Hubbard, Alfred · Solares, Edwin · Hemming-Schroeder, Elizabeth

88 rows · 18 KB · fasta

These are the files needed to run the Broad Institute's malaria amplicon pipeline for the PvGAP Plasmodium vivax panel, described in detail here . They consist of FASTA files containing the forward and reverse primers and another FASTA file containing reference sequences for each target, derived from the PvP01 reference genome.

Yuan, Guangyuan

72 rows × 13 cols · 6.0 KB · csv, fasta

11 numeric · 2 categorical

This dataset supports the findings of the manuscript "Root anatomical traits modulate the assembly and nitrogen transformation potential of root-associated microbiomes in a temperate steppe" (NPH-MS-2026-55667). It contains root traits data, bacterial 16S rRNA gene absolute abundances, functional genes relative abundances, DNA extraction metadata, and phylogenetic marker sequences for 37 plant species from a temperate steppe ecosystem. The dataset includes the following files: 1. root traits.csv - Root traits including average diameter (AD), specific root length (SRL), specific root area (SRA), root tissue density (RTD), root nitrogen content (RNC), root carbon content (RCC), carbon‑nitrogen ratio (RCN), cortex layer number (CLN), cortex thickness (CT), and the ratio of cortex thickness to root diameter (CTRD). The first column lists plant species names. 2. Absolute abundance of 16S rRNA gene.csv - Quantitative PCR (qPCR) derived absolute abundances of bacterial 16S rRNA gene copies (copies/ng DNA) across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 3. DNA extraction sample weight.csv - Fresh weight (grams) of root material used for DNA extraction for each sample, linked by SampleID to the abundance data. 4. DNA extraction concentration.csv - Qubit‑measured DNA concentrations (ng/μL) and the sample volume (μL) used for quality control, together with sample metadata. 5. 37species.fasta - DNA sequences of two chloroplast markers (matK and rbcL) for the 37 plant species included in the study. The sequences are in FASTA format with headers formatted as ">Species". These were used for host phylogeny construction and Pagel's λ analyses. 6. Quantitative PCR results of functional gene.csv - Quantitative PCR (qPCR) derived relative abundances of bacterial 16S rRNA gene and functional genes across different root compartments (rhizosphere, rhizoplane, endosphere), host species, root orders, and cotyledon classes (monocot/dicot). 7. README.md - A detailed description of each file, column headers, abbreviations, units, and any missing value codings (NA). All data are provided to ensure transparency and reproducibility of the analyses. For methodological details, please refer to the Materials and Methods section of the associated publication. These data are under embargo until the associated research article is published. After that date, they will be freely available under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. During the embargo period, the metadata (title, authors, abstract) and the DOI remain publicly visible, but the data files are not accessible. For access requests before the embargo expires, please contact the corresponding author.

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

Requena Rolanía, Jose María · Greif, Gonzalo · ROBELLO, CARLOS

1 files · 8.0 MB · fasta

This dataset contains the genome sequence for Trypanosoma cruzi (strain Dm28c). This genome sequence was de novo assembled using PacBio Hi-Fi and Illumina sequencing platforms by Greif et al (2026. PMID: 41501640). The genome was assembled into 32 contigs, which represent complete chromosomes. The provided Fasta file also contains an additional contig corresponding to the maxicircle (mitochondrial genome) sequence. The Fasta files included in this dataset were downloaded from GenBank (assembly GCA_044048535.1; May 22, 2026). Additional information about the Dm28cT2T genome assembly and gene annotations may be accessed through the link: https://cruzi.pasteur.uy/

Burman, Nathaniel · Buyukyoruk, Murat · Wiegand, Tanner · et al.

4 files · 8.0 MB · fasta

This folder contains a multiple sequence alignment of Cas7 homologs in .fasta format, the domain-level annotations from PFAM and CasFinder, and an associated phylogenetic tree in .newick format.

Xu, Tao

3 files · 100 MB · rar, xlsx

The deepmd_data dataset comprises energy data for 375,781 structures and force data for more than 45 million atoms, generated from six hierarchical active learning iterations. The init directory stores the non-periodic molecular configurations established at the initialization stage. The iter directories contain structures labeled by both AIMD and DPMD-FP methods for each iteration. Each folder is named according to the scheme of solvent molecule index followed by lithium salt designation. The finetuned_data folder contains SEI reaction simulation data used for fine-tuning the MLFFs. Comprehensive details regarding the solvent molecules are available in the solvent_with_smiles.xlsx file.

Yuezong Wang · Yu Niu · Jiqiang Chen

2 files · 100 MB · rar, zip

This dataset contains raw experimental images, video sequences of real test samples, simulated microscopic image data from the manuscript " A robust method for microscopic 3D shape restoration via shape-from-focus" , as well as focal volume datasets collected before vibration simulation, after vibration simulation, and post anti-vibration processing. All provided data enable the validation of conclusions and reproducibility of experimental results obtained via the computational pipeline proposed in this paper.

Daugavietis, Jānis

6 files · 3.3 GB · jpeg, rardeclared

Skala Bünte, Süki Vagonu Hallē [2026.07.08.] Koncerta beigu telefona foto/ video. SKALA BÜNTE X SÜKI FACE2FACE https://fb.me/e/7dycfN2gI Details Event by John Dow Vagonu Hall Public · Anyone on or off Facebook 8TH OF JULY VAGONU HALLE TWO BANDS TWO BACKLINES MOSHPIT IN THE MIDDLE ONCE IN A LIFETIME FACE2FACE MASSACRE PROVIDED BY SKALA BÜNTE & SÜKI 🔪🔪🔪 DOORS 19:00 7€

Geisler, Jan · Rakhimberdiev, Eldar · Boom, Michiel P. · et al.

29 files · 124 MB · csv, shapefiledeclared

1. Many migratory birds now reach their Arctic breeding grounds earlier in order to keep pace with advancing springs and shifting nutrient peaks, either by departing earlier from non-breeding grounds or by travelling faster. For dark-bellied brent geese, there is limited potential to travel faster, as their migration to the Siberian breeding grounds is already among the fastest of Arctic geese and swans. Earlier departure would require reaching departure body mass earlier, either through a faster accumulation of energy stores during spring staging or via adjustments earlier in the annual cycle. 2. We examined long-term shifts in spring staging phenology and changes in winter and spring body mass trajectories of brent geese at the population level, with particular emphasis on the effects of winter temperature on body mass and spring body mass on departure timing. 3. We used more than five decades of body mass measurements from individuals caught in the United Kingdom and France, and in the Dutch Wadden Sea to reconstruct changes in spring and winter mass trajectories, respectively. These data were combined with over five decades of migration counts in the Netherlands and more than two decades of counts in Denmark to quantify changes in spring staging phenology. 4. We found that brent geese have not shifted their spring arrival in the Wadden Sea but have advanced departure timing. Furthermore, brent geese were heavier during and after milder winters, and have changed mass trajectories over recent decades. They no longer lose mass during winter and the second spring staging phase, and fuelling rates in the first spring staging phase have declined. Annual variation in body mass was not related to annual departure timing. 5. These results suggest that milder winters have relaxed energetic constraints and improved body condition in brent geese throughout the non-breeding season. Our findings highlight the importance of considering the full annual cycle when assessing how animals with limited capacity to adjust migration timing or speed respond to global change.

Murilo Coelho · de Sousa Amâncio, Francisco Dione · Paixao, Matheus · et al.

3 files · 742 KB · rardeclared

This repository contains the replication package for the paper "More Productive, but at What Cost? Understanding How GenAI Shapes Developers' Work Across the SPACE Dimensions", accepted at the 40th Brazilian Symposium on Software Engineering (SBES 2026), São Paulo, Brazil. The package includes: (i) the complete survey instrument and sanitized participant responses; (ii) qualitative coding artifacts, including the codebook, category consolidation, and classification analysis; (iii) inter-rater reliability materials (Cohen's Kappa = 0.81); (iv) quantitative datasets and statistical analysis outputs (SPACE composite scores, Cronbach's alpha, Kruskal-Wallis, Mann-Whitney U, and Dunn's post-hoc tests); and (v) supporting literature review material. All participant data were anonymized prior to disclosure. The survey materials are in Portuguese, the language of data collection.

Abbas, Syed Hassan

1 files · 86 MB · rardeclared

Abbas H, et al. "GenixRL- " The VUS were extracted from CLinVar database (downloaded [Date: August 2025]) and scored using the GenixRL framework. This dataset provides the foundation for the VUS reclassification analysis presented in the main manuscript. The dataset is provided as a single compressed CSV file: GenixRL_VUS_Scored.csv.gz Key Coulmn Descriptions: [Variant Identifier Columns, e.g., CHROM, POS, REF, ALT]: Standard genomic coordinates for each variant. SYMBOL: The official gene symbol. GenixRL_Score: The continuous pathogenicity score generated by GenixRL, ranging from 0 (most likely benign) to 1 (most likely pathogenic). GenixRL_Classification: The tiered classification based on the manuscript's thresholds: 'Likely Benign': Score < 0.53 'Likely Pathogenic': Score >= 0.53 and < 0.709 'High-Confidence Pathogenic': Score >= 0.709 [Other relevant columns]: The file also includes intermediate scores from other predictors and allele frequencies used for validation.

Cao, Shiyuan · Li, Yaning

8 files · 18 MB · csv, rardeclared

This repository provides the supporting materials for the manuscript "A Confidence-Guided Sports Multi-Object Tracking Method via Jersey Semantic Fusion." The archived materials include evaluation summaries, final tracking outputs, environment records, dataset mapping files, protocol reproduction materials, intermediate summary files, and revision evidence used to support the reported SportsMOT validation results. The reported formal results were obtained from the real detector, real frame-level semantic feature extraction, confidence partitioning, cascaded association, and TrackEval evaluation pipeline. The original public benchmark datasets, including SportsMOT, TeamTrack, SoccerNet Tracking, MOT17, and MOT20, are not redistributed in this repository and should be obtained from their original providers.

Nie, Yong · Huang, Bo

1 files · 1.5 KB · rardeclared

BI tree

Nie, Yong · Huang, Bo

1 files · 9.1 KB · rardeclared

Alignments for phylogen

Kavanagh, Jack · Anthony, Patrick

6 files · 11 MB · geojson, geopackage, shapefiledeclared

A historical map showing a segment of the boundaries of New Spain in c. 1800. This map is fully open to fellow researchers and is available in multiple open source formats (SHP, GPKG, GeoJSON).

Kavanagh, Jack · Anthony, Patrick

6 files · 9.3 MB · geojson, geopackage, shapefiledeclared

A historical map of the boundaries of Prussia in c. 1795. This map is fully open to fellow researchers and is available in multiple open source formats (SHP, GPKG, GeoJSON).

Rui, Jin · Cai, Chenfan

1 files · 3.7 MB · rardeclared

This dataset provides a paper-aligned 6-km grid-level perceived informality index for Southeast Asia. It is prepared as the data-release package associated with the manuscript "Unveiling the environmental drivers of urban informality in Southeast Asia through citizen science and explainable machine learning", intended for submission to npj Urban Sustainability. The release retains the ten countries used in the manuscript: Philippines, Indonesia, Vietnam, Cambodia, Myanmar, Thailand, Malaysia, Laos, Brunei and Timor-Leste. Singapore and unassigned grid cells from an earlier draft package were excluded to align the deposited data with the manuscript scope. The primary variable is informality_index, a min-max normalized 0-1 perceived informality index. Higher values indicate stronger predicted perceived urban informality. The original large-valued model output is retained as raw_informality_score for provenance, but informality_index should be used as the main manuscript-ready variable. Normalization was calculated over the retained ten-country grid cells. The package is organized into four main folders. The data/ folder contains the authoritative GeoPackage spatial layer, CSV exports, centroid-coordinate tables, administrative boundaries, country-level summary statistics and whole-dataset summary statistics. The docs/ folder contains a data dictionary, a methodology note and a processing log documenting how the release was generated. The figures/ folder contains quick-look visual summaries, including the informality-index histogram, country-level mean chart and spatial preview map. The checksums/ folder contains SHA-256 checksums for verifying file integrity. The GeoPackage file SEA_Perceived_Informality_6km_Grid.gpkg is the authoritative spatial dataset and includes grid geometries, country assignment, raw_informality_score and informality_index. The CSV files are provided for users who prefer tabular workflows or do not use GIS software. The centroid CSV includes approximate longitude and latitude for each grid cell centroid. Summary-statistics files report country-level and overall distributions of the normalized perceived informality index, with additional raw-score summaries retained for provenance. This release is intended to support reproducibility, spatial visualization and further research on perceived urban informality, environmental exposure and urban sustainability in Southeast Asia. Raw satellite imagery, Google Street View imagery and third-party geospatial layers are not redistributed in this package because they are subject to the access terms and licensing conditions of their original providers.

Haider, Haroon

1 files · 146 MB · rardeclared

This dataset provides global gridded soil nitrous oxide (N₂O) emissions for the period 1961-2019, distributed as a stack of annual NetCDF files ( N2O_soil_emissions_YYYY.nc ), one per year, giving 59 files in total. Each file resolves emissions on a regular 0.5° × 0.5° longitude-latitude mesh (720 longitude columns by 360 latitude rows) covering the full globe. Grid-cell centres are given by the lat (degrees_north) and lon (degrees_east) coordinate variables, with longitude running from -180° to +180°; the environmental-response field was rolled from its native 0-360° convention to -180-180° so that every layer shares this common grid. Ocean and other missing cells are flagged with a fill value of NaN . Within each annual file, emissions are stored as twelve monthly fields ( n2o_january through n2o_december ) together with an annual total ( n2o_annual ). The monthly fields report soil N₂O emission per grid cell in grams of N₂O-N per cell per month, and the annual field, expressed in grams of N₂O-N per cell per year, is the sum of the twelve monthly layers. Because the stored values are absolute per-cell masses rather than per-area fluxes, a regional or global total is obtained by summing cells directly and converting from grams to teragrams (dividing the summed grams by 1 × 10&sup1;²). Grid-cell emissions were computed as the product of a fertiliser-driven emission field, an environmental scaling term, and a mean precipitation modifier. Each file preserves the full provenance of this calculation through its global attributes, which record the dataset title, the reference year, the input and output units, the calculation string, the longitude-fix note, and a UTC creation timestamp, so that every layer can be traced back to its inputs and processing steps.

Francescone, Marco

14 files · 380 KB · shapefile, zipdeclared

This dataset contains original geomorphic mapping of surface fault traces along the Dixie Valley Fault (DVF) range front and piedmont zone, central Nevada, USA. Traces were mapped directly from a 1-m bare-earth lidar digital elevation model (DEM), using hillshade and slope-raster visualizations. This dataset accompanies the manuscript: Francescone, M., et al. (in review), LiDAR-Based Fault-Scarp Analysis and Rupture Hazard Assessment: Earthquake Scenarios of the Dixie Valley Fault System (Nevada, USA). See Section 3.1 ("Fault Trace Mapping") of the manuscript for full methodological details