cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48436/zjkky-pgs18
title: Data for binary classification experiments

description: Research context

This zip archive contains all the data and scripts which are neccessary to reproduce the results of the following paper,  co-authored by Markus Kattenbeck, Ioannis Giannopoulos, Negar Alinaghi, Antonia Golab, and Daniel R. Montello:

Predicting spatial familiarity by exploiting head and eye movements during pedestrian navigation in the real world

This paper will be published in Springer Nature Scientific Reports.

File overview

The structure of the archive is the following:



Folder "01_data" contains all the data files needed and a readme file describing the structure of each of these data files. These data files are:



lsp.csv [contains demographic data about participants]

matched_gaze_imu.csv [contains the segmented behavioral data, i.e. both gaze features and imu features]

matched_gaze_imu_feature_description.pdf [contains a description of the features contained in matched_gaze_imu.csv]

walking_dates.csv [contains an overview on which date participants walked the familiar and unfamiliar routes]

users_polygons.csv [contains one or more polygons per participant in which they are familiar]

polygons_markers.csv [contains locations of POIs per polygon for which participants reported to be familiar with]

user_routes.csv [containes the route participants provided between a randomly selected pair of POIs they have provided for a given polygon]



Folder "02_scripts" contains the data analysis scripts; they are organized in two subfolders:



01_ml_scripts: these are the scripts for the XGBoost classification; they are organized as two python files in which further instructions for use are given.



80_20_code.py is the python file which runs the ML experiments using an 80/20 train/test split

L5O4T_code.py is the python file which runs the ML experiments leaving the full data of five different participants per condition as unseen data for the test.

requirements.txt states the used Python package versions



02_r_scripts: 



cleaned_script.Rmd This is an R notebook which can be easily opened in R-Studio and provides the analysis scripts for the descriptive statistics presented in the paper. 

package_versions.txt states the used R package versions






Licenses

The code is licensed under MIT, the data is licensed under CC-BY.
DOI: 10.15468/dl.v2dqsf
title: Occurrence Download

description: A dataset containing 3541666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Africa",
 "TaxonKey is Plantae",
 "Year 1000-1975"
 ]
}

 The dataset includes 3541666 records from 541 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003454-250221090833381/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.28238684
title: Association between epigenetic aging and atrioventricular block: a two-sample Mendelian randomization study

description: Atrioventricular block (AVB) is a prevalent bradyarrhythmia. This study aims to investigate the causal effects of epigenetic aging, as inferred from DNA methylation profiles on the prevalence of AVB by Mendelian randomization (MR) analysis. Genetic instruments for epigenetic aging and AVB were obtained from genome-wide association study data in the Edinburgh DataShare and FinnGen biobanks. Univariable and multivariable MR analyses were conducted to evaluate causal associations. Additionally, we employed sensitivity tests to assess the robustness of the MR findings. MR analysis showed that genetically predicted GrimAge acceleration was significantly associated with a higher risk of AVB (inverse variance-weighted: <i>p</i> = 0.010, 95% confidence interval (CI) = 1.024–1.196; weighted median: <i>p</i> = 0.031, 95% CI = 1.009–1.215). However, no evidence supported a causal relationship between AVB and epigenetic aging. The association between epigenetic aging and AVB was established using multivariate MR analysis after adjusting for various risk factors. Sensitivity analyses confirmed the reliability and robustness of the results. Our findings suggest that epigenetic aging in GrimAge may increase the risk of AVB, emphasizing the importance of addressing epigenetic aging in strategies for AVB prevention. Atrioventricular block (AVB) is a heart problem that makes the heart beat too slowly. This can cause serious health problems. Getting older is one cause, but scientists are also studying ”biological aging.” This means how the body ages based on changes in genes, not just how many years a person has lived. We looked at different ways to measure biological aging. One measure called GrimAge, showed that people who age faster have a higher chance of getting AVB. Slowing down biological aging, mainly GrimAge, might help keeping from AVB.
DOI: 10.6084/m9.figshare.28238684.v1
title: Association between epigenetic aging and atrioventricular block: a two-sample Mendelian randomization study

description: Atrioventricular block (AVB) is a prevalent bradyarrhythmia. This study aims to investigate the causal effects of epigenetic aging, as inferred from DNA methylation profiles on the prevalence of AVB by Mendelian randomization (MR) analysis. Genetic instruments for epigenetic aging and AVB were obtained from genome-wide association study data in the Edinburgh DataShare and FinnGen biobanks. Univariable and multivariable MR analyses were conducted to evaluate causal associations. Additionally, we employed sensitivity tests to assess the robustness of the MR findings. MR analysis showed that genetically predicted GrimAge acceleration was significantly associated with a higher risk of AVB (inverse variance-weighted: <i>p</i> = 0.010, 95% confidence interval (CI) = 1.024–1.196; weighted median: <i>p</i> = 0.031, 95% CI = 1.009–1.215). However, no evidence supported a causal relationship between AVB and epigenetic aging. The association between epigenetic aging and AVB was established using multivariate MR analysis after adjusting for various risk factors. Sensitivity analyses confirmed the reliability and robustness of the results. Our findings suggest that epigenetic aging in GrimAge may increase the risk of AVB, emphasizing the importance of addressing epigenetic aging in strategies for AVB prevention. Atrioventricular block (AVB) is a heart problem that makes the heart beat too slowly. This can cause serious health problems. Getting older is one cause, but scientists are also studying ”biological aging.” This means how the body ages based on changes in genes, not just how many years a person has lived. We looked at different ways to measure biological aging. One measure called GrimAge, showed that people who age faster have a higher chance of getting AVB. Slowing down biological aging, mainly GrimAge, might help keeping from AVB.
DOI: 10.6084/m9.figshare.28331233
title: Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis

description: Necrotizing enterocolitis (NEC) is an often fatal intestinal injury that primarily affects preterm infants for which screening tools are lacking. We performed a pilot analysis of DNA methylation in peripheral blood samples from preterm infants with and without NEC to identify potential NEC biomarkers. Peripheral blood samples were collected from infants at NEC diagnosis (<i>n</i> = 15) or from preterm controls (<i>n</i> = 13). Targeted genome-wide analysis was performed to identify DNA methylation differences between cases and controls. Broad differences between NEC cases and controls were identified in distinct genomic elements. Differences between surgical NEC cases and controls were frequently associated with inflammation. Deconvolution analysis to identify cell type-specific DNA signatures revealed increases in ileal, vascular endothelial, and cardiomyocyte cell type proportions and decreases in colonic and neuronal cell type proportions in blood from NEC cases relative to controls. We identified marked differences in DNA methylation of peripheral blood samples from preterm infants with and without NEC. Increased ileal cell-specific methylation signatures in the blood of infants with NEC relative to controls, with a marked increase seen in surgical cases, provides rationale for further analysis of intestinal DNA methylation signatures as biomarkers of NEC.
DOI: 10.6084/m9.figshare.28331233.v1
title: Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis

description: Necrotizing enterocolitis (NEC) is an often fatal intestinal injury that primarily affects preterm infants for which screening tools are lacking. We performed a pilot analysis of DNA methylation in peripheral blood samples from preterm infants with and without NEC to identify potential NEC biomarkers. Peripheral blood samples were collected from infants at NEC diagnosis (<i>n</i> = 15) or from preterm controls (<i>n</i> = 13). Targeted genome-wide analysis was performed to identify DNA methylation differences between cases and controls. Broad differences between NEC cases and controls were identified in distinct genomic elements. Differences between surgical NEC cases and controls were frequently associated with inflammation. Deconvolution analysis to identify cell type-specific DNA signatures revealed increases in ileal, vascular endothelial, and cardiomyocyte cell type proportions and decreases in colonic and neuronal cell type proportions in blood from NEC cases relative to controls. We identified marked differences in DNA methylation of peripheral blood samples from preterm infants with and without NEC. Increased ileal cell-specific methylation signatures in the blood of infants with NEC relative to controls, with a marked increase seen in surgical cases, provides rationale for further analysis of intestinal DNA methylation signatures as biomarkers of NEC.
DOI: 10.6084/m9.figshare.28233783
title: DNA methylation at birth and IgE trajectories from birth to adolescence, different patterns between White and Asian

description: We aim to assess association of DNA methylation (DNAm) at birth with total immunoglobulin E (IgE) trajectories from birth to late adolescence and whether such association is ethnicity-specific. We examined the association of total IgE trajectories from birth to late adolescence with DNAm at birth in two independent birth cohorts, the Isle of wight birth cohort (IOWBC) in UK (<i>n</i> = 796; White) and the maternal and infant cohort study (MICS) in Taiwan (<i>n</i> = 60; Asian). Biological pathways and methylation quantitative trait loci (methQTL) for associated Cytosine-phosphate-Guanine sites were studied. Two total IgE trajectories, high vs. low, were inferred from each of the two cohorts. Associations of DNAm at 103 CpGs with IgE trajectories in IOWBC and at 476 CpGs in MICS were identified. Between the two cohorts, of the identified CpGs, one was in common, methQTL site cg16711274 (mapped to gene MINAR1), and 17 pathways were common with at least four linked to airway diseases. The findings suggest at-birth epigenetics may explain ethnicity differences in total IgE trajectories later in life.
DOI: 10.6084/m9.figshare.28233783.v1
title: DNA methylation at birth and IgE trajectories from birth to adolescence, different patterns between White and Asian

description: We aim to assess association of DNA methylation (DNAm) at birth with total immunoglobulin E (IgE) trajectories from birth to late adolescence and whether such association is ethnicity-specific. We examined the association of total IgE trajectories from birth to late adolescence with DNAm at birth in two independent birth cohorts, the Isle of wight birth cohort (IOWBC) in UK (<i>n</i> = 796; White) and the maternal and infant cohort study (MICS) in Taiwan (<i>n</i> = 60; Asian). Biological pathways and methylation quantitative trait loci (methQTL) for associated Cytosine-phosphate-Guanine sites were studied. Two total IgE trajectories, high vs. low, were inferred from each of the two cohorts. Associations of DNAm at 103 CpGs with IgE trajectories in IOWBC and at 476 CpGs in MICS were identified. Between the two cohorts, of the identified CpGs, one was in common, methQTL site cg16711274 (mapped to gene MINAR1), and 17 pathways were common with at least four linked to airway diseases. The findings suggest at-birth epigenetics may explain ethnicity differences in total IgE trajectories later in life.
DOI: 10.6084/m9.figshare.28464641
title: Impacts of Birds vs. Invertebrate Predators on Rocky Intertidal Community Structure

description: Most studies of species interactions in rocky intertidal communities focus on invertebrate predators and herbivores interacting with sessile invertebrates and macrophytes. However, shorebirds are usually a conspicuous presence on rocky shores and eat sessile and mobile invertebrate prey, often including invertebrate predators and herbivores. Inspired by classic studies of strong bird predation effects in rocky intertidal habitats in Washington state (USA) and South Africa, I tested the effects of bird and invertebrate (sea stars, whelks) predation at multiple sites, wave exposures and zones on the central Oregon coast from spring 1996 to fall 1997. To gain insight into the effects of birds relative to effects of invertebrate predators, I used a crossed design, with bird exclusions (present and absent) and invertebrate predator removal (present and reduced). Compared to Washington state and South Africa, birds had little effect on abundance of sessile or mobile prey in wave-exposed mid, wave-exposed low, and wave-protected mid zones at 2-4 sites. I suggest that differences between Oregon results and those in Washington and South Africa were driven by differences in bird abundance associated with whether the study site had resident colonies of shorebirds (primarily gulls, crows, and oystercatchers). That is, offshore islands often have resident breeding colonies such as in the Washington and South African studies, while sites in this study were all on the mainland where gulls were mostly transient visitors while resident oystercatchers were usually limited to one or two pairs per site. Comparison with other marine and terrestrial experimental tests suggests that top-down effects of birds often vary in strength, and thus, future investigations should seek to understand the factors that underlie this variation.
DOI: 10.15468/dl.tbzyu9
title: Occurrence Download

description: A dataset containing 38637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-3299.0",
 "Geometry POLYGON((-24.77518 31.54319,74.69308 31.54319,74.69308 77.3574,-24.77518 77.3574,-24.77518 31.54319))",
 "OccurrenceStatus is Present",
 "TaxonKey is Pimpinella major (L.) Huds.",
 "Year 1960-2025"
 ]
}

 The dataset includes 38637 records from 364 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003467-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsz2n8
title: Occurrence Download

description: A dataset listing the 168846 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 168846 records were derived from 1768 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003463-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2lnk50
title: CCDC 2403032: Experimental Crystal Structure Determination

description: Related Article: J. T. Mague, J. P. Donahue, J. Taylor|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnkc6
title: CCDC 2403038: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnkd7
title: CCDC 2403039: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnkf8
title: CCDC 2403040: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnkkd
title: CCDC 2403044: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnkmg
title: CCDC 2403046: Experimental Crystal Structure Determination

description: Related Article: Dmitry Zverev|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnqkk
title: CCDC 2403199: Experimental Crystal Structure Determination

description: Related Article: J. T. Mague, Y. El Bakri|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2lnqnn
title: CCDC 2403202: Experimental Crystal Structure Determination

description: Related Article: Anna M. Obukhova, Maksim V. Dmitriev, Andrey N. Maslivets|2024|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mjlqh
title: CCDC 2429027: Experimental Crystal Structure Determination

description: Related Article: wang haixu|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.6mhx3b
title: Occurrence Download

description: A dataset containing 202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brassica rapa var. oleifera DC.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 202 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006141-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.suahr8
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is one of (Japan, Korea, Republic of, China, United States of America, Chinese Taipei, Germany, New Zealand, Belgium, Netherlands, unknown or invalid)",
 "TaxonKey is Pinellia ternata (Thunb.) Breitenb."
 ]
}

 The dataset's 1 records were derived from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006137-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvcxyg
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.77693 44.10317,10.83183 44.10317,10.83183 44.12515,10.77693 44.12515,10.77693 44.10317))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rana temporaria Linnaeus, 1758"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006142-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyr7p2
title: Occurrence Download

description: A dataset containing 20233 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coccinella undecimpunctata Linnaeus, 1758"
 ]
}

 The dataset includes 20233 records from 261 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006143-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9uxuph
title: Occurrence Download

description: A dataset containing 2594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-93.92770 6.92316,-82.43216 6.92316,-82.43216 11.51935,-93.92770 11.51935,-93.92770 6.92316))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Centris Fabricius, 1804"
 ]
}

 The dataset includes 2594 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006143-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.