cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5883/bold:aao7571
title: Barcode Index Number BOLD:AAO7571

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aao7595
title: Barcode Index Number BOLD:AAO7595

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.15468/dl.q7zuee
title: Occurrence Download

description: A dataset containing 19969147 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trochilidae"
 ]
}

 The dataset includes 19969147 records from 1079 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008567-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y8guvt
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Delphinium hellenicum Pawl.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080956-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ntszfh
title: Occurrence Download

description: A dataset containing 4399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Physocarpus (Cambess.) Raf.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4399 records from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014073-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9yc2zf
title: Occurrence Download

description: A dataset containing 54839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Karenia G.Hansen & Moestrup, 2000"
 ]
}

 The dataset includes 54839 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008456-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9tqd75
title: Occurrence Download

description: A dataset containing 549 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neocaridina davidi (Bouvier, 1904)"
 ]
}

 The dataset includes 549 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080963-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfj27f
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-93.4 36.5,-83.4 36.5,-83.4 43.75,-93.4 43.75,-93.4 36.5))",
 "HasCoordinate is true",
 "TaxonKey is Carex bicknellii Britton & A.Br.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 119 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014085-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7rudpd
title: Occurrence Download

description: A dataset containing 2460 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-43.00388 -58.28543,-36.12305 -24.43359,-70.04883 -14.94141,-82.5293 -56.07422,-43.00388 -58.28543))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aeschynomene L."
 ]
}

 The dataset includes 2460 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0324702-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7zmsj4
title: Occurrence Download

description: A dataset containing 1580 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dethawia splendens (Lapeyr.) Kerguélen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1580 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081005-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cywagb
title: Occurrence Download

description: A dataset containing 7076556 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Great Backyard Bird Count"
 ]
}

 The dataset includes 7076556 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014067-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e8j2az
title: Occurrence Download

description: A dataset containing 942 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Melanerpes erythrocephalus (Linnaeus, 1758)",
 "Year is 1989"
 ]
}

 The dataset includes 942 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220106-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.37nspy
title: Occurrence Download

description: A dataset containing 3033 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Descurainia tanacetifolia (L.) Prantl",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3033 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081003-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r42bzt
title: Occurrence Download

description: A dataset containing 726 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-121.40582 39.46072,-119.83565 39.46072,-119.83565 41.961,-121.40582 41.961,-121.40582 39.46072))",
 "TaxonKey is Tenebrionidae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 726 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014083-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzma8h
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dioscorea cuspidata Humb. & Bonpl. ex Willd."
 ]
}

 The dataset includes 61 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0153979-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2uebxy
title: Occurrence Download

description: A dataset containing 35723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lymantria monacha Linnaeus, 1758"
 ]
}

 The dataset includes 35723 records from 221 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008457-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ssdcam
title: Occurrence Download

description: A dataset containing 2633 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus tenuis (Duméril & Bibron, 1837)"
 ]
}

 The dataset includes 2633 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0153980-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjmx5u
title: Occurrence Download

description: A dataset containing 226935 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sisymbrium officinale (L.) Scop.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 226935 records from 1278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080999-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60656/396e3c5fe4a64986
title: Custom collection of lidar data from Bucharest, Chilbolton, Granada, Hyytiälä, Jülich, and 8 other sites between 1 and 31 Jan 2021
DOI: 10.15468/dl.z6pryf
title: Occurrence Download

description: A dataset containing 993 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ROC RSPB Farmland Species Survey Dataset"
 ]
}

 The dataset includes 993 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000053-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dhd3za
title: Occurrence Download

description: A dataset containing 14486 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyanea capillata (Linnaeus, 1758)"
 ]
}

 The dataset includes 14486 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000054-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14112853
title: Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition

description: Here we provide a spatiotemporal dataset of triple negative breast cance (TNBC), featuring matched primary tumors and longitudinal biopsies of metastatic lesions collected before and during ICI treatment (specifically anti-PD1) in the context of a prospective clinical trial. We generated multiplexed imaging data of pathology sections for each patient at different timepoints to conduct in-depth analysis of how spatial proteomic characteristics evolve through disease progression and immunotherapy in TNBC and their association with patient response. 

 

All analysis scripts for this data can be found here. 

Top Level Folders


analysis_files: This directory should initially contain a cell table (generated with Mesmer and annotated by Pixie). The scripts expect a column named "cell_meta_cluster" containing the cell clusters, as well "fov" with the specific image name. This folder will also contain the final data tables generated by the TNBC scripts.

output_files: This directory stores the per core and per timepoint data files for each feature. These are aggregated to form the final data tables stored in analysis_files.

intermediate_files: This directory contains subfolders storing any fov and cell level feature analysis done on the data. In addition, there is a subdirectory containing the metadata about each fov, each timepoint, and each patient.



Directory Tree




TONIC_Cohort (base directory)



analysis_files

output_files

intermediate_files



metadata

post_processing - contains specifications for the filtering of the data tables in output_files

fiber_segmentation_processed_data - image level fiber analysis (code)



tile_stats_512 - 512x512 tile analysis



spatial_analysis



neighborhood_mats - neighboring cell count/frequency at specified pixel radius and cell cluster level

mixing_score - image level mixing score of various cell population combinations (code)

cell_neighbor_analysis - data detailing cell diversity and linear distance between cell populations in an image (code)

neighborhood_analysis - kmeans neighborhood analysis (code)



ecm - generated in 4_ecm_preprocessing.py

ecm_pixel_clustering - generated in ECM_Pixie_Cluster_Pixels.ipynb and ECM_pixel_clustering_stats.ipynb
DOI: 10.5281/zenodo.14728650
title: Pengaruh Penerapan Model Pembelajaran Kooperatif Tipe Inquiri Untuk Meningkatkan Proses Berpikir Kritis Siswa Pada Materi Operasi Hitung Bilangan Bulat Siswa Kelas VII SMP Negeri 47 Halmahera Selatan

description: Kemampuan berpikir kritis merupakan aspek yang sangat penting dalam perkembangan pendidikan saat ini. Salah satu metode pembelajaran yang dapat meningkatkan kemampuan berpikir kritis adalah model pembelajaran inquiri Tujuan penelitian ini adalah untuk mengetahui apakah ada pengaruh penerapan model pembelajaran kooperatif tipe inquiri untuk meningkatkan proses berpikir kritis siswa pada materi operasi bilangan bulat siswa kelas VII SMP Negeri 47 Halmahera Selatan. Metode penelitian yang digunakan adalah penelitian kuantitatif tipe eksperimen dengan desain penelitian Pretest-Posttest Control Group Design yang menggunaakan dua kelas yaitu kelas control dan kelas eksperimen. Sampel ditentukan berdasarkan kemampuan berpikir kritis siswa, dengan siswa kelas VII A yang berjumlah 22 siswa sebagai kelas kontrol dan kelas VII B yang berjumlah 22 siswa sebagai kelas eksperimen. Teknik pengumpulan data melalui tes dan observasi. Teknik analisis data menggunakan uji prasyarat yaitu uji normallitas, uji homogenitas, uji hipotesis, dan uji data observasi. 

Hasil peneltian menunjukkan model pembelajaran inquiri efektif dalam meningkatkan proses berfikir kritis siswa, kesimpulan ini dapat dilihat dari hasil perhitungan kelas VII A (kelas Kontrol) diperoleh nilai rata-rata 70,32 sementara kelas VII B (kelas Eksperimen) diperoleh nilai rata-rata adalah 78,27. Data tersebut membuktikan adanya perbedaan proses berpikir kritis antara siswa kelas eksperimen dan kelas kontrol. Kesimpulan penelitian ini adalah penerapan model pembelajaran inquiri terhadap proses berpikir kritis siswa materi operasi hitung bilangan bulat kelas VII SMP Negeri 47 Halmahera Selatan berpengaruh dan terdapat perbedaan. Hal ini dibuktikan dengan adanya perbedaan rata-rata antara kelas eksperimen dan kelas kontrol. Rata-rata kelas eksperimen lebih besar daripada rata-rata kelas kontrol.
DOI: 10.5281/zenodo.14728651
title: Pengaruh Penerapan Model Pembelajaran Kooperatif Tipe Inquiri Untuk Meningkatkan Proses Berpikir Kritis Siswa Pada Materi Operasi Hitung Bilangan Bulat Siswa Kelas VII SMP Negeri 47 Halmahera Selatan

description: Kemampuan berpikir kritis merupakan aspek yang sangat penting dalam perkembangan pendidikan saat ini. Salah satu metode pembelajaran yang dapat meningkatkan kemampuan berpikir kritis adalah model pembelajaran inquiri Tujuan penelitian ini adalah untuk mengetahui apakah ada pengaruh penerapan model pembelajaran kooperatif tipe inquiri untuk meningkatkan proses berpikir kritis siswa pada materi operasi bilangan bulat siswa kelas VII SMP Negeri 47 Halmahera Selatan. Metode penelitian yang digunakan adalah penelitian kuantitatif tipe eksperimen dengan desain penelitian Pretest-Posttest Control Group Design yang menggunaakan dua kelas yaitu kelas control dan kelas eksperimen. Sampel ditentukan berdasarkan kemampuan berpikir kritis siswa, dengan siswa kelas VII A yang berjumlah 22 siswa sebagai kelas kontrol dan kelas VII B yang berjumlah 22 siswa sebagai kelas eksperimen. Teknik pengumpulan data melalui tes dan observasi. Teknik analisis data menggunakan uji prasyarat yaitu uji normallitas, uji homogenitas, uji hipotesis, dan uji data observasi. 

Hasil peneltian menunjukkan model pembelajaran inquiri efektif dalam meningkatkan proses berfikir kritis siswa, kesimpulan ini dapat dilihat dari hasil perhitungan kelas VII A (kelas Kontrol) diperoleh nilai rata-rata 70,32 sementara kelas VII B (kelas Eksperimen) diperoleh nilai rata-rata adalah 78,27. Data tersebut membuktikan adanya perbedaan proses berpikir kritis antara siswa kelas eksperimen dan kelas kontrol. Kesimpulan penelitian ini adalah penerapan model pembelajaran inquiri terhadap proses berpikir kritis siswa materi operasi hitung bilangan bulat kelas VII SMP Negeri 47 Halmahera Selatan berpengaruh dan terdapat perbedaan. Hal ini dibuktikan dengan adanya perbedaan rata-rata antara kelas eksperimen dan kelas kontrol. Rata-rata kelas eksperimen lebih besar daripada rata-rata kelas kontrol.
DOI: 10.34740/kaggle/dsv/10565062
title: Daftar Pengadilan Indonesia
DOI: 10.15468/dl.rrfe5s
title: Occurrence Download

description: A dataset listing the 17 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ochroma pyramidale (Cav.) Urb."
 ]
}

 The dataset's 17 records were derived from 362 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000046-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q8en25
title: Occurrence Download

description: A dataset containing 109336 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-12-29",
 "EventDate is less than or equal to 2025-01-28",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 109336 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003257-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14728676
title: Bam files
DOI: 10.5281/zenodo.14728677
title: Bam files
DOI: 10.5281/zenodo.14728678
title: Bam files
DOI: 10.17632/y4s9vf7dtj.1
title: Association between skin microbiota and keratinocyte carcinomas: insight from mendelian randomization

description: Keratinocyte carcinomas (KCs), specifically cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC), have been associated with alterations in the skin microbiome. However, it remains unclear whether the alterations reflect carcinogenic or anticancer properties, or if they merely represent an ecological niche. Mendelian randomization (MR) is a robust approach to estimate causal effects between traits. Here, we conducted a two-sample MR and Meta-analysis to investigate the causal association between skin microbiota and KCs (cSCC and BCC) among European populations.
DOI: 10.17632/r6h24d2d3y.2
title: Gallblader Diseases Dataset

description: The dataset is composed of ultrasound images of the GB organ from inside the gastrointestinal tract. The dataset includes 9 classes according to anatomical landmarks. Each class represents a GB disease.
DOI: 10.17632/r6h24d2d3y.1
title: Gallblader Diseases Dataset

description: The dataset is composed of ultrasound images of the GB organ from inside the gastrointestinal tract. The dataset includes 9 classes according to anatomical landmarks. Each class represents a GB disease.
DOI: 10.5281/zenodo.14510075
title: Data associated with Leuthold et al. - "Decadal persistence of grassland soil organic matter derived from litter and pyrogenic inputs"

description: These are data associated with the manuscript, "Decadal persistence of grassland soil organic matter derived from litter and pyrogenic inputs", by Leuthold et al., published in Nature Geoscience on January 24, 2025. Included herein are 4 spreadsheets that contain information on the chemical and isotopic composition of soil organic matter fractions isolated via the combined-size density fractionation of soils sampled at the Konza Prarie LTER site in Kansas, USA. While data are present for depths below 5 cm, the bulk of the data are associated with samples from 0 - 2, and 2 - 5 cm. Two different experimental treatments are represented in the data. In one experimental treatment, isotopically enriched (13C and 15N) litter material (Andropogon gerardii) was applied to the soil surface and tracked into the soil organic matter over the course of 10 years. In the other, isotopically enriched (13C and 15N) pyrogenic organic matter was applied to the soil and similarly tracked for 9 years. Information about analysis instrumentation and addtional details available upon request.

 

The analysis code, including the mixing models, statistics, and code for the data visualization are available on Github, in the linked repository. Any additional questions about the data can be directed to Dr. Sam Leuthold (sam.leuthold@colostate.edu).
DOI: 10.5281/zenodo.14728665
title: Interview Transcripts for "Community scientists provide knowledge and public education and help enforce environmental regulations in social-ecological systems"

description: Anonymized interview transcripts for the manuscript "Community scientists provide knowledge and public education and help enforce environmental regulations in social-ecological systems" publiushed in Nature Communications: Earth and Environment.
DOI: 10.5281/zenodo.14728664
title: Interview Transcripts for "Community scientists provide knowledge and public education and help enforce environmental regulations in social-ecological systems"

description: Anonymized interview transcripts for the manuscript "Community scientists provide knowledge and public education and help enforce environmental regulations in social-ecological systems" publiushed in Nature Communications: Earth and Environment.
DOI: 10.15468/dl.rvj2tx
title: Occurrence Download

description: A dataset listing the 364 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "GadmGid is CAN.9.50.1_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata",
 "Year 2024-2025"
 ]
}

 The dataset's 364 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000051-250123221155621/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.28267031
title: Data for "Arctic lake trout (<i>Salvelinus namaycush</i>) show evidence of seasonal acclimation of cardiac adrenergic sensitivity but not heat tolerance"

description: Heart rate, waveform, and thermal tolerance data for the Journal of Fish Biology article titled: Arctic lake trout (<i>Salvelinus namaycush</i>) show evidence of seasonal acclimation of cardiac adrenergic sensitivity but not heat tolerance
DOI: 10.6084/m9.figshare.28267031.v1
title: Data for "Arctic lake trout (<i>Salvelinus namaycush</i>) show evidence of seasonal acclimation of cardiac adrenergic sensitivity but not heat tolerance"

description: Heart rate, waveform, and thermal tolerance data for the Journal of Fish Biology article titled: Arctic lake trout (<i>Salvelinus namaycush</i>) show evidence of seasonal acclimation of cardiac adrenergic sensitivity but not heat tolerance