cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3886/e195641v1
title: Data and Code for: Increasing Organ Donor Registration as a Means to Increase Transplantation: An Experiment With Actual Organ Donor Registrations

description: The U.S. has a severe shortage of organs for transplant. Recently --- inspired by research based on hypothetical choices --- jurisdictions have tried to increase organ donor registrations by changing how the registration question is asked. We evaluate these changes with a novel "field-in-the-lab" experiment, in which subjects change their real organ donor status, and with new donor registration data collected from U.S. states. A "yes/no" frame is not more effective than an "opt-in" frame, contradicting conclusions based on hypothetical choices, but other question wording can matter and asking individuals to reconsider their donor status increases registrations.
description: Waves 1 and 2 included people with a Massachussetts driver's license, learner's permit, or state identification card and a social security number. Wave 3 also included Massachussetts residents and required the same credentials, but was a Qualtrics panel rather than conducted in-person in the lab. The Next of Kin study included participants from Amazon's Mechanical Turk  . Smallest Geographic Unit: DMV data: state
DOI: 10.48804/0jqlk7
title: Dataset of The Greek Source of the Slavonic Version of Ignatius' Letter to the Romans? A Comparison between MSS Taur. C.I.10, Ath. Chil. 644 and Vindob. Slav. 33

description: This dataset includes the transcriptions of the Greek codex Taurinensis BNU C.I.10 and the Slavonic codices Athos, Chilandaricus Slav. 644 and Vindobonensis Slav. 33. This is the data I used for my article “The Greek Source of the Slavonic Version of Ignatius' Letter to the Romans. A Comparison between MSS Taur. C.I.10, Ath. Chil. 644 and Vindob. Slav. 33” (forthc.). Concerning the Greek transcription, I wrote the nomina sacra in full and I indicated proper names with capital letters. In the Slavonic transcription, the nomina sacra are written in its abbreviated form. I used the TEI guidelines (P5 Version 4.9.0., last updated on 24th January 2025, revision f73186978) for making my transcriptions electronically available with a text-critical scope. It emphasizes the textual content of Ignatius of Antioch’s Letter to the Romans, but the dataset does not give a detailed description of the palaeographic context of the codices.
DOI: 10.5281/zenodo.15125548
title: Wetland Land-Cover Segmentation and Classification in the Netherlands (Sentinel-2 satellite imagery and Dynamic World labels)

description: This dataset contains preprocessed Sentinel-2 imagery and corresponding Dynamic World land-cover labels for six wetland areas in the Netherlands. It was created to support land-cover classification and segmentation tasks in ecologically dynamic floodplain environments. The data covers the period January 2017 to November 2024 and includes only scenes with less than 5% cloud cover.

Sentinel-2 imagery was retrieved using the Google Earth Engine (GEE) API from the COPERNICUS/S2 SR HARMONIZED collection, which provides Harmonized Level-2A data at 10 m spatial resolution. From the 26 available bands, 9 were selected based on their relevance for wetland delineation: RGB, Red Edge 1–3, Near-Infrared (NIR), and Shortwave Infrared (SWIR 1–2). The imagery was tiled into 256×256 pixel patches and filtered for quality (e.g., excluding patches with >10% black pixels).

Dynamic World land-cover labels (Brown et al., 2022) were used to generate pixel-wise semantic segmentation masks by selecting the most probable class (out of 9 land-cover types) for each pixel. The resulting masks are single-band images where pixel values 0–8 represent land-cover classes as follows:

0: Water  1: Trees  2: Grass  3: Flooded Vegetation  4: Crops  5: Shrub & Scrub  6: Built  7: Bare  8: Snow & Ice

The dataset includes the following splits:





Training set: Gelderse Poort, Oostvaardersplassen, Loosdrechtse Plassen, Land van Saeftinghe (1,701 images)




Validation set: Lauwersmeer (948 images)




Test set: Biesbosch (1,140 images)



This resource enables benchmarking of supervised and self-supervised learning methods for wetland classification in medium-resolution optical satellite data.

Reference:Brown, C.F., Brumby, S.P., Guzder-Williams, B., Birch, T., Hyde, S.B., Mazzariello, J., Czerwinski, W., Pasquarella, V.J., Haertel, R., Ilyushchenko, S., Schwehr, K., Weisse, M., Stolle, F., Hanson, C., Guinan, O., Moore, R., & Tait, A.M. (2022). Dynamic World, Near real-time global 10 m land use land cover mapping. Scientific Data, 9(1). https://doi.org/10.1038/s41597-022-01307-4
DOI: 10.5281/zenodo.15125549
title: Wetland Land-Cover Segmentation and Classification in the Netherlands (Sentinel-2 satellite imagery and Dynamic World labels)

description: This dataset contains preprocessed Sentinel-2 imagery and corresponding Dynamic World land-cover labels for six wetland areas in the Netherlands. It was created to support land-cover classification and segmentation tasks in ecologically dynamic floodplain environments. The data covers the period January 2017 to November 2024 and includes only scenes with less than 5% cloud cover.

Sentinel-2 imagery was retrieved using the Google Earth Engine (GEE) API from the COPERNICUS/S2 SR HARMONIZED collection, which provides Harmonized Level-2A data at 10 m spatial resolution. From the 26 available bands, 9 were selected based on their relevance for wetland delineation: RGB, Red Edge 1–3, Near-Infrared (NIR), and Shortwave Infrared (SWIR 1–2). The imagery was tiled into 256×256 pixel patches and filtered for quality (e.g., excluding patches with >10% black pixels).

Dynamic World land-cover labels (Brown et al., 2022) were used to generate pixel-wise semantic segmentation masks by selecting the most probable class (out of 9 land-cover types) for each pixel. The resulting masks are single-band images where pixel values 0–8 represent land-cover classes as follows:

0: Water  1: Trees  2: Grass  3: Flooded Vegetation  4: Crops  5: Shrub & Scrub  6: Built  7: Bare  8: Snow & Ice

The dataset includes the following splits:





Training set: Gelderse Poort, Oostvaardersplassen, Loosdrechtse Plassen, Land van Saeftinghe (1,701 images)




Validation set: Lauwersmeer (948 images)




Test set: Biesbosch (1,140 images)



This resource enables benchmarking of supervised and self-supervised learning methods for wetland classification in medium-resolution optical satellite data.

Reference:Brown, C.F., Brumby, S.P., Guzder-Williams, B., Birch, T., Hyde, S.B., Mazzariello, J., Czerwinski, W., Pasquarella, V.J., Haertel, R., Ilyushchenko, S., Schwehr, K., Weisse, M., Stolle, F., Hanson, C., Guinan, O., Moore, R., & Tait, A.M. (2022). Dynamic World, Near real-time global 10 m land use land cover mapping. Scientific Data, 9(1). https://doi.org/10.1038/s41597-022-01307-4
DOI: 10.6073/pasta/537d876206a554a58f988499177401bd
title: Topobathymetric DEMs of Short Prong marsh and tidal flat in Hog Island Bay, VA 2022-2023

description: Seamless DEMs of the marsh edge and tidal flat at Short Prong in 2022 and 2023 were created using a combination of aerial photogrammetry and boat-mounted single-beam echosounding. Aerial photogrammetry surveys of the subaerial intertidal flat and marsh edge were completed during low tide using a DJI Phantom 4 RTK drone. Positioning was determined using six surveyed ground control points and drone on-board RTK. During high tide, a single beam echosounder was used to survey six cross-shore transects of the subtidal and one alongshore transect near the marsh edge. The same flight plan and echosounding survey path was used both years, with surveys taking place on 7/19/22 and 7/11/23. Photogrammetric data was processed in Agisoft Metashape to produce a DEM and a photomosaic. Echosounding data was processed in Hydromagic and interpolated using the natural neighbor method in GIS. Overlap of survey extent between photogrammetric and echosounding DEMs were stitched together in GIS to create seamless DEMs with a cellsize of 3 cm from the lower elevations of the marsh platform into the subtidal flat for 2022 and 2023.
DOI: 10.3886/e194342v1
title: Data and Code for Pay Transparency and Gender Equality

description: Since 2018, UK firms with at least 250 employees have been mandated to publicly disclose gender equality indicators. Exploiting variations in this mandate across firm size and time, we show that pay transparency closes 19 percent of the gender pay gap by reducing men’s wage growth. By combining different sources of data, we also provide suggestive evidence that the public availability of the equality indicators influences employers’ response as worse performing firms and employers potentially more exposed to public scrutiny seem to reduce their gender pay gap the most.
description: British Firms with 200-300 employees.
DOI: 10.5281/zenodo.14973674
title: Comparing AI and Human Decision-Making Mechanisms in Daily Collaborative Experiments
DOI: 10.5281/zenodo.14973673
title: Comparing AI and Human Decision-Making Mechanisms in Daily Collaborative Experiments
DOI: 10.5281/zenodo.15111406
title: Comparing AI and Human Decision-Making Mechanisms in Daily Collaborative Experiments
DOI: 10.3886/e202824
title: Code for: Aggressive Pivots and Entrepreneurial Skill

description: Replication code for the paper titled "Aggressive Pivots and Entrepreneurial Skill"<br>
DOI: 10.3886/e202824v1
title: Code for: Aggressive Pivots and Entrepreneurial Skill

description: Replication code for the paper titled "Aggressive Pivots and Entrepreneurial Skill"<br>
DOI: 10.15139/s3/se5abu
title: Monmouth University National Poll, Number 293

description: This survey was conducted using a national sample and addresses President Joe Biden's pardon of Hunter Biden and President Donald Trump's past and potential future pardons. Also, opinion of Trump winning the 2024 election, his policy proposals, and the possibility of him suspending laws and constitutional provisions to go after his political enemies.
DOI: 10.6084/m9.figshare.27894048
title: Source Data

description: The source data underlying visualizations presented in Figs. 2(a)-(i), 3(a)-(i), 4(a)-(i), 5(a)-(d), and 6.<br>
DOI: 10.6084/m9.figshare.27894048.v1
title: Source Data

description: The source data underlying visualizations presented in Figs. 2(a)-(b), 3(a)-(e), 4(a)-(i), 5(a)-(i), 6(a)-(d), and 7
DOI: 10.48323/7ca6e-v7x51
title: MS_XevoTQXS_2024_November

description: TKI05AAAMP02ABMHO03CF - AEX, HSST3Meth Dev CoAs CSHRLI01AF
DOI: 10.48323/rahy5-re126
title: MS_XevoTQXS_2024_November

description: TKI05AAAMP02ABMHO03CF - AEX, HSST3Meth Dev CoAs CSHRLI01AF
DOI: 10.48323/jrvks-enr77
title: TSC Proteomics

description: MHO01AF

Hek293T TSC2KO +/- MK-2206

Proteome Data

n=6
DOI: 10.48323/r5kcf-1g472
title: TSC Proteomics

description: MHO01AF

Hek293T TSC2KO +/- MK-2206

Proteome Data

n=6
DOI: 10.6084/m9.figshare.28715867
title: Cortical Microcircuit Model for Excitatory/Inhibitory balance

description: A computational microcircuit model with biologically plausible layer 2/3 of visual cortex that combined excitatory pyramidal neurons with three subtypes of inhibitory interneurons (parvalbumin [PV], somatostatin [SOM], and vasoactive intestinal polypeptide [VIP]).
DOI: 10.5281/zenodo.15125948
title: Kawasaki-Pyroptosis
DOI: 10.5281/zenodo.15125949
title: Kawasaki-Pyroptosis
DOI: 10.5281/zenodo.15125969
title: agrostis_congestiflora_spades_01.fasta.gz
DOI: 10.5281/zenodo.15125970
title: agrostis_congestiflora_spades_01.fasta.gz
DOI: 10.5281/zenodo.15119623
title: Supplementary Files for "Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen"

description: Supplementary files for "Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen" by Baril, Puccetti, and Croll, 2025. 

 

Abstract:

Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies affect TE dynamics remains unknown. Fungal pathogens in agriculture provide unique frameworks to address such questions due to the availability of spatially explicit sampling and well-characterized niche conditions. We characterised TE evolutionary dynamics using an extensive intraspecies sampling of 1,953 genomes across the global distribution range of the major fungal wheat pathogen Zymoseptoria tritici. Employing a pangenomic approach, we characterise genomic diversity and benchmark methods to robustly infer TE insertion polymorphism, before systematically assessing TEs as a source of adaptive variation. We annotated ~3.2 million TE loci among genomes, finding substantial variation in TE content within and among populations. TE activity surged during the pathogen's expansion from its centre of origin in the Middle East, with unique TE activity profiles arising in derived populations. TE-mediated adaptation emerged from distinct waves of TE mobilization. The highest rates of TE activity were observed over timescales as short as 25 years. 45 TE loci showing local adaptation signatures within 1kb of 49 host genes were identified, with adaptive TE insertions likely related to adaptation to antifungals and the plant host environment. This work highlights the power of vast genomic datasets to unravel intraspecies TE invasion histories and pinpoint factors likely driving recent adaptation. This argues for a shift in focus to incorporate deep population-level TE activity surveys in our pursuit to uncover the molecular drivers of adaptive evolution. 

 

README contains description of files contained in this repository. All supplementary materials related to this manuscript are supplied in this repository.
DOI: 10.5281/zenodo.15125975
title: Supplementary Files for "Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen"

description: Supplementary files for "Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen" by Baril, Puccetti, and Croll, 2025. 

 

Abstract:

Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies affect TE dynamics remains unknown. Fungal pathogens in agriculture provide unique frameworks to address such questions due to the availability of spatially explicit sampling and well-characterized niche conditions. We characterised TE evolutionary dynamics using an extensive intraspecies sampling of 1,953 genomes across the global distribution range of the major fungal wheat pathogen Zymoseptoria tritici. Employing a pangenomic approach, we characterise genomic diversity and benchmark methods to robustly infer TE insertion polymorphism, before systematically assessing TEs as a source of adaptive variation. We annotated ~3.2 million TE loci among genomes, finding substantial variation in TE content within and among populations. TE activity surged during the pathogen's expansion from its centre of origin in the Middle East, with unique TE activity profiles arising in derived populations. TE-mediated adaptation emerged from distinct waves of TE mobilization. The highest rates of TE activity were observed over timescales as short as 25 years. 45 TE loci showing local adaptation signatures within 1kb of 49 host genes were identified, with adaptive TE insertions likely related to adaptation to antifungals and the plant host environment. This work highlights the power of vast genomic datasets to unravel intraspecies TE invasion histories and pinpoint factors likely driving recent adaptation. This argues for a shift in focus to incorporate deep population-level TE activity surveys in our pursuit to uncover the molecular drivers of adaptive evolution. 

 

README contains description of files contained in this repository. All supplementary materials related to this manuscript are supplied in this repository.
DOI: 10.25345/c5qv3cg51
title: MassIVE MSV000097493 - Abnormal Lipid Metabolism and Altered Neuronal Support by Astrocytes Lacking Akap11, a Risk Gene for Schizophrenia and Bipolar Disorder
title: A-Kinase Anchoring Protein 11 (AKAP11) is a shared genetic risk factor for schizophrenia and bipolar disorder, yet its role in the brain remains poorly understood. Through multi-omic analysis of Akap11 mutant mouse brains and cultured astrocytes, we identified significant transcriptomic, proteomic, and metabolomic alterations. Key findings include the upregulation of cholesterol and fatty acid metabolic pathways, accumulation of lipid species such as cholesteryl esters, triacylglycerols, ceramides, and glycerophospholipids, and elevated levels of 3',5'-cyclic AMP and protein kinase A (PKA) signaling. These metabolic perturbations manifested as increased lipid droplet accumulation in Akap11 mutant astrocytes, highlighting AKAP11's critical role in regulating intracellular lipid homeostasis. Mechanistically, we demonstrate that AKAP11 functions as an autophagy receptor mediating PKA degradation and interacts with endoplasmic reticulum-resident proteins VAP-A and VAP-B through its FFAT motif, providing molecular insight into AKAP11's regulation of lipid metabolism. Additionally, co-culture experiments with human induced pluripotent stem cell-derived neurons demonstrated that Akap11 mutant astrocytes increase excitatory neurotransmission and neuronal activity. Collectively, these findings link AKAP11-mediated lipid and synaptic dysregulation to psychiatric disease risk, highlighting the importance of astrocytes in these disorders, and suggesting new therapeutic targets for investigation.
DOI: 10.5281/zenodo.15125203
title: Synthetic Dataset for Slice Performance Forecasting

description: This synthetic dataset was created from simulated data that underwent thorough analysis to identify patterns of seasonality and correlations among variables. Its primary aim is to support the training and evaluation of various forecasting strategies for slice performance in 5G networks, as detailed in the article:

"A Comparative Study of Training Strategies for Slice Performance Forecasting in B5G Networks".

The dataset comprises synthetic canonical series that accurately mirror the characteristics of the original data. These series are stored in Parquet format, facilitating efficient access. They are specifically designed to aid in the comparison and assessment of different forecasting methods within the context of 5G networks.
DOI: 10.57745/7cb4vq
title: interactive_figure_abundanceASV_LabelRougebroilers.html

description: :unav
DOI: 10.57745/99jxnf
title: interactive_figure_percentageASV_Conventionalbroilers.html

description: :unav
DOI: 10.57745/f1gr5r
title: interactive_figure_percentageASV_LabelRougebroilers.html

description: :unav
DOI: 10.57745/iw8dck
title: interactive_figure_abundanceASV_Conventionalbroilers.html

description: :unav
DOI: 10.57745/nmv4cd
title: interactive_figure_abundanceASV_free-rangebroilers.html

description: :unav
DOI: 10.57745/xxbvzm
title: interactive_figure_abundanceASV_LabelRougebroilers.html

description: :unav
DOI: 10.5281/zenodo.15125896
title: Egg translocation across a local range boundary reduces hatch rates in a trailing-edge population of a migratory songbird, Setophaga caerulescens (Black-throated Blue Warbler)

description:  Data and Code for:

Egg translocation across a local range boundary reduces hatch rates in a trailing-edge population of a migratory songbird, the Black-throated Blue Warbler (2025)Ornithology, ukaf007, https://doi.org/10.1093/ornithology/ukaf007Samuel A Merker, T Scott Sillett, Benjamin G Freeman, Robert J Cooper, Richard B Chandler

This repository contains data and R scripts to recreate the analyses in the paper.Each script should be independent and should load the required and associated data to run the script and recreate figures in the manuscript.In most instances, the necessary packages are loaded at the beginning of each script.We encourage the use of RStudio to complete the analysis.

1. **Egg translocation manipulation data**

            -Translocation_Analysis.R            -Translocation_Data.gzip            2. **Female effort data**                        -Female_behavior.R            -female_behavior.gzip            3. **Internal and external (ambient) nest temperature data**

            -Describing_nest_climate_analyses.R            -microclimate_on_hatching.R            -micro_climate_data.gzip            -Nest_Climate_Data.gzip            -insums.R            -outsums.R

5. **Nestling measurement data**

            -Nestlings.R            -Nestlings.gzip   6. **Range Map**               -Range_Maps.R            -btbw_howa_map_data.gzip   7. **Nest Dates**               -nest dates.R            -nest_dates.gzip   8. **Time eggs out of nest**               -time_out_of_nests.R            -time_data.gzip
DOI: 10.5281/zenodo.15125897
title: Egg translocation across a local range boundary reduces hatch rates in a trailing-edge population of a migratory songbird, Setophaga caerulescens (Black-throated Blue Warbler)

description:  Data and Code for:

Egg translocation across a local range boundary reduces hatch rates in a trailing-edge population of a migratory songbird, the Black-throated Blue Warbler (2025)Ornithology, ukaf007, https://doi.org/10.1093/ornithology/ukaf007Samuel A Merker, T Scott Sillett, Benjamin G Freeman, Robert J Cooper, Richard B Chandler

This repository contains data and R scripts to recreate the analyses in the paper.Each script should be independent and should load the required and associated data to run the script and recreate figures in the manuscript.In most instances, the necessary packages are loaded at the beginning of each script.We encourage the use of RStudio to complete the analysis.

1. **Egg translocation manipulation data**

            -Translocation_Analysis.R            -Translocation_Data.gzip            2. **Female effort data**                        -Female_behavior.R            -female_behavior.gzip            3. **Internal and external (ambient) nest temperature data**

            -Describing_nest_climate_analyses.R            -microclimate_on_hatching.R            -micro_climate_data.gzip            -Nest_Climate_Data.gzip            -insums.R            -outsums.R

5. **Nestling measurement data**

            -Nestlings.R            -Nestlings.gzip   6. **Range Map**               -Range_Maps.R            -btbw_howa_map_data.gzip   7. **Nest Dates**               -nest dates.R            -nest_dates.gzip   8. **Time eggs out of nest**               -time_out_of_nests.R            -time_data.gzip
DOI: 10.71795/7vc4-d928
title: Backbone Thesaurus
title: BBT