Zhang, Song · Wang, Xiaoyu · Zhang, Jiayi · et al.

17 files · 1.4 MB · csv, xlsx, zip

This dataset contains raw and processed data underlying the study on Vibrio-phage interactions, including genome sequences, CRISPR arrays, spacer-protospacer mappings, defense system annotations, phylogenetic analyses, and structural modeling outputs. It also includes scripts used for analysis and figure generation. All raw sequencing reads are deposited in NCBI SRA and genome accession numbers are provided in Supplementary files.

guo, na · pan, jiachen · li, tiantian · et al.

14 files · 100 MB · csv, rar, tsv

ADM_LSIR is a physics-inspired laparoscopic aerosol degradation dataset for aerosol-aware surgical image analysis and image restoration. The v1.0.0 release contains: - 21,916 clean clinical laparoscopic frames (clean/) - 9,562 real intraoperative aerosol-degraded frames (degraded/) - 36,052 simulated aerosol masks, including 19,701 smoke-like masks and 16,351 trajectory masks (mask/) - Blender simulation/cache materials (ADM_LSIR_Blender_simulation_files_v1.0.rar) - metadata_quality_report_v1.0.csv - recommended_splits_v1.0.csv - video_mapping_v1.0.csv - parts_manifest.txt - checksums_v1.0.tsv - release_manifest_v1.0.json All released clinical frames are de-identified and stored as lossless PNG files. Filenames use anonymized video identifiers, e.g., C-V##-####.png for clean frames and D-V##-####.png for degraded frames. The recommended split is defined at the source_video_id/public_video_label level to reduce leakage across frames from the same source video. The public video labels in video_mapping_v1.0.csv provide privacy-safe source-video identifiers (video1-video19). The Blender archive documents the smoke and trajectory mask simulation setup and supports reuse, but it is not a guaranteed exact per-mask reproduction package. The released pre-rendered mask library is the primary reusable dataset component. Source code for synthesis and quality screening is available at: https://github.com/SweetDeathh/ADM_LSIR

Winter, Henry · Severino, MaryKay · Volunteer Scientist

16 files · 100 MB · csv, pdf, zip

These are audio recordings taken by an Eclipse Soundscapes (ES) Data Collector during the week of the April 08, 2024 Total Solar Eclipse. It was decided to include only raw, unprocessed audio data files in each site-specific ZIP archive and in each Zenodo record. This decision was so that any researcher can independently verify, reproduce, and extend the analysis performed. As a result, some sites have WAV files with 0 bytes of data or timestamps outside the range of probable recording times. Procedures used by the Eclipse Soundscapes team to process audio data for its purposes are outlined in the Data Management reports located in the Eclipse Soundscapes Zenodo community. Data with 0 bytes of data were included for completeness. Data Site location information: Latitude: 44.46311 Longitude: -71.68203 Local Eclipse Type: Total Solar Eclipse Solar Eclipse Eclipse Percent (%): 100 WAV files Time & Date Settings: Set with Automated AudioMoth Time Chime (More information on TimeStamp Setting below) Data Collector Start Time Notes: N/A Included Data: Audio files in WAV format with the date and time in UTC within the file name: YYYYMMDD_HHMMSS meaning YearMonthDay_HourMinuteSecond For example, 20240411_141600.WAV means that this audio file starts on April 11, 2024 at 14:16:00 Coordinated Universal Time (UTC) CONFIG Text file: Includes AudioMoth device setting information, such as sample rate in Hertz (Hz), gain, firmware, etc. README.md: Markdown formatted file with information about the recording and recording site. file_list.csv: A machine and human file that gives the following information on each file in the record: File Name, File Type, Description, File Size in kilobytes, Name of Associated Data Dictionary with the file, calculated SHA-512 Hash of the file as a unique identifier to insure data integrity during transfer and compression. total_eclipse_data.csv: A machine and human readable file that gives the following information about the site where the audio data recording was taken: ESID#, Latitude, Longitude, Eclipse_type, CoveragePercent, Eclipse Start UTC (1st contact), Totality Start UTC (2nd contact), Totality End UTC (3rd Contact), Eclipse End UTC (4th Contact), Max Eclipse Time UTC License.txt: A human readable file that explains the terms and conditions under which the data can be used. AudioMoth_Operation_Manual.pdf: A human readable document that explains the use of an AudioMoth device. The document is current up to the time of the AudioMoth's use in the Eclipse Soundscapes project. file_list_data_dict.csv: A machine and human data dictionary file that gives information on the variables contained within the file_list.csv file. CONFIG_data_dict.csv: A machine and human data dictionary file that gives information on the variables contained within the CONFIG.TXT file. eclipse_data_data_dict.csv: A machine and human data dictionary file that gives information on the variables contained within the total_eclipse_data.csv file. WAV_data_dict.csv: A machine and human data dictionary file that gives information on the variables contained within the *.WAV files. ES_Data_Management_Pre-Eclipse_Data_Infrastructure_Stage_0.pdf: PDF document that describes Stage 0 (Pre-Eclipse Infrastructure and Data Stewardship Planning) of the Eclipse Soundscapes (ES) data lifecycle. ES_Data_Management_Receipt_Sorting_and_Metadata_Organization_Stage_1.pdf: PDF document that describes Stage 1 (Receipt, Sorting, and Metadata Organization) of the Eclipse Soundscapes (ES) data lifecycle. ES_Data_Management_Data_Processing_Stage_2.pdf: PDF document that describes Stage 2 (Data Processing) of the Eclipse Soundscapes (ES) data Volunteer Scientists. 2023 and 2024 solar eclipse soundscapes audio datalifecycle. ES_Data_Management_Data_Sharing_Stage_3.pdf: PDF document that describes Stage 3 (Public Data Sharing) of the Eclipse Soundscapes (ES) data lifecycle. Eclipse Information for this location: Eclipse Date: April 08, 2024 Eclipse Start Time (UTC) (1st Contact): 18:16:15 Totality Start Time (UTC) (2nd Contact): [N/A if partial eclipse] 19:28:56 Eclipse Maximum Time [when the most possible amount of the Sun in blocked] (UTC): 19:29:25 Totality End Time (UTC) (3rd Contact): [N/A if partial eclipse] 19:29:53 Eclipse End Time (UTC) (4th Contact): [N/A if partial eclipse] 20:38:30 Audio Data Collection During Eclipse Week ES Data Collectors used AudioMoth devices to record audio data, known as soundscapes, over a 5-day period during the eclipse week: 2 days before the eclipse, the day of the eclipse, and 2 days after. The complete raw audio data collected by the Data Collector at the location mentioned above is provided here. This data may or may not cover the entire requested timeframe due to factors such as availability, technical issues, or other unforeseen circumstances. ES ID# Information: Each AudioMoth recording device was assigned a unique Eclipse Soundscapes Identification Number (ES ID#). This identifier connects the audio data, submitted via a MicroSD card, with the latitude and longitude information provided by the data collector through an online form. The ES team used the ES ID# to link the audio data with its corresponding location information and then uploaded this raw audio data and location details to Zenodo. This process ensures the anonymity of the ES Data Collectors while allowing them to easily search for and access their audio data on Zenodo. TimeStamp Information: The ES team and the Data Collectors took care to set the date and time on the AudioMoth recording devices using an AudioMoth time chime before deployment, ensuring that the recordings would have an automatic timestamp. However, participants also manually noted the date and start time as a backup in case the time chime setup failed. The notes above indicate whether the WAV audio files for this site were timestamped manually or with the automated AudioMoth time chime. Common Timestamp Error: Some AudioMoth devices experienced a malfunction where the timestamp on audio files reverted to a date in 1970 or before, even after initially recording correctly. Despite this issue, the affected data was still included in this ES site's collected raw audio dataset. Latitude & Longitude Information: The latitude and longitude for each site was taken manually by data collectors and submitted to the ES team, either via a web form or on paper. It is shared in Decimal Degrees format. General Project Information: The Eclipse Soundscapes Project is a NASA Volunteer Science project funded by NASA Science Activation that is studying how eclipses affect life on Earth during the October 14, 2023 annular solar eclipse and the April 8, 2024 total solar eclipse. Eclipse Soundscapes revisits an eclipse study from almost 100 years ago that showed that animals and insects are affected by solar eclipses! Like this study from 100 years ago, ES asked for the public's help. ES uses modern technology to continue to study how solar eclipses affect life on Earth! Eclipse Soundscapes is an enterprise of ARISA Lab, LLC and is supported by NASA award No. 80NSSC21M0008. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Aeronautics and Space Administration. Eclipse map/figure/table/predictions courtesy of Fred Espenak, NASA/Goddard Space Flight Center, from eclipse.gsfc.nasa.gov . Eclipse Data Version Definitions {1st digit = year, 2nd digit = Eclipse type (1=Total Solar Eclipse, 9=Annular Solar Eclipse, 0=Partial Solar Eclipse), 3rd digit is unused and in place for future use} 2023.9.0 = Week of October 14, 2023 Annular Eclipse Audio Data, Path of Annularity (Annular Eclipse) 2023.0.0 = Week of October 14, 2023 Annular Eclipse Audio Data, OFF the Path of Annularity (Partial Eclipse) 2024.1.0 = Week of April 8, 2024 Total Solar Eclipse Audio Data, Path of Totality (Total Solar Eclipse) 2024.0.0 = Week of April 8, 2024 Total Solar Eclipse Audio Data , OFF the Path of Totality (Partial Solar Eclipse) *Please note that this dataset's version number is listed below. Eclipse Soundscapes Data Collector Role Training and Implementation Resources Manual (2023-2024) (Archival Copy) This site-level record includes the Eclipse Soundscapes Data Collector Role Training and Implementation Resources Manual (2023-2024) . The manual documents the participant training, device setup procedures, metadata submission requirements, ES ID system, timestamp protocols, data return workflow, and public archiving processes used during the October 14, 2023 annular solar eclipse and the April 8, 2024 total solar eclipse. The manual is preserved for transparency and reproducibility and reflects the procedures under which this dataset was collected and processed. (DOI 10.5281/zenodo.18623442) Data Receipt, Processing, and Analysis Methods All programs supporting Stages 1–3 are openly available in the: Eclipse Soundscapes GitHub repository: https://github.com/ARISA-Lab-LLC/ESCSP Data Management Lifecycle The following section documents the relationship of this record to the full Eclipse Soundscapes (ES) data lifecycle, a multi-stage workflow designed to support large-scale participatory science, long-term data stewardship, open science, and scientific reuse. Each stage addressed a different operational need, beginning before eclipse deployment and continuing through validation, public archiving, and scientific analysis. Together, these stages transformed distributed volunteer-submitted audio recordings into structured, documented, publicly accessible NASA-funded research assets. Stage 0: Pre-Eclipse Infrastructure and Deployment Preparation Severino, M., & Winter, H. (2026). Eclipse Soundscapes Data Management: Pre-Eclipse Infrastructure and Deployment Preparation (Stage 0). Zenodo. https://doi.org/10.5281/zenodo.20413370 Stage 0 focused on building the operational foundation required to support geographically distributed eclipse data collection at national scale. This stage included AudioMoth device preparation, accessibility modifications, ES ID # assignment systems, metadata collection workflows, participant training materials, deployment logistics, and planning for downstream data stewardship and archival workflows. The 2023 annular eclipse served as both a scientific investigation and a large-scale operational beta test that informed improvements for the 2024 total solar eclipse campaign. Related Citations and Resources: Severino, M., & Kline, T. (2025, November 24). Eclipse Soundscapes Apprentice Role Curriculum: Solar Eclipses and Multi-Sensory Observing (Informal Education). Zenodo. https://doi.org/10.5281/zenodo.17703003 Severino, M., & Bauer, D. J. (2026). Eclipse Soundscapes Observer Role Training and Resources Manual (2023–2024). Zenodo. https://doi.org/10.5281/zenodo.18633602< /li> Severino, M., Winter, H., & Bauer, D. J. (2026). Eclipse Soundscapes Data Collector Role Training and Implementation Manual (2023–2024). Zenodo. https://doi.org/10.5281/zenodo.18623443 Stage 1: Receipt, Sorting, and Metadata Organization Severino, M., & Winter, H. (2026). Eclipse Soundscapes Data Management: Receipt, Sorting, and Metadata Organization (Stage 1). Zenodo. https://doi.org/10.5281/zenodo.19471425 Stage 1 transformed returned participant materials into organized, traceable site-level records. This included receiving mailed microSD cards, consolidating participant-submitted metadata, reconciling handwritten and online records, organizing physical audio media by ES ID #, and deriving eclipse timing and coverage information using NASA eclipse prediction datasets. The outputs of Stage 1 established the structured metadata relationships required for downstream validation, processing, archiving, and analysis workflows. Related Citations and Resources: Winter, H., & Goncalves, J. (2026). EPTT (Eclipse Phase Timing Tool) [Computer software]. GitHub. https://github.com/ARISA-Lab-LLC/ESCSP-Eclipse-Phase-Timing-Tool /li> Espenak, F. (n.d.). Eclipse predictions by Fred Espenak, NASA's GSFC Eclipse Web Site. NASA Goddard Space Flight Center. http://eclipse.gsfc.nasa.gov/eclipse.html Stage 2: Data Processing and Validation Severino, M., & Winter, H. (2026). Eclipse Soundscapes Data Management: Data Processing (Stage 2). Zenodo. https://doi.org/10.5281/zenodo.18683402 Stage 2 focused on centralized audio ingestion, validation, timestamp verification, metadata reconciliation, and preparation of datasets for analysis and public sharing. During this stage, returned audio recordings were processed using custom open-source tools developed by the ES team, including ES WAVES and ES AMES. The project implemented scalable infrastructure capable of processing large volumes of participant-submitted microSD cards while preserving all raw audio data without modification. Stage 2 established the validated dataset structure required for long-term preservation and scientific analysis. Related Citations and Resources: Winter, H., & Goncalves, J. (2026). ES WAVES (Eclipse Soundscapes WAV Audio Validation & Extraction Suite) [Computer software]. GitHub. https://github.com/ARISA-Lab-LLC/ESCSP-ES-WAV-Audio-Validation-Extraction-Suite Winter, H., & Goncalves, J. (2026). ES AMES (Eclipse Soundscapes AudioMoth Metadata Extractor Suite) [Computer software]. GitHub. https://github.com/ARISA-Lab-LLC/ESCSP-ES-AMES-AudioMoth-Metadata-Extractor-Suite Stage 3: Public Data Sharing and Open Archiving Severino, M., & Winter, H. (2026). Eclipse Soundscapes Data Management: Public Audio Data Sharing (Stage 3). Zenodo. https://doi.org/10.5281/zenodo.18683437 Stage 3 transformed validated site-level datasets into publicly archived, DOI-assigned research records published through the Eclipse Soundscapes Zenodo Community. This stage included dataset packaging, metadata standardization, README generation, integrity verification, DOI assignment, and automated repository upload workflows using the Automated Zenodo Upload Software (AZUS). These workflows established the project's long-term open-science infrastructure and ensured that datasets remained findable, accessible, interoperable, reusable, and citable for future scientific and educational use. Related Citations and Resources: Winter, H., & Goncalves, J. (2026). AZUS (Automated Zenodo Upload Software) [Computer software]. GitHub. https://github.com/ARISA-Lab-LLC/AZUS-Automated-Zenodo-Upload-Software Stage 4: Scientific Analysis and Research Use Stage 4 involves the scientific analysis and interpretation of validated eclipse soundscape datasets. Analysis workflows utilized datasets verified during earlier stages to investigate eclipse-related environmental and animal vocalization changes across hundreds of recording sites. This stage also includes broader scientific interpretation, publication development, and continued reuse of Eclipse Soundscapes datasets and infrastructure for future research, education, and open-science applications. Related Citations and Resources: Pease, B., Gilbert, N., & Severino, M. (2026). Eclipse Soundscapes Preliminary Findings – How Eclipses Affect Nature as determined by Sound (Recorded Webinar). Zenodo. https://doi.org/10.5281/zenodo.18613979 Gilbert, N. A., Pease, B. S., Severino, M., & Winter, H. III. (2026). Photic niche explains avian behavioral responses to solar eclipses. Ecology and Evolution, 16(2), e73090. https://doi.org/10.1002/ece3.73090 Analysis code repository: https://github.com/BrentPease1/eclipse-traits Companion Zenodo record archiving structured analysis scripts and derived outputs: https://doi.org/10.5281/zenodo.15790879[r] Public Archiving, Privacy, and Data Transparency The Eclipse Soundscapes Data Collector Role Training and Implementation Manual (2023-2024) includes a detailed explanation of how Eclipse Soundscapes audio data are publicly archived on Zenodo, how participant privacy is protected through the ES ID system, and how transparency and traceability are maintained. It also outlines the criteria for determining which recordings are included in the public archive, as well as the distinction between publicly shared archival data and datasets used for ES-led scientific analyses. Participants and data users can consult this section for full documentation of the project's open science and privacy practices. Severino, M., & Winter, H. (2026). Eclipse Soundscapes Data Collector Role Training and Implementation Manual (2023–2024). Zenodo. https://doi.org/10.5281/zenodo.18623443 Citations Individual Site Citation: APA Citation (7th edition) Winter, H., Severino, M., & Volunteer Scientist. (2026). 2024 solar eclipse soundscapes audio data [Audio dataset, ES ID# 292]. Zenodo.{Insert DOI} Collected by volunteer scientists as part of the Eclipse Soundscapes Project. This project is supported by NASA award No. 80NSSC21M0008. Eclipse Community Citation Winter, H., Severino, M., & Volunteer Scientists. 2023 and 2024 solar eclipse soundscapes audio data [Collection of audio datasets]. Eclipse Soundscapes Community, Zenodo. https://zenodo.org/communities/eclipsesoundscapes/ Collected by volunteer scientists as part of the Eclipse Soundscapes Project This project is supported by NASA award No. 80NSSC21M0008.

Aalborg, Trine

7 files · 8.0 MB · csv, gzip

README - Data for "Genomic constraint and hypervariability in tetraploid potatoes" Trine Aalborg, May 2026 The data applied in the study includes phenotypic and genotypic information on the MASPOT panel (768 F1 progeny of an 18-parent diallel cross - property of Danespo A/S). The genotypic data was generated using genotyping-by-sequencing technology as described in the paper. Following genotype calling and filtration (5-60x read depth, < 50 % missing rate, > 1 % MAF), the total SNP set includes 151,164 biallelic SNPs. Coordinates of these SNPs relative to the DMv6.1 potato reference genome are provided. In addition to genotypes across the clones, the estimated GERP score of that SNP from (Wu et al., 2023) is reported. The manuscript analyses only consider markers with reliable GERP scores (MSA alignment depth > 50, and neutral score > 2), which corresponded to 97,815 of the total 151,164 biallelic SNPs. SNPeff annotations of the markers (based on the DMv6.1 reference genome) are also appended. The phenotypes were collected across 1-2 field trials, depending on the traits, and includes a minimum of two replicates per clone from a randomized block design. There are phenotypes for eight traits: dry matter content [%], yield (hkg/ha), senescence [1-9], flesh color [1-9], tubers/plant, tuber length [mm], tuber diameter [mm], and tuber size [mm^3]. Metadata includes phenotyping year and block location of the plot as well as pedigree of the diallel offspring. File descriptions: gt_MASPOT.csv - .csv file of the non-imputed genotypic data of 151,164 SNPs for the 768 F1 clones (those with GERP scores). Columns 1-3 are SNP coordinates and SNP IDs. Column names from column 4 and onwards are clone IDs. gt_MASPOT_imputed.csv - .csv file holding the imputed (random forest, missRanger algorithm) genotypic data of 151,164 SNPs for the 768 F1 clones. gt_MASPOT_recoded.csv - .csv file of the recoded, imputed genotypic data of 151,164 SNPs for the 768 F1 clones. The SNPs are recoded from original MASPOT ref/alt allele (based on AF in the MASPOT panel) to the alternative allele = the derived allele in the 100-Solanaceae panel. pt_MASPOT.csv - .csv file holding the phenotypic data (eight traits) of the 768 F1 clones (Clone_ID). The number of observations varies across traits. Also including metadata: year of phenotyping (Year), block number (Block, Line_in_block), clone parents (Mother, Father, Family). GERP_MASPOT.csv - .csv file holding the GERP scores (including alignment depth, neutral scores, and a marker annotation based on GERP score thresholds (deleterious, neutral, hypervariable, or low quality)), SNPeff annotations, and the derived allele in the 100-Solanaceae panel from (Wu et al., 2023) [MASPOT_Alt_Allele_Is_Sol_Derived_Allele - used for recoding of the genotypes] of the MASPOT SNPs with GERP scores. snps.MASPOT_F1.vcf.gz - zipped .vcf file of the GBS MASPOT genotypic data (both discrete genotype calls and allele frequencies) called to the DMv6.1 potato reference genome. Filtered to read depth 5x, MQ > 30. A total of 160,920 biallelic SNPs. Includes the 768 F1 progeny analyzed. Literature: Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G. P., Zhou, S., et al. (2023). Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 186, 2313-2328.e15. doi: 10.1016/j.cell.2023.04.008