cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0445433
title: Shade Mapping for UBC Vancouver Neighbourhood Climate Adaptation and Community Wellbeing

description: Shade is important to urban environments as they provide comfort, reduce heat-related stress, and enhance overall wellbeing. This report presents a comprehensive study on shade mapping for Neighbourhood climate adaptation and community wellbeing within the University of British Columbia Vancouver (UBCV) campus. The primary objectives are to develop methodologies for shade mapping, identify areas with insufficient shade coverage, and provide actionable recommendations for improving shade distribution. Using high-resolution LiDAR data and sun position data, a Digital Surface Model (DSM) was created to represent campus elevation, and hillshade analysis was employed to simulate shade coverage at 15-minute intervals. Findings reveal that pedestrian areas have the highest mean shade coverage (0.69507), while concrete areas such as buildings and structures have the lowest (0.434512). Significant variations exist across Neighbourhoods, with East Campus and Hampton Place showing high, consistent shade, while Stadium and UBlvd require improvement. Bus stations also exhibit variability in shade, with UBC Exchange Bay 8 having the lowest coverage (0.160035). Recommendations include enhancing shade consistency in pedestrian areas, providing shelters in open concrete spaces, and increasing shade in Neighbourhoods like Wesbrook Place and UBlvd. Limitations of the study include the hillshade method's inability to account for shaded areas underneath trees or structures and the need for ground-truth validation. Future work should explore 3D multipatch analysis, incorporate detailed tree inventory data, and integrate shade analysis into broader urban planning efforts. This methodology-driven research aims to inspire further enhancements to the campus environment, ensuring optimized shade coverage and contributing to a more comfortable and sustainable urban landscape.
DOI: 10.15468/dl.z2rkh5
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Osmeriformes",
 "Geometry POLYGON ((33.4566 -25.7816, 35.1352 -25.1504, 26.9648 -25.1504, 26.9648 -34.0826, 27.209 -34.0314, 28.1962 -33.4486, 30.3395 -31.6744, 31.7308 -29.6968, 32.7846 -28.846, 33.3559 -27.1274, 33.4566 -25.7816))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 18 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008309-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4qqkgs
title: Occurrence Download

description: A dataset containing 57005 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Otis tarda Linnaeus, 1758"
 ]
}

 The dataset includes 57005 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011145-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7w4kkz
title: Occurrence Download

description: A dataset containing 5383 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((178.4057 -9.435511, 179.8634 -9.435511, 179.8634 -7.448171, 178.4057 -7.448171, 178.4057 -9.435511))"
 ]
}

 The dataset includes 5383 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013033-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29117336
title: Figure S4, Circular map of <i>H. volcanii </i>PC0224 plasmid pHA3

description: Circular map of <i>H. volcanii </i>PC0224 plasmid pHA3
DOI: 10.6084/m9.figshare.29117336.v1
title: Figure S4, Circular map of <i>H. volcanii </i>PC0224 plasmid pHA3

description: Circular map of <i>H. volcanii </i>PC0224 plasmid pHA3
DOI: 10.15468/dl.ctpzdz
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Farysporium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 78 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038592-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uqm8sq
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orphanomyces",
 "HasCoordinate is true"
 ]
}

 The dataset includes 104 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038593-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17627831
title: Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus.

description: Poorly dispersing pseudoscorpions (Arachnida: Pseudoscorpiones) are often considered suitable models for biogeography studies. Several lineages show interesting distribution patterns, such as the genus Parobisium Chamberlin, 1930 that occurs in the western U.S.A. and eastern Asia but is absent in Europe and central Asia. Here we review the pseudoscorpion genus Parobisium using an integrative taxonomic approach and describe two new species from South Korea based on morphological and molecular data: Parobisium namkungi sp. nov. and P. troglophilum sp. nov. Phylogenetic analyses using three genetic markers, cytochrome c oxidase subunit I (COI), histone H3A, and 28S ribosomal DNA also reveal that two former subspecies, P. magnum ohuyeanum (Morikawa, 1952) and P. magnum chejuense (Morikawa, 1970), are genetically distinct enough to recognize them as separate species, P. ohuyeanum stat nov. and. P. chejuense stat. nov..

Table S1. PCR conditions to generate DNA sequences for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.

Table S2. Primers used to generate DNA sequences used for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.

Table S3. GenBank accession numbers for DNA sequences of the 28S rDNA (28S), histone H3A (H3), and Cytochrome c Oxidase subunit I (COI) used for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.
DOI: 10.5281/zenodo.17627832
title: Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus.

description: Poorly dispersing pseudoscorpions (Arachnida: Pseudoscorpiones) are often considered suitable models for biogeography studies. Several lineages show interesting distribution patterns, such as the genus Parobisium Chamberlin, 1930 that occurs in the western U.S.A. and eastern Asia but is absent in Europe and central Asia. Here we review the pseudoscorpion genus Parobisium using an integrative taxonomic approach and describe two new species from South Korea based on morphological and molecular data: Parobisium namkungi sp. nov. and P. troglophilum sp. nov. Phylogenetic analyses using three genetic markers, cytochrome c oxidase subunit I (COI), histone H3A, and 28S ribosomal DNA also reveal that two former subspecies, P. magnum ohuyeanum (Morikawa, 1952) and P. magnum chejuense (Morikawa, 1970), are genetically distinct enough to recognize them as separate species, P. ohuyeanum stat nov. and. P. chejuense stat. nov..

Table S1. PCR conditions to generate DNA sequences for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.

Table S2. Primers used to generate DNA sequences used for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.

Table S3. GenBank accession numbers for DNA sequences of the 28S rDNA (28S), histone H3A (H3), and Cytochrome c Oxidase subunit I (COI) used for “Two new species of Parobisium (Pseudoscorpiones: Neobisiidae) Chamberlin, 1930 from South Korea, with a preliminary phylogeny of the genus”.
DOI: 10.5281/zenodo.17627772
title: Dataset Journal Artificial Intelligence & Digital Marketing
title: Dataset
DOI: 10.5281/zenodo.17627773
title: Dataset Journal Artificial Intelligence & Digital Marketing
title: Dataset
DOI: 10.5281/zenodo.17627912
title: Precipitation dominates forest net primary productivity variations with distinct regional differences in Yunnan Province, China

description: Precipitation dominates forest net primary productivity variations with distinct regional differences in Yunnan Province, China
DOI: 10.5281/zenodo.17627913
title: Precipitation dominates forest net primary productivity variations with distinct regional differences in Yunnan Province, China

description: Precipitation dominates forest net primary productivity variations with distinct regional differences in Yunnan Province, China
DOI: 10.15468/dl.9tnfht
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Planetella",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038594-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.18415.09125
title: low budget FSM speed test
DOI: 10.5281/zenodo.17561469
title: Underwater images collected by a Kite surf in Le-Morne-Manawa, Mauritius - 2019-09-14

description: This dataset was collected by a Kite surf in Le-Morne-Manawa, Mauritius - 2019-09-14. 

            Underwater or aerial images collected by scientists or citizens can have a wide variety of use for science, management, or conservation.
            These images can be annotated and shared to train IA models which can in turn predict the objects on the images.
            We provide a set of tools (hardware and software) to collect marine data, predict species or habitat, and provide maps.

            This dataset is part of larger collection referencing numerous underwater and aerial images Seatizen Altas. 
            Methods, tools and scientific objectives are also described in a dedicated data paper.

            
                
                                       
                
                
 GPS information: 

                No GPS.
            
                    
                

                
            

            
 Generic folder structure 
            
            YYYYMMDD_COUNTRYCODE-optionalplace_device_session-number 
            ├── DCIM :  folder to store videos and photos depending on the media collected. 
            ├── GPS :  folder to store any positioning related file. If any kind of correction is possible on files (e.g. Post-Processed Kinematic thanks to rinex data) then the distinction between device data and base data is made. If, on the other hand, only device position data are present and the files cannot be corrected by post-processing techniques (e.g. gpx files), then the distinction between base and device is not made and the files are placed directly at the root of the GPS folder. 
            │   ├── BASE :  files coming from rtk station or any static positioning instrument. 
            │   └── DEVICE : files coming from the device. 
            ├── METADATA : folder with general information files about the session. 
            ├── PROCESSED_DATA : contain all the folders needed to store the results of the data processing of the current session. 
            │   ├── BATHY :  output folder for bathymetry raw data extracted from mission logs. 
            │   ├── FRAMES :  output folder for georeferenced frames extracted from DCIM videos. 
            │   ├── IA :  destination folder for image recognition predictions. 
            │   └── PHOTOGRAMMETRY :  destination folder for reconstructed models in photogrammetry. 
            └── SENSORS : folder to store files coming from other sources (bathymetry data from the echosounder, log file from the autopilot,  mission plan etc.).       
            

            
 Software 
            All the raw data was processed using our worflow. All predictions were generated by our inference pipeline. You can find all the necessary scripts to download this data in this repository. Enjoy your data with SeatizenDOI!
DOI: 10.5281/zenodo.17627613
title: Underwater images collected by a Kite surf in Le-Morne-Manawa, Mauritius - 2019-09-14

description: This dataset was collected by a Kite surf in Le-Morne-Manawa, Mauritius - 2019-09-14. 

            Underwater or aerial images collected by scientists or citizens can have a wide variety of use for science, management, or conservation.
            These images can be annotated and shared to train IA models which can in turn predict the objects on the images.
            We provide a set of tools (hardware and software) to collect marine data, predict species or habitat, and provide maps.

            This dataset is part of larger collection referencing numerous underwater and aerial images Seatizen Altas. 
            Methods, tools and scientific objectives are also described in a dedicated data paper.

            
                
                                       
                
                
 GPS information: 

                No GPS.
            
                    
                

                
            

            
 Generic folder structure 
            
            YYYYMMDD_COUNTRYCODE-optionalplace_device_session-number 
            ├── DCIM :  folder to store videos and photos depending on the media collected. 
            ├── GPS :  folder to store any positioning related file. If any kind of correction is possible on files (e.g. Post-Processed Kinematic thanks to rinex data) then the distinction between device data and base data is made. If, on the other hand, only device position data are present and the files cannot be corrected by post-processing techniques (e.g. gpx files), then the distinction between base and device is not made and the files are placed directly at the root of the GPS folder. 
            │   ├── BASE :  files coming from rtk station or any static positioning instrument. 
            │   └── DEVICE : files coming from the device. 
            ├── METADATA : folder with general information files about the session. 
            ├── PROCESSED_DATA : contain all the folders needed to store the results of the data processing of the current session. 
            │   ├── BATHY :  output folder for bathymetry raw data extracted from mission logs. 
            │   ├── FRAMES :  output folder for georeferenced frames extracted from DCIM videos. 
            │   ├── IA :  destination folder for image recognition predictions. 
            │   └── PHOTOGRAMMETRY :  destination folder for reconstructed models in photogrammetry. 
            └── SENSORS : folder to store files coming from other sources (bathymetry data from the echosounder, log file from the autopilot,  mission plan etc.).       
            

            
 Software 
            All the raw data was processed using our worflow. All predictions were generated by our inference pipeline. You can find all the necessary scripts to download this data in this repository. Enjoy your data with SeatizenDOI!
DOI: 10.15468/dl.9grwpt
title: Occurrence Download

description: A dataset containing 228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Testicularia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 228 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038596-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gq5wqz
title: Occurrence Download

description: A dataset containing 5775 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triodanis perfoliata biflora, Cyperus alternifolius flabelliformis, Mimosa diplotricha inermis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Material sample)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 5775 records from 313 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038597-251025141854904/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.25359355
title: Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries

description: 5-Methylcytosine methyltransferases (m<sup>5</sup>C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a complete understanding of the archaeal counterparts is lacking. In this study, the identification and characterization of archaeal RNA m<sup>5</sup>C MTases were performed. As a case study, a hyperthermophilic archaeon, <i>Pyrococcus horikoshii</i> OT3, which possesses five putative RNA m<sup>5</sup>C MTases, was chosen. Among the five putative RNA m<sup>5</sup>C MTases, two proteins (PH0851 and PH1991) have been characterized as homologs of a bacterial rRNA MTase (RsmB) and eukaryal tRNA MTase (NSUN6), respectively. The in-depth characterization of the remaining three putative RNA m<sup>5</sup>C MTases (PH1078, PH1374, and PH1537) in this study suggests the presence of the signature architecture and catalytic residues plausibly involved in the binding of their cognate RNA substrates. Additionally, the results also suggest the existence of two RsmB-like proteins (PH0851 and PH1078) belonging to the same subfamily IV of m<sup>5</sup>C RNA MTase. However, the proteins PH1374 and PH1537 belong to the same subfamily V but bind to different substrates, rRNA and tRNA, respectively. The findings further indicate that archaeal RNA m<sup>5</sup>C MTases link those from bacteria and eukarya.
DOI: 10.6084/m9.figshare.25359355.v1
title: Distinct characteristics of putative archaeal 5-methylcytosine RNA methyltransferases unveil their substrate specificities and evolutionary ancestries

description: 5-Methylcytosine methyltransferases (m<sup>5</sup>C MTases) are known to be involved in the modification of RNA. Although these enzymes have been relatively well characterized in bacteria and eukarya, a complete understanding of the archaeal counterparts is lacking. In this study, the identification and characterization of archaeal RNA m<sup>5</sup>C MTases were performed. As a case study, a hyperthermophilic archaeon, <i>Pyrococcus horikoshii</i> OT3, which possesses five putative RNA m<sup>5</sup>C MTases, was chosen. Among the five putative RNA m<sup>5</sup>C MTases, two proteins (PH0851 and PH1991) have been characterized as homologs of a bacterial rRNA MTase (RsmB) and eukaryal tRNA MTase (NSUN6), respectively. The in-depth characterization of the remaining three putative RNA m<sup>5</sup>C MTases (PH1078, PH1374, and PH1537) in this study suggests the presence of the signature architecture and catalytic residues plausibly involved in the binding of their cognate RNA substrates. Additionally, the results also suggest the existence of two RsmB-like proteins (PH0851 and PH1078) belonging to the same subfamily IV of m<sup>5</sup>C RNA MTase. However, the proteins PH1374 and PH1537 belong to the same subfamily V but bind to different substrates, rRNA and tRNA, respectively. The findings further indicate that archaeal RNA m<sup>5</sup>C MTases link those from bacteria and eukarya.
DOI: 10.6084/m9.figshare.27959770
title: The impact of DNA point mutations and epigenetic modifications on the nucleosome wrapping energy

description: Nucleosome positioning and mobility, which plays an important role in gene expression and regulation, is in turn modulated by DNA sequence and its underlying mechanical properties. The free energy, required to deform a 147 bp linear DNA fragment into a nucleosomal configuration, is a way to quantify DNA mechanical propensity for nucleosome formation. This work explores how such energy, referred to as the nucleosome wrapping energy, is altered by DNA sequence mutations and epigenetic modifications. The nucleosome wrapping energy is computed using a newly developed computational method based on minimising the <i>cgNA+</i> coarse-grain model energy with elastic constraints on phosphate positions. We find that the effect of sequence mutations and epigenetic modifications is highly dependent on the positions along the sequence of the modified bases. Most point mutations as well as cytosine methylation and hydroxymethylation, depending on their positions, can lead both to an increase and decrease in the nucleosome wrapping energy. We use the data of mutation-caused energy changes to identify sequence patterns in specific positions, leading to the smallest and highest wrapping energy values. Furthermore, we construct sequences corresponding to extremely low and high nucleosome wrapping energies, compared to energy distribution for human genome sequences. We believe that our findings are helpful for better understanding the role of DNA sequence and its epigenetic modifications in nucleosome positioning. Furthermore, our constructed minimum energy sequence could be used as a candidate for producing stable synthetic nucleosomes.
DOI: 10.6084/m9.figshare.27959770.v1
title: The impact of DNA point mutations and epigenetic modifications on the nucleosome wrapping energy

description: Nucleosome positioning and mobility, which plays an important role in gene expression and regulation, is in turn modulated by DNA sequence and its underlying mechanical properties. The free energy, required to deform a 147 bp linear DNA fragment into a nucleosomal configuration, is a way to quantify DNA mechanical propensity for nucleosome formation. This work explores how such energy, referred to as the nucleosome wrapping energy, is altered by DNA sequence mutations and epigenetic modifications. The nucleosome wrapping energy is computed using a newly developed computational method based on minimising the <i>cgNA+</i> coarse-grain model energy with elastic constraints on phosphate positions. We find that the effect of sequence mutations and epigenetic modifications is highly dependent on the positions along the sequence of the modified bases. Most point mutations as well as cytosine methylation and hydroxymethylation, depending on their positions, can lead both to an increase and decrease in the nucleosome wrapping energy. We use the data of mutation-caused energy changes to identify sequence patterns in specific positions, leading to the smallest and highest wrapping energy values. Furthermore, we construct sequences corresponding to extremely low and high nucleosome wrapping energies, compared to energy distribution for human genome sequences. We believe that our findings are helpful for better understanding the role of DNA sequence and its epigenetic modifications in nucleosome positioning. Furthermore, our constructed minimum energy sequence could be used as a candidate for producing stable synthetic nucleosomes.