cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13889602
title: Datasets for the article "Light-dependent flavin redox and adduct states control the conformation and DNA binding activity of the transcription factor EL222"

description: #Figures

All spectra (NMR, infrared, UV/Visible), molecular models, and plots presented in the main text and Supplementary Information are available in this directory. 

# Classical Molecular Dynamic (MD) and Metadynamics Simulations (metaD) Data and Analysis

This part of the repository contains data, parameters and scripts used in classical MD (oxi_MD, cov_MD and red_MD models) and meta-dynamics simulations (oxi_metaD, cov_metaD and red_metaD models) presented in our publication, including files essential for running metaD simulations, collective variable (COLVAR) analysis, and data processing for publication figures. Each directory contains a README file with instructions on file usage, script dependencies, and suggested analysis methods.

## Contents

#### MD and metaD Simulation Files

- Input Files: MD and metaD input files used to initialize and configure the simulations, including system setup, force field parameters, and environment settings.

- MetaD Parameters: Parameter files used for metaD simulations, detailing the biasing parameters, collective variables, and simulation controls.

#### HILLS and COLVAR Files

- HILLS Files: Files containing the metaD hills added during simulations, providing information on biasing potentials over time.

- COLVAR Files: Files capturing the values of the collective variables (CVs) during the simulations, enabling analysis of CV-based system evolution

#### Post-Processing Scripts

- Data Analysis and Plotting Scripts: these scripts used to analyze metaD data, including COLVAR data parsing and bias potential extraction and plotting investigated variables over simulation time.

- Extracting Max Bias during metaD Simulations: Provides the script used for extracting the maximum bias values from COLVAR files in metaD models.
DOI: 10.5281/zenodo.13889603
title: Datasets for the article "Light-dependent flavin redox and adduct states control the conformation and DNA binding activity of the transcription factor EL222"

description: #Figures

All spectra (NMR, infrared, UV/Visible), molecular models, and plots presented in the main text and Supplementary Information are available in this directory. 

# Classical Molecular Dynamic (MD) and Metadynamics Simulations (metaD) Data and Analysis

This part of the repository contains data, parameters and scripts used in classical MD (oxi_MD, cov_MD and red_MD models) and meta-dynamics simulations (oxi_metaD, cov_metaD and red_metaD models) presented in our publication, including files essential for running metaD simulations, collective variable (COLVAR) analysis, and data processing for publication figures. Each directory contains a README file with instructions on file usage, script dependencies, and suggested analysis methods.

## Contents

#### MD and metaD Simulation Files

- Input Files: MD and metaD input files used to initialize and configure the simulations, including system setup, force field parameters, and environment settings.

- MetaD Parameters: Parameter files used for metaD simulations, detailing the biasing parameters, collective variables, and simulation controls.

#### HILLS and COLVAR Files

- HILLS Files: Files containing the metaD hills added during simulations, providing information on biasing potentials over time.

- COLVAR Files: Files capturing the values of the collective variables (CVs) during the simulations, enabling analysis of CV-based system evolution

#### Post-Processing Scripts

- Data Analysis and Plotting Scripts: these scripts used to analyze metaD data, including COLVAR data parsing and bias potential extraction and plotting investigated variables over simulation time.

- Extracting Max Bias during metaD Simulations: Provides the script used for extracting the maximum bias values from COLVAR files in metaD models.
DOI: 10.15468/dl.n6jzht
title: Occurrence Download

description: A dataset containing 15419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Fiji",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 15419 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007375-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjea65
title: Occurrence Download

description: A dataset containing 1461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Passifloraceae"
 ]
}

 The dataset includes 1461 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007453-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5efhx
title: Occurrence Download

description: A dataset containing 363582 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Monarch Watch"
 ]
}

 The dataset includes 363582 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007373-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fh9arr
title: Occurrence Download

description: A dataset containing 841 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 841 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007376-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpfvc6
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Stelis pulchella Kunth"
 ]
}

 The dataset includes 270 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007377-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvuuqc
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.07603 46.15738,6.07442 46.15568,6.07648 46.15472,6.07676 46.15761,6.07603 46.15738))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 73 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007455-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p13kkwbr
title: Field Validation Data for Live Tree Presence/Absence Following Two Large Wildfires in California, USA

description: This data file contains observations recorded during field surveys of post-fire vegetation in the 2021 Caldor and 2022 Mosquito Fires in the Sierra Nevada of California. The surveys were performed in summer 2023. All tree species were surveyed and treated the same.
DOI: 10.15468/dl.q33qsn
title: Occurrence Download

description: A dataset containing 1080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Guam",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 1080 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007456-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqgtwb
title: Occurrence Download

description: A dataset containing 2608 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Glyptemys insculpta (Le Conte, 1830))"
 ]
}

 The dataset includes 2608 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007378-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4spj7d
title: Occurrence Download

description: A dataset containing 5216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Otospermophilus variegatus (Erxleben, 1777)"
 ]
}

 The dataset includes 5216 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007457-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fz8e4x
title: Occurrence Download

description: A dataset containing 53318 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Pseudacris crucifer (Wied-Neuwied, 1838))"
 ]
}

 The dataset includes 53318 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007371-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdcvye
title: Occurrence Download

description: A dataset containing 1570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Xerospermophilus spilosoma (Bennett, 1833)"
 ]
}

 The dataset includes 1570 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007379-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8rmgnf
title: Occurrence Download

description: A dataset containing 20080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Melanerpes flavifrons (Vieillot, 1818)",
 "Year 1000-2024"
 ]
}

 The dataset includes 20080 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007380-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3wyw2
title: Occurrence Download

description: A dataset containing 2608 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Glyptemys insculpta (Le Conte, 1830))"
 ]
}

 The dataset includes 2608 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007382-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dr44n4
title: Occurrence Download

description: A dataset containing 1012 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Stelis pusilla Kunth"
 ]
}

 The dataset includes 1012 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007458-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h9cpb7
title: Occurrence Download

description: A dataset containing 2814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Uruguay, Argentina)",
 "TaxonKey is Picumnus nebulosus Sundevall, 1866",
 "Year 1000-2024"
 ]
}

 The dataset includes 2814 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007381-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60594/w4f59x
title: Transect Data from the 2022 Department of Defense Wildland Fire Science Initiative Fort Stewart Campaign

description: To characterize fine-scale variations in vegetation structure, quantify heterogeneity, and capture fuel estimation and consumption, transects were utilized to sample coarse woody debris, fuel types, and fuelbed heights across the F units. This dataset provides transect data collected before (February 2022) and after (March 2022) the prescribed burns.This dataset is part of the Wildland Fire Science Initiative (WFSI) research burn campaign held at Fort Stewart from March 2 to 5, 2022. In addition, pre- and post-fire data collection occurred before and after these dates. See the most recent version of the contextual dataset “Fort Stewart 2022: Contextual data for Wildland Fire Science Initiative (WFSI) Research Burn Campaign” for more information about the campaign (see Annotations section for has Metadata link).
DOI: 10.17632/rng92psg4h.1
title: Anthropogenic forcing has impacted precipitation variability in the North China Monsoon Marginal Region

description: Climate change has significant impacts on ecosystems and socioeconomic sustainable development globally or regionally. Moreover, the feedback mechanism between the coupling of anthropogenic with natural internal variability and climate change in Asian Summer Monsoon (ASM) region remains unclear. Here, we present a robust annual precipitation reconstruction for the period 1770-2020, based on the tree ring oxygen isotope data and the simple linear regression model in the North China Monsoon Marginal Region (NCMMR). Multisource proxy records detected widespread drought trends within the NCMMR since 1950s. The multiple linear regression (MLR) modelling and water vapor flux analysis from ensemble means of Community Earth System Model-Last Millennium Ensemble suggested that the precipitation variability in the NCMMR is strong influenced by the Indian Ocean Dipole, El Niño-Southern Oscillation, Atlantic Multidecadal Oscillation and Interdecadal Pacific Oscillation. Meanwhile, the ASM system changes are driven by internal variability, and regulate interannual precipitation. The fingerprint results based on the Coupled Model Intercomparison Project Phase 6 diagnostic revealed that the middle 20th century rise in anthropogenic aerosol emissions may have counteracted the influence of greenhouse gases, but the pronounced greenhouse gases forcing signal has been strongly detected since the early 21st century. The MLR has been widely used in climate change driver studies because of its reliability and accuracy, and fingerprint detection can qualitatively determine the influence of external forcing on climate change. Accordingly, the NCMMR precipitation reduction since 1950s is likely driven by the combination of anthropogenic factors and changes in the ASM caused by internal variability.
DOI: 10.17632/rng92psg4h.2
title: Anthropogenic forcing has impacted precipitation variability in the North China Monsoon Marginal Region

description: The Asian Summer Monsoon (ASM) is a crucial driver of precipitation, sustaining ecological balance and socio-economic development in North China. However, the extent to which climate change has influenced this monsoonal system, leading to detectable and attributable modifications in precipitation regimes, remains unclear. Here, we present a robust annual precipitation reconstruction spanning 1770-2020, derived from tree-ring stable oxygen isotope data and a simple linear regression model in the North China Monsoon Marginal Region (NCMMR). Reconstructed precipitation and independent hydroclimatic records reveal a pronounced drying trend across the NCMMR since the 1950s. Multiple linear regression (MLR) modelling, water vapor transport analyses using ensemble means from the Community Earth System Model-Last Millennium Ensemble, and correlation analysis indicate that precipitation variability in the NCMMR is modulated by the Indian Ocean Dipole, El Niño-Southern Oscillation, Atlantic Multidecadal Oscillation, and Interdecadal Pacific Oscillation. Nevertheless, fingerprint analysis suggests that the observed precipitation decline since the 1950s is strongly associated with greenhouse gas concentrations, albeit partially offset by the effects of anthropogenic aerosol emissions and internal variability. The impact of greenhouse gas forcing on precipitation variability is expected to intensify in the coming decades.
DOI: 10.15468/dl.99e7ve
title: Occurrence Download

description: A dataset containing 101155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Apera spica-venti (L.) P.Beauv.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 101155 records from 656 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007426-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ru7qk9
title: Occurrence Download

description: A dataset listing the 227877 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset's 227877 records were derived from 2829 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007454-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1049399.10fu
title: SH1049399.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1049407.10fu
title: SH1049407.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1049415.10fu
title: SH1049415.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.kngk6b
title: Occurrence Download

description: A dataset containing 265375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.HKG",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2019-2020"
 ]
}

 The dataset includes 265375 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000327-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bk974w
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "StateProvince is Tolima",
 "TaxonKey is Primates"
 ]
}

 The dataset includes 76 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000346-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kzuyqd
title: Occurrence Download

description: A dataset containing 305568 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melanerpes rubricapillus (Cabanis, 1862)"
 ]
}

 The dataset includes 305568 records from 353 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000323-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jd96ve
title: Occurrence Download

description: A dataset containing 471986 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Rockfish Recruitment and Ecosystem Assessment Survey, Catch Data"
 ]
}

 The dataset includes 471986 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000339-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.