Morales Trujillo, Leticia · García García, Julián Alberto · Domínguez Mayo, Francisco José · et al.

11 rows × 3 cols · 1.1 KB · csv, png

3 categorical

This package provides the TRASYS validation and verification metamodel diagrams together with concise specifications of the model-to-model and model-to-text transformations documented in the doctoral thesis Continuous Traceability Management in Assisted Reproduction Processes. The materials describe the derivation of a preliminary verification model from a validation model and the generation of traceability-rule and data-structure code from the verification model. No clinical data, personal data, production code, Enterprise Architect project files, credentials, or proprietary artifacts are included.

Lopez, Annalaura · Greco, Margherita · Marcolli, Beatrice · et al.

4 files · 17 KB · docx, xlsx

This dataset originates from a study aiming to valorise Ciuta sheep, a local breed native from the Italian Central Alps, through the characterization of nutritional quality and chemical composition of fresh meat (loins) and one traditional dry-cured product. Specifically, the research focused on determining the chemical composition of Ciuta sheep meat and on identifying key changes in its chemical profile during dry curing process, hypothesizing that such chemical fingerprint may suggest some markers linked to the production system, geographical origin, and traditional processing techniques. For this reason, for bthe dry-cured product, both an aliquot of fresh meat before and after transformation and dry-curing was sampled and analysed. Regarding loins, three commercial categories (lambs, hoggets and mutton) were considered, in order to define any possible difference induced by age of the sheep (and physiological factors, such as rumen development). The dataset includes chemical data regarding the proximate composition (moisture, protein, fat, ash, salt content for the dry-cured product) and energy content of fresh and dry-cured meat; the fatty acids content of fresh and dry-cured meat product; the volatile profile of fresh and dry-cured meat product. Results from analysis performed in our study suggested that the development of high-quality dry-cured products could provide a strategy to valorise Ciuta sheep meat, especially from adult animals (culled ewes and rams), while fresh meat production could focus on lambs. The complex volatile profile detected was influenced by both the farming system and traditional processing methods.

Kantor, Rose · Shakya, Migun · Ruth, Nelson · et al.

2,095 rows · 907 KB · fasta, tsv

A virus genome database representing 21,015 near-complete virus genomes collected from untargeted ultra-deep RNA/DNA combined sequencing of wastewater. Sequence data was provided by the CASPER consortium and raw data may be found on NCBI SRA under bioprojects PRJNA1247874 and PRJNA1198001. Data underwent read trimming, rRNA and human read removal, de novo assembly, and selection of high-quality viral contigs. Contigs were clustered at 95% identity and 85% query coverage to dereplicate. Chimera-checking required at least two independent assemblies of the same viral genome or presence of the genome in another reference database. Annotation made use of RdRpCATCH, geNomad, checkV, BLASTN against NCBI core-nt, and RNAVirHost. The RdRp fasta files contain representative RdRp sequences identified through homology to major RdRp reference databases and clustered at 90% sequence identity over 75% sequence coverage. Included sequences contain all three conserved RdRp motifs (A, B, and C) arranged in either the canonical ABC configuration or the permuted CAB configuration.

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.

Budzinski, Lisa · Beenken, Anne Elisabeth · Sempert, Toni · et al.

9 rows × 1 cols · 743 B · csv, docx, zip

1 categorical

We have investigated an IgG4-RD (IgG4-RD) cohort by our multi-parameter microbiota flow cytometry approach to characterise the microbiota on single-cell level for attributes of the disease. The microbiota is isolated from stool samples and stained according to the published protocol for (a) host immunoglobulins IgA1, IgA2, IgM, IgG and (b) agglutinin binding to mannose, galactose or N-Acetyl-glucosamine surface sugar moieties. For all samples we also determined the microbiome composition by 16S rRNA (V3-V4) sequencing on the illumina MiSeq platform. We provide the raw .fcs and FASTQ files of 40 IgG4-RD patients. For comparison we additionally analysed 36 healthy donors. All .fcs files were generated on BD Influx®. The metadata is collected in the provided meta.csv. The staining parameters are summarized in provided panel.csv.

Li, Zhiyao · Wang, Ningbo · Zhong, Jiahao

6 files · 48 MB · docx, zip

GIFT-BDS is a regional ionospheric total electron content (TEC) and TEC-gradient dataset over China derived from BeiDou geostationary Earth orbit (GEO) observations and a dense ground-based GNSS receiver network. The dataset is designed to provide high-resolution observations of ionospheric TEC variability and horizontal TEC-gradient structures over China and adjacent regions. The versioned release covers the period from 19 July 2024 to 31 December 2025, corresponding to DOY 201 of 2024 to DOY 365 of 2025. The geographical coverage is 15°N-50°N and 95°E-135°E. The dataset is provided in daily NetCDF files and contains two product levels. Level-1 products provide observation-level GEO-derived slant TEC (STEC) and rate of TEC index (ROTI) records for individual receiver-GEO satellite lines of sight, with a temporal resolution of 30 s. Level-2 products provide gridded regional TEC and TEC-gradient variables, including VTEC, VTEC t , ROTI, GIX, GIX std , GIX x , GIX y , GIX t,x , and GIX t,y , with a temporal resolution of 15 min. IPP-based variables are provided on a 1° × 1° grid, while inter-IPP-gradient variables are provided on a 0.25° × 0.25° grid. The main processing steps include observation screening, cycle-slip and data-gap detection, continuous-arc segmentation, carrier-to-code leveling, satellite and receiver DCB correction, IPP calculation, inter-IPP pair selection, gradient estimation, and gridding. Quality control is applied before release. Missing values may occur because of station outages, data gaps, quality-control exclusions, or insufficient valid samples within a grid cell. Users should check the NetCDF variable attributes, including units and fill values, before analysis. The dataset is suitable for regional ionospheric studies, TEC-gradient monitoring, space-weather-related analyses, and investigations of ionospheric effects on GNSS positioning applications.

Jungmyoung, Son · Sihoon, Lee · Jiyeon, Hong

3 files · 20 KB · docx, xlsx

This dataset provides the complete double-coding matrix, PRISMA 2020 checklist, and search strategy supporting the systematic review "Representation-to-AI Transformation in K-12 Generative AI Learning: A Theory-Building Systematic Review of Semantic Transformation Mechanisms." It includes: (1) study-level tier classification (Core/Supporting/Context) for two independent coders and consensus tier for all 18 included studies; (2) the full semantic transformation unit (STU) coding matrix (18 studies x 10 STUs = 180 cells) with pre-consensus and consensus scores; (3)evidence-weighting consensus scores; (4) inter-rater reliability statistics (Cohen's kappa); (5) the completed PRISMA 2020 checklist; and (6) the full database-specific Boolean search strategy.

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.

Kovaliov, Michael

1 files · 100 MB · parquet

Madhusudan, Gujral

6 files · 29 MB · parquetdeclared

Large language models (LLMs) are trained on massive, publicly available text datasets comprising trillions of tokens, enabling them to excel at general language tasks like next-token prediction. However, LLMs often struggle with domain-specific prompts, exhibiting reduced accuracy or generating inaccurate information (hallucinations). This is because they lack sufficient subject matter expertise. Two primary approaches exist to address this limitation for augmenting LLMs knowledge: Retrieval-Augmented Generation (RAG) and fine-tuning. This presentation focuses on fine-tuning smaller LLMs with domain-specific instruct datasets using the LoRA (Low-Rank Adaptation) technique on Gaudi hardware. We will leverage publicly available LLMs and datasets from the Hugging Face Hub for this demonstration. Though it is possible to fine tune LLMs with plain text data - sourced from documents, articles, and other materials.

Azziz, Ricardo

1 files · 1.6 MB · docxdeclared

Supplemental Table 1. Meeting Agenda of the 2024 PCOS Challenge-CDC Stakeholder Meeting on Testosterone Reference Interval Standardization. August 26, 2024. Centers for Disease Control and Prevention, Atlanta, Georgia. Supplemental Table 2. Proposed Four-Stage Workflow for Developing Standardized Testosterone Reference Intervals Using Existing Study Data.

Austin, Timothy · do Valle Chagas Azaneu, Marina · Roughan, Moninya

26 files · 29 MB · netcdf, pdf, pngdeclared

Data collected from a temperature mooring at Lord Howe Island maintained by UNSW Sydney and funded by Parks Australia. The mooring position is longitude = 158.97°E and latitude = -31.51°, and local depth of approximately 52 m. The data were sampled using a series of thermistors (aqualogger 520PTs) deployed on a mooring line at 4m intervals through the water column, with shallowest instrument at 13 m and deepest at 53 m. The time period spans between 14-05-2025 and 22-04-2026. IMOS standard data quality assurance and quality control processes have been followed and the data formatted following IMOS conventions. Data quality control includes automated routines and visual inspection (expert QC) and flagging of obvious errors. File are c.f. compliant NetCDF files, and file name format follows IMOS conventions and includes sampling period in the format: UNSW_Lord_Howe_Marine_Park_TZ_ yyyymmddThhmmss Z_LH050_FV01_ LH050-2511-Aqualogger-AQUAlogger-520PT16-max160m-13_END- yyyymmddThhmmssZ.

Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.

1 files · 894 KB · pngdeclared

FIG. 14. — T3 (A, B), T8 (C, D), T11 (E, F), and T12 (G, H) of Zygorhiza kochii (Reichenbach in Carus & Koch, 1847), specimen TM 8501 in anterior (A, C, E, G) and lateral (B, D, F, H) views. Abbreviations: C, centrum; CF, capitular facet; NC, neural canal; POZ, postzygapophysis; PRZ, prezygapophysis; TF, tubercular facet; TP, transverse process. Scale bar: 10 cm. Figure: Jonas W. P. Hakkens.

Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.

1 files · 1.4 MB · pngdeclared

FIG. 9. — Preserved elements of Zygorhiza kochii (Reichenbach in Carus & Koch, 1847), specimen TM 8501 as located in-situ (A) and in articulation (B). Colors indicate anteroposterior location of element. Abbreviations: BH, basihyal; CX, cervical vertebra X; DR, distal rib segment; LM, left mandible; MN, manubrium; MS, mesosternal segment; RM, right mandible; Rx, Rib X; TB, tympanic bulla; TX, thoracic vertebra X. Scale bar: 10 cm. Figure: Jonas W. P. Hakkens.

Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.

1 files · 303 KB · pngdeclared

FIG. 7. — Skulls of Zygorhiza kochii (Reichenbach in Carus & Koch,1847) USNM 11962, and Dorudon serratus Gibbes, 1845 MMNS VP 130 in lateral and dorsal views highlighting diagnostic features: 1, nuchal crest bearing a posteriorly directed point at mid-height (Zygorhiza kochii) vs is generally round (Dorudon serratus) in lateral view; 2, crenulated cingula on P2-4 (Zygorhiza kochii) vs smooth cingula on P2-4 (Dorudon serratus); 3, medial margin of maxillae contact frontals (Zygorhiza kochii) vs do not contact the frontals (Dorudon serratus); 4, large anterior process on frontals (Zygorhiza kochii) vs no anterior process on frontals (Dorudon serratus); 5, narial process of premaxilla extends along almost the entire length of the nasals (Zygorhiza kochii) vs halfway along lateral margin of the nasals (Dorudon serratus). Not shown: p1 with single pinched root (Zygorhiza kochii) vs double-rooted p1 (Dorudon serratus). Not to scale. Drawings: Jonas W. P. Hakkens.

Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.

1 files · 429 KB · pngdeclared

FIG. 6. — Skulls of Zy. kochii (Reichenbach in Carus & Koch, 1847) (A-D) and D. serratus Gibbes, 1845 (E-I) in lateral view, specimens are scaled to equal condylobasal length. Grey sections represent anatomy obscured by matrix, other bones, or broken surfaces; brown indicates structures from the left lateral side. Not to scale. Drawings: Jonas W. P. Hakkens.

Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.

1 files · 365 KB · pngdeclared

FIG. 5. — Skulls of Zy. kochii (Reichenbach in Carus & Koch, 1847) (A-D) and D. serratus Gibbes, 1845 (E-I) in dorsal view. Grey sections represent anatomy obscured by matrix, other bones, or broken surfaces. Scaled to equal condylobasal length. Drawings: Jonas W. P. Hakkens.