cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10732311
title: DICOM WG-26 Whole Slide Imaging Annotations Connectathon: Imaging Data Commons entry

description: This data descriptor contains DICOM Slide Microscopy (SM modality) images and DICOM 2D point and polygon Bulk Annotations (ANN modality) submitted by the Imaging Data Commons team as part of the participation in the 2024 DICOM Working Group 26 Annotations Connectathon (https://dicom-wg26-connectathons.github.io/2024-annotations/).

Detailed content of the descriptor is as follows:



Images correspond to 3 series selected from the DICOM-converted slides incuded in the TCGA-READ collection (originally shared in vendor-specific format in https://portal.gdc.cancer.gov/projects/TCGA-READ) and available from NCI Imaging Data Commons [1] at https://portal.imaging.datacommons.cancer.gov/explore/filters/?collection_id=tcga_read. Specifically, the following series are included, as defined by their `PatientID`, `StudyInstanceUID` and `SeriesInstanceUID` values. Each individual series contains multiple files corresponding to different resolution layers, shared as zip files. 



`TCGA-AF-2687.zip`: series `1.3.6.1.4.1.5962.99.1.2251401802.152239158.1638633974346.2.0` https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.213661963103110408605329613498871186883/series/1.3.6.1.4.1.5962.99.1.2251401802.152239158.1638633974346.2.0

`TCGA-AF-2689.zip`: series `1.3.6.1.4.1.5962.99.1.2259090539.712983657.1638641663083.2.0` https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.312916405820155829215771528638931942827/series/1.3.6.1.4.1.5962.99.1.2259090539.712983657.1638641663083.2.0

`TCGA-AF-2690.zip`: series `1.3.6.1.4.1.5962.99.1.2247972296.1080138101.1638630544840.2.0` https://viewer.imaging.datacommons.cancer.gov/slim/studies/2.25.158926540358526295486644564130790202309/series/1.3.6.1.4.1.5962.99.1.2247972296.1080138101.1638630544840.2.0



`polygon_annotations.zip`: 2D polygon annotations of the boundary of the cell nuclei. Conversion into DICOM ANN was performed from the original content shared in [2].

`point_annotations.zip`: 2D point annotations corresponding to the centroids of the cell nuclei defined in the prior polygon annotations.

`rectangle_annotations.zip`: 2D rectangle annotations corresponding to the axis-aligned bounding box of the cell nuclei defined in the prior polygon annotations.

`ellipse_annotations.zip`: 2D ellipse annotations corresponding to the ellipse fit to the cell nuclei defined in the prior polygon annotations.

`screenshots.pdf`: screenshots demonstrating visualization of the included annotations in the open source Slim viewer (https://github.com/ImagingDataCommons/slim) (note these visualizations were produced using a development branch of the software)

`run_verify.sh`: script that was used to run `dciodvfy` validator and save validation results.


Zip files with the annotations also include the output of the `dciodvfy` validator (https://dclunie.com/dicom3tools/dciodvfy.html) version `20240227102104` for each of the files.
DOI: 10.5281/zenodo.10821837
title: CoUDlabs_TA_USFD_02_ANNULAR_Regueiro. Time series analysis of sewer temperatures in an annular flume to estimate sediment accumulation

description: This dataset contains the results of the experimental campaign and how data were collected on the the Co-UDlabs Transnational Access project: Temperature time series analysis for predicting sedimentation in sewer systems, by Regueiro-Picallo et al. The Transnational Access project was funded under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101008626.

The experiments were designed to further develop an innovative methodology for measuring sediment bed deposits in UDS based on temperature data analysis (Regueiro-Picallo et al., 2023; Regueiro-Picallo et al., 2024). Particularly, the aim of these experiments was to study the influence of the sewer hydrodynamics for estimating the sediment accumulation using temperature-based methods. Therefore, the main tasks of this project were the design of a temperature-control system for the ANNULAR flume to reproduce sewer temperature patterns, and the development of an experimental campaign including different flow, sediment depth and temperature pattern conditions. The purpose of these measurements is to prove the use of simplified systems to monitor sediment accumulation in sewer systems.

The data are described so that others can use and reproduce.
DOI: 10.5281/zenodo.10821838
title: CoUDlabs_TA_USFD_02_ANNULAR_Regueiro. Time series analysis of sewer temperatures in an annular flume to estimate sediment accumulation

description: This dataset contains the results of the experimental campaign and how data were collected on the the Co-UDlabs Transnational Access project: Temperature time series analysis for predicting sedimentation in sewer systems, by Regueiro-Picallo et al. The Transnational Access project was funded under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101008626.

The experiments were designed to further develop an innovative methodology for measuring sediment bed deposits in UDS based on temperature data analysis (Regueiro-Picallo et al., 2023; Regueiro-Picallo et al., 2024). Particularly, the aim of these experiments was to study the influence of the sewer hydrodynamics for estimating the sediment accumulation using temperature-based methods. Therefore, the main tasks of this project were the design of a temperature-control system for the ANNULAR flume to reproduce sewer temperature patterns, and the development of an experimental campaign including different flow, sediment depth and temperature pattern conditions. The purpose of these measurements is to prove the use of simplified systems to monitor sediment accumulation in sewer systems.

The data are described so that others can use and reproduce.
DOI: 10.6084/m9.figshare.25421140
title: ftdna_nk

description: nonplblic
DOI: 10.6084/m9.figshare.25421140.v1
title: ftdna_nk

description: nonplblic
DOI: 10.21966/6zp4-ye07
title: Mobile Invertebrate Rocky Intertidal Surveys - BC Central Coast - 2016-2018
title: Relevés intertidaux rocheux d'invertébrés mobiles - Côte centrale de la Colombie-Britannique - 2016-2018

description: The mobile invertebrate community associated with three primary habitat types (mussels, barnacle and Fucus distichus) was assessed from 2016-2018 at three coastal sites along the northwest edge of Calvert Island on the central coast of British Columbia. All sites were exposed rocky shorelines with distinct zones of mussels, barnacles, and Fucus distichus algae. We surveyed the abundance and diversity of the mobile invertebrate community within permanent plots in each zone. Counts were performed using the point intercept method with a strung quadrat and size was measured for a subset of species. Plots were also subsampled using smaller unstrung quadrats, within which smaller limpets and littorine snails were counted. The Sites were surveyed on an approximately monthly basis from May-September, and two winter surveys in November and February. We conducted 6 surveys in 2018, 5 in 2017, and 3 in 2016.
description: La communauté mobile d'invertébrés associée à trois types d'habitats principaux (moules, balanes et Fucus distichus) a été évaluée de 2016 à 2018 sur trois sites côtiers le long de la limite nord-ouest de l'île Calvert, sur la côte centrale de la Colombie-Britannique. Tous les sites étaient des rivages rocheux exposés avec des zones distinctes de moules, de balanes et d'algues Fucus distichus. Nous avons étudié l'abondance et la diversité de la communauté d'invertébrés mobiles dans des parcelles permanentes de chaque zone. Les dénombrements ont été effectués à l'aide de la méthode d'interception ponctuelle avec un quadrat cordé et la taille a été mesurée pour un sous-ensemble d'espèces. Les parcelles ont également été sous-échantillonnées à l'aide de plus petits quadrats non cordés, dans lesquels des patelles et des escargots littorins plus petits ont été dénombrés Les sites ont été étudiés approximativement tous les mois de mai à septembre, et deux relevés hivernaux en novembre et février. Nous avons mené 6 enquêtes en 2018, 5 en 2017 et 3 en 2016.
DOI: 10.5281/zenodo.10823127
title: CNF Encoded Isomorphic and Optimized Miters from Hardware Model Checking Competition 2012 Models

description: These miter benchmarks are used in a paper on congruence closure in 2024.

The miter AIGs in the [`aig`](aig) directory are the same as those used togenerate CNFs of miter benchmarks submitted to the SAT Challenge in 2012.Some of them have regularly been used in the SAT Competitions since then.

The AIGs are separated into two sets:

- [`aig/iso`](aig/iso) miters of isomorphic circuits- [`aig/opt`](aig/opt) miters of optimized versus original circuit

The first set checks equivalence of one circuit with itself in the[`aig/iso`](aig/iso) (isomorphic) sub-directory and second set containsequivalence checking problems (aka miters) comparing the original circuitwith an optimized version in the [`aig/opt`](aig/opt) (optimized)sub-directory.  The optimized versions of the circuits were obtained in 2012by the `dc2` script for [ABC](https://people.eecs.berkeley.edu/~alanmi/abc).We did not re-run ABC with a newer version in order to make sure we have asbase-line in our experiments the same CNFs, as they are well-known, i.e., they have been used in the SAT competitions for several years.

Note that the original AIGER models have state elements (called "latches"in AIGER terminology), but both the optimization with ABC as well as ourequivalence checking is purely combinational, by treating latches asadditional pseudo inputs, and next-state functions as output-functions.  Themiters were accordingly generated (by the 2011 version) of `aigmiter` usingthe `-c` option.  For the same reason as for ABC explained above, we did notrerun `aigmiter` either.

We then encoded the two sets of AIGs into CNF in two different ways.The first encoding just uses a simple Tseitin encoding, withoutPlaisted-Greenbaum optimization, i.e., using the `--no-pg` option, as in 2012.Even though we use a new version of `aigtocnf` in `src/aiger/aigtocnf.c` wemade sure that identical CNFs are generated for this first encoding variantby checking that the MD5 sum of the (actually compressed) CNF files match.This required to disable a newly introduced cone-of-influence (COI)optimization with `--no-coi` which skips unreachable gates even when thePlaisted-Greenbaum optimization is disabled.

The second variant of the encoding detects XOR and ITE gates by patternmatching and produces more concise CNFs by skipping internal AND gatesof detected XOR and ITE gates producing a direct encoding instead.

This gives the following sets of CNFs;

- [`cnf/ands/iso`](cnf/ands/iso) isomorphic circuits with ANDs only- [`cnf/ands/opt`](cnf/ands/opt) optimized versus original with ANDs only- [`cnf/xits/iso`](cnf/xits/isor) isomorphic circuits with ANDs, XORs, ITEs- [`cnf/xits/opt`](cnf/xits/opt) optimized versus original with ANDs, XORs, ITEs

All the CNFs in these directories have the same original file name of theAIGER model to simplify run-time comparison.  In `cnf/all` we furtherprovide links with qualified names to distinguish them.
DOI: 10.5281/zenodo.10822951
title: Reduced Gun Violence Frame Corpus data set for the Text2Story 2024 article: "Evaluating the Ability of Computationally Extracted Narrative Maps to Encode Media Framing"

description: Title: Simplified Gun Violence Frame Corpus (GVFC) Subset

Description:This data set is a simplified subset of the Gun Violence Frame Corpus (GVFC) from Liu et al. (2019). The original GVFC consists of 1300 news articles in English from multiple U.S. based sources extracted during the year 2018, focusing on media frames commonly used when reporting the issue of Gun Violence. The original data set has 9 types of frames, including both issue-specific and generic frames. Due to high computational costs in our analysis methods, we decreased the data set size from 1300 articles to 131 articles using stratified sampling, maintaining the original distribution of the frame labels. We also manually searched for the original sources of each article based on its headline and added the missing temporal information and news source to the data set, as it was required by our algorithms.

To further reduce the complexity of the framing model and account for the smaller data set size, we grouped the original nine frames into three higher-level frames:

1. Frame 1: Political Issues - Combining the first, second, and third frames, which focus on political issues mostly related to gun control.2. Frame 2: Public Services - Combining the fourth and fifth frames, which focus on mental healthcare issues, as well as school and public safety.3. Frame 3: Cultural and Societal Issues - Combining the last four frames, which are oriented towards cultural or societal issues, including discussions around race and ethnicity, public opinion, and economic consequences.

The resulting simplified data set contains 131 news articles, each labeled with one of the three higher-level frames, along with the necessary temporal information and news source for the narrative extraction process.

If you use this data set, please make sure to cite the original GVFC paper and our workshop paper please. 

References:



Liu et al. (2019) "Detecting Frames in News Headlines and Its Application to Analyzing News Framing Trends Surrounding US Gun Violence", 23rd Conference on Computational Natural Language Learning (CoNLL 2019).

Concha Macías, Sebastián and Keith Norambuena, Brian (2024). "Evaluating the Ability of Computationally Extracted Narrative Maps to Encode Media Framing", Text2Story 2024 Workshop, ECIR 2024.
DOI: 10.5281/zenodo.10822952
title: Reduced Gun Violence Frame Corpus data set for the Text2Story 2024 article: "Evaluating the Ability of Computationally Extracted Narrative Maps to Encode Media Framing"

description: Title: Simplified Gun Violence Frame Corpus (GVFC) Subset

Description:This data set is a simplified subset of the Gun Violence Frame Corpus (GVFC) from Liu et al. (2019). The original GVFC consists of 1300 news articles in English from multiple U.S. based sources extracted during the year 2018, focusing on media frames commonly used when reporting the issue of Gun Violence. The original data set has 9 types of frames, including both issue-specific and generic frames. Due to high computational costs in our analysis methods, we decreased the data set size from 1300 articles to 131 articles using stratified sampling, maintaining the original distribution of the frame labels. We also manually searched for the original sources of each article based on its headline and added the missing temporal information and news source to the data set, as it was required by our algorithms.

To further reduce the complexity of the framing model and account for the smaller data set size, we grouped the original nine frames into three higher-level frames:

1. Frame 1: Political Issues - Combining the first, second, and third frames, which focus on political issues mostly related to gun control.2. Frame 2: Public Services - Combining the fourth and fifth frames, which focus on mental healthcare issues, as well as school and public safety.3. Frame 3: Cultural and Societal Issues - Combining the last four frames, which are oriented towards cultural or societal issues, including discussions around race and ethnicity, public opinion, and economic consequences.

The resulting simplified data set contains 131 news articles, each labeled with one of the three higher-level frames, along with the necessary temporal information and news source for the narrative extraction process.

If you use this data set, please make sure to cite the original GVFC paper and our workshop paper please. 

References:



Liu et al. (2019) "Detecting Frames in News Headlines and Its Application to Analyzing News Framing Trends Surrounding US Gun Violence", 23rd Conference on Computational Natural Language Learning (CoNLL 2019).

Concha Macías, Sebastián and Keith Norambuena, Brian (2024). "Evaluating the Ability of Computationally Extracted Narrative Maps to Encode Media Framing", Text2Story 2024 Workshop, ECIR 2024.
DOI: 10.6084/m9.figshare.25370821
title: Data from: Trophic impact of an invasive mysid shrimp depends on zooplankton community composition: a mesocosm experiment

description: Data are from:Patonai K., Endrédi A., Horváth Z., Borza P., Pálffy K., Dobosy P. & Vad C.F. Trophic impact of an invasive mysid shrimp depends on zooplankton community composition: a mesocosm experiment. <i>Freshwater</i> <i>Biology </i>doi: 10.1111/FWB.14233
DOI: 10.6084/m9.figshare.25370821.v1
title: Data from: Trophic impact of an invasive mysid shrimp depends on zooplankton community composition: a mesocosm experiment

description: Data are from:Patonai K., Endrédi A., Horváth Z., Borza P., Pálffy K., Dobosy P. & Vad C.F. Trophic impact of an invasive mysid shrimp depends on zooplankton community composition: a mesocosm experiment. <i>Freshwater</i> <i>Biology </i>doi: 10.1111/FWB.14233
DOI: 10.5281/zenodo.7004070
title: Biosurfer data files for analysis

description: This repository contains data used for running Biosurfer, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.



	
The first zip file (biosurfer_gencode_toy_data.zip) is a small subset of the GENCODE Human version 38 for the purpose of trial run and testing.
	
The second zip file (biosurfer_gencode_v41_data.zip) contains GENCODE Human version 41.
	
The third zip file (biosurfer_gencode_v42_data.zip) contains GENCODE Human version 42.
	
The fourth zip file (biosurfer_wtc11_data.zip) contain karyotypically normal human stem cell line data (WTC11).
DOI: 10.5281/zenodo.7004071
title: The Human GENCODE release 38 toy data

description: This is a small subset of the GENCODE Human version 38 for the purpose of trial run and testing of Biosurfer, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
DOI: 10.5281/zenodo.7182809
title: Biosurfer data files for analysis

description: This repository contains data used for running Biosurfer, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology. Hybrid analysis, a pipeline of Biosurfer was performed using the following data that has a gene annotation files (GTF), a reference sequences (genome, transcriptome), and a protein feature files (e.g., Pfam mappings). The first zip file (biosurfer_gencode_toy_data.zip) is a small subset of the GENCODE Human version 38 for the purpose of trial run and testing. The second zip file (biosurfer_gencode_v41_data.zip) contains GENCODE Human version 41. The third zip file (biosurfer_wtc11_data.zip) contain karyotypically normal human stem cell line data (WTC11).
DOI: 10.5281/zenodo.7297008
title: Biosurfer data files for analysis

description: This repository contains data used for running Biosurfer, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.



	
The first zip file (biosurfer_gencode_toy_data.zip) is a small subset of the GENCODE Human version 38 for the purpose of trial run and testing.
	
The second zip file (biosurfer_gencode_v41_data.zip) contains GENCODE Human version 41.
	
The third zip file (biosurfer_gencode_v42_data.zip) contains GENCODE Human version 42.
	
The fourth zip file (biosurfer_wtc11_data.zip) contain karyotypically normal human stem cell line data (WTC11).
DOI: 10.25612/837.erv954gkdkln
title: HCAD Median Year Structure Built for Residential Buildings

description: Median year structure built datasets at block, block group, census tract, and CTA level for residential buildings in Harris County. Calculated using HCAD data.
DOI: 10.21966/82bd-ks94
title: Kelp extent for the McNaughton Group Islands (2017), Manley Island (2017), and Serpent Group Islands (2016), British Columbia, Canada
title: Étendue de varech pour les îles McNaughton Group (2017), Manley Island (2017) et Serpent Group Islands (2016), Colombie-Britannique, Canada

description: This is a polygon layer mapping kelp canopy extent for the McNaughton Group islands, Manley Island, and Serpent Group Islands.

Kelp canopy extent was mapped from imagery taken using an unoccupied aerial system (UAS). McNaughton Imagery was taken in late May 2017, the Manley images were captured in late July 2017, and the Serpent Group images were made in early July 2016. The images were captured using a DJI Phantom 3 professional UAS equipped with a commercial grade 4k RGB (See attached UAS methods). Kelp bed polygons were drawn manually in ArcGIS 10.5.1. Only beds containing greater than ~3 fronds were mapped. Beds were considered connected when less than ~5m separated them. Single fronds and single frond outliers were not digitized. Vertices were placed every 4m or less (more vertices were used on complex shapes). The attributes in this table are limited to the perimeter length (m) and area (m^2) of each kelp bed polygon. Area was determined in the NAD_1983_CSRS_BC_Environment_Albers projection. Species and bed density were not recorded for this dataset.
description: Il s'agit d'une couche polygonale qui cartographie l'étendue de la canopée de varech pour les îles McNaughton Group, Manley Island et Serpent Group Islands.

L'étendue du couvert de varech a été cartographiée à partir d'images prises à l'aide d'un système aérien inoccupé (UAS). McNaughton Imagery a été prise fin mai 2017, les images de Manley ont été capturées fin juillet 2017 et les images du Serpent Group ont été réalisées début juillet 2016. Les images ont été capturées à l'aide d'un UAS professionnel DJI Phantom 3 équipé d'un RVB 4K de qualité commerciale (voir méthodes UAS ci-jointes). Les polygones de lit de varech ont été dessinés manuellement dans ArcGIS 10.5.1. Seuls les lits contenant plus de 3 frondes ont été cartographiés. Les lits étaient considérés comme connectés lorsque moins de 5 m les séparaient. Les frondes simples et les valeurs aberrantes à une seule fronde n'ont pas été numérisées. Les sommets étaient placés tous les 4 m ou moins (plus de sommets étaient utilisés sur des formes complexes). Les attributs de ce tableau sont limités à la longueur périmétrique (m) et à la surface (m^2) de chaque polygone de lit de varech. La surface a été déterminée dans la projection NAD_1983_CSRS_BC_Environment_Albers. Les espèces et la densité de lit n'ont pas été enregistrées pour cet ensemble de données.
DOI: 10.5281/zenodo.10822957
title: Gene expression count matrix for 4 T cell subtypes from ROSMAP participants

description: Peripheral blood mononuclear cells (PBMCs) from participants in the Rush Religious Orders Study/Memory and Aging Project (ROSMAP) were isolated by Ficoll gradient centrifugation, then sorted by high-speed flow cytometry into the following T cell subtypes:  CD4+CD45RO-, CD4+CD45RO+, CD8+CD45RO-, and CD8+CD45RO+.  Total RNA was extracted using buffer TCL (Qiagen), then RNA-seq libraries were prepared according to the Single Cell RNA Barcoding and Sequencing method originally developed for single-cell RNA-seq, adapted for extracted total RNA.  RNA libraries were collected on a single 384-well plate and sequenced on the Illumina HiSeq using the High-throughput 3’ Digital Gene Expression (DGE) library.  The "RNA count matrix" file is the raw counts from the 384-well plate, while the "ROSMAP_Tcell_DGE_PlateMap" file contains metadata for the wells on the plate, by well position.