cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7819303
title: Rescued Phased VCF for GIAB HG001

description: <strong>The GIAB VCF file contained anomalies that elicited run-time errors from both LRphase and WhatsHap. This VCF is noncompliant with the VCF 4.3 specification (https://samtools.github.io/hts-specs/VCFv4.3.pdf) in at least two ways: 1) Phase Set (PS) tags within genotype fields contain strings instead of 32-bit integers. 2) Sample columns in the VCF column header are labeled ”INTEGRATION” rather than containing the sample name. We also found ~25,000 records with malformed genotype records, which contained extra fields not defined in the format string. Finally, we encountered errors from WhatsHap that suggested at least a subset of indel records are also malformed. Neither program would run successfully without correcting these errors, but we were able to rescue the VCF using a custom Python script. Briefly, we transliterated PS tag strings to integer values by concatenating a unique integer with the chromosome number for each record (24, 25, and 26, for chromosomes X, Y, and M, respectively). This ensured that all phase sets have integer labels and only included variants on the same chromosome. We defined an additional format tag, OPS, under which we stored the original PS tag values. Likewise, the “INTEGRATION” label in the column name header was replaced with the sample name, “HG001”. Variants with malformed genotype fields were rescued by removing the fields not defined in the format string. Since we were unable to identify the direct cause for WhatsHap errors related to indel record parsing, we filtered out all records for indels and structural variants, leaving only SNV records in the VCF.</strong>
DOI: 10.5281/zenodo.10257128
title: Rescued Phased VCF for GIAB HG001

description: The GIAB VCF file contained anomalies that elicited run-time errors from both LRphase and WhatsHap. This VCF is noncompliant with the VCF 4.3 specification (https://samtools.github.io/hts-specs/VCFv4.3.pdf) in at least two ways: 1) Phase Set (PS) tags within genotype fields contain strings instead of 32-bit integers. 2) Sample columns in the VCF column header are labeled ”INTEGRATION” rather than containing the sample name. We also found ~25,000 records with malformed genotype records, which contained extra fields not defined in the format string. Finally, we encountered errors from WhatsHap that suggested at least a subset of indel records are also malformed. Neither program would run successfully without correcting these errors, but we were able to rescue the VCF using a custom Python script. Briefly, we transliterated PS tag strings to integer values by concatenating a unique integer with the chromosome number for each record (24, 25, and 26, for chromosomes X, Y, and M, respectively). This ensured that all phase sets have integer labels and only included variants on the same chromosome. We defined an additional format tag, OPS, under which we stored the original PS tag values. Likewise, the “INTEGRATION” label in the column name header was replaced with the sample name, “HG001”. Variants with malformed genotype fields were rescued by removing the fields not defined in the format string. Since we were unable to identify the direct cause for WhatsHap errors related to indel record parsing, we filtered out all records for indels and structural variants, leaving only SNV records in the VCF.
DOI: 10.5281/zenodo.10256919
title: 16s_1L14_1H14_SL14_SH14
DOI: 10.5281/zenodo.10256920
title: 16s_1L14_1H14_SL14_SH14
DOI: 10.5281/zenodo.10254976
title: XSum and CNN with paraphrases of summaries

description: These datasets contain the original datasets and paraphrases of the summaries.
CNN/DailyMail is available at https://huggingface.co/datasets/cnn_dailymail released under the Apache 2.0 license. 
XSum is available at https://huggingface.co/datasets/EdinburghNLP/xsum and was originally released under the MIT license.
The paraphraser is https://huggingface.co/humarin/chatgpt_paraphraser_on_T5_base available under the OpenRAIL license.
DOI: 10.5281/zenodo.10254975
title: XSum and CNN with paraphrases of summaries

description: These datasets contain the original datasets and paraphrases of the summaries.
CNN/DailyMail is available at https://huggingface.co/datasets/cnn_dailymail released under the Apache 2.0 license. 
XSum is available at https://huggingface.co/datasets/EdinburghNLP/xsum and was originally released under the MIT license.
The paraphraser is https://huggingface.co/humarin/chatgpt_paraphraser_on_T5_base available under the OpenRAIL license.
DOI: 10.6073/pasta/f219113373913f2daf421732e28d3c38
title: Ecological Impacts of Hurricanes Across the Yucatan Peninsula 1851-2000

description: This study used computer modeling to study the impacts of hurricanes across the Yucatan Peninsula since 1851. For details on methods and results please see the published paper (Boose, E. R., D. R. Foster, A. Barker Plotkin and B. Hall. 2003. Geographical and historical variation in hurricanes across the Yucatan Peninsula. In Lowland Maya Area: Three Millennia at the Human-Wildland Interface. A. Gomez-Pompa, M. F. Allen, S. Fedick and J. J. Jimenez-Osornio, eds. Haworth Press, New York, NY. In press). The Abstract from the paper is reproduced below. "The ecological impacts of hurricanes across the Yucatan Peninsula over the last 150 years were investigated using a simple meteorological model (HURRECON) developed at Harvard Forest as well as a database of historical hurricane data (HURDAT) maintained by the U. S. National Hurricane Center. All hurricanes over the period 1851-2000 with sustained winds of hurricane force (33 meters/sec) within 300 kilometers of the study region were analyzed (n = 105). Each storm was reconstructed to produce estimates of wind damage on the Fujita scale across the region. Individual reconstructions were then compiled to study cumulative impacts of all 105 storms. "Results showed considerable variation in hurricane activity from year to year, and from decade to decade, while at the half-century scale there was an increase in hurricane intensity since the mid-nineteenth century. Ninety percent of the hurricanes causing F1 damage or higher (on the Fujita scale) occurred in the months of August, September, and October. A strong spatial gradient in hurricane frequency and intensity extended across the region from northeast to southwest, resulting from (1) the greater number of hurricanes to the north, (2) the east to west movement of most hurricanes across the area, and (3) the tendency for most hurricanes to weaken significantly after landfall. For example, during the study period, northeastern parts of the peninsula experienced a minimum of one F3 hurricane, six F2 hurricanes, and thirty F1 hurricanes, while southwestern parts experienced no F2 or F3 damage and fewer than five F1 storms. Though a significant disturbance across much of the Yucatan Peninsula, hurricanes may have shorter-lived and less severe ecological impacts than fire or human land use. The interaction of these factors (e.g., fires following hurricanes), however, may be very significant and deserves further study."
DOI: 10.7924/r4c82h56b
title: Data from: Contraceptive Use Following Gestational Trophoblastic Disease: A Systematic Review

description: Contraceptive use following diagnosis of gestational trophoblastic disease or gestational trophoblastic neoplasia is key to allow for careful monitoring of beta-hCG without the risk of new incident pregnancy. However, there is lack of clarity regarding risks and benefits of different contraceptive methods to help guide patient and provider shared decision making on this topic.  Our aim was to systematically review the effect of contraceptive methods following gestational trophoblastic disease (GTD) on timing of beta-hCG remission, risk of post-molar gestational trophoblastic neoplasia (GTN), risk of unintended incident pregnancy, and interactions between contraceptive methods and disease treatment. Our findings suggest that hormonal contraception does not have an impact on beta-hCG normalization or the risk of developing post-molar gestational trophoblastic neoplasia. There was insufficient data to comment on interactions with cancer-directed treatment.
DOI: 10.6073/pasta/3345f86b68a9dc514387e3735c0944b9
title: Net Carbon Exchange of a Young Upper-Slope Deciduous Forest at Harvard Forest LPH Tower 2002-2010

description: This data set contains sensible heat exchange, water vapor exchange and carbon exchange as well as environmental data for a deciduous forest dominated by red oak (Quercus rubra). It is 1.1 km WNW of the EMS tower where continuous eddy covariance measurements began in 1992 (see HF004). The High Deciduous site is about 385 m a.s.l., or 35 m higher in elevation than the EMS, which is situated in a relatively low area near a stream. The forest near this eddy covariance tower is broadly similar in species composition to the EMS site, but it is younger and shorter in stature. The site was cleared for pasture, but not deeply plowed or planted, in the 18th and19th centuries. Agriculture on the site was abandoned near the end of the 19th century. The forest within 200 to 300 m of the eddy covariance tower to the NW, W, SW, and S burned in an intense fire in 1957, which left few or no surviving trees.
DOI: 10.24400/527896/a01-2023.001
title: Experimental products including CFOSat Topography for wave current interactions studies

description: 3 datasets are proposed 1/ along-track L3 across-track geostrophic velocities (from sea level anomaly and absolute dynamic topography) filtered at 15 and 60 km, with angle values (giving the positive across-track direction) of CFOSat mission, 2/ gridded L4 sea level anomalies and geostrophic velocities from 8 merged missions including CFOSat (Sentinel-6, Jason-3, Sentinel-3A, Sentinel-3B, Altika, Cryosat, HY2B, CFOSat) 3/ gridded L4 Sea level anomalies and geostrophic velocities from 7 merged missions without CFOsat (Sentinel-6, Jason-3, Sentinel-3A, Sentinel-3B, Altika, Cryosat, HY2B). Sea level measurements from CFOsat used for computing L3 and L4 products were retrieved using the latest version of CFOsat processing. For the L4 products, the geostrophic current is derivated from sea level anomaly maps generated with MIOST multiscale and multivariate mapping tool (Ballarotta et al., 2023, https://doi.org/10.5194/essd-15-295-2023) with level 3 altimetric data distributed by the EU Copernicus Marine Service (product SEALEVEL_GLO_PHY_L3_MY_008_062, https://doi.org/10.48670/moi-00146). Details in Jenn-Alet et al., OSTST 2023, CFOSAT Sea level and current demonstration products.
DOI: 10.5281/zenodo.10257229
title: SDSS DR72 Large Scale Structure random catalog

description: This is a catalog of random points in the footprint of the Sloan Digitial Sky Survey (specifically the NYU-VAGC) used for defining the angular mask of the survey. This dataset was originally created/hosted by Michael Blanton at NYU as part of the Sloan Digital Sky Survey.
DOI: 10.5281/zenodo.10257228
title: SDSS DR72 Large Scale Structure random catalog

description: This is a catalog of random points in the footprint of the Sloan Digitial Sky Survey (specifically the NYU-VAGC) used for defining the angular mask of the survey. This dataset was originally created/hosted by Michael Blanton at NYU as part of the Sloan Digital Sky Survey.
DOI: 10.6073/pasta/396d959f8125d6285bd3d4406d09b922
title: Long-Term Dynamics of Oak and Chestnut in Central Massachusetts from 3500 BP to Present

description: Despite decades of study we have limited insights into the nature of the pre-European landscape of the northeastern USA and the forces and changes that shaped modern forest patterns. Information on such long-term forest dynamics would provide critical insights into the relationships among environmental change, land-use history and biotic responses and is greatly needed for conservation planning. To address these issues we used modern, historical, and paleoecological approaches to reconstruct the 3500-year history of a New England upland region dominated by oak and (formerly) chestnut forests and to interpret the interactions among climate change, natural and human disturbance, and site factors in controlling vegetation patterns and dynamics at different spatial scales. The results indicate that stand, landscape and regional forest dynamics were most strongly driven by climate, notably an apparent cooling and increase in moisture availability c. 1500 yr BP, and European land-use activities commencing 260 yr BP. However, the abundance of oak and chestnut (fire-tolerant, sprouting species) and the distribution of hemlock (fire-intolerant) at a stand to landscape scale were also influenced by fire, which, in turn, varied with climate and human activity. Despite, or perhaps as a consequence of ongoing disturbance by fire and presumably windstorms in this hurricane-prone region, the pre-European period was marked by two 1000+ year periods of remarkably stable forest composition, separated by an abrupt compositional shift. In contrast, over the past 260 years the vegetation has changed rather continuously in response to human activity, producing stand, landscape and regional patterns that are novel as well as recent in origin. Chestnut was a major component of some pre-European landscapes in New England, in part because of occasional fire, and that cultural and physical factors have interacted over millennia to control vegetation patterns and dynamics. Our analyses also suggest that the composition of low diversity forests can be remarkably stable over millennia. The range of ecological, cultural and management insights afforded by this study underscores the fundamental utility of very long-term research in science and policy development.
DOI: 10.5281/zenodo.10257205
title: Data supporting "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables"

description: This repository contains the set of data and the code to reproduce the results shown in "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables" published on Journal of Chemical Engineering and Data (DOI: 10.1021/acs.jced.3c00538).
DOI: 10.5281/zenodo.10257206
title: Data supporting "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables"

description: This repository contains the set of data and the code to reproduce the results shown in "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables" published on Journal of Chemical Engineering and Data (DOI: 10.1021/acs.jced.3c00538).
DOI: 10.6073/pasta/9329fd9e05ad60b40f53f649a9b857bb
title: Development and Expansion of Peatlands in Central New England from 14000 BP to Present

description: As peatlands form they create a temporal archive of community development, allowing the reconstruction of vegetation dynamics through the analysis of sediments and the development of detailed chronologies of successional change. Peatland formation occurs through two mechanisms: (i) terrestrialization, when a water body fills with sediments and peat; and (ii) paludification, the conversion of dry land to peatland. In temperate regions, where high summer temperatures may limit peat accumulation, general models of peatland development suggest that allogenic factors such as climate change control peatland development and that terrestrialization is the primary mechanism of formation. This study evaluates this widely accepted model by comparing the developmental histories of three peatlands within the same climate region in New England in order to: (i) describe the development and timing of successional events among peatlands; (ii) document the roles of paludification and terrestrialization as developmental mechanisms; and (iii) evaluate the importance of climate change vs. autogenic factors in peatland development in this temperate region. Basin morphometry, sediment stratigraphies, and chronologies of community change determined through radiocarbon dating indicate that peatland development at each site involved terrestrialization followed by paludification, with no apparent influence of broad-scale climate change on the timing of these processes. Paludification was consistently initiated coincident with the consolidation of a shrub mat across each lake-basin, and was controlled in extent and rate by the topography of the adjoining uplands. The timing of stratigraphic changes varied among sites, suggesting that autogenic factors associated with the accumulation of peat rather than regional climate change controlled development. These results provide the foundation for a model of temperate peatland development driven by autogenic factors and caution against the use of temperate peatland development as a proxy for climatic reconstruction.
DOI: 10.18112/openneuro.ds004847.v1.0.0
title: Associations between neighborhood resources and youth’s response to reward omission in a task modeling negatively biased environments
DOI: 10.18742/24468220.v1
title: Diversity representation in SBAQs raw data nonidentifiable

description: Mixed methods RCT exploring the use of gender, sexuality, and ethnicity as demographic identifiers in written assessments for undergraduate medical education, and the impact on question performance by medical students.
DOI: 10.5281/zenodo.8360494
title: FASTA 16s gene sequencing files for Control points for design of taxonomic composition in synthetic human gut consortia

description: FASTA file output from Illumina MiSeq. Processed tally files (reads / species used to calculate relative abundances) are available in the other Zenodo repository listed in the key resources table, under ~ BC###/rawData/tallyfile.xlsx
DOI: 10.5281/zenodo.8360495
title: FASTA 16s gene sequencing files for Control points for design of taxonomic composition in synthetic human gut consortia

description: FASTA file output from Illumina MiSeq. Processed tally files (reads / species used to calculate relative abundances) are available in the other Zenodo repository listed in the key resources table, under ~ BC###/rawData/tallyfile.xlsx
DOI: 10.5281/zenodo.8356546
title: Code and processed data - Control points for design of taxonomic composition in synthetic human gut consortia

description: Code, optical density data, and sequencing tally files (relative abundance from 16S sequencing of defined communities) for Control points for design of taxonomic composition in synthetic human gut consortia. Files are organized by experiment with a readme file contained within the .zip file. "Setup" folders have information about expeirmental design, "rawData" folders have optical density and tallyfiles, "analysis" folders have scripts used to analyze data and generate models.
DOI: 10.5281/zenodo.8356547
title: Code and processed data - Control points for design of taxonomic composition in synthetic human gut consortia

description: Code, optical density data, and sequencing tally files (relative abundance from 16S sequencing of defined communities) for Control points for design of taxonomic composition in synthetic human gut consortia. Files are organized by experiment with a readme file contained within the .zip file. "Setup" folders have information about expeirmental design, "rawData" folders have optical density and tallyfiles, "analysis" folders have scripts used to analyze data and generate models.
DOI: 10.5281/zenodo.10192411
title: DCE-MRI DRO Data (Daniel Barboriak)

description: This is the digital reference object (DRO) data created to validate software build to analyse DCE-MRI with the General Kinetic Model (GKM) or extended GKM (eGKM) as well as software for evaluating T1 mapping using the variable flip angle (VFA) method.
The data has been produced for the Quantitative Imaging Biomarkers Alliance (QIBA) and was moved from the retired Quantitative Imaging Data Warehouse (QIDW).
It can be used to evaluate software packages for their conformance to the quantitative DCE-MRI Profile 2.0 soon to be release.
DOI: 10.5281/zenodo.10192412
title: DCE-MRI DRO Data (Daniel Barboriak)

description: This is the digital reference object (DRO) data created to validate software build to analyse DCE-MRI with the General Kinetic Model (GKM) or extended GKM (eGKM) as well as software for evaluating T1 mapping using the variable flip angle (VFA) method.
The data has been produced for the Quantitative Imaging Biomarkers Alliance (QIBA) and was moved from the retired Quantitative Imaging Data Warehouse (QIDW).
It can be used to evaluate software packages for their conformance to the quantitative DCE-MRI Profile 2.0 soon to be release.
DOI: 10.5281/zenodo.10257261
title: DCE-MRI DRO Data (Daniel Barboriak)

description: This is the digital reference object (DRO) data created to validate software build to analyse DCE-MRI with the General Kinetic Model (GKM) or extended GKM (eGKM) as well as software for evaluating T1 mapping using the variable flip angle (VFA) method.
The data has been produced for the Quantitative Imaging Biomarkers Alliance (QIBA) and was moved from the retired Quantitative Imaging Data Warehouse (QIDW).
It can be used to evaluate software packages for their conformance to the quantitative DCE-MRI Profile 2.0 soon to be release.
DOI: 10.5281/zenodo.8219552
title: Tropical Andes Land Cover Dataset (TALANDCOVER)

description: The Tropical Andes Land Cover Dataset (TALANDCOVER) was built for the department of Antioquia Colombia and consists of three folders for the three types of sampling.

Random: 5000 images
Balanced of minimum 50% coverage per class: 1389 images
Balanced of minimum 70% coverage per class:731 images
The coordinate system of each dataset is EPSG:3857 - WGS 84 / Pseudo-Mercator with spatial resolution of 4.77 meters and 128*128px.
Example of image and corresponding label name:

image_PNICFI_D2019-05_T586-1068_C1_N100.tif
label_PNICFI_D2019-05_T586-1068_C1_N100.tif
Pixel values for label are:
0 Bare-degraded lands1 Grasslands2 Heterogeneous agricultural areas3 Dense forest4 Water bodies5 Built-up areas
There are multiple keywords intentionally inserted in each image name or label name that enable the split of the name in pieces of information about each image and label metadata.
Spliting the image or label name by the keywords, would get 6 items:

The item (image/label) describe if the file correspond to a patch image or a patch label.
The second item (Keyword "_P") gives the name of the product NICFI (https://assets.planet.com/docs/NICFI_User_Guide_v4_EN.pdf)
The third item (keyword "_D") gives a date for the composite
The fourth (keyword "_T") gives the tile number, as stated in the planet scope visual base map documentation: "The name of each basemap quad within the Basemaps API is designed to represent the x and y position of the quad within the two dimensional grid which makes up the basemap. It is generally {X}-{Y}, where X and Y are the x and y position of the quad in the grid". https://developers.planet.com/docs/data/visual-basemaps/
The fifth (keyword "_C") when available gives the cover class used by the slidding windows to extract the patch, resulting in at least a minimum of 50% or 70% of the pixels within the image correspond to that specific cover class, depending on the selected sample dataset.
Take into account that random samples dont have this keyword since the patches where collected at random from a 2d grid without regard of the cover classes present
 
Article : "Land Cover Classification in the Antioquia Region of the Tropical Andes Using NICFI Satellite Data Program Imagery and Semantic Segmentation Techniques".