cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26170021
title: Mechanistic insights from the atomic-level quaternary structure of short-lived GPCR oligomers in live cells

description: The functional significance of the interactions between proteins in living cells to form short-lived quaternary structures cannot be overemphasized. Yet, quaternary structure information is not captured by current methods, neither can those methods determine structure within living cells. The dynamic versatility, abundance, and functional diversity of G protein-coupled receptors (GPCRs) pose myriad challenges to existing technologies but also present these proteins as the ideal testbed for new technologies to investigate the complex inter-regulation of receptor-ligand, receptor-receptor, and receptor-downstream effector interfaces in living cells. Here, we present development and use of a novel method capable of overcoming existing challenges by combining distributions (or spectrograms) of FRET efficiencies from populations of fluorescently tagged proteins associating into oligomeric complexes in live cells with diffusion-like trajectories of FRET donors and acceptors obtained from coarse-grained molecular dynamics (CGMD) simulations. Our approach provides an atom-level picture of the binding interfaces within oligomers of the human secretin receptor (hSecR) in live cells and allows for extraction of mechanistic insights into the function of GPCRs oligomerization. This FRET-MD spectrometry approach is a robust platform for investigating protein-protein binding mechanisms and opens a new avenue for investigating stable as well as fleeting quaternary structures of any membrane proteins in living cells.
DOI: 10.6084/m9.figshare.26170021.v4
title: Mechanistic insights from the atomic-level quaternary structure of short-lived GPCR oligomers in live cells

description: The functional significance of the interactions between proteins in living cells to form short-lived quaternary structures cannot be overemphasized. Yet, quaternary structure information is not captured by current methods, neither can those methods determine structure within living cells. The dynamic versatility, abundance, and functional diversity of G protein-coupled receptors (GPCRs) pose myriad challenges to existing technologies but also present these proteins as the ideal testbed for new technologies to investigate the complex inter-regulation of receptor-ligand, receptor-receptor, and receptor-downstream effector interfaces in living cells. Here, we present development and use of a novel method capable of overcoming existing challenges by combining distributions (or spectrograms) of FRET efficiencies from populations of fluorescently tagged proteins associating into oligomeric complexes in live cells with diffusion-like trajectories of FRET donors and acceptors obtained from coarse-grained molecular dynamics (CGMD) simulations. Our approach provides an atom-level picture of the binding interfaces within oligomers of the human secretin receptor (hSecR) in live cells and allows for extraction of mechanistic insights into the function of GPCRs oligomerization. This FRET-MD spectrometry approach is a robust platform for investigating protein-protein binding mechanisms and opens a new avenue for investigating stable as well as fleeting quaternary structures of any membrane proteins in living cells.
DOI: 10.6084/m9.figshare.26170021.v3
title: Revealing the amino acid-level structure of GPCR oligomeric complexes via a novel fusion of advanced FRET spectrometry and MD simulations-based data fitting

description: The functional significance of the interactions between proteins in living cells to form short-lived quaternary structures cannot be overemphasized. Yet, quaternary structure information is not captured by current methods, neither can those methods determine structure within living cells. The dynamic versatility, abundance, and functional diversity of G protein-coupled receptors (GPCRs) pose myriad challenges to existing technologies but also present these proteins as the ideal testbed for new technologies to investigate the complex inter-regulation of receptor-ligand, receptor-receptor, and receptor-downstream effector interfaces in living cells. Here, we present development and use of a novel method capable of overcoming existing challenges by combining distributions (or spectrograms) of FRET efficiencies from populations of fluorescently tagged proteins associating into oligomeric complexes in live cells with diffusion-like trajectories of FRET donors and acceptors obtained from molecular dynamics (MD) simulations. Our approach provides an atom-level picture of the binding interfaces within oligomers of the human secretin receptor (hSecR) in live cells and allows for extraction of mechanistic insights into the function of GPCRs oligomerization. This FRET-MD spectrometry approach is a robust platform for investigating protein-protein binding mechanisms and opens a new avenue for investigating stable as well as fleeting quaternary structures of any membrane proteins in living cells.
DOI: 10.5281/zenodo.14247722
title: Supporting data for: "ntSynt-viz: Visualizing synteny patterns across multiple genomes"

description: Here, we provide the files used to generate the chromosome painting ribbon plots for the manuscript "ntSynt-viz: Visualizing synteny patterns across multiple genomes".

For each file (human or hoverfly tar.gz), there are sub-folders with the input files for running ntSynt-viz and the comparator tool NGenomeSyn.
DOI: 10.5281/zenodo.14247723
title: Supporting data for: "ntSynt-viz: Visualizing synteny patterns across multiple genomes"

description: Here, we provide the files used to generate the chromosome painting ribbon plots for the manuscript "ntSynt-viz: Visualizing synteny patterns across multiple genomes".

For each file (human or hoverfly tar.gz), there are sub-folders with the input files for running ntSynt-viz and the comparator tool NGenomeSyn.
DOI: 10.15468/dl.a856hu
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thinobius newberyi Scheerpeltz, 1925",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 26 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071739-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14658079
title: P=NP proof

description: https://chatgpt.com/share/6788036b-8f6c-8005-b325-b75db93d3874
DOI: 10.5281/zenodo.14658080
title: P=NP proof

description: https://chatgpt.com/share/6788036b-8f6c-8005-b325-b75db93d3874
DOI: 10.15468/dl.fqb7c3
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes albarracinus (Wagner, 1928)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 119 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071740-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aaqpta
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes chersinus Delabie, 1954",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071741-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7k3f2
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes escorialensis (Jekel, 1866)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071742-241126133413365/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.28200344.v1
title: <b>Comparative analysis ENM methods for abundance-suitability relationship</b>

description: Data from the comparative analysis of the performance of different ENM methods for predicting the spatial distribution of bird abundance in North America.
DOI: 10.6084/m9.figshare.28200344
title: <b>Comparative analysis ENM methods for abundance-suitability relationship</b>

description: Data from the comparative analysis of the performance of different ENM methods for predicting the spatial distribution of bird abundance in North America.
DOI: 10.15468/dl.c56vrp
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-5.6888 35.85969,-3.71932 36.14938,-3.7947 37.50701,-6.39555 38.28039,-6.98922 36.68776,-5.6888 35.85969))",
 "HasGeospatialIssue is false",
 "TaxonKey is Olea europaea L."
 ]
}

 The dataset includes 217 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071744-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2mcqn
title: Occurrence Download

description: A dataset containing 246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes geminatus (Gené, 1839)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 246 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071746-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14649072
title: WHHW Peptide Metal Binding DFT

description: using ORCA 5.0.3
DOI: 10.5281/zenodo.14649073
title: WHHW Peptide Metal Binding DFT

description: using ORCA 5.0.3
DOI: 10.15468/dl.a7g3ww
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes hernandezi (López-Colón, 1988)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071748-241126133413365/datasets/export for details.
DOI: 10.15468/dl.kpwc9x
title: Occurrence Download

description: A dataset containing 86154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((4.24424 52.10522,5.30146 52.04674,5.23623 52.53711,5.32846 52.73281,5.29472 52.82278,5.162 52.91726,5.06977 53.02748,4.90782 53.17369,4.82668 53.21838,4.7841 53.18719,4.64464 53.02523,4.65813 52.86552,4.6064 52.70806,4.58615 52.62484,4.53667 52.49212,4.48943 52.37965,4.24424 52.10522))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Malacostraca"
 ]
}

 The dataset includes 86154 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071747-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/75dbjkmy9g.1
title: soybeans-noted-augumented-cut

description: The dataset contains 20,539 images of grains annotated with bounding boxes in YOLOv8 format. These images have been pre-processed and augmented to enhance model training for grain classification and defect detection. The following pre-processing steps were applied to each image:

 Auto-orientation of pixel data (with EXIF-orientation stripping)
 Resize to 600x600 pixels (stretching)
 Grayscale conversion (CRT phosphor)
 Auto-contrast via histogram equalization

Additionally, the following augmentation techniques were applied to create three versions of each source image:

 50% probability of horizontal flip
 50% probability of vertical flip
 Random rotation between -15 and +15 degrees
 Random brightness adjustment between -15% and +15%

This dataset was created to support computer vision models by providing a diverse range of augmented data for better model generalization and accuracy. The images are in JPG format and are annotated to identify grain defects such as moldy, burnt, pecky, scorched, greenish, and good grains.

Format: YOLOv8 bounding box annotations.
Image Size: Resized to 600x600 pixels.
Number of Images: 20,539 images (with augmentations generating additional versions of each source image).
DOI: 10.15468/dl.wqvdrg
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes intermedius (Costa, 1839)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 402 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071749-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14641540
title: Westside Raw Sequences and Phyloseqs

description: The Westside_SPUN_Willing md5 and tar files were directly downloaded from the Northwest Genomics Center and contain the raw sequence reads for the first ~250 samples in the library prepared by Ellie in falll 2024. SPUN_Westside_Willing.rds is a phyloseq object classifying and merging these reads with the metadata file in the FML Drive. SPUN_Westside_Willing_with_FungalTraits.rds additionally has the FungalTraits database merged within the taxonomy table (so each taxa has additional functional trait data when known) and has been rarefied to the 10,000 reads per sample (which removed 8 samples and 290 rare taxa).
DOI: 10.5281/zenodo.14641541
title: Westside Raw Sequences and Phyloseqs

description: The Westside_SPUN_Willing md5 and tar files were directly downloaded from the Northwest Genomics Center and contain the raw sequence reads for the first ~250 samples in the library prepared by Ellie in falll 2024. SPUN_Westside_Willing.rds is a phyloseq object classifying and merging these reads with the metadata file in the FML Drive. SPUN_Westside_Willing_with_FungalTraits.rds additionally has the FungalTraits database merged within the taxonomy table (so each taxa has additional functional trait data when known) and has been rarefied to the 10,000 reads per sample (which removed 8 samples and 290 rare taxa).
DOI: 10.15468/dl.cbwz48
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes marginatus (Poiret, 1787)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071750-241126133413365/datasets/export for details.
DOI: 10.15468/dl.cfrhxh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes nitidus (Jekel, 1866)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071752-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bm96dz
title: Occurrence Download

description: A dataset containing 45341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-100.551 36.917,-71.79 36.917,-71.79 49.612,-100.551 49.612,-100.551 36.917))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Osmerus mordax (Mitchill, 1814), Gymnocephalus cernua (Linnaeus, 1758))",
 "Year 1970-2025"
 ]
}

 The dataset includes 45341 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071751-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5k9ue
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thorectes punctatissimus (Chevrolat, 1840)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071754-241126133413365/datasets/export for details.
DOI: 10.15468/dl.v2vcug
title: Occurrence Download

description: A dataset listing the 1300 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is one of (Germany, France, Netherlands, Switzerland, United Kingdom of Great Britain and Northern Ireland, Belgium)",
 "TaxonKey is Orthoptera"
 ]
}

 The dataset's 1300 records were derived from 5248 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071745-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c7c52s
title: Occurrence Download

description: A dataset containing 3115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Norway",
 "TaxonKey is Gadus morhua Linnaeus, 1758"
 ]
}

 The dataset includes 3115 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011066-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kwgpss
title: Occurrence Download

description: A dataset containing 25550 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Platismatia glauca (L.) W.L.Culb. & C.F.Culb., Platycerus caraboides (Linneaus, 1758), Platycladus orientalis (L.) Franco)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 25550 records from 344 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0324779-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4j5bd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "Geometry POLYGON((-55.21729 -27.09948,-46.86768 -27.09948,-46.86768 -21.45435,-55.21729 -21.45435,-55.21729 -27.09948))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Orchesticus Cabanis, 1851"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0170896-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akcv6a
title: Occurrence Download

description: A dataset containing 386 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cinchona macrocalyx Pav. ex DC."
 ]
}

 The dataset includes 386 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019090-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.atepq7
title: Occurrence Download

description: A dataset containing 2640 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anguilla marmorata Quoy & Gaimard, 1824"
 ]
}

 The dataset includes 2640 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0324408-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vh41jk
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Rund um die Sausenburg"
 ]
}

 The dataset includes 63 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001701-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqku6z
title: Occurrence Download

description: A dataset containing 377590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 377590 records from 643 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022220-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.erkrus
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Menidia colei Hubbs, 1936"
 ]
}

 The dataset includes 241 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0340892-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nkkf72
title: Occurrence Download

description: A dataset containing 574858 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Venezuela (Bolivarian Republic of), Chile, Peru, Colombia, Argentina, Ecuador, Bolivia (Plurinational State of))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Poaceae, Asteraceae)"
 ]
}

 The dataset includes 574858 records from 795 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010535-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.