two lakes with amendments of soils extracts from below and above the treeline and incubated in-situ during 72h. Compositional metrics were derived from Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to evaluate differences in DOM composition between the treatments. There are three files in this Annex:



Catalan_et_al_2024_TREELINE_Crosstab_singletons_removed.txt: containing the data on FT-ICR-MS

Catalan_et_al_2024_TREELINE_samples.txt: containing the list of samples analyzed by FT-ICR-MS

Catalan_et_al_2024_TREELINE_ancilary.txt: Data on other variables measured, such as DOC degradation and concentrations, fluorescence spectroscopy indices or nutrients. File


Annex2. Code to produce figures 1, 2 and 3 of the main text. The language used was R 4.3.1., using RStudio. The files in Annex 1 and 2 are used here. 



Catalan_et_al_2024_TREELINE_Fig1_Enrichment

Catalan_et_al_2024_TREELINE_Fig2_Chemodiversity

Catalan_et_al_2024_TREELINE_Fig3_DOM_decay


Annex3. PARAFAC model components for DOM excitation-emission fluorcescence matrices. Also available in OpenFluor, with accession number 18555



Catalan_et_al_2024_TREELINE_PARAFAC_model.xlsx
DOI: 10.6084/m9.figshare.22605979
title: Additional file 6 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

description: Additional file 6: Table S5. The information of 134 transcripts including repeated sequence, number of repeated sequences, position of repeated sequence and length of transcripts.
DOI: 10.6084/m9.figshare.22606130
title: Additional file 1 of Distribution of endotoxin in maternal and fetal body with intrahepatic cholestasis of pregnancy and its association with adverse fetal outcome

description: Additional file 1.
DOI: 10.6084/m9.figshare.22606282.v1
title: Additional file 2 of Iris lactea var. chinensis plant drought tolerance depends on the response of proline metabolism, transcription factors, transporters and the ROS-scavenging system

description: Additional file 2.
DOI: 10.5281/zenodo.10534068
title: Native MS dataset for: "Structural Insights into the Interaction Between Adenovirus 5C Hexon and Human Lactoferrin"

description: Native mass spectrometry dataset used in: Structural Insights into the Interaction Between Adenovirus 5C Hexon and Human Lactoferrin. Arun Dhillon, B. David Persson, Oleksandr Volkov, Hagen Sülzen, Alan Kádek, Petr Pompach, Sami Kereïche, Charlotte Uetrecht, Martin Lepšík, Niklas Arnberg and Sebastian Zoll. The Journal of Virology (2024). doi: 10.1128/jvi.01576-23

Description:

Native mass spectrometry (MS) analysis of the effect of solution ionic strength on the stoichiometry of interaction between human adenovirus HAdV-C5 hexon and human lactoferin.

Sample processing:

Prior to native MS measurements, hexon:Lf complex purified in buffer D was buffer exchanged into 20 mM aqueous ammonium acetate solution pH 7.0 (AA; ≥99.99% trace metals basis, Honeywell Research Chemicals) using two cycles of spin gel-filtration (MicroBioSpin P-6, Bio-Rad). The complex was subsequently diluted by 20 mM AA to 0.5 µM (estimated based on 3+3 stoichiometry). Alternatively, for low ionic strength conditions, the dilution was performed with LC-MS grade water instead, resulting in 5.85 mM AA concentration. Reference spectra of isolated Hexon and LF were obtained from 5 µM (monomer) samples in 150 mM AA pH 7.0.

After short equilibration on ice, the samples were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (Thermo Scientific) via static nanoelectrospray ionization. The samples were electrosprayed from gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments) prepared in-house essentially as described before (PMID: 17406634, PMID: 33658206). The mass spectrometer was tuned for best signal quality and intensity, while maintaining minimal ion activation. Specifically, electrospray voltage was kept at 1.25 kV, source desolvation temperature 120°C, in-source trapping -50 V, ion transfer profile “high m/z”, analyzer profile “low m/z”, analyzer target resolution 1500 acquiring in mass range 1000 – 20000 m/z, averaging 5 microscans. Further desolvation and collisional cooling in HCD cell was performed with nitrogen at relative gas pressure setting 8.0 with gentle collisional activation by 10 V HCD voltage gradient.

Data processing:

Raw spectra were averaged over at least 50 scans in Thermo Xcalibur Qual Browser 4.2.47 (Thermo Scientific) and mass deconvoluted in UniDec 6.0.3 package (PMID: 25799115). The averaged spectra were exported for ZENODO deposition as single-scan Thermo .raw files (including instrumental parameters metadata) and in plain m/z vs intensity .txt files.
DOI: 10.5281/zenodo.10534069
title: Native MS dataset for: "Structural Insights into the Interaction Between Adenovirus 5C Hexon and Human Lactoferrin"

description: Native mass spectrometry dataset used in: Structural Insights into the Interaction Between Adenovirus 5C Hexon and Human Lactoferrin. Arun Dhillon, B. David Persson, Oleksandr Volkov, Hagen Sülzen, Alan Kádek, Petr Pompach, Sami Kereïche, Charlotte Uetrecht, Martin Lepšík, Niklas Arnberg and Sebastian Zoll. The Journal of Virology (2024). doi: 10.1128/jvi.01576-23

Description:

Native mass spectrometry (MS) analysis of the effect of solution ionic strength on the stoichiometry of interaction between human adenovirus HAdV-C5 hexon and human lactoferin.

Sample processing:

Prior to native MS measurements, hexon:Lf complex purified in buffer D was buffer exchanged into 20 mM aqueous ammonium acetate solution pH 7.0 (AA; ≥99.99% trace metals basis, Honeywell Research Chemicals) using two cycles of spin gel-filtration (MicroBioSpin P-6, Bio-Rad). The complex was subsequently diluted by 20 mM AA to 0.5 µM (estimated based on 3+3 stoichiometry). Alternatively, for low ionic strength conditions, the dilution was performed with LC-MS grade water instead, resulting in 5.85 mM AA concentration. Reference spectra of isolated Hexon and LF were obtained from 5 µM (monomer) samples in 150 mM AA pH 7.0.

After short equilibration on ice, the samples were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (Thermo Scientific) via static nanoelectrospray ionization. The samples were electrosprayed from gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments) prepared in-house essentially as described before (PMID: 17406634, PMID: 33658206). The mass spectrometer was tuned for best signal quality and intensity, while maintaining minimal ion activation. Specifically, electrospray voltage was kept at 1.25 kV, source desolvation temperature 120°C, in-source trapping -50 V, ion transfer profile “high m/z”, analyzer profile “low m/z”, analyzer target resolution 1500 acquiring in mass range 1000 – 20000 m/z, averaging 5 microscans. Further desolvation and collisional cooling in HCD cell was performed with nitrogen at relative gas pressure setting 8.0 with gentle collisional activation by 10 V HCD voltage gradient.

Data processing:

Raw spectra were averaged over at least 50 scans in Thermo Xcalibur Qual Browser 4.2.47 (Thermo Scientific) and mass deconvoluted in UniDec 6.0.3 package (PMID: 25799115). The averaged spectra were exported for ZENODO deposition as single-scan Thermo .raw files (including instrumental parameters metadata) and in plain m/z vs intensity .txt files.
DOI: 10.6084/m9.figshare.22606258
title: Additional file 2 of Transcriptomic changes in single yeast cells under various stress conditions

description: Additional file 2. Table S1. Summary of mapping results of the scRNA-seq libraries. Table S2. Summary of mapping results of the bulk RNA-seq libraries
DOI: 10.6084/m9.figshare.22606261.v1
title: Additional file 3 of Transcriptomic changes in single yeast cells under various stress conditions

description: Additional file 3. Table S3. Raw Counts of Samples and Genes used for DEG. Table S4. Summary of DEGs under AAS. Table S5. Summary of DEGs under GS.
DOI: 10.25549/usctheses-ouc11256087
title: 00001.tif
DOI: 10.6084/m9.figshare.22606261
title: Additional file 3 of Transcriptomic changes in single yeast cells under various stress conditions

description: Additional file 3. Table S3. Raw Counts of Samples and Genes used for DEG. Table S4. Summary of DEGs under AAS. Table S5. Summary of DEGs under GS.
DOI: 10.6084/m9.figshare.22606258.v1
title: Additional file 2 of Transcriptomic changes in single yeast cells under various stress conditions

description: Additional file 2. Table S1. Summary of mapping results of the scRNA-seq libraries. Table S2. Summary of mapping results of the bulk RNA-seq libraries
DOI: 10.6084/m9.figshare.22606285.v1
title: Additional file 3 of Iris lactea var. chinensis plant drought tolerance depends on the response of proline metabolism, transcription factors, transporters and the ROS-scavenging system

description: Additional file 3.
DOI: 10.25549/usctheses-ouc11256089
title: Microsoft Word - Dissertation_Niu_1031.docx
DOI: 10.6084/m9.figshare.21557560
title: Additional file 10 of Grapevine (Vitis vinifera) responses to salt stress and alkali stress: transcriptional and metabolic profiling

description: Additional file 10: Table S9. The DAMs involved in Chl biosynthesis and photosynthesis.
DOI: 10.6084/m9.figshare.21557563.v1
title: Additional file 11 of Grapevine (Vitis vinifera) responses to salt stress and alkali stress: transcriptional and metabolic profiling

description: Additional file 11: Table S10. The DAMs related to organic acids.
DOI: 10.6084/m9.figshare.13698179.v1
title: Additional file 1 of Genome-wide identification and functional analysis of the ERF2 gene family in response to disease resistance against Stemphylium lycopersici in tomato

description: Additional file 1: Table S1. Identification and Analysis of Physical and Chemical Properties of ERF
DOI: 10.5281/zenodo.10629837
title: NPClassifier predictions of COCONUT compounds

description: Class predictions as returned by NPClassifier of COCONUT compounds.

Used NPClassifier between 2024.01.03~2024.01.15. Used COCONUT version 2022.01.01

 

 

References:



Kim, H. W. et al. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. J. Nat. Prod. 84, 2795–2807 (2021). 10.1021/acs.jnatprod.1c00399

Sorokina, M., Merseburger, P., Rajan, K., Yirik, M. A. & Steinbeck, C. COCONUT online: Collection of Open Natural Products database. J. Cheminformatics 13, 2 (2021). https://doi.org/10.1186/s13321-020-00478-9
DOI: 10.5281/zenodo.10629838
title: NPClassifier predictions of COCONUT compounds

description: Class predictions as returned by NPClassifier of COCONUT compounds.

Used NPClassifier between 2024.01.03~2024.01.15. Used COCONUT version 2022.01.01

 

 

References:



Kim, H. W. et al. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. J. Nat. Prod. 84, 2795–2807 (2021). 10.1021/acs.jnatprod.1c00399

Sorokina, M., Merseburger, P., Rajan, K., Yirik, M. A. & Steinbeck, C. COCONUT online: Collection of Open Natural Products database. J. Cheminformatics 13, 2 (2021). https://doi.org/10.1186/s13321-020-00478-9