cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18203970
title: SyntheFluor-RL Data

description: This dataset accompanies the paper:

Sayana, R., Callon, K., Xu, J., Deutsch, J., Chu, S., Zou, J., Janetzko, J., Shivnaraine, R.V., Swanson, K. Generating readily synthesizable small molecule fluorophore scaffolds with reinforcement learning. The 2nd Workshop on Generative AI and Biology, ICML, 2025.The dataset is organized into the following folders:

 

building_block_prep: Intermediate files generated while conducting initial scoring of building blocks for generation. Final input building block file for generation is in synthefluor_generation.

 

chemfluor_data: Chemfluor data files including post-processed files used for training the property prediction models.

 

gaussian_logs: Example Gaussian log files generated in our workflow. Gaussian outputs the results of its calculations (e.x geometry optimization, frequency analysis, energy calculations) as it runs, which we pipe into `.log` files for further analysis.

 

generated_molecule_analysis: intermediate files created to analyze generated molecules and compare with a random set of 10,000 molecules from the REAL space

 

property_prediction_models: Chemprop-RDKit and Chemprop-Morgan models trained to predict PLQY, absorption, or emission properties of molecules.

 

supplementary_figures: UV/HPLC and mass spectrometry analysis of the top three compounds generated by SyntheFluor-RL.

 

supplementary_tables: The supplementary tables referenced in the paper, including model performance of the property prediction models and brightness of the generated molecules.

 

supplementary_software: A custom MATLAB script that was used to quantify mean pixel intensity across fluorescence-only images.

 

synthefluor_generation: Molecules generated by SyntheFluor-RL. This folder additionally includes the building blocks file used as input for generation and the clustering data and analysis of the generated molecules which was used for candidate selection.
DOI: 10.5281/zenodo.18203969
title: SyntheFluor-RL Data

description: This dataset accompanies the paper:

Sayana, R., Callon, K., Xu, J., Deutsch, J., Chu, S., Zou, J., Janetzko, J., Shivnaraine, R.V., Swanson, K. Generating readily synthesizable small molecule fluorophore scaffolds with reinforcement learning. The 2nd Workshop on Generative AI and Biology, ICML, 2025.The dataset is organized into the following folders:

 

building_block_prep: Intermediate files generated while conducting initial scoring of building blocks for generation. Final input building block file for generation is in synthefluor_generation.

 

chemfluor_data: Chemfluor data files including post-processed files used for training the property prediction models.

 

gaussian_logs: Example Gaussian log files generated in our workflow. Gaussian outputs the results of its calculations (e.x geometry optimization, frequency analysis, energy calculations) as it runs, which we pipe into `.log` files for further analysis.

 

generated_molecule_analysis: intermediate files created to analyze generated molecules and compare with a random set of 10,000 molecules from the REAL space

 

property_prediction_models: Chemprop-RDKit and Chemprop-Morgan models trained to predict PLQY, absorption, or emission properties of molecules.

 

supplementary_figures: UV/HPLC and mass spectrometry analysis of the top three compounds generated by SyntheFluor-RL.

 

supplementary_tables: The supplementary tables referenced in the paper, including model performance of the property prediction models and brightness of the generated molecules.

 

supplementary_software: A custom MATLAB script that was used to quantify mean pixel intensity across fluorescence-only images.

 

synthefluor_generation: Molecules generated by SyntheFluor-RL. This folder additionally includes the building blocks file used as input for generation and the clustering data and analysis of the generated molecules which was used for candidate selection.
DOI: 10.15468/dl.o8agio
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017333-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sav5bm
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anax nigrofasciatus nigrofasciatus",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 206 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184827-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2vqpa9
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sinochlora longifissa (Matsumura & Shiraki, 1908)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 68 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184945-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bfaul8
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005313-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.twh6em
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0089723-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffkvcf
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-85.93392 -3.13710,-58.55770 -3.13710,-58.55770 7.80096,-85.93392 7.80096,-85.93392 -3.13710))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Berberis sumacana Camargo"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184980-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hycb0c
title: Occurrence Download

description: A dataset containing 139083138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 139083138 records from 2824 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085520-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ds5r22
title: Occurrence Download

description: A dataset containing 917604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Locality ~*Lake Superior*",
 "Locality ~*Lake Michigan*",
 "Locality ~*Lake Huron*",
 "Locality ~*Lake Erie*",
 "Locality ~*Lake Ontario*",
 "Locality ~*St. Marys River*",
 "Locality ~*Huron Erie Corridor*",
 "Locality ~*St. Clair River*",
 "Locality ~*Lake St. Clair*",
 "Locality ~*Detroit River*",
 "Locality ~*Niagara River*",
 "Locality ~*L. Superior*",
 "Locality ~*L Superior*",
 "Locality ~*L. Michigan*",
 "Locality ~*L Michigan*",
 "Locality ~*L. Huron*",
 "Locality ~*L Huron*",
 "Locality ~*L. Erie*",
 "Locality ~*L Erie*",
 "Locality ~*L. Ontario*",
 "Locality ~*L Ontario*",
 "Locality ~*St. Mary's R*",
 "Locality ~*St Marys R*",
 "Locality ~*St Mary's R*",
 "Locality ~*Ste. Marys R*",
 "Locality ~*Ste Marys R*",
 "Locality ~*Ste. Mary's R*",
 "Locality ~*Ste Mary's R*",
 "Locality ~*Saint Marys R*",
 "Locality ~*Saint Mary's R*",
 "Locality ~*Sainte Marys R*",
 "Locality ~*Sainte Mary's R*",
 "Locality ~*Huron-Erie Corridor*",
 "Locality ~*St Clair R*",
 "Locality ~*Ste. Clair R*",
 "Locality ~*Ste Clair R*",
 "Locality ~*St. Claire R*",
 "Locality ~*St Claire R*",
 "Locality ~*Ste. Claire R*",
 "Locality ~*Ste Claire R*",
 "Locality ~*Saint Clair R*",
 "Locality ~*Sainte Clair R*",
 "Locality ~*Saint Claire R*",
 "Locality ~*Sainte Claire R*",
 "Locality ~*Lake S* Cla*",
 "Locality ~*Lakes S* Cla*",
 "Locality ~*L. S* Cla*",
 "Locality ~*L S* Cla*",
 "Locality ~*Detroit R*",
 "Locality ~*Detroite R*",
 "Locality ~*D. R*",
 "Locality ~*D R*",
 "Locality ~*Niagara R*",
 "Locality ~*Niagra R*",
 "Locality ~*Great Lake*"
 ]
 }
 ]
}

 The dataset includes 917604 records from 771 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137180-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2r4j4
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "WaterBody is one of (Lake Superior, Lake Superior (lake & creek tribs), Lake Superior shore, Lake superior, LAKE MICHIGAN-LAKE HURON, Lake Michigan, Lake Michigan (lake & creek tribs), Lake michigan, LAKE HURON ?, Lake Huron, Lake Huron (lake & creek tribs), Lake Huron, Duncan Bay, Lake Huron, MI, Lake Hurron, Lake huron, Lake Erie, Lake Erie (lake & creek tribs), Lake Erie, La Plaisance Bay, Lake Erie, Misery Bay, Lake Erie; Ohio, Lake erie, Lake Ontario, Lake Ontario (lake & creek tribs), Lake ontario, St Mary's, Niagara River, Niagara Falls, Niagara, Niagara River (upper), Niagara River near Rose-Hill, Niagara River, East Branch, Niagara river, HURON R., HURON RIVER-LAKE ERIE, Huron R., Huron R. (MI), Huron River, Huron River - Lake Erie, Huron River, St. Lawrence River, Huron river, Erie Lake, Erie/Huron, Ontario lake, Michigan Lake)"
 ]
}

 The dataset includes 29 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009127-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.42hjzc
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhabdosargus globiceps (Valenciennes, 1830)",
 "Year 2000-2025"
 ]
}

 The dataset includes 99 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009900-250515123054153/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.28715213
title: Supplementary Material for: Associations between Luteinizing Hormone/Chorionic Gonadotropin Receptor Polymorphisms and Assisted Reproductive Technology Outcomes: A Systematic Review and Meta-analysis

description: Introduction: Variants of the luteinizing hormone/chorionic gonadotropin receptor (LHCGR) gene have been investigated for their close associations with assisted reproductive technology (ART) outcomes. However, available data are controversial. This meta-analysis aimed to elucidate the associations of LHCGR N312S polymorphism (rs2293275) with ART outcomes.
Methods: A thorough search was performed in the databases of PubMed, EMBASE, Web of Science, and Cochrane Library from their inception to July 19, 2024. The analysis included five studies, encompassing 2,692 patients with infertility and subfertility. RevMan 5.4 was used for further comprehensive data analysis.
Results: In this study, A allele homozygotes encoded asparagine (N/N), and G allele homozygotes encoded serine (S/S). The number of oocytes retrieved was higher in AA homozygotes than in GG homozygotes (mean difference [MD] 1.07, 95% confidence interval [CI] 0.09 to 2.05, I2 = 7%, P = 0.03) or AG heterozygotes (MD 1.26, 95% CI 0.32 to 2.20, I2 = 45%, P = 0.008). The number of mature oocytes and the distribution of the LHCGR (rs2293275) genotype (MD 0.60, 95% CI −0.25 to 1.45, I2 = 49%, P = 0.17; MD 0.85, 95% CI 0.02 to 1.68, I2 = 76%, P = 0.05; MD −0.36, 95% CI −1.20 to 0.49, I2 = 56%, P = 0.41) were not significantly different. G allele homozygotes and heterozygotes exhibited an increasing trend in the number of clinical pregnancies compared with A allele homozygotes (odds ratio [OR] 1.69, 95% CI 1.21 to 2.36, I2 = 0%, P = 0.002; OR 1.30, 95% CI 1.09 to 1.54, I2 = 0%, P = 0.003).
Conclusion: This study revealed associations of LHCGR polymorphism with ART outcomes, implying that the LHCGR N312S polymorphism (rs2293275) may serve as a predictor for certain ART outcomes.
DOI: 10.6084/m9.figshare.28715213.v2
title: Supplementary Material for: Associations between Luteinizing Hormone/Chorionic Gonadotropin Receptor Polymorphisms and Assisted Reproductive Technology Outcomes: A Systematic Review and Meta-analysis

description: Introduction: Variants of the luteinizing hormone/chorionic gonadotropin receptor (LHCGR) gene have been investigated for their close associations with assisted reproductive technology (ART) outcomes. However, available data are controversial. This meta-analysis aimed to elucidate the associations of LHCGR N312S polymorphism (rs2293275) with ART outcomes.
Methods: A thorough search was performed in the databases of PubMed, EMBASE, Web of Science, and Cochrane Library from their inception to July 19, 2024. The analysis included five studies, encompassing 2,692 patients with infertility and subfertility. RevMan 5.4 was used for further comprehensive data analysis.
Results: In this study, A allele homozygotes encoded asparagine (N/N), and G allele homozygotes encoded serine (S/S). The number of oocytes retrieved was higher in AA homozygotes than in GG homozygotes (mean difference [MD] 1.07, 95% confidence interval [CI] 0.09 to 2.05, I2 = 7%, P = 0.03) or AG heterozygotes (MD 1.26, 95% CI 0.32 to 2.20, I2 = 45%, P = 0.008). The number of mature oocytes and the distribution of the LHCGR (rs2293275) genotype (MD 0.60, 95% CI −0.25 to 1.45, I2 = 49%, P = 0.17; MD 0.85, 95% CI 0.02 to 1.68, I2 = 76%, P = 0.05; MD −0.36, 95% CI −1.20 to 0.49, I2 = 56%, P = 0.41) were not significantly different. G allele homozygotes and heterozygotes exhibited an increasing trend in the number of clinical pregnancies compared with A allele homozygotes (odds ratio [OR] 1.69, 95% CI 1.21 to 2.36, I2 = 0%, P = 0.002; OR 1.30, 95% CI 1.09 to 1.54, I2 = 0%, P = 0.003).
Conclusion: This study revealed associations of LHCGR polymorphism with ART outcomes, implying that the LHCGR N312S polymorphism (rs2293275) may serve as a predictor for certain ART outcomes.
DOI: 10.6084/m9.figshare.28890230
title: Supplementary Material for: Thromboxane A2 or activated platelets slightly low-er Fgf23 expression in vitro

description: Introduction: Fibroblast growth factor 23 (FGF23) has emerged as an important endocrine regulator of renal phosphate and vitamin D metabolism and as a factor implicated in patho-physiological processes in further organs including heart. In myocardial infarction, elevations of plasma FGF23 can be observed that may be related to left ventricular hypertrophy or fibro-sis. A critical event in the development of myocardial infarction and thrombosis is platelet aggregation due to thromboxane A2 (TxA2) formation. We studied whether TxA2 is a regula-tor of FGF23. Methods: Experiments were performed in rat UMR-106 osteoblast-like cells and mouse MC3T3-E1 upon exposure to TxA2, pharmacological manipulation of TxA2 sig-naling, or co-incubation with platelets isolated from healthy volunteers. Fgf23 transcripts were analyzed by qRT-PCR and FGF23 protein by ELISA. Results: As a result, TxA2 or stable TxA2 receptor agonists I-BOP or U46619 significantly suppressed Fgf23 gene expres-sion, an effect abrogated by TxA2 receptor antagonist SQ29548. TxA2 signaling also down-regulated FGF23 protein concentration in the cell culture supernatant. Co-incubation of UMR-106 cells with freshly isolated human thrombocytes activated with thrombin, but not with non-activated platelets or thrombin alone significantly lowered Fgf23 gene expression in UMR-106 cells. Conclusion: Taken together, TxA2 signaling suppresses FGF23 production in UMR-106 and MC3T3-E1 bone cells. TxA2-dependent regulation of FGF23 synthesis may be particularly relevant for common diseases associated with enhanced platelet aggregation.

Keywords: Thrombin, myocardial infarction, thrombocytes
DOI: 10.6084/m9.figshare.28890230.v2
title: Supplementary Material for: Thromboxane A2 or activated platelets slightly low-er Fgf23 expression in vitro

description: Introduction: Fibroblast growth factor 23 (FGF23) has emerged as an important endocrine regulator of renal phosphate and vitamin D metabolism and as a factor implicated in patho-physiological processes in further organs including heart. In myocardial infarction, elevations of plasma FGF23 can be observed that may be related to left ventricular hypertrophy or fibro-sis. A critical event in the development of myocardial infarction and thrombosis is platelet aggregation due to thromboxane A2 (TxA2) formation. We studied whether TxA2 is a regula-tor of FGF23. Methods: Experiments were performed in rat UMR-106 osteoblast-like cells and mouse MC3T3-E1 upon exposure to TxA2, pharmacological manipulation of TxA2 sig-naling, or co-incubation with platelets isolated from healthy volunteers. Fgf23 transcripts were analyzed by qRT-PCR and FGF23 protein by ELISA. Results: As a result, TxA2 or stable TxA2 receptor agonists I-BOP or U46619 significantly suppressed Fgf23 gene expres-sion, an effect abrogated by TxA2 receptor antagonist SQ29548. TxA2 signaling also down-regulated FGF23 protein concentration in the cell culture supernatant. Co-incubation of UMR-106 cells with freshly isolated human thrombocytes activated with thrombin, but not with non-activated platelets or thrombin alone significantly lowered Fgf23 gene expression in UMR-106 cells. Conclusion: Taken together, TxA2 signaling suppresses FGF23 production in UMR-106 and MC3T3-E1 bone cells. TxA2-dependent regulation of FGF23 synthesis may be particularly relevant for common diseases associated with enhanced platelet aggregation.

Keywords: Thrombin, myocardial infarction, thrombocytes
DOI: 10.6084/m9.figshare.28890230.v1
title: Supplementary Material for: Thromboxane A2 or activated platelets slightly low-er Fgf23 expression in vitro

description: Introduction: Fibroblast growth factor 23 (FGF23) has emerged as an important endocrine regulator of renal phosphate and vitamin D metabolism and as a factor implicated in patho-physiological processes in further organs including heart. In myocardial infarction, elevations of plasma FGF23 can be observed that may be related to left ventricular hypertrophy or fibro-sis. A critical event in the development of myocardial infarction and thrombosis is platelet aggregation due to thromboxane A2 (TxA2) formation. We studied whether TxA2 is a regula-tor of FGF23. Methods: Experiments were performed in rat UMR-106 osteoblast-like cells and mouse MC3T3-E1 upon exposure to TxA2, pharmacological manipulation of TxA2 sig-naling, or co-incubation with platelets isolated from healthy volunteers. Fgf23 transcripts were analyzed by qRT-PCR and FGF23 protein by ELISA. Results: As a result, TxA2 or stable TxA2 receptor agonists I-BOP or U46619 significantly suppressed Fgf23 gene expres-sion, an effect abrogated by TxA2 receptor antagonist SQ29548. TxA2 signaling also down-regulated FGF23 protein concentration in the cell culture supernatant. Co-incubation of UMR-106 cells with freshly isolated human thrombocytes activated with thrombin, but not with non-activated platelets or thrombin alone significantly lowered Fgf23 gene expression in UMR-106 cells. Conclusion: Taken together, TxA2 signaling suppresses FGF23 production in UMR-106 and MC3T3-E1 bone cells. TxA2-dependent regulation of FGF23 synthesis may be particularly relevant for common diseases associated with enhanced platelet aggregation.

Keywords: Thrombin, myocardial infarction, thrombocytes
DOI: 10.6084/m9.figshare.29110043
title: Supplementary Material for: Drug Removal by Hemoadsorption

description: Background: There is growing interest in hemoadsorption (HA) therapies in critically ill patients although their precise indications remain to be established. Several devices are available on the market with heterogeneous properties and capabilities. 
Summary: Due to the non-specific removal associated with most HA techniques, concerns have been raised on their unintended removal of drugs such as anti-infectives in sepsis. On the other hand, drug removal might be beneficial in certain situations for instance antithrombotic medications in patients requiring emergency surgery or in case of accidental or self-induced intoxication. In this review, we summarize available in vitro, in vivo, and clinical studies reporting on the influence of various HA techniques on drugs pharmacokinetics. 
Key message: We conclude that further studies should aim at providing drug dosing recommendations during HA and confirm its safety, efficacy, and practicalities when used for intoxications.