cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ans6t4
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-118.2041806999999949 33.8660203000000024, -118.2041806999999949 33.8673029999999997, -118.2041806999999949 33.8693553199999968, -118.2041806999999949 33.8705525100000031, -118.2041806999999949 33.8720062299999967, -118.2041806999999949 33.8734599599999981, -118.2041806999999949 33.8746571499999973, -118.2041806999999949 33.8766239500000026, -118.2041806999999949 33.8779921699999989, -118.2041806999999949 33.8795314099999985, -118.2041806999999949 33.8814126999999985, -118.2026405499999981 33.8814126999999985, -118.2005014500000044 33.8814126999999985, -118.1993891200000064 33.8814126999999985, -118.1974211400000030 33.8814126999999985, -118.1956243000000057 33.8814126999999985, -118.1956243000000057 33.8800444900000031, -118.1956243000000057 33.8778211400000018, -118.1956243000000057 33.8767949799999997, -118.1956243000000057 33.8753412499999982, -118.1956243000000057 33.8737165000000005, -118.1956243000000057 33.8726903399999983, -118.1956243000000057 33.8711510999999987, -118.1956243000000057 33.8695263500000010, -118.1956243000000057 33.8676450500000001, -118.1956243000000057 33.8660203000000024, -118.1979345299999977 33.8660203000000024, -118.2000736300000057 33.8660203000000024, -118.2023838599999976 33.8660203000000024, -118.2041806999999949 33.8660203000000024))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 47 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091222-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.btsauy
title: Occurrence Download

description: A dataset containing 28536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Sphinx pinastri Linnaeus, 1758",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28536 records from 174 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029761-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14629937
title: mri2femii-chp5-dataset
DOI: 10.5281/zenodo.14629938
title: mri2femii-chp5-dataset
DOI: 10.15468/dl.rq3ee2
title: Occurrence Download

description: A dataset containing 1407 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 Aedes scapularis Rondani, 1848"
 ]
}

 The dataset includes 1407 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064123-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69vp8z
title: Occurrence Download

description: A dataset containing 308 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fish species in recreational fishing catches in the Zaporizhia (Dnipro) reservoir and in the upper part of the Kaniv reservoir"
 ]
}

 The dataset includes 308 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064124-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14629992
title: mycteria_ibis_zanfona_1.fasta.gz
DOI: 10.5281/zenodo.14629993
title: mycteria_ibis_zanfona_1.fasta.gz
DOI: 10.15468/dl.5m42dd
title: Occurrence Download

description: A dataset containing 468 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 Aedes scutellaris (Walker, 1858)"
 ]
}

 The dataset includes 468 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064128-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xe8cxt
title: Occurrence Download

description: A dataset containing 15252 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "Geometry POLYGON((-5.22137 36.72832,-5.53279 36.81995,-5.9014 36.97751,-6.14926 36.99781,-6.34628 36.8759,-6.65134 36.73341,-6.65134 36.45277,-6.45433 36.13004,-5.97767 35.98618,-5.74887 36.22751,-5.43746 36.44765,-5.22137 36.72832))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 15252 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064130-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8pteku
title: Occurrence Download

description: A dataset containing 19 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 Aedes septemstriatus Dyar & Knab, 1907"
 ]
}

 The dataset includes 19 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064131-241126133413365/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.28046612
title: Blue frogs data & code

description: Data used for analyses within the manuscript - <i>The Blue Frogs Project: leveraging community science data to document axanthism hotspots across the globe</i>
DOI: 10.15468/dl.nvf268
title: Occurrence Download

description: A dataset containing 775 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 Aedes serratus (Theobald, 1901)"
 ]
}

 The dataset includes 775 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064132-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sjk6tr
title: Occurrence Download

description: A dataset containing 5227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is one of (Albania, Croatia, Italy, Portugal, Spain, France, Greece)",
 "DatasetKey is one of (Loggerhead satellite tracking data from Rethymno, Crete, Greece, Marine turtle sightings, strandings and captures in French waters 1990-2003, Long-term cetacean monitoring in the Azores based on whale watching observations (2009-2020), Observation.org, Nature data from around the World, Registro de varamientos de tortugas marinas en las Illes Balears, iNaturalist Research-grade Observations, Amphibiens et Reptiles de France (Enquête 2), POPA- Fisheries Observer Program of the Azores: Turtle sightings in the Azores tuna fishery from 2000 on: during navigation or search mode., Inventario Español de Especies Terrestres (MAGRAMA), Réseau Tortues Marines de Méditerranée Française (RTMMF)-Captures accidentelles de tortues marines rapportées par les RTMMF en Méditerranée française)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caretta caretta (Linnaeus, 1758)"
 ]
}

 The dataset includes 5227 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064133-241126133413365/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.26499487
title: The Impact of “Negligible” Cross-Loadings in Investigations of Measurement Invariance with MGCFA and MGESEM

description: Measurement invariance (MI) is an essential part of validity evidence concerned with ensuring that tests function similarly across groups, contexts, and time. Most evaluations of MI involve multigroup confirmatory factor analyses (MGCFA) that assume simple structure. However, recent research has shown that constraining non-target indicators to zero when cross-loadings are present results in biased estimates of latent variable associations. Using Monte Carlo simulation, we investigate the behavior of fit statistics for identifying non-invariance when the target measurement model is the same for both groups, and the source of non-invariance is the presence and magnitude of non-zero cross-loadings in one group, but not in another. We consider differences between MGCFA and multigroup ESEM (MGESEM), and combined and separate group tests of configural invariance. Implications for applied researchers are provided.
DOI: 10.6084/m9.figshare.26499487.v1
title: The Impact of “Negligible” Cross-Loadings in Investigations of Measurement Invariance with MGCFA and MGESEM

description: Measurement invariance (MI) is an essential part of validity evidence concerned with ensuring that tests function similarly across groups, contexts, and time. Most evaluations of MI involve multigroup confirmatory factor analyses (MGCFA) that assume simple structure. However, recent research has shown that constraining non-target indicators to zero when cross-loadings are present results in biased estimates of latent variable associations. Using Monte Carlo simulation, we investigate the behavior of fit statistics for identifying non-invariance when the target measurement model is the same for both groups, and the source of non-invariance is the presence and magnitude of non-zero cross-loadings in one group, but not in another. We consider differences between MGCFA and multigroup ESEM (MGESEM), and combined and separate group tests of configural invariance. Implications for applied researchers are provided.
DOI: 10.6084/m9.figshare.26359754.v1
title: Semiparametric Structural Equation Models with Interval-Censored Data

description: Structural equation models offer a valuable tool for delineating the complicated interrelationships among multiple variables, including observed and latent variables. Over the last few decades, structural equation models have successfully analyzed complete and right-censored survival data, exemplified by wide applications in psychological, social, or genomic studies. However, the existing methodology for structural equation modeling is not concerned with interval-censored data, a type of coarse survival data arising typically from periodic examinations for the occurrence of asymptomatic disease. The present study aims to fill this gap and provide a flexible semiparametric structural equation modeling framework. A general class of factor-augmented transformation models is proposed to model the interval-censored outcome of interest in the presence of latent risk factors. An expectation–maximization algorithm is subtly designed to conduct the nonparametric maximum likelihood estimation. Furthermore, the asymptotic properties of the proposed estimators are established by leveraging the empirical process theory. The numerical results obtained from extensive simulations and an application to the Alzheimer’s disease data set demonstrate the proposed method’s empirical performance and practical utility.
DOI: 10.6084/m9.figshare.27105964
title: Latent Vector Autoregressive Modeling: A Stepwise Estimation Approach

description: Researchers often study dynamic processes of latent variables in everyday life, such as the interplay of positive and negative affect over time. An intuitive approach is to first estimate the measurement model of the latent variables, then compute factor scores, and finally use these factor scores as observed scores in vector autoregressive modeling. However, this approach neglects the uncertainty in the factor scores, leading to biased parameter estimates and threatening the validity of conclusions about the dynamic process. We propose Three-Step Latent Vector Autoregression that adheres to this stepwise procedure while correcting for the factor scores’ uncertainty. Stepwise approaches offer various advantages, for example the ability to visualize and inspect the factor scores. A simulation study demonstrates that the method performs well in obtaining correct parameter estimates of a dynamic process. We also provide an empirical example and scripts for implementation in the open-source software R using the <i>lavaan</i> package.
DOI: 10.6084/m9.figshare.27105964.v2
title: Latent Vector Autoregressive Modeling: A Stepwise Estimation Approach

description: Researchers often study dynamic processes of latent variables in everyday life, such as the interplay of positive and negative affect over time. An intuitive approach is to first estimate the measurement model of the latent variables, then compute factor scores, and finally use these factor scores as observed scores in vector autoregressive modeling. However, this approach neglects the uncertainty in the factor scores, leading to biased parameter estimates and threatening the validity of conclusions about the dynamic process. We propose Three-Step Latent Vector Autoregression that adheres to this stepwise procedure while correcting for the factor scores’ uncertainty. Stepwise approaches offer various advantages, for example the ability to visualize and inspect the factor scores. A simulation study demonstrates that the method performs well in obtaining correct parameter estimates of a dynamic process. We also provide an empirical example and scripts for implementation in the open-source software R using the <i>lavaan</i> package.
DOI: 10.15468/dl.z8wsrb
title: Occurrence Download

description: A dataset containing 89 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 Aedes sexlineatus (Theobald, 1901)"
 ]
}

 The dataset includes 89 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064134-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p4gpsb
title: Occurrence Download

description: A dataset containing 4379 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 Aedes sollicitans (Walker, 1856)"
 ]
}

 The dataset includes 4379 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064137-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7ms6a
title: Occurrence Download

description: A dataset listing the 220 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-115.65199 32.67432,-115.48871 32.66743,-115.49028 32.85798,-115.65356 32.85547,-115.65231 32.72447,-115.65199 32.67432))"
 ]
}

 The dataset's 220 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064125-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrvz3m
title: Occurrence Download

description: A dataset listing the 208 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-99.77589 23.47363,-99.78574 23.45804,-99.80146 23.42116,-99.80193 23.39641,-99.78891 23.38916,-99.781 23.35586,-99.76287 23.35287,-99.73869 23.35159,-99.70892 23.34732,-99.70892 23.35928,-99.70846 23.37934,-99.70892 23.40367,-99.71264 23.44164,-99.71915 23.47108,-99.77589 23.47363))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 208 records were derived from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064129-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sf7vjx
title: Occurrence Download

description: A dataset listing the 733 species recorded in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-123.50514 48.50005,-123.51057 48.50035,-123.51497 48.50033,-123.51939 48.49831,-123.52459 48.49596,-123.52748 48.49289,-123.52946 48.49117,-123.5325 48.48537,-123.53407 48.47464,-123.53047 48.46733,-123.52385 48.46467,-123.51786 48.46301,-123.50976 48.46098,-123.49913 48.46287,-123.48825 48.46575,-123.48075 48.47099,-123.47808 48.48319,-123.4819 48.49032,-123.48797 48.4946,-123.49382 48.49768,-123.49819 48.49874,-123.5016 48.49962,-123.50514 48.50005))"
 ]
}

 The dataset's 733 records were derived from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064126-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14010444
title: CryoXKit virtual screening set

description: Virtual screening dataset used in Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Modification of LIT-PCBA dataset. The dataset used for TRPV1 is available from Llanos et al.

 

Also included are 

run_bias.template.qsub

submit.sh

Together, these scripts provide examples of how to set-up and run screening density-guided simulations on a SLURM-based HPC cluster. Please note that this dataset does not include the structural density files associated with each receptor. These must be downloaded separately from the RCSB PDB (hyperlinks for each receptor may be found in SI Table 2 of the associated publication for this dataset).

 

Targets included:

ADRB2

ALDH1

FEN1

GBA

HSP90a

MAPK1

MTORC1

PKM2

VDR
DOI: 10.5281/zenodo.14010445
title: CryoXKit virtual screening set

description: Virtual screening dataset used in Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Modification of LIT-PCBA dataset. The dataset used for TRPV1 is available from Llanos et al.

 

Targets included:

ADRB2

ALDH1

FEN1

GBA

HSP90a

MAPK1

MTORC1

PKM2

VDR
DOI: 10.5281/zenodo.14110144
title: CryoXKit virtual screening set

description: Virtual screening dataset used in Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Modification of LIT-PCBA dataset. The dataset used for TRPV1 is available from Llanos et al.

 

Targets included:

ADRB2

ALDH1

FEN1

GBA

HSP90a

MAPK1

MTORC1

PKM2

VDR
DOI: 10.5281/zenodo.14629749
title: CryoXKit virtual screening set

description: Virtual screening dataset used in Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Modification of LIT-PCBA dataset. The dataset used for TRPV1 is available from Llanos et al.

 

Also included are 

run_bias.template.qsub

submit.sh

Together, these scripts provide examples of how to set-up and run screening density-guided simulations on a SLURM-based HPC cluster. Please note that this dataset does not include the structural density files associated with each receptor. These must be downloaded separately from the RCSB PDB (hyperlinks for each receptor may be found in SI Table 2 of the associated publication for this dataset).

 

Targets included:

ADRB2

ALDH1

FEN1

GBA

HSP90a

MAPK1

MTORC1

PKM2

VDR
DOI: 10.15468/dl.82dcbx
title: Occurrence Download

description: A dataset containing 10208 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 Aedes sticticus (Meigen, 1835)"
 ]
}

 The dataset includes 10208 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064138-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14500640
title: ATLANTIC SPATIAL - Hydrological

description: ATLANTIC SPATIAL is a data set when we make available more than 500 raster layers with a fine-scale spatial information (resolution = 30 m) for the entire Atlantic Forest extent for the year 2020. Hydrological metrics comprise potential springs and its kernel and potential streams and respective distances.
DOI: 10.5281/zenodo.14500641
title: ATLANTIC SPATIAL - Hydrological

description: ATLANTIC SPATIAL is a data set when we make available more than 500 raster layers with a fine-scale spatial information (resolution = 30 m) for the entire Atlantic Forest extent for the year 2020. Hydrological metrics comprise potential springs and its kernel and potential streams and respective distances.
DOI: 10.15468/dl.n9usd9
title: Occurrence Download

description: A dataset containing 3467 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 Aedes stimulans (Walker, 1848)"
 ]
}

 The dataset includes 3467 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064140-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mf2zte
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Altica palustris (Weise, 1888)",
 "PhylumKey is Arthropoda",
 "Year is greater than or equal to 1992",
 "Year is less than or equal to 2012",
 "Geometry POLYGON((-26 34, 42 34, 42 70, -26 70, -26 34))"
 ]
}

 The dataset includes 408 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023173-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.