cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.b3n69v
title: Occurrence Download

description: A dataset containing 1232 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scabiosa nitens Roem. & Schult.",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 1232 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033930-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x3szvg
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Macroteleia absona Muesebeck, 1977)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033931-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnb57e
title: Occurrence Download

description: A dataset containing 555 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iberochondrostoma lusitanicum (Collares-Pereira, 1980)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 555 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033932-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2yynq
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caseolus commixtus (R.T.Lowe, 1855)",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033934-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/w8f33nv5k9.1
title: From Phenotype to Molecules: Unveiling the Genetic and Immunological Bridges Between Autoimmune Diseases and Vitiligo

description: This study investigates the causal relationships between 21 autoimmune diseases and Vitiligo through Mendelian randomization analysis, identifying causal associations with seven autoimmune diseases.
DOI: 10.5281/zenodo.11212015
title: Structural Homology of Epitope Pair Candidates for Molecular Mimicry Trigger  of Type 1 Diabetes Mellitus

description: Background: Molecular mimicry, where foreign and self-peptides contain similar epitopes, can induce autoimmune responses. Identifying potential molecular mimics and studying their properties is key to understanding the onset of autoimmune diseases such as type 1 diabetes mellitus (T1DM). Previous work identified pairs of infectious epitopes (EINF) and T1DM epitopes (ET1D) that demonstrated sequence homology; however, structural homology was not considered. Correlating sequence homology with structural properties is important for streamlining translational investigation of potential molecular mimics. Therefore, the purpose of this work is to compare sequence homology with structural homology by calculating the structures and electrostatic potential surfaces of the epitope pairs identified in previous work from our laboratory. 

 Results:  For each epitope pair the root mean square deviation (RMSD) was calculated between their predicted structures and their electrostatic potentials were compared. Structures were predicted using the AlphaFold software program. Of the 52 epitope pairs considered here only 10 do not exhibit any matching (i.e. less than 3 residues overlap). When considering all residues the RMSD ranges from 0.33 Å to 11.66 Å with an average of 2.68 Å. Twenty-two pairs (42%) have RMSD of less than 1.5 Å and 30 (58%) less than 3 Å. Even some of the matching pairs show some electrostatic similarities that need to be considered. In general there is good agreement between the folding predicted for the isolated EINF and ET1D epitopes and the folding of the corresponding amino acid sequence in the parent antigen, but in some cases there are deviation that need to be considered, even when the RMDS is small.

 Conclusions: Despite differences, most of the EINF/ET1D pairs selected by sequence homology show similar structural and electrostatic distributions, indicating that the EINF may bind to the same protein targets, the major histocompatibility complex molecules, for T1DM, leading to molecular mimicry onset of the disease. These findings suggest that searching for epitope pairs using sequence homology, a much less computationally demanding approach, leads to strong candidates for molecular mimicry that should be considered for further study. Still structure and full docking calculations will be necessary to advance the in-silico molecular mimicry predictions.  Here we presnt the following files:

·         Fasta files of all epitopes studied.

·         Alphafold calculated Structures of all epitopes.

·         Antigen structures.

·         Epitope pair structure comparison and their electrostatics.
DOI: 10.5281/zenodo.11212016
title: Structural Homology of Epitope Pair Candidates for Molecular Mimicry Trigger  of Type 1 Diabetes Mellitus

description: Background: Molecular mimicry, where foreign and self-peptides contain similar epitopes, can induce autoimmune responses. Identifying potential molecular mimics and studying their properties is key to understanding the onset of autoimmune diseases such as type 1 diabetes mellitus (T1DM). Previous work identified pairs of infectious epitopes (EINF) and T1DM epitopes (ET1D) that demonstrated sequence homology; however, structural homology was not considered. Correlating sequence homology with structural properties is important for streamlining translational investigation of potential molecular mimics. Therefore, the purpose of this work is to compare sequence homology with structural homology by calculating the structures and electrostatic potential surfaces of the epitope pairs identified in previous work from our laboratory. 

 Results:  For each epitope pair the root mean square deviation (RMSD) was calculated between their predicted structures and their electrostatic potentials were compared. Structures were predicted using the AlphaFold software program. Of the 52 epitope pairs considered here only 10 do not exhibit any matching (i.e. less than 3 residues overlap). When considering all residues the RMSD ranges from 0.33 Å to 11.66 Å with an average of 2.68 Å. Twenty-two pairs (42%) have RMSD of less than 1.5 Å and 30 (58%) less than 3 Å. Even some of the matching pairs show some electrostatic similarities that need to be considered. In general there is good agreement between the folding predicted for the isolated EINF and ET1D epitopes and the folding of the corresponding amino acid sequence in the parent antigen, but in some cases there are deviation that need to be considered, even when the RMDS is small.

 Conclusions: Despite differences, most of the EINF/ET1D pairs selected by sequence homology show similar structural and electrostatic distributions, indicating that the EINF may bind to the same protein targets, the major histocompatibility complex molecules, for T1DM, leading to molecular mimicry onset of the disease. These findings suggest that searching for epitope pairs using sequence homology, a much less computationally demanding approach, leads to strong candidates for molecular mimicry that should be considered for further study. Still structure and full docking calculations will be necessary to advance the in-silico molecular mimicry predictions.  Here we presnt the following files:

·         Fasta files of all epitopes studied.

·         Alphafold calculated Structures of all epitopes.

·         Antigen structures.

·         Epitope pair structure comparison and their electrostatics.
DOI: 10.15468/dl.nn5nv7
title: Occurrence Download

description: A dataset containing 4926 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Chinese Taipei",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Fagaceae"
 ]
}

 The dataset includes 4926 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033936-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/dzgmzs55p9.1
title: Dataset: Adani Energy Solutions Limited (ADANIENSOL.NS) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.15468/dl.4sq2gu
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lampetra auremensis Mateus, Alves, Quintella & Almeida, 2013",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033937-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/jgbbfw2tzk.4
title: Data from GCA article "Thermodynamic property estimations for aqueous primary, secondary, and tertiary alkylamines, benzylamines, and their corresponding aminiums across temperature and pressure are validated by measurements from experiments"

description: Abstract:
On Earth and beyond, organic chemistry often occurs in the presence of water within environments that deviate drastically from ambient conditions (25°C and 1 bar). Accurately predicting aqueous organic reaction pathways is crucial toward understanding planetary scale processes such as the cycling of elements crucial for life (e.g., carbon and nitrogen). Advanced thermodynamic modeling can be utilized to determine the favorability of various organic reactions based on geologically relevant ranges of temperature and pressure, as well as compositional variables (e.g., pH). However, data that would otherwise allow for a diversity of organic compounds and environmental conditions to be modeled are sparse and rarely tested with experiments, particularly with regard to organic-nitrogen compounds. In this work, we develop a framework to estimate thermodynamic properties at ambient conditions that can then be extrapolated across ranges of temperature and pressure for aqueous primary, secondary, and tertiary amines and aminiums (protonated amines), specifically those structures containing linear alkyl chains and benzyl functional groups. We also performed hydrothermal experiments (250°C, ~40 bar) involving reactions of methylamines to test our resulting thermodynamic models, and we compare our models for other alkylamines and benzylamines to previous empirical measurements from the literature. Specifically, we use existing thermodynamic data along with our estimates at ambient conditions in combination with a variety of existing extrapolation methods related to the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate temperature- and pressure-dependent predictions of acid dissociation constants (i.e., pKa values) that strongly agree with previous empirical measurements. We use similar methods to predict product distributions for reactions involving primary, secondary, and tertiary amines/aminiums, as well as ammonia/ammonium and corresponding alcohols whose collective distributions depend on reversible substitution reactions. Our predictions are in good agreement with our experimental results involving the methylamine reaction system as well as previous experiments involving the benzylamine reaction system, for which we also produced thermodynamic estimates involving benzyl alcohol. The agreement between independent theoretical predictions and experimental measurements suggests that our estimated properties can be applied to modeling amine chemistry in other experimental and natural aqueous systems that range in temperature and pressure, providing new tools for planetary exploration.
DOI: 10.17632/jgbbfw2tzk.3
title: Data from GCA article "Thermodynamic property estimations for aqueous primary, secondary, and tertiary alkylamines, benzylamines, and their corresponding aminiums across temperature and pressure are validated by measurements from experiments"

description: Abstract:
On Earth and beyond, organic chemistry often occurs in the presence of water within environments that deviate drastically from ambient conditions (25°C and 1 bar). Accurately predicting aqueous organic reaction pathways is crucial toward understanding planetary scale processes such as the cycling of elements crucial for life (e.g., carbon and nitrogen). Advanced thermodynamic modeling can be utilized to determine the favorability of various organic reactions based on geologically relevant ranges of temperature and pressure, as well as compositional variables (e.g., pH). However, data that would otherwise allow for a diversity of organic compounds and environmental conditions to be modeled are sparse and rarely tested with experiments, particularly with regard to organic-nitrogen compounds. In this work, we develop a framework to estimate thermodynamic properties at ambient conditions that can then be extrapolated across ranges of temperature and pressure for aqueous primary, secondary, and tertiary amines and aminiums (protonated amines), specifically those structures containing linear alkyl chains and benzyl functional groups. We also performed hydrothermal experiments (250°C, ~40 bar) involving reactions of methylamines to test our resulting thermodynamic models, and we compare our models for other alkylamines and benzylamines to previous empirical measurements from the literature. Specifically, we use existing thermodynamic data along with our estimates at ambient conditions in combination with a variety of existing extrapolation methods related to the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate temperature- and pressure-dependent predictions of acid dissociation constants (i.e., pKa values) that strongly agree with previous empirical measurements. We use similar methods to predict product distributions for reactions involving primary, secondary, and tertiary amines/aminiums, as well as ammonia/ammonium and corresponding alcohols whose collective distributions depend on reversible substitution reactions. Our predictions are in good agreement with our experimental results involving the methylamine reaction system as well as previous experiments involving the benzylamine reaction system, for which we also produced thermodynamic estimates involving benzyl alcohol. The agreement between independent theoretical predictions and experimental measurements suggests that our estimated properties can be applied to modeling amine chemistry in other experimental and natural aqueous systems that range in temperature and pressure, providing new tools for planetary exploration.
DOI: 10.15468/dl.f77uts
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stipa danubialis Dihoru & Roman",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033938-240506114902167/datasets/export for details.
DOI: 10.17632/jgbbfw2tzk.2
title: Data from GCA article "Thermodynamic property estimations for aqueous primary, secondary, and tertiary alkylamines, benzylamines, and their corresponding aminiums across temperature and pressure are validated by measurements from experiments"

description: Abstract:
On Earth and beyond, organic chemistry often occurs in the presence of water within environments that deviate drastically from ambient conditions (25°C and 1 bar). Accurately predicting aqueous organic reaction pathways is crucial toward understanding planetary scale processes such as the cycling of elements crucial for life (e.g., carbon and nitrogen). Advanced thermodynamic modeling can be utilized to determine the favorability of various organic reactions based on geologically relevant ranges of temperature and pressure, as well as compositional variables (e.g., pH). However, data that would otherwise allow for a diversity of organic compounds and environmental conditions to be modeled are sparse and rarely tested with experiments, particularly with regard to organic-nitrogen compounds. In this work, we develop a framework to estimate thermodynamic properties at ambient conditions that can then be extrapolated across ranges of temperature and pressure for aqueous primary, secondary, and tertiary amines and aminiums (protonated amines), specifically those structures containing linear alkyl chains and benzyl functional groups. We also performed hydrothermal experiments (250°C, ~40 bar) involving reactions of methylamines to test our resulting thermodynamic models, and we compare our models for other alkylamines and benzylamines to previous empirical measurements from the literature. Specifically, we use existing thermodynamic data along with our estimates at ambient conditions in combination with a variety of existing extrapolation methods related to the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate temperature- and pressure-dependent predictions of acid dissociation constants (i.e., pKa values) that strongly agree with previous empirical measurements. We use similar methods to predict product distributions for reactions involving primary, secondary, and tertiary amines/aminiums, as well as ammonia/ammonium and corresponding alcohols whose collective distributions depend on reversible substitution reactions. Our predictions are in good agreement with our experimental results involving the methylamine reaction system as well as previous experiments involving the benzylamine reaction system, for which we also produced thermodynamic estimates involving benzyl alcohol. The agreement between independent theoretical predictions and experimental measurements suggests that our estimated properties can be applied to modeling amine chemistry in other experimental and natural aqueous systems that range in temperature and pressure, providing new tools for planetary exploration.
DOI: 10.15468/dl.t5f3fg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Triturus vulgaris ampelensis Fuhn, 1951",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033940-240506114902167/datasets/export for details.
DOI: 10.15468/dl.gecn6r
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trissolcus basalis (Wollaston, 1858))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 431 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033939-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wu9zsw
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gortyna borelii lunata Freyer, 1837",
 "BasisOfRecord is one of (Human Observation, Observation)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Country is one of (Finland, Ireland, Sweden, Cyprus, Portugal, Netherlands, France, Bulgaria, Romania, Spain, Poland, Czechia, Malta, United Kingdom of Great Britain and Northern Ireland, Austria, Croatia, Slovenia, Slovakia, Germany, Denmark, Italy, Belgium, Gibraltar, Lithuania, Greece, Luxembourg, Latvia, Estonia, Hungary)"
 ]
}

 The dataset includes 73 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033941-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.