cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12910461.v1
title: Additional file 9 of Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

description: Additional file 9: Table S9. GC percent and codon usage for Avena plastomes computed by CodonW v.1.4.2 [38]. a Genomic GC percent and codon usage statistic analysis. b The third codon usage statistic analysis.
DOI: 10.5281/zenodo.10671748
title: Quantifying potential trade-offs and win-wins between arthropod diversity and yield on cropland under agri-environment schemes–A meta-analysis
DOI: 10.5281/zenodo.10671749
title: Quantifying potential trade-offs and win-wins between arthropod diversity and yield on cropland under agri-environment schemes–A meta-analysis
DOI: 10.6084/m9.figshare.12386183
title: Additional file 1 of The Glycosylphosphatidylinositol biosynthesis pathway in human diseases

description: Additional file 1: Supplementary Table S1. The genotype and the clinical data of PIG/PIGP genes.
DOI: 10.6084/m9.figshare.12386183.v1
title: Additional file 1 of The Glycosylphosphatidylinositol biosynthesis pathway in human diseases

description: Additional file 1: Supplementary Table S1. The genotype and the clinical data of PIG/PIGP genes.
DOI: 10.6084/m9.figshare.17104787
title: RNA-seq reveals that multiple plant hormones are regulated by <i>Bacillus cereus</i> G2 in <i>Glycyrrhiza uralensis</i> subjected to salt stress

description: <i>Bacillus cereus</i> G2 can alleviate the adverse effect caused by salt in <i>Glycyrrhiza uralensis</i> Fisch. Transcriptome in the salt (S) treatment and control (CK) groups with or without G2 (CK + B or S + B) were sequenced to identify G2 regulate genes and response pathways under salt stress in <i>G. uralensis</i>. A total of 3608 differentially expressed genes (DEGs) were identified, of which 1589, 623, 469, and 927 DEGs were identified in S vs CK, CK + B vs CK, S + B vs S and S + B vs CK + B comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that G2 improved salt-tolerance mainly by regulating phytohormone in <i>G. uralensis</i>. Specifically, G2 up-regulated the DEGs related to auxin (IAA) signal transduction, abscisic acid (ABA) biosynthesis, signal transduction, and catabolism, and jasmonic acid (JA) biosynthesis and signal transduction under salt stress. Overall, multiple phytohormones were involved in the interaction of salt stress and G2 in <i>G. uralensis</i>.
DOI: 10.5281/zenodo.10418768
title: Supplementary material for: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.

description: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.

Supplementary material

This deposition contains supplementary material for a paper on coordinate system calibration in 4D STEM. A preprint of the paper is available at https://arxiv.org/abs/2403.08538.

Contents



20221025_154811.zip: Overfocused 4D STEM test dataset

 

overfocus.sif: Apptainer image with complete software stack. apptainer run --writable overfocus.sif to execute. It starts a Jupyterlab instance with two notebooks, one to genreate test data and the other to perform the interactive adjustment. This documents the software version that was used for the figures in the paper.

 

requirements.txt: Python package versions of dependencies in overfocus.sif. 

 

COM - Jupyter Notebook - Google Chrome 2023-01-25 12-40-07_processed.mp4: Screen capture video with explanation of the first live calibration with an early prototype.

 

video description.docx: Explanation of the plots and adjustment process in the screen capture video.

 

Microscope-Calibration.tar.gz: Repository archive of the software and examples for calibration in the version used in the paper.

 

TemGym.tar.gz: Repository archive of TemGym Basic in the version used in the paper.
DOI: 10.5281/zenodo.10418769
title: Supplementary material for: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.

description: Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin.

Supplementary material

This deposition contains supplementary material for a paper on coordinate system calibration in 4D STEM. A preprint of the paper is available at https://arxiv.org/abs/2403.08538.

Contents



20221025_154811.zip: Overfocused 4D STEM test dataset

 

overfocus.sif: Apptainer image with complete software stack. apptainer run --writable overfocus.sif to execute. It starts a Jupyterlab instance with two notebooks, one to genreate test data and the other to perform the interactive adjustment. This documents the software version that was used for the figures in the paper.

 

requirements.txt: Python package versions of dependencies in overfocus.sif. 

 

COM - Jupyter Notebook - Google Chrome 2023-01-25 12-40-07_processed.mp4: Screen capture video with explanation of the first live calibration with an early prototype.

 

video description.docx: Explanation of the plots and adjustment process in the screen capture video.

 

Microscope-Calibration.tar.gz: Repository archive of the software and examples for calibration in the version used in the paper.

 

TemGym.tar.gz: Repository archive of TemGym Basic in the version used in the paper.
DOI: 10.5281/zenodo.10912462
title: Throughput measures of IP traffic on top of NDN gateway

description: Results of the tests carried out as part of the NDNoverIP software experiment.
DOI: 10.5281/zenodo.10912463
title: Throughput measures of IP traffic on top of NDN gateway

description: Results of the tests carried out as part of the NDNoverIP software experiment.
DOI: 10.15468/dl.syhxxq
title: Occurrence Download

description: A dataset containing 3383 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is HiDaFernPT: Historical data of spore availability for 121 spontaneous and cultivated fern and lycopod taxa in Portugal (1926 – 2013)"
 ]
}

 The dataset includes 3383 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092210-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pg2a5w
title: Occurrence Download

description: A dataset containing 3383 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is HiDaFernPT: Historical data of spore availability for 121 spontaneous and cultivated fern and lycopod taxa in Portugal (1926 – 2013)"
 ]
}

 The dataset includes 3383 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092211-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/pr4d-w8zc
title: Measurement of Nitrogen_monoxide at Payerne

description: Measurement of Nitrogen_monoxide at Payerne
DOI: 10.25345/c5v11vx3w
title: MassIVE MSV000094461 - GNPS Streptomyces sp. ACT015_CultureMediaVariation
title: ACT015 strain was growth in four different culture media: A1, TSB, TSBY and ISP2 in order to compare the metabolism production. AcOEt exctratcts were analysed through UPLC-MS/MS and MS data was processed using NP3_MS_workflow.
DOI: 10.15468/dl.xh3vwq
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Atta cephalotes (Linnaeus, 1758)"
 ]
}

 The dataset includes 112 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092213-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/pyku-f5vz
title: Measurement of Nitrogen_monoxide at Payerne

description: Measurement of Nitrogen_monoxide at Payerne
DOI: 10.48597/bumd-rz98
title: Measurement of Nitrogen_monoxide at Payerne

description: Measurement of Nitrogen_monoxide at Payerne
DOI: 10.48597/qpwt-uu67
title: Nitrogen_monoxide at Payerne

description: Measurement of Nitrogen_monoxide at Payerne
DOI: 10.6084/m9.figshare.23806170
title: Data from: Alien flora are accumulating steadily in China over the last 80 years

description: In this study, we assessed the temporal pattern of new alien flora accumulation at a national scale (China) and deciphered the relative influence of ten biotic and abiotic variables on the minimum residence time of the alien plant species of different invasion stages (introduced, naturalized, and invasive).The data set uploaded here has two files:1) The .xlsx file has the information on species identity and taxonomy, minimum residence time, biotic variables, and abiotic variables 2) The zip file has the HTML version of the R codes used to analyze the data. The associated data are also provided.
DOI: 10.6084/m9.figshare.23806170.v1
title: Data from: Alien flora are accumulating steadily in China over the last 80 years

description: In this study, we assessed the temporal pattern of new alien flora accumulation at a national scale (China) and deciphered the relative influence of ten biotic and abiotic variables on the minimum residence time of the alien plant species of different invasion stages (introduced, naturalized, and invasive).The data set uploaded here has two files:1) The .xlsx file has the information on species identity and taxonomy, minimum residence time, biotic variables, and abiotic variables 2) The zip file has the HTML version of the R codes used to analyze the data. The associated data are also provided.
DOI: 10.6084/m9.figshare.25140002.v1
title: Adaptive response of <i>Pseudomonas aeruginosa</i> under serial ciprofloxacin exposure

description: Supplementary Material for 'Adaptive response of <i>Pseudomonas aeruginosa</i> under serial ciprofloxacin exposure', as described in<i> Microbiology. </i><br>Understanding the evolution of antibiotic resistance is important for combating drug-resistant bacteria. In this work, we investigated the adaptive response of <i>Pseudomonas aeruginosa</i>to ciprofloxacin. Ciprofloxacin-susceptible<i> P. aeruginosa </i>ATCC 9027, CIP-E1 which was exposed to ciprofloxacin for 14 days and CIP-E2 strain which was CIP-E1 cultured in antibiotic-free broth for 10 days were comparatively analyzed. Phenotypic response including cell morphology and production of pyoverdine, pyocyanin, and rhamnolipid were assessed. Proteomic responses were evaluated using comparative iTRAQ labeling LC-MS/MS to figure out differentially expressed proteins (DEPs).
DOI: 10.6084/m9.figshare.25140002
title: Adaptive response of <i>Pseudomonas aeruginosa</i> under serial ciprofloxacin exposure

description: Supplementary Material for 'Adaptive response of <i>Pseudomonas aeruginosa</i> under serial ciprofloxacin exposure', as described in<i> Microbiology. </i><br>Understanding the evolution of antibiotic resistance is important for combating drug-resistant bacteria. In this work, we investigated the adaptive response of <i>Pseudomonas aeruginosa</i>to ciprofloxacin. Ciprofloxacin-susceptible<i> P. aeruginosa </i>ATCC 9027, CIP-E1 which was exposed to ciprofloxacin for 14 days and CIP-E2 strain which was CIP-E1 cultured in antibiotic-free broth for 10 days were comparatively analyzed. Phenotypic response including cell morphology and production of pyoverdine, pyocyanin, and rhamnolipid were assessed. Proteomic responses were evaluated using comparative iTRAQ labeling LC-MS/MS to figure out differentially expressed proteins (DEPs).
DOI: 10.15468/dl.cuk9pd
title: Occurrence Download

description: A dataset containing 8666 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Seabird observations in Australian and adjacent seas from voyages of the RV Franklin, RV Southern Surveyor, Southern Supporter and RV Aurora Australis (1988-2012)"
 ]
}

 The dataset includes 8666 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092214-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ef3bzw
title: Occurrence Download

description: A dataset containing 2817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Canada",
 "TaxonKey is one of (Asclepias incarnata L.)"
 ]
}

 The dataset includes 2817 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092215-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrcxh9
title: Occurrence Download

description: A dataset containing 222334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Ipomoea L."
 ]
}

 The dataset includes 222334 records from 905 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092208-240321170329656/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.25521913
title: Genomes of methanotrophs with nitrous oxide reductase

description: Genomes of newly sequenced N<sub>2</sub>OR-containing <i>Methylocystis </i>species (strains IM2, IM3, and IM4) and a previously sequenced MAG of <i>Ca</i>. Methylotropicum kingii. Annotation files for the genomes of <i>Methylocystis</i> species (strains IM2, IM3, and IM4), <i>Methylocella tundrae</i> T4, <i>Methylacidiphilum caldifontis </i>IT6, and <i>Ca</i>. Methylotropicum kingii. are also included.
DOI: 10.6084/m9.figshare.25521913.v2
title: Genomes of methanotrophs with nitrous oxide reductase

description: Genomes of newly sequenced N<sub>2</sub>OR-containing <i>Methylocystis </i>species (strains IM2, IM3, and IM4) and a previously sequenced MAG of <i>Ca</i>. Methylotropicum kingii. Annotation files for the genomes of <i>Methylocystis</i> species (strains IM2, IM3, and IM4), <i>Methylocella tundrae</i> T4, <i>Methylacidiphilum caldifontis </i>IT6, and <i>Ca</i>. Methylotropicum kingii. are also included.
DOI: 10.6084/m9.figshare.25521913.v1
title: Genomes of methanotrophs with nitrous oxide reductase

description: Genomes of newly sequenced N<sub>2</sub>OR-containing <i>Methylocystis</i> species (strain IM2, IM3, and IM4) and previously sequenced MAG of <i>Ca</i>. Methylotropicum kingii.
DOI: 10.15468/dl.hmnym3
title: Occurrence Download

description: A dataset containing 2066 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acacia mangium Willd., Octacanthium octocorne (Ralfs) Compère, Xanthidium octocorne Ehrenb. ex Ralfs)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2066 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092217-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t83n59
title: Occurrence Download

description: A dataset containing 21707 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Euphorbia hirta L.)"
 ]
}

 The dataset includes 21707 records from 519 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092216-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2dby4v
title: CCDC 2215047: Experimental Crystal Structure Determination

description: Related Article: Trong Duc Le, Tien Cong Nguyen, Thi My Nuong Bui, Thi Kim Dung Hoang, Quoc Trung Vu, Chien Thang Pham, Chau Phi Dinh, Jibril Abdullahi Alhaji, Luc Van Meervelt|2023|J.Mol.Struct.|1284|135321|doi:10.1016/j.molstruc.2023.135321
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dby5w
title: CCDC 2215048: Experimental Crystal Structure Determination

description: Related Article: Trong Duc Le, Tien Cong Nguyen, Thi My Nuong Bui, Thi Kim Dung Hoang, Quoc Trung Vu, Chien Thang Pham, Chau Phi Dinh, Jibril Abdullahi Alhaji, Luc Van Meervelt|2023|J.Mol.Struct.|1284|135321|doi:10.1016/j.molstruc.2023.135321
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b96wr
title: CCDC 2153814: Experimental Crystal Structure Determination

description: Related Article: Ruchika Sharma, Mulveer Singh, Palthad Jayarama Srijana, Kamal, Badiadka Narayana, Balladka Kunhanna Sarojini, Ullal Likhitha, Saminathan Murugavel, Jayakumar Mohan Raj, Rajni Kant|2023|J.Mol.Struct.|1284|135309|doi:10.1016/j.molstruc.2023.135309
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d0rjq
title: CCDC 2205263: Experimental Crystal Structure Determination

description: Related Article: Rui Shen, Jie Zhang, Xi Wang|2023|J.Mol.Struct.|1284|135348|doi:10.1016/j.molstruc.2023.135348
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7933067
title: Should I stay or should I go? The effect of London's terrorist attack on the educational choices of Muslims

description: Files to replicate the empirical analysis reported in the paper.
DOI: 10.5281/zenodo.7933068
title: Should I stay or should I go? The effect of London's terrorist attack on the educational choices of Muslims

description: Files to replicate the empirical analysis reported in the paper.
DOI: 10.20351/29gd20230428
title: MICOLOR-1 Cruise, RV García del Cid

description: Oceanographic data acquired during the MICOLOR-1 Cruise (29GD20230428) on board the Research Vessel García del Cid in 2023.
DOI: 10.6084/m9.figshare.21758738
title: MATLAB function

description: A MATLAB function that is used by the provided script to make histogram plots of the data.
DOI: 10.6084/m9.figshare.21758738.v1
title: MATLAB function

description: A MATLAB function that is used by the provided script to make histogram plots of the data.
DOI: 10.6084/m9.figshare.22730171.v1
title: December 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730174.v1
title: January 2022 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730174
title: January 2022 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730171
title: December 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730180.v1
title: September 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730183
title: May 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730186
title: June 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730189
title: August 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730192
title: March 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730180
title: September 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730183.v1
title: May 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730195
title: February 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730198
title: October 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730201.v1
title: April 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730204
title: November 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730204.v1
title: November 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730246
title: July 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730252
title: Dataset in CSV format

description: Compressed file containing the same dataset as the matlab files, only in comma delimited file (*.csv) format.
DOI: 10.6084/m9.figshare.22730201
title: April 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730246.v1
title: July 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.6084/m9.figshare.22730198.v1
title: October 2021 WIM data

description: MATLAB table file containing weigh in motion records from the A3 highway in Italy.
DOI: 10.34740/kaggle/dsv/5689917
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.34740/kaggle/dsv/5689929
title: UNET Lung Segmentation Weights for Chest X Rays