cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d12018
title: The Evolution of Function within the Nudix Superfamily: 340 select Nudix proteins

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: The Excel file "340 select nudix proteins.xlsx" contains information of 340 select Nudix proteins, the subsets of which comprise of all alignments discussed in the paper except the "Nudix-clan alignment". The information related to the PDB structures is reprinted in Table 3. Columns K, L, M and N indicates the starting and ending residues of domains used in the alignments. For each protein, the best-characterized activity with the highest confidence score, when available, is recorded in Columns O, P and Q; such information was obtained from "Initial_score_assignment.xlsx" (doi:10.6078/d1vc7g).
DOI: 10.6078/d15p47
title: The Evolution of Function within the Nudix Superfamily: 76-PDB sequence alignment in FASTA format

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: 76-PDB sequence alignment in FASTA format; can be opened by most sequence alignment visualization software such as Jalview (Waterhouse et al. 2009 doi:10.1093/bioinformatics/btp033).
DOI: 10.6078/d1pp4w
title: The Evolution of Function within the Nudix Superfamily: GOA analysis results

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Comparison between our literature-based study of Nudix functions and those in GOA. The sheet "GOA_Comparison" shows the final comparison result between our Nudix database and UniProt GOA (release 2013-12-11). The main content in this sheet is reprinted as Table 5 in the main text of the paper. The sheet "Statistics" contains information to derive the GOA-related statistics mentioned in the abstract, introduction, and result part of the main text. The sheet "MySQL_040614" contains the same protein-function-score tuples as in the "Final Score Assignment" Excel file (doi:10.6078/d1qp46), and in addition provides curated function assignments (Columns D and E) resulting from the GOA comparison. The three sheets "UniProt_GOA_121113-EXP/NONEXP/NONF" contains all GO assignments to Nudix proteins in GOA release 2013-12-11. The sheet "GO_Terms" contains the complete proposed and current GO terms used in this paper to describe the Nudix protein collection; the main content in this sheet is reprinted as Tables 1 and 2. The sheet "GO_Hierarchy_proposed" contains the proposed GO hierarchy, and is reprinted as Figure 3. Finally, the sheet "GO_Hierarchy_010114" is an archive of the existed GO hierarchy for Nudix-related terms as of 2014-01-01.
DOI: 10.15468/dl.748ucx
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Iris ventricosa",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002907-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x36sgr
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas gibberifrons",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002908-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mez2tp
title: Occurrence Download

description: A dataset containing 2427 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tapirus pinchaque"
 ]
}

 The dataset includes 2427 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002909-250920141307145/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.30174130
title: Cognitive Behavioral Micro-Modules for Dental Anxiety: Development and Theoretical Integration into Preoperative Dental Care

description: Background: Dental anxiety affects approximately 16–20% of adults, making them avoid necessary dental treatments such as root canal therapy (RCT), extractions, and oral surgeries. Brief, scalable interventions are indeed needed to mitigate preoperative anxiety without requiring therapist involvement. Objective: This study describes the development and theoretical foundation of an Android-based application delivering cognitive-behavioural therapy (CBT) micro-modules (2–5 minutes) designed to reduce dental anxiety before procedures. Methods: The app was adapted from an evidence-based HTML5 intervention into a native Android application. It incorporates five core CBT techniques: cognitive restructuring, body scanning, controlled breathing, procedural visualization, and coping statements. The design emphasizes usability, scientific validity, and standalone functionality. Results: The app provides a structured, self-guided intervention that can be completed in under 15 minutes. Theoretical integration draws from the Health Belief Model (HBM), the Transactional Model of Stress and Coping, and principles of digital micro-interventions. Conclusions: Mobile CBT micro-modules offer a feasible, cost-effective method for reducing preoperative dental anxiety. Future clinical trials should assess efficacy in RCT, extraction, and surgical settings.
DOI: 10.6084/m9.figshare.30174130.v1
title: Cognitive Behavioral Micro-Modules for Dental Anxiety: Development and Theoretical Integration into Preoperative Dental Care

description: Background: Dental anxiety affects approximately 16–20% of adults, making them avoid necessary dental treatments such as root canal therapy (RCT), extractions, and oral surgeries. Brief, scalable interventions are indeed needed to mitigate preoperative anxiety without requiring therapist involvement. Objective: This study describes the development and theoretical foundation of an Android-based application delivering cognitive-behavioural therapy (CBT) micro-modules (2–5 minutes) designed to reduce dental anxiety before procedures. Methods: The app was adapted from an evidence-based HTML5 intervention into a native Android application. It incorporates five core CBT techniques: cognitive restructuring, body scanning, controlled breathing, procedural visualization, and coping statements. The design emphasizes usability, scientific validity, and standalone functionality. Results: The app provides a structured, self-guided intervention that can be completed in under 15 minutes. Theoretical integration draws from the Health Belief Model (HBM), the Transactional Model of Stress and Coping, and principles of digital micro-interventions. Conclusions: Mobile CBT micro-modules offer a feasible, cost-effective method for reducing preoperative dental anxiety. Future clinical trials should assess efficacy in RCT, extraction, and surgical settings.
DOI: 10.15468/dl.khqnxc
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Iva angustifolia",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 36 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002912-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuexgv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas hottentota",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002913-250920141307145/datasets/export for details.
DOI: 10.15468/dl.dfvefq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas hottentota",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002914-250920141307145/datasets/export for details.
DOI: 10.15468/dl.bev5ju
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dichotomyctere ocellatus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002916-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqxcmf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas hottentota",
 "Country is Slovenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002915-250920141307145/datasets/export for details.
DOI: 10.15468/dl.nkvc4s
title: Occurrence Download

description: A dataset containing 424 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Iva axillaris",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 424 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002917-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3rm4hx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas hottentota",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002918-250920141307145/datasets/export for details.
DOI: 10.15468/dl.py8fes
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pterocryptis cucphuongensis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002919-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.45ad2f
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ixeris polycephala",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 118 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002920-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sk7zgd
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas laysanensis",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002922-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcfy5s
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas laysanensis",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002921-250920141307145/datasets/export for details.
DOI: 10.15468/dl.9usvhm
title: Occurrence Download

description: A dataset containing 65017 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vultur gryphus",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation",
 "Year is greater than or equal to 2018"
 ]
}

 The dataset includes 65017 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002878-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9322f
title: Occurrence Download

description: A dataset containing 24050 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chinese Taipei",
 "Geometry POLYGON((121.93365 24.83406,121.96518 24.83435,121.96504 24.85099,121.93372 24.85078,121.93365 24.83406))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 24050 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002924-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2je8ny
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudancistrus coquenani)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002925-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.0cftw25c
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (11 records)
DOI: 10.15468/dl.3fr7zv
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas luzonica",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002928-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6usn9x
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anas luzonica",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002927-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25976/3k29-vs78
title: CIMP 215: Aquatic ecosystems in the Fort Good Hope area as indicators of environmental change

description: Global warming is causing large-scale transformations of the northern landscape. In particular, permafrost thaw has wide implications for northern ecosystems and the communities living in this transitioning landscape. As climate continues to warm, previously frozen soils may release carbon and nutrients to aquatic ecosystems. These environmental changes may push aquatic ecosystems beyond tipping points, so that the functions and services they provide to communities are at risk. This project is directly addressing concerns about changes in water quality expressed by community members in Fort Good Hope in the Sahtú Settlement Area. We used a YSI multiparametric sonde and 2L polycarbonate bottles for water sampling. Ultimately, the results from the project will help anticipate cumulative effects of climate warming and anthropogenic disturbances such as land-use on aquatic health.
description: We used a YSI multiparametric sonde and 2L polycarbonate bottles for water sampling in Fort Good Hope in the Sahtú Settlement Area.
description: Analysis for metals and nutrients were done at the GRIL laboratory at Université du Québec in Montréal. Analyses for dissolved organic carbon (DOC) were done at Université du Québec in Trois-Rivières.