cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/pmk2cb3nt2
title: FKBP12 inhibits hepcidin expression by modulating BMP receptors interaction and ligand responsiveness in hepatocytes

description: The expression of the iron regulatory hormone hepcidin in hepatocytes is regulated by the BMP-SMAD pathway through the type I receptors ALK2 and ALK3, the type II receptors ACVR2A and BMPR2, and the ligands BMP2 and BMP6. We previously
identified the immunophilin FKBP12 as a new hepcidin inhibitor that acts by blocking ALK2. Both the physiologic ALK2 ligand BMP6 and the immunosuppressive drug Tacrolimus (TAC) displace FKBP12 from ALK2 and activate the signaling. However,
the molecular mechanism whereby FKBP12 regulates BMP-SMAD pathway activity and thus hepcidin expression remains unclear. Here, we show that FKBP12 acts by modulating BMP receptor interactions and ligand responsiveness. We first demonstrate that in primary murine hepatocytes TAC regulates hepcidin expression exclusively via FKBP12. Downregulation of the BMP receptors reveals that ALK2, to a lesser extent ALK3, and ACVR2A are required for hepcidin upregulation in response to both BMP6 and TAC. Mechanistically, TAC and BMP6 increase ALK2 homooligomerization and ALK2–ALK3 hetero-oligomerization and the interaction between ALK2 and the type II receptors. By acting on the same receptors, TAC and BMP6 cooperate in BMP pathway activation and hepcidin expression both in vitro and in vivo. Interestingly, the activation state of ALK3 modulates its interaction with FKBP12, which may explain the cell-specific activity of FKBP12. Overall, our results identify the mechanism whereby FKBP12 regulates the BMP-SMAD pathway and hepcidin expression in hepatocytes, and suggest that FKBP12–ALK2 interaction is a potential pharmacologic target in disorders caused by defective BMP-SMAD signaling and characterized by low hepcidin and high BMP6 expression. 
Complete data files relative to the manuscript "Pettinato M. et al., FKBP12 inhibits hepcidin expression by modulating BMP receptors interaction and ligand responsiveness in hepatocytes. Am J Hematol. 2023 Aug;98(8):1223-1235. doi: 10.1002/ajh.26961. Epub 2023 May 18. PMID: 37199280".
DOI: 10.17632/pmk2cb3nt2.1
title: FKBP12 inhibits hepcidin expression by modulating BMP receptors interaction and ligand responsiveness in hepatocytes

description: The expression of the iron regulatory hormone hepcidin in hepatocytes is regulated by the BMP-SMAD pathway through the type I receptors ALK2 and ALK3, the type II receptors ACVR2A and BMPR2, and the ligands BMP2 and BMP6. We previously
identified the immunophilin FKBP12 as a new hepcidin inhibitor that acts by blocking ALK2. Both the physiologic ALK2 ligand BMP6 and the immunosuppressive drug Tacrolimus (TAC) displace FKBP12 from ALK2 and activate the signaling. However,
the molecular mechanism whereby FKBP12 regulates BMP-SMAD pathway activity and thus hepcidin expression remains unclear. Here, we show that FKBP12 acts by modulating BMP receptor interactions and ligand responsiveness. We first demonstrate that in primary murine hepatocytes TAC regulates hepcidin expression exclusively via FKBP12. Downregulation of the BMP receptors reveals that ALK2, to a lesser extent ALK3, and ACVR2A are required for hepcidin upregulation in response to both BMP6 and TAC. Mechanistically, TAC and BMP6 increase ALK2 homooligomerization and ALK2–ALK3 hetero-oligomerization and the interaction between ALK2 and the type II receptors. By acting on the same receptors, TAC and BMP6 cooperate in BMP pathway activation and hepcidin expression both in vitro and in vivo. Interestingly, the activation state of ALK3 modulates its interaction with FKBP12, which may explain the cell-specific activity of FKBP12. Overall, our results identify the mechanism whereby FKBP12 regulates the BMP-SMAD pathway and hepcidin expression in hepatocytes, and suggest that FKBP12–ALK2 interaction is a potential pharmacologic target in disorders caused by defective BMP-SMAD signaling and characterized by low hepcidin and high BMP6 expression. 
Complete data files relative to the manuscript "Pettinato M. et al., FKBP12 inhibits hepcidin expression by modulating BMP receptors interaction and ligand responsiveness in hepatocytes. Am J Hematol. 2023 Aug;98(8):1223-1235. doi: 10.1002/ajh.26961. Epub 2023 May 18. PMID: 37199280".
DOI: 10.15468/dl.3hp2qw
title: Occurrence Download

description: A dataset containing 632 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "OccurrenceStatus is Present",
 "TaxonKey is Rosalia alpina",
 "Year 2005-2025"
 ]
}

 The dataset includes 632 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009636-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jmwjea
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gloydius lipipengi)",
 "DecimalLatitude is greater than or equal to 0",
 "DecimalLatitude is less than or equal to 60",
 "DecimalLongitude is greater than or equal to 60",
 "DecimalLongitude is less than or equal to 150",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009639-251120083545085/datasets/export for details.
DOI: 10.15468/dl.acy98t
title: Occurrence Download

description: A dataset containing 3510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to -10.914722",
 "DecimalLatitude is less than or equal to -5.914722",
 "DecimalLongitude is greater than or equal to -145.0",
 "DecimalLongitude is less than or equal to -140.0",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 3510 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009637-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/7096
title: Synthetic-LungNotes-10K
DOI: 10.15468/dl.yu9a4c
title: Occurrence Download

description: A dataset containing 18907 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ulmus pumila"
 ]
}

 The dataset includes 18907 records from 428 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009638-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yy2xnu
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trimeresurus yunnanensis)",
 "Country is one of (China, India, Indonesia, Pakistan, Bangladesh, Japan, Philippines, Viet Nam, Türkiye, Iran (Islamic Republic of), Thailand, Myanmar, Korea, Republic of, Korea (Democratic People’s Republic of), Iraq, Afghanistan, Saudi Arabia, Uzbekistan, Malaysia, Yemen, Nepal, Sri Lanka, Kazakhstan, Syrian Arab Republic, Cambodia, Jordan, Azerbaijan, United Arab Emirates, Tajikistan, Israel, Lao People’s Democratic Republic, Lebanon, Kyrgyzstan, Turkmenistan, Singapore, Oman, Palestine, State of, Kuwait, Georgia, Mongolia, Armenia, Qatar, Bahrain, Timor-Leste, Cyprus, Bhutan, Maldives, Brunei Darussalam)",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 44 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007476-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.etmjnc
title: Occurrence Download

description: A dataset containing 26316 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 第四次森林資源調查野生動物調查錄音檔案監聽辨識及資料分析 Sound Identification and Data Analysis of Wildlife Field Survey Recordings from the Fourth National Forest Resources Survey"
 ]
}

 The dataset includes 26316 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007475-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwdd54
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((6.07001 52.03171,6.12631 52.03171,6.12631 52.07531,6.07001 52.07531,6.07001 52.03171))",
 "HasGeospatialIssue is false",
 "TaxonKey is Apidae",
 "Year 2024-2025"
 ]
}

 The dataset includes 181 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007478-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.355p2h
title: Occurrence Download

description: A dataset containing 32760 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "OccurrenceStatus is Present",
 "TaxonKey is Asimina triloba"
 ]
}

 The dataset includes 32760 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007477-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17709219
title: Optimizing management to close yield gaps for China's major cereals: A meta-analysis and spatial assessment

description: The data support the article " Optimizing management to close yield gaps for China's major cereals: A meta-analysis and spatial assessment   " published in Global Change Biology.
DOI: 10.5281/zenodo.17709220
title: Optimizing management to close yield gaps for China's major cereals: A meta-analysis and spatial assessment

description: The data support the article " Optimizing management to close yield gaps for China's major cereals: A meta-analysis and spatial assessment   " published in Global Change Biology.
DOI: 10.13140/rg.2.2.33557.18400
title: Bollettino sismico Regione Umbria 2019 per Google Earth
DOI: 10.34740/kaggle/dsv/13862919
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.5s9j2s
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Geonoma chococola",
 "HasCoordinate is true"
 ]
}

 The dataset includes 82 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007480-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wyv9p5
title: Occurrence Download

description: A dataset containing 320 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Tunisia",
 "OccurrenceStatus is Present",
 "TaxonKey is Cephalaspidea"
 ]
}

 The dataset includes 320 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007481-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vhprqe
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vipera berus)",
 "Country is one of (China, India, Indonesia, Pakistan, Bangladesh, Japan, Philippines, Viet Nam, Türkiye, Iran (Islamic Republic of), Thailand, Myanmar, Korea, Republic of, Korea (Democratic People’s Republic of), Iraq, Afghanistan, Saudi Arabia, Uzbekistan, Malaysia, Yemen, Nepal, Sri Lanka, Kazakhstan, Syrian Arab Republic, Cambodia, Jordan, Azerbaijan, United Arab Emirates, Tajikistan, Israel, Lao People’s Democratic Republic, Lebanon, Kyrgyzstan, Turkmenistan, Singapore, Oman, Palestine, State of, Kuwait, Georgia, Mongolia, Armenia, Qatar, Bahrain, Timor-Leste, Cyprus, Bhutan, Maldives, Brunei Darussalam)",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007483-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57h6uf
title: Occurrence Download

description: A dataset containing 301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "TaxonKey is Geocoris"
 ]
}

 The dataset includes 301 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007482-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcj2xr
title: Occurrence Download

description: A dataset containing 2997478 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Year is 1981"
 ]
}

 The dataset includes 2997478 records from 560 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007435-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcbtf5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "OccurrenceStatus is Present",
 "ScientificName is Gulo gulo",
 "TaxonKey is Gulo gulo",
 "Year 1980-2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007485-251120083545085/datasets/export for details.
DOI: 10.15468/dl.wcya2d
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vipera renardi)",
 "Country is one of (China, India, Indonesia, Pakistan, Bangladesh, Japan, Philippines, Viet Nam, Türkiye, Iran (Islamic Republic of), Thailand, Myanmar, Korea, Republic of, Korea (Democratic People’s Republic of), Iraq, Afghanistan, Saudi Arabia, Uzbekistan, Malaysia, Yemen, Nepal, Sri Lanka, Kazakhstan, Syrian Arab Republic, Cambodia, Jordan, Azerbaijan, United Arab Emirates, Tajikistan, Israel, Lao People’s Democratic Republic, Lebanon, Kyrgyzstan, Turkmenistan, Singapore, Oman, Palestine, State of, Kuwait, Georgia, Mongolia, Armenia, Qatar, Bahrain, Timor-Leste, Cyprus, Bhutan, Maldives, Brunei Darussalam)",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2025",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 268 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007486-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17709398
title: National Open Access Monitor, Ireland - Research product metadata

description: This dataset contains the foundational data for the National Open Access Monitor under an open license. OpenAIRE will routinely provide monthly data dumps to Zenodo, encompassing a comprehensive set of data and indicators related to the Open Access Monitor. This collaborative effort ensures accessibility and openness in sharing the data, promoting transparency and facilitating its use for research and analysis purposes.The dataset comprises of the metadata of the research products metadata stored in the parquet format. The file contains two columns ("id", "xml"), the first of which is the OpenAIRE identifier of the research product and the the second the xml representation of the metadata. The schema of the metadata can be found in https://www.openaire.eu/schema/1.0/oaf-1.0.xsd and a detailed description of the contents can be found in https://graph.openaire.eu/docs/ and https://zenodo.org/records/2643199
DOI: 10.5281/zenodo.17453610
title: Supplementary data: Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control

description: Supplementary data for the paper:

Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control

Abstract

Controlling cell population dynamics and phenotypic diversification is a key objective in systems and synthetic biology, particularly for ensuring uniform responses from engineered gene circuits. While cell-machine interfaces have been employed to modulate host-gene circuit interactions, environmental perturbations typical of industrial bioreactor conditions remain underexplored. In this study, we investigate the impact of such perturbations on the general stress response in Escherichia coli and Saccharomyces cerevisiae. Using scale-down bioreactor experiments, we evaluate the performance of the Segregostat, a real-time control system that leverages automated flow cytometry to induce dynamic nutrient shifts. The Segregostat achieves robust stress response control, even under severe perturbations such as extended residence times in a two-compartment reactor. We hypothesize that this robustness arises from the system’s ability to amplify host-compatible fluctuations beyond bioreactor-induced perturbations. Our findings highlight the importance of integrating environmental factors into control strategies for reliable gene circuit behavior in industrial bioprocessing environments.
description: Dataset contains automated flow cytometry data and additional culture measurements.




A_LabScale
Contains the raw data from the reactors experiments performed in lab-scale bioreactor.


B_ScaleDown
Contains the raw data from the reactors experiments performed in scale-down bioreactor.


BZ_Pulses
Contains the raw data from the reactors experiments performed in lab-scale bioreactor with feeding by pulses (in Supp. Materials only).


C_Changestats
Contains the raw data from the reactors experiments of accelerostats and decelerostats performed in lab-scale bioreactor (in Supp. Materials only).


CytometerCalibration
Contains the data for calibrations of cytometers (from Delvenne et al., 2025)


Paper_FEC
Contains parts of previously published data (Delvenne et al., 2025) required for the computation of the trade-off between growth and targeted gene expression




For each cultivation in bioreactor, summary plots are provided together with the raw data. These plots include measured and computed parameters such as fluorescence time-scatter plots from flow cytometry with the corresponding Shannon entropy, cell biomass, pH, acid/base addition, temperature, mixing, and dissolved oxygen.
DOI: 10.5281/zenodo.17453611
title: Supplementary data: Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control

description: Supplementary data for the paper:

Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control

Abstract

Controlling cell population dynamics and phenotypic diversification is a key objective in systems and synthetic biology, particularly for ensuring uniform responses from engineered gene circuits. While cell-machine interfaces have been employed to modulate host-gene circuit interactions, environmental perturbations typical of industrial bioreactor conditions remain underexplored. In this study, we investigate the impact of such perturbations on the general stress response in Escherichia coli and Saccharomyces cerevisiae. Using scale-down bioreactor experiments, we evaluate the performance of the Segregostat, a real-time control system that leverages automated flow cytometry to induce dynamic nutrient shifts. The Segregostat achieves robust stress response control, even under severe perturbations such as extended residence times in a two-compartment reactor. We hypothesize that this robustness arises from the system’s ability to amplify host-compatible fluctuations beyond bioreactor-induced perturbations. Our findings highlight the importance of integrating environmental factors into control strategies for reliable gene circuit behavior in industrial bioprocessing environments.
description: Dataset contains automated flow cytometry data and additional culture measurements.




A_LabScale
Contains the raw data from the reactors experiments performed in lab-scale bioreactor.


B_ScaleDown
Contains the raw data from the reactors experiments performed in scale-down bioreactor.


BZ_Pulses
Contains the raw data from the reactors experiments performed in lab-scale bioreactor with feeding by pulses (in Supp. Materials only).


C_Changestats
Contains the raw data from the reactors experiments of accelerostats and decelerostats performed in lab-scale bioreactor (in Supp. Materials only).


CytometerCalibration
Contains the data for calibrations of cytometers (from Delvenne et al., 2025)


Paper_FEC
Contains parts of previously published data (Delvenne et al., 2025) required for the computation of the trade-off between growth and targeted gene expression




For each cultivation in bioreactor, summary plots are provided together with the raw data. These plots include measured and computed parameters such as fluorescence time-scatter plots from flow cytometry with the corresponding Shannon entropy, cell biomass, pH, acid/base addition, temperature, mixing, and dissolved oxygen.
DOI: 10.5281/zenodo.17191019
title: Data underlying the publication "Experiments on rapidly rotating convection: the role of the Prandtl number"

description: This dataset underlies the paper "Experiments on rapidly rotating convection: the role of the Prandtl number" by Hannah M. Clercx and Rudie P.J. Kunnen. This experimental investigation produced time records of several temperature sensors and heating power inputs from a rotating Rayleigh-Bénard convection cell.
DOI: 10.5281/zenodo.17710180
title: Data underlying the publication "Experiments on rapidly rotating convection: the role of the Prandtl number"

description: This dataset underlies the paper "Experiments on rapidly rotating convection: the role of the Prandtl number" by Hannah M. Clercx and Rudie P.J. Kunnen. This experimental investigation produced time records of several temperature sensors and heating power inputs from a rotating Rayleigh-Bénard convection cell.
DOI: 10.15468/dl.v4frbs
title: Occurrence Download

description: A dataset containing 908 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Attalea allenii",
 "HasCoordinate is true"
 ]
}

 The dataset includes 908 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007488-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.