cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12672626
title: Data from: Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT

description: Abstract

In this dataset, we present supplementary material from the paper by Bujny et al. (2024). The material includes STL models of aorta segmented in contrast Computed Tomography (CT) scans by a medical expert and using the Machine Learning (ML) model described in the paper. A gallery of ML-based segmentations of the aortic root in non-contrast CT, with the corresponding scans and aortic valve meshes registered from contrast CT using the Iterative Closest Point (ICP) algorithm is provided, as well. Finally, we include the source code of the ICP-based accuracy evaluation method proposed in the paper, with an example in Jupyter Notebook. All of the data included in the dataset has been generated based on the CT scans from the openly available orCaScore dataset (Wolterink et al. 2016).

 

Dataset organization

The root folder contains 3 catalogs:



contrast_aorta_stls – set of 19 Ground Truth (GT) segmentations of aorta in contrast CT, with the corresponding inferences of the contrast ML model described in the paper, for the scans from the open-source orCaScore dataset (Wolterink et al. 2016).

icp_code – Python code of the ICP-based accuracy evaluation method proposed in the paper.

icp_gallery – HTML gallery of aorta segmentations based on the non-contrast ML model described in the paper, with the corresponding CT scans and meshes of the aortic valves segmented in contrast CT, which were rigidly registered to the non-contrast scans using the proposed ICP-based approach. In the CT scans, blue and red contours were used to depict non-contrast-based and registered contrast-based ML segmentations, respectively.


 

References

M. Bujny, K. Jesionek, J. Nalepa, T. Bartczak, K. Miszalski-Jamka, M. Kostur, “Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT,” 27th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Marrakesh, Morocco, 2024 [accepted].

J. M. Wolterink et al., “An evaluation of automatic coronary artery calcium scoring methods with cardiac CT using the orCaScore framework: Evaluation of cardiac CT-based automatic coronary calcium scoring,” Med. Phys., vol. 43, no. 5, pp. 2361–2373, 2016.
DOI: 10.5281/zenodo.13236390
title: Data from: Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT

description: Abstract

In this dataset, we present supplementary material from the paper by Bujny et al. (2024). The material includes STL models of aorta segmented in contrast Computed Tomography (CT) scans by a medical expert and using the Machine Learning (ML) model described in the paper. A gallery of ML-based segmentations of the aortic root in non-contrast CT, with the corresponding scans and aortic valve meshes registered from contrast CT using the Iterative Closest Point (ICP) algorithm is provided, as well. Finally, we include the source code of the ICP-based accuracy evaluation method proposed in the paper, with an example in Jupyter Notebook. All of the data included in the dataset has been generated based on the CT scans from the openly available orCaScore dataset (Wolterink et al. 2016).

 

Dataset organization

The root folder contains 3 catalogs:



contrast_aorta_stls – set of 19 Ground Truth (GT) segmentations of aorta in contrast CT, with the corresponding inferences of the contrast ML model described in the paper, for the scans from the open-source orCaScore dataset (Wolterink et al. 2016).

icp_code – Python code of the ICP-based accuracy evaluation method proposed in the paper.

icp_gallery – HTML gallery of aorta segmentations based on the non-contrast ML model described in the paper, with the corresponding CT scans and meshes of the aortic valves segmented in contrast CT, which were rigidly registered to the non-contrast scans using the proposed ICP-based approach. In the CT scans, blue and red contours were used to depict non-contrast-based and registered contrast-based ML segmentations, respectively.


 

References

M. Bujny, K. Jesionek, J. Nalepa, T. Bartczak, K. Miszalski-Jamka, M. Kostur, “Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT,” 27th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Marrakesh, Morocco, 2024 [accepted].

J. M. Wolterink et al., “An evaluation of automatic coronary artery calcium scoring methods with cardiac CT using the orCaScore framework: Evaluation of cardiac CT-based automatic coronary calcium scoring,” Med. Phys., vol. 43, no. 5, pp. 2361–2373, 2016.
DOI: 10.15468/dl.jhn2b8
title: Occurrence Download

description: A dataset containing 648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oncorhynchus gorbuscha (Walbaum, 1792)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 648 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051823-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6rcz89
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((141.97122 -37.110115, 141.97122 -37.11236, 141.977958 -37.11236, 141.977958 -37.110115, 141.97122 -37.110115)), ((141.977958 -37.11236, 141.977958 -37.114606, 141.986941 -37.114606, 141.986941 -37.11236, 141.977958 -37.11236)), ((141.986941 -37.114606, 141.986941 -37.119098, 141.973466 -37.119098, 141.973466 -37.121344, 141.989187 -37.121344, 141.989187 -37.119098, 141.993678 -37.119098, 141.993678 -37.114606, 141.986941 -37.114606)), ((141.993678 -37.119098, 141.993678 -37.123589, 141.995924 -37.123589, 141.995924 -37.134818, 141.99817 -37.134818, 141.99817 -37.137064, 142.002662 -37.137064, 142.002662 -37.130327, 141.99817 -37.130327, 141.99817 -37.128081, 142.004907 -37.128081, 142.004907 -37.123589, 141.99817 -37.123589, 141.99817 -37.119098, 141.993678 -37.119098)), ((141.995924 -37.134818, 141.982449 -37.134818, 141.982449 -37.137064, 141.980204 -37.137064, 141.980204 -37.13931, 141.986941 -37.13931, 141.986941 -37.143802, 141.989187 -37.143802, 141.989187 -37.137064, 141.995924 -37.137064, 141.995924 -37.134818)), ((142.004907 -37.123589, 142.009399 -37.123589, 142.009399 -37.121344, 142.004907 -37.121344, 142.004907 -37.123589)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051824-240626123714530/datasets/export for details.
DOI: 10.15468/dl.97ddxs
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.645735 -35.057454, 148.645735 -35.077667, 148.654718 -35.077667, 148.654718 -35.10237, 148.661456 -35.10237, 148.661456 -35.084404, 148.65921 -35.084404, 148.65921 -35.079912, 148.656964 -35.079912, 148.656964 -35.075421, 148.652472 -35.075421, 148.652472 -35.064192, 148.650227 -35.064192, 148.650227 -35.057454, 148.645735 -35.057454))"
 ]
}

 The dataset includes 38 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051825-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m29brd
title: Occurrence Download

description: A dataset containing 972 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((144.56961 -37.123589, 144.556135 -37.123589, 144.556135 -37.130327, 144.558381 -37.130327, 144.558381 -37.134818, 144.551643 -37.134818, 144.551643 -37.137064, 144.558381 -37.137064, 144.558381 -37.13931, 144.556135 -37.13931, 144.556135 -37.152785, 144.56961 -37.152785, 144.56961 -37.150539, 144.565118 -37.150539, 144.565118 -37.146047, 144.562872 -37.146047, 144.562872 -37.13931, 144.571856 -37.13931, 144.571856 -37.150539, 144.574101 -37.150539, 144.574101 -37.152785, 144.580839 -37.152785, 144.580839 -37.150539, 144.58533 -37.150539, 144.58533 -37.128081, 144.580839 -37.128081, 144.580839 -37.130327, 144.571856 -37.130327, 144.571856 -37.134818, 144.565118 -37.134818, 144.565118 -37.130327, 144.56961 -37.130327, 144.56961 -37.123589), (144.565118 -37.130327, 144.562872 -37.130327, 144.562872 -37.128081, 144.565118 -37.128081, 144.565118 -37.130327)), ((144.558381 -37.080919, 144.558381 -37.083165, 144.562872 -37.083165, 144.562872 -37.085411, 144.565118 -37.085411, 144.565118 -37.089902, 144.56961 -37.089902, 144.56961 -37.09664, 144.562872 -37.09664, 144.562872 -37.098886, 144.565118 -37.098886, 144.565118 -37.101131, 144.562872 -37.101131, 144.562872 -37.105623, 144.556135 -37.105623, 144.556135 -37.101131, 144.551643 -37.101131, 144.551643 -37.105623, 144.549398 -37.105623, 144.549398 -37.107869, 144.547152 -37.107869, 144.547152 -37.114606, 144.551643 -37.114606, 144.551643 -37.119098, 144.558381 -37.119098, 144.558381 -37.114606, 144.562872 -37.114606, 144.562872 -37.119098, 144.565118 -37.119098, 144.565118 -37.121344, 144.56961 -37.121344, 144.56961 -37.123589, 144.571856 -37.123589, 144.571856 -37.119098, 144.574101 -37.119098, 144.574101 -37.101131, 144.578593 -37.101131, 144.578593 -37.09664, 144.571856 -37.09664, 144.571856 -37.092148, 144.58533 -37.092148, 144.58533 -37.089902, 144.587576 -37.089902, 144.587576 -37.083165, 144.58533 -37.083165, 144.58533 -37.080919, 144.558381 -37.080919), (144.565118 -37.107869, 144.571856 -37.107869, 144.571856 -37.114606, 144.565118 -37.114606, 144.565118 -37.107869)), ((144.578593 -37.101131, 144.578593 -37.107869, 144.580839 -37.107869, 144.580839 -37.11236, 144.58533 -37.11236, 144.58533 -37.107869, 144.587576 -37.107869, 144.587576 -37.105623, 144.58533 -37.105623, 144.58533 -37.101131, 144.578593 -37.101131)))"
 ]
}

 The dataset includes 972 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051827-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fgk3w8
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((149.977494 -35.061946, 149.977494 -35.064192, 149.973002 -35.064192, 149.973002 -35.073175, 149.977494 -35.073175, 149.977494 -35.095633, 149.981985 -35.095633, 149.981985 -35.097879, 149.986477 -35.097879, 149.986477 -35.100125, 149.990969 -35.100125, 149.990969 -35.095633, 149.986477 -35.095633, 149.986477 -35.079912, 149.981985 -35.079912, 149.981985 -35.073175, 149.990969 -35.073175, 149.990969 -35.077667, 149.99546 -35.077667, 149.99546 -35.079912, 149.990969 -35.079912, 149.990969 -35.08665, 149.997706 -35.08665, 149.997706 -35.077667, 150.004443 -35.077667, 150.004443 -35.064192, 149.999952 -35.064192, 149.999952 -35.070929, 149.99546 -35.070929, 149.99546 -35.068683, 149.990969 -35.068683, 149.990969 -35.064192, 149.986477 -35.064192, 149.986477 -35.061946, 149.977494 -35.061946)), ((149.990969 -35.100125, 149.990969 -35.10237, 149.997706 -35.10237, 149.997706 -35.100125, 149.990969 -35.100125)))"
 ]
}

 The dataset includes 61 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051829-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13236574
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Joseph Henri Rispaud, http://www.wikidata.org/entity/Q128490596. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q128490596
DOI: 10.5281/zenodo.13236575
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Joseph Henri Rispaud, http://www.wikidata.org/entity/Q128490596. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q128490596
DOI: 10.5281/zenodo.13236576
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Americus Featherman, http://www.wikidata.org/entity/Q21512731. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21512731
DOI: 10.5281/zenodo.13236577
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Americus Featherman, http://www.wikidata.org/entity/Q21512731. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21512731
DOI: 10.48323/g20ag-rw259
title: Dataset Stability of selected exhaled breath volatiles stored in Tenax® TA adsorbent tubes at -80 °C

description: Agilent GC/MS records
DOI: 10.5281/zenodo.13236579
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Otto Uttendörfer, http://www.wikidata.org/entity/Q124737. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q124737
DOI: 10.15468/dl.zcm4fz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((143.087383 -37.137064, 143.087383 -37.13931, 143.091874 -37.13931, 143.091874 -37.137064, 143.087383 -37.137064)), ((143.091874 -37.13931, 143.091874 -37.143802, 143.09412 -37.143802, 143.09412 -37.13931, 143.091874 -37.13931)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051831-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.13236581
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Max Wetschky, http://www.wikidata.org/entity/Q27683890. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q27683890
DOI: 10.15468/dl.z8eajb
title: Occurrence Download

description: A dataset containing 697 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tetraloniella dentata (Germar, 1839)"
 ]
}

 The dataset includes 697 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051830-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpmspx
title: Occurrence Download

description: A dataset containing 695492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus suber L."
 ]
}

 The dataset includes 695492 records from 400 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051819-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5278/bb1a0238-2c65-4ef7-87b3-fc1b5412802d
title: Data on characterisation and bioactivity assessment of Salicornia ramosissima, Tripolium pannonicum, and Crithmum maritimum extracts

description: Data of the measurements regarding fatty acid profile, phytochemical content, and in vitro bioactivity.
DOI: 10.35003/ctpaxc/c5eevo
title: 10.1029-2018JE005590Figure210250012.pptx

description: :unav
DOI: 10.35003/ctpaxc/da1zjs
title: 10.1029-2018JE005590Figure210250005.pptx

description: :unav
DOI: 10.35003/ctpaxc/f6d1tk
title: 10.1029-2018JE005590Figure210250006.pptx

description: :unav
DOI: 10.35003/ctpaxc/isjhsd
title: 10.1029-2018JE005590Figure210250010.pptx

description: :unav
DOI: 10.35003/ctpaxc/pnzv8m
title: 10.1029-2018JE005590Figure210250009.pptx

description: :unav
DOI: 10.35003/ctpaxc/imxxz8
title: 10.1029-2018JE005590Figure210250014.pptx

description: :unav
DOI: 10.35003/ctpaxc/iym3nu
title: 10.1029-2018JE005590Figure210250003.pptx

description: :unav
DOI: 10.35003/ctpaxc/t3r9ue
title: 10.1029-2018JE005590Figure210250011.pptx

description: :unav
DOI: 10.35003/ctpaxc/vya4r9
title: 10.1029-2018JE005590Figure210250016.pptx

description: :unav
DOI: 10.35003/ctpaxc/00qkpi
title: 10.1029-2018JE005590Figure210250004.pptx

description: :unav
DOI: 10.35003/ctpaxc/dprixx
title: 10.1029-2018JE005590Figure210250001.pptx

description: :unav
DOI: 10.35003/ctpaxc/nhmrbk
title: 10.1029-2018JE005590Figure210250008.pptx

description: :unav
DOI: 10.35003/ctpaxc/xc17kn
title: 10.1029-2018JE005590Figure210250002.pptx

description: :unav
DOI: 10.35003/ctpaxc/yefapu
title: 10.1029-2018JE005590Figure210250018.pptx

description: :unav
DOI: 10.35003/ctpaxc/zba4n5
title: 10.1029-2018JE005590Figure210250007.pptx

description: :unav
DOI: 10.35003/ctpaxc
title: Replication Data for: Geologic History of the Northern Portion of the South Pole-Aitken Basin on the Moon

description: Key Points: • A geological map of the northern portion of South Pole-Aitken basin was made • Conﬁrmed and potential volcanic materials make up ~8% of the basin ﬂoor • The pre-SPA lunar crust was likely stratified with respect to iron
DOI: 10.35003/ctpaxc/9ukrux
title: 10.1029-2018JE005590Figurejgre21025fig0013.pptx

description: :unav
DOI: 10.35003/ctpaxc/iqfp8y
title: 10.1029-2018JE005590Figure210250017.pptx

description: :unav
DOI: 10.35003/ctpaxc/rsovlm
title: Table_1.tab

description: :unav
DOI: 10.35003/ctpaxc/tjffxt
title: 10.1029-2018JE005590Figure210250015.pptx

description: :unav
DOI: 10.15468/dl.7nfyxs
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.681668 -35.08665, 148.681668 -35.088896, 148.683914 -35.088896, 148.683914 -35.097879, 148.688405 -35.097879, 148.688405 -35.08665, 148.681668 -35.08665))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051833-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5278/3d8f5bf9-7a54-43ab-898a-ff865eb4df15
title: Data on characterisation of Salicornia europaea, Tripolium pannonicum, and Crithmum maritimum

description: Data on biomass green fractionation and chemical characterisation of fractions.
DOI: 10.15468/dl.x6ps4u
title: Occurrence Download

description: A dataset containing 4285 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cacatua goffiniana C.S.Roselaar & Michaels, 2004"
 ]
}

 The dataset includes 4285 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051832-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g9m98z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((141.944271 -37.13931, 141.944271 -37.146047, 141.948762 -37.146047, 141.948762 -37.13931, 141.944271 -37.13931))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051834-240626123714530/datasets/export for details.
DOI: 10.15468/dl.7ncpsh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.796204 -35.088896, 148.796204 -35.093387, 148.802941 -35.093387, 148.802941 -35.091141, 148.798449 -35.091141, 148.798449 -35.088896, 148.796204 -35.088896))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051835-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.13224473
title: Mouse culture and tissue aging - epigenetic clock pt2

description: Aging is associated with dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are unknown. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes using in vitro models. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissues in vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time point via reduced representation bisulfite sequencing. By developing a measure that tracked cellular aging in vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti‐aging interventions modulate this measure. Our measure, termed CultureAGE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be induced in vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re‐programmed to iPSCs. Enrichment and clustering analysis implicated EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be induced in vitro and used to uncover mechanistic insights into epigenetic aging.