cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23298467.v3
title: ORDerly benchmarks of chemical reactions

description: Benchmark datasets generated by ORDerly for chemical reaction predictionORDerly-condition: Reaction condition prediction (predict solvents and agents given reactants and products)ORDerly-forward: Forward reaction prediction (predict reaction products given reactants, solvents, and agents)ORDerly-retro: Retrosynthesis prediction (prediction reactants given a desired product)Not-USPTO: Datasets containing all non-USPTO data from ORD (as of August 2023) you can use as an additional test set for forward/retrosynthesis.Paper: https://chemrxiv.org/engage/chemrxiv/article-details/64ca5d3e4a3f7d0c0d78ca42Code: https://github.com/sustainable-processes/orderlyA full overview of the datasets used in the paper, and the configs used to generate these datasets, can be found here: https://doi.org/10.6084/m9.figshare.23502372.v1Feel free to email me, Daniel Wigh, at dsw46@cam.ac.uk<br><br>
DOI: 10.5281/zenodo.10622292
title: Multi-omics for Understanding Climate Change (MUCC) database v1.0.0

description: This is the Multi-omics for Understanding Climate Change (MUCC database) version 1.0.0. This current version is based on metagenomic and metatranscriptomic sequencing of Old Woman Creek wetland soils, but will be expanded in the future to include data from additional wetlands. Files and datasets included here: 



MAGs.zip Dereplicated database of 2,502 MAGs (fasta files)

OWC_HQMQ_DB_genes.faa.gz MAG amino acid gene sequences derived from DRAM gene calls (fasta file)

OWC_HQMQ_DB_ANNOTATIONS_20220208.txt.gz MAG DRAM annotations 

owc_metat_table_mags.csv Metatranscriptomic expression per MAG across 133 metatranscriptomes (csv table)

owc_metat_table_mags_genes.csv Metatranscriptomic expression per gene across 133 metatranscriptomes (csv table)

owc_metat_table_mags_genes_annotations.csv corresponding DRAM annotations to #5 for transcribed genes (csv table)

 gtdbtk.ar53.decorated.tree newick file for tree in figure S4
DOI: 10.5281/zenodo.8194032
title: Multi-omics for Understanding Climate Change (MUCC) database v1.0.0

description: This is the Multi-omics for Understanding Climate Change (MUCC database) version 1.0.0. This current version is based on metagenomic and metatranscriptomic sequencing of Old Woman Creek wetland soils, but will be expanded in the future to include data from additional wetlands. Files and datasets included here: 



MAGs.zip Dereplicated database of 2,502 MAGs (fasta files)

OWC_HQMQ_DB_genes.faa.gz MAG amino acid gene sequences derived from DRAM gene calls (fasta file)

OWC_HQMQ_DB_ANNOTATIONS_20220208.txt.gz MAG DRAM annotations 

owc_metat_table_mags.csv Metatranscriptomic expression per MAG across 133 metatranscriptomes (csv table)

owc_metat_table_mags_genes.csv Metatranscriptomic expression per gene across 133 metatranscriptomes (csv table)

owc_metat_table_mags_genes_annotations.csv corresponding DRAM annotations to #5 for transcribed genes (csv table)

 gtdbtk.ar53.decorated.tree newick file for tree in figure S4
DOI: 10.5281/zenodo.8194033
title: Multi-omics for Understanding Climate Change (MUCC) database v1.0.0

description: This is the Multi-omics for Understanding Climate Change (MUCC database) version 1.0.0. This current version is based on metagenomic and metatranscriptomic sequencing of Old Woman Creek wetland soils, but will be expanded in the future to include data from additional wetlands. Files and datasets included here: 



	
MAGs.zip Dereplicated database of 2,502 MAGs (fasta files)
	
OWC_HQMQ_DB_genes.faa.gz MAG amino acid gene sequences derived from DRAM gene calls (fasta file)
	
OWC_HQMQ_DB_ANNOTATIONS_20220208.txt.gz MAG DRAM annotations 
	
owc_metat_table_mags.csv Metatranscriptomic expression per MAG across 133 metatranscriptomes (csv table)
	
owc_metat_table_mags_genes.csv Metatranscriptomic expression per gene across 133 metatranscriptomes (csv table)
	
owc_metat_table_mags_genes_annotations.csv corresponding DRAM annotations to #5 for transcribed genes (csv table)
DOI: 10.6084/m9.figshare.25148886
title: Supplementary tables (Table S1-15) from Marine transmissible cancer navigates urbanized waters, threatening to spillover

description: This document contains all raw data, environemental data sources, primers sequences, PCR results and statistical results. Each table is referred in the main document.
DOI: 10.6084/m9.figshare.25148886.v1
title: Supplementary tables (Table S1-15) from Marine transmissible cancer navigates urbanized waters, threatening to spillover

description: This document contains all raw data, environemental data sources, primers sequences, PCR results and statistical results. Each table is referred in the main document.
DOI: 10.15131/shef.data.21397485
title: Data for: "Atomic-scale modelling of organic matter in soil: Adsorption of organic molecules and biopolymers on the hydroxylated alpha-Al2O3 (0001) surface"

description: Coordinates (xyz format) of adsorption configurations of methanol, methylamine, acetamide, methylacetate, acetic acid, cellulose, chitin, chitosan and pectin on the hydroxylated alpha-Al2O3 (0001) surface.
<br>
The files with small molecules adsorbed on the alpha-Al2O3 slab are labelled "Al2O3-OH-221-12L-{molecule}-{number}.xyz", where "221" refers to the 2x2x1 extended surface supercell, 12L refers to 12 atomic layers - the thickness of the Al2O3 slab, {molecule} is the molecule name, and {number} is the number of the adsorption configuration, in the order of stability.
<br>
The files with biomolecules adsorbed on the alpha-Al2O3 slab are labelled "Al2O3-OH-661-12L-{molecule}-{label}.xyz", where "661" refers to the 6x6x1 extended surface supercell, 12L refers to 12 atomic layers - the thickness of the Al2O3 slab, {molecule} is the biomolecule name, and {label } is the letter label of the adsorption configuration.
<br>
The lattice parameters for the 2x2x1 supercell where small molecules were adsorbed are:
A     9.575184417    0.000000000    0.000000000
B    -4.787592208    8.292352951    0.000000000
C     0.000000000    0.000000000   50.000000000
<br>
The lattice parameters for the 6x6x1 supercell where biomolecules were adsorbed are:
A    28.725553251    0.000000000    0.000000000
B   -14.362776624   24.877058853    0.000000000
C     0.000000000    0.000000000   50.000000000
<br>
DOI: 10.15131/shef.data.21397485.v1
title: Data for: "Atomic-scale modelling of organic matter in soil: Adsorption of organic molecules and biopolymers on the hydroxylated alpha-Al2O3 (0001) surface"

description: Coordinates (xyz format) of adsorption configurations of methanol, methylamine, acetamide, methylacetate, acetic acid, cellulose, chitin, chitosan and pectin on the hydroxylated alpha-Al2O3 (0001) surface.
<br>
The files with small molecules adsorbed on the alpha-Al2O3 slab are labelled "Al2O3-OH-221-12L-{molecule}-{number}.xyz", where "221" refers to the 2x2x1 extended surface supercell, 12L refers to 12 atomic layers - the thickness of the Al2O3 slab, {molecule} is the molecule name, and {number} is the number of the adsorption configuration, in the order of stability.
<br>
The files with biomolecules adsorbed on the alpha-Al2O3 slab are labelled "Al2O3-OH-661-12L-{molecule}-{label}.xyz", where "661" refers to the 6x6x1 extended surface supercell, 12L refers to 12 atomic layers - the thickness of the Al2O3 slab, {molecule} is the biomolecule name, and {label } is the letter label of the adsorption configuration.
<br>
The lattice parameters for the 2x2x1 supercell where small molecules were adsorbed are:
A     9.575184417    0.000000000    0.000000000
B    -4.787592208    8.292352951    0.000000000
C     0.000000000    0.000000000   50.000000000
<br>
The lattice parameters for the 6x6x1 supercell where biomolecules were adsorbed are:
A    28.725553251    0.000000000    0.000000000
B   -14.362776624   24.877058853    0.000000000
C     0.000000000    0.000000000   50.000000000
<br>
DOI: 10.6084/m9.figshare.25148945
title: OpenFE v1.0 rc results.tar.gz

description: Results of tyk2 benchmark set using openfe v1.0 rc1
DOI: 10.6084/m9.figshare.25148945.v1
title: OpenFE v1.0 rc results.tar.gz

description: Results of tyk2 benchmark set using openfe v1.0 rc1
DOI: 10.15131/shef.data.22303282
title: Dataset for Observation of Zitterbewegung in photonic microcavities

description: Dataset for Observation of Zitterbewegung in photonic microcavities
DOI: 10.15131/shef.data.22303282.v1
title: Dataset for Observation of Zitterbewegung in photonic microcavities

description: Dataset for Observation of Zitterbewegung in photonic microcavities
DOI: 10.6084/m9.figshare.25148991
title: Input file to run the vertex model simulations using TiFoSi from Choice of friction coefficient deeply affects tissue behaviour in stochastic epithelial vertex models

description: To understand the mechanisms that coordinate the formation of biological tissues, the use of numerical implementations is necessary. The complexity of such models involves many assumptions and parameter choices that result in unpredictable consequences, obstructing the comparison with experimental data. Here, we focus on vertex models, a family of spatial models used extensively to simulate the dynamics of epithelial tissues. Usually, in the literature, the choice of the friction coefficient is not addressed using quasi-static deformation arguments that generally do not apply to realistic scenarios. In this manuscript, we discuss the role that the choice of friction coefficient has on the relaxation times and consequently in the conditions of cell cycle progression and division. We explore the effects that these changes have on the morphology, growth rate and topological transitions of the tissue dynamics. These results provide a deeper understanding of the role that an accurate mechanical description plays in the use of vertex models as inference tools.This article is part of the theme issue ‘Causes and consequences of stochastic processes in development and disease’.
DOI: 10.6084/m9.figshare.25148991.v1
title: Input file to run the vertex model simulations using TiFoSi from Choice of friction coefficient deeply affects tissue behaviour in stochastic epithelial vertex models

description: To understand the mechanisms that coordinate the formation of biological tissues, the use of numerical implementations is necessary. The complexity of such models involves many assumptions and parameter choices that result in unpredictable consequences, obstructing the comparison with experimental data. Here, we focus on vertex models, a family of spatial models used extensively to simulate the dynamics of epithelial tissues. Usually, in the literature, the choice of the friction coefficient is not addressed using quasi-static deformation arguments that generally do not apply to realistic scenarios. In this manuscript, we discuss the role that the choice of friction coefficient has on the relaxation times and consequently in the conditions of cell cycle progression and division. We explore the effects that these changes have on the morphology, growth rate and topological transitions of the tissue dynamics. These results provide a deeper understanding of the role that an accurate mechanical description plays in the use of vertex models as inference tools.This article is part of the theme issue ‘Causes and consequences of stochastic processes in development and disease’.
DOI: 10.17632/vkbc59rmsx.1
title: Original western blot-231105wyf

description: Original western blot for the article "Sirt6 deficiency causes excessive proliferation of neural precursor cells and delays cortical neurogenesis in mice"
DOI: 10.17632/t792k7f42b.2
title: Données brutes des protéines identifiées par spectrométrie de masse dans le protéome proximal de RipAA

description: Vous trouverez dans le fichier excel les données brutes de la spectrométrie de masse du protéome proximal de RipAA
DOI: 10.17632/t792k7f42b.1
title: Données brutes des protéines identifiées par spectrométrie de masse dans le protéome proximal de RipAA

description: Vous trouverez dans le fichier excel les données brutes de la spectrométrie de masse du protéome proximal de RipAA
DOI: 10.17632/k2kvf949ht.2
title: Microplastics in the water column of the Rhine River near Basel: 22 months of sampling

description: Data generated for the publication titled "Microplastics in the water column of the Rhine River near Basel: 22 months of sampling".

Abstract
Measured microplastic concentrations in river surface waters fluctuate greatly. This variability is affected by season, and is co-driven by factors, such as sampling methodologies, sampling site, or sampling position within site. Unfortunately, most studies comprise single-instance measurements, whereas extended sampling periods are better suited to assess the relevance of such factors. Moreover, microplastic concentrations in riverine water column remain underexplored. Similar to the oceans however, this compartment likely holds significant amounts of microplastics. By representatively sampling the entire Rhine River cross-section near Basel through five sampling points over 22 months, we show that microplastic (50–3000 µm) concentration in the water column was not well explained by river discharge. This suggests a chemodynamic export regime, in which occasional high discharge events, as observed here, can nonetheless over short time periods lead to peak microplastic concentrations (highest = 1.23 × 102 n m-3, median = 4.48 n m-3). These are perhaps re-suspended particles from the bed load, or stem from shores as diffuse input. This study addresses a gap in research by examining time-resolved microplastic pollution in a major European river. It offers data on microplastic levels in the water column and in suspended particulate matter.
DOI: 10.15131/shef.data.22568431
title: Local Priests and their Siblings: Appendix - Bibliography

description:  Appendix to Alice Hicklin,  ‘Local Priests and their Siblings c. 900–c. 1100: The Documentary Evidence’, <em>Frühmittelalterliche Studien </em>(2023)
<br>
ABSTRACT: Priests’ relationships with their brothers and sisters are richly evidenced in tenth- and eleventh-century documentary sources across the Latin West. But the looming shadow of the ‘Gregorian Reform’ has focused historians’ attentions on clerical marriage and vertical familial relationships (fathers and sons, or uncles and nephews). This article redresses the balance, arguing that sibling relationships have been underestimated in their importance to the lived experience of local priests, their families and communities in the tenth and eleventh centuries in post-Carolingian western Francia and the Iberian peninsula. It examines how priests and their brothers and sisters managed estates, co-operated to pool resources, and developed inheritance strategies with particular emphasis on how such records may reflect both practice on the ground and the concerns of the scribes, draftsmen and archivists who recorded, copied and edited them.
<br>
<br>
The following list comprises all published editions of charters or notices of local priests with siblings that I have investigated at the date of submission of the article (November 2022). Entries are alphabetised by location.
DOI: 10.15131/shef.data.22568431.v1
title: Local Priests and their Siblings: Appendix - Bibliography

description:  Appendix to Alice Hicklin,  ‘Local Priests and their Siblings c. 900–c. 1100: The Documentary Evidence’, <em>Frühmittelalterliche Studien </em>(2023)
<br>
ABSTRACT: Priests’ relationships with their brothers and sisters are richly evidenced in tenth- and eleventh-century documentary sources across the Latin West. But the looming shadow of the ‘Gregorian Reform’ has focused historians’ attentions on clerical marriage and vertical familial relationships (fathers and sons, or uncles and nephews). This article redresses the balance, arguing that sibling relationships have been underestimated in their importance to the lived experience of local priests, their families and communities in the tenth and eleventh centuries in post-Carolingian western Francia and the Iberian peninsula. It examines how priests and their brothers and sisters managed estates, co-operated to pool resources, and developed inheritance strategies with particular emphasis on how such records may reflect both practice on the ground and the concerns of the scribes, draftsmen and archivists who recorded, copied and edited them.
<br>
<br>
The following list comprises all published editions of charters or notices of local priests with siblings that I have investigated at the date of submission of the article (November 2022). Entries are alphabetised by location.
DOI: 10.6084/m9.figshare.25148330
title: Data from Valadao-Mendes et al. 2023 - Plant pollination interactions in Brazil

description: Dataset including papers, biomes, plant and pollinator species, and the pollination interaction in Brazil.
DOI: 10.6084/m9.figshare.25148330.v1
title: Data from Valadao-Mendes et al. 2023 - Plant pollination interactions in Brazil

description: Dataset including papers, biomes, plant and pollinator species, and the pollination interaction in Brazil.
DOI: 10.6084/m9.figshare.25148855
title: Global slowdown in community turnover despite accelerating climate change

description: R Script S1_Turnover_breakpoint_allmetrics_lags_5_20_Jan2024.r: R script used to compute turnover rates for each community and break year.R Script S2_Simulation_lag5_Uncentered_30Nov23.r: This is an R script used to simulate changes in turnover rate in response to environmental change and degradation.Study_gridding_community_partitioning: The R script used for spatial partitioning of BioTIME community time series data.processed_data: This zipped file contains all files required to be loaded at the different stages in the analyses.
DOI: 10.15131/shef.data.20715328.v2
title: Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes

description: Title:  <strong>Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes</strong> 
<br>
This was a qualitative research project for a Doctorate in Education.  Its aim was to ascertain whether students of English for Academic Purposes (EAP) found that exploring certain psychological and sociological factors affecting human thinking helped them with their own critical thinking. I did this with EAP students at the University of Sheffield in a series of workshops.  I then interviewed the participants and analysed the resulting data using thematic analysis and code development.  
The project received ethical approval from the University of Sheffield; the Reference Number is 023437. See the READ ME document for further details.
DOI: 10.15131/shef.data.20715328
title: Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes

description: Title:  <strong>Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes</strong> 
<br>
This was a qualitative research project for a Doctorate in Education.  Its aim was to ascertain whether students of English for Academic Purposes (EAP) found that exploring certain psychological and sociological factors affecting human thinking helped them with their own critical thinking. I did this with EAP students at the University of Sheffield in a series of workshops.  I then interviewed the participants and analysed the resulting data using thematic analysis and code development.  
The project received ethical approval from the University of Sheffield; the Reference Number is 023437. See the READ ME document for further details.
DOI: 10.15131/shef.data.20715328.v3
title: Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes

description: Title:  <strong>Exploring the psychological and sociological factors affecting critical thinking with students of English for Academic Purposes</strong> 
<br>
This was a qualitative research project for a Doctorate in Education.  Its aim was to ascertain whether students of English for Academic Purposes (EAP) found that exploring certain psychological and sociological factors affecting human thinking helped them with their own critical thinking. I did this with EAP students at the University of Sheffield in a series of workshops.  I then interviewed the participants and analysed the resulting data using thematic analysis and code development.  
The project received ethical approval from the University of Sheffield; the Reference Number is 023437. See the READ ME document for further details.
DOI: 10.15131/shef.data.22211635
title: All UK media mentions of University of Sheffield research pre 2020. Altmetric dataset.

description: This is a Excel dataset of international, national, regional and local media coverage of research that is affiliated with the University of Sheffield. The data was obtained on the 14th August 2020 through Altmetric.com.
The spreadsheet contains:
UK Media Mentions with URL
UK National Media with URL
UK Regional news sites with URL 
All UK National Media 
<br>
Please note that the Altmetric score for each output is dated for the 14th August 2020. Many of these scores will have now changed. 
<br>
Please note that Column Q is the Altmetric.com details page URL. 
<br>
<br>
<br>
<br>
<br>
DOI: 10.15131/shef.data.22211635.v1
title: All UK media mentions of University of Sheffield research pre 2020. Altmetric dataset.

description: This is a Excel dataset of international, national, regional and local media coverage of research that is affiliated with the University of Sheffield. The data was obtained on the 14th August 2020 through Altmetric.com.
The spreadsheet contains:
UK Media Mentions with URL
UK National Media with URL
UK Regional news sites with URL 
All UK National Media 
<br>
Please note that the Altmetric score for each output is dated for the 14th August 2020. Many of these scores will have now changed. 
<br>
Please note that Column Q is the Altmetric.com details page URL. 
<br>
<br>
<br>
<br>
<br>
DOI: 10.5281/zenodo.10616598
title: The source of energy, the fifth dimension and definition of time
title: 5th dimension
title: Definition of Time and source of energy

description: https://drive.google.com/file/d/1--cqmd2_An1OjazKfMZX0cl_nIHcjNFx/view?usp=drivesdk
description: The fifth dimension is the temporal energy and time is the beginning of the every phenomenon of life
DOI: 10.5281/zenodo.10616599
title: The source of energy, the fifth dimension and definition of time
title: 5th dimension
title: Definition of Time and source of energy

description: https://drive.google.com/file/d/1--cqmd2_An1OjazKfMZX0cl_nIHcjNFx/view?usp=drivesdk
description: The fifth dimension is the temporal energy and time is the beginning of the every phenomenon of life
DOI: 10.6084/m9.figshare.22277602
title: Supplementary Material 1.xlsx

description: <br><i>A global review on chromosome number and genome size for the filmy ferns family (Hymenophyllaceae Mart., Polypodiopsida)</i><br>Uma revisão global para o número de cromossomos e tamanho do genoma na família das samambaias transparentes (Hymenophyllaceae Mart., Polypodiopsida)
DOI: 10.6084/m9.figshare.22277602.v2
title: Supplementary Material 1.xlsx

description: <br><i>A global review on chromosome number and genome size for the filmy ferns family (Hymenophyllaceae Mart., Polypodiopsida)</i><br>Uma revisão global para o número de cromossomos e tamanho do genoma na família das samambaias transparentes (Hymenophyllaceae Mart., Polypodiopsida)
DOI: 10.5281/zenodo.10480938
title: Backscattering of Ions Impacting Ganymede's Surface as a Source for Energetic Neutral Atoms (Dataset)

description: This dataset for the manuscript "Backscattering of Ions Impacting Ganymede's Surface as a Source for Energetic Neutral Atoms" contains the SDTrimSP simulation results of backscattered Energetic Neutral Atoms (ENAs) from the surface of Ganymede, as described in the manuscript and shown in the figures therein.