Chen, Jianyong
6 files · 1.5 GB · gzip
hybrid · semantic + lexical · 1483 datasets ranked · 2.45s
Chen, Jianyong
6 files · 1.5 GB · gzip
A first sequence of the Ae. speltoides B chromosome has been available since 2020 (RUBAN et al. 2020b), but this assembly represents ~16% of the B only and thus cannot be used to uncover B-encoded genes. Now, high-molecular-weight DNA from +B leaf tissue of the clonally propagated +B plant was used to generate a chromosome-scale genome assembly. A total of 154 Gb of PacBio HiFi reads and 36.4 Gb of Nanopore reads (>25 kb) were generated for primary assembly using hifiasm (Cheng et al. 2026). The resulting 5.47 Gb assembly achieved 93.7% BUSCO completeness (contig N50 = 17.1 Mb). Approximately 104 Gb of Hi-C sequencing data derived from leaf tissue of the same +B plant were employed to scaffold the primary contigs. The assembly yielded eight large scaffolds (398-835 Mb), each displaying a characteristic Rabl configuration. Alignment of these scaffolds to the reference genome of Ae. speltoides accession AEG-9674-1 without B chromosome (Avni et al. 2022) revealed that seven of the eight scaffolds showed strong synteny with the standard A chromosomes 1S-7S. To determine whether the remaining large scaffold corresponded to the B chromosome, we generated ~60 Gb of whole-genome sequencing (WGS) data from 0B AR-derived lateral root tissue of the same plant, as well as approximately 36 Gb of WGS data from +B leaf tissue. Comparative read-mapping analyses showed that the eighth scaffold exhibited normal sequencing coverage in +B leaf-derived data but substantially reduced coverage in 0B AR-derived data. Thus, the 398 Mb scaffold represents the B chromosome, accounting for 69% of its size as estimated by flow cytometry. Additionally, 4.81 Gb of contigs were assigned to the seven pairs of A chromosomes, representing 91% of their estimated size (1C=5.27 Gb). Consequently, we produced a high-quality chromosome-scale assembly of Ae. speltoides carrying B chromosomes. To identify genes associated with the B chromosome elimination process, RNA-seq was performed across developmental stages and different tissues in which B chromosome behavior differs. Using all +B RNA-seq datasets, we annotated the Ae. speltoides genome assembly containing the B chromosome. This annotation identified 59,981 transcripts and 47792 protein-coding genes on the seven A chromosomes and 5,940 transcripts and 4,196 protein-coding genes on the B chromosome.
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.
Hakkens, Jonas W. P. · Reumer, Jelle W. F. · Schulp, Anne S.
1 files · 6.2 MB · pngdeclared
FIG. 1. — Photographs of TM 8501 as displayed in Teylers Museum in dorsal (A), left lateral (B) and right lateral (C) views (note the presence of matrix obscuring details of the anterior snout, temporal openings, and associated postcrania); D, localities of Zy. kochii (Reichenbach in Carus & Koch, 1847), D. serratus Gibbes, 1845, and C. healyorum Uhen & Gingerich, 2001; colors indicate: Bartonian (bright orange circle), Early Priabonian (blue squares), Late Priabonian (brown diamonds). Numbered occurrences are specimens discussed in this study: 1, MMNS VP 130; 2, USNM 11962, USNM 16638, USNM 16639, USNM 13773, USNM 4678, USNM 4679, FMNH PM-459, TM 8501; 3, MSC 3927/AUMP 2368, MB.Ma.43248; 4, SCSM 87.195; 5, MCZ 8763. Data and map are traced from the paleobiology database. More detailed localities for 2 can be found in Gingerich 2015b. Scale bar: 10 cm. Map: Jonas W. P. Hakkens; photos: Vannessa Timmermans (Teylers Museum).
Lopez-Gomez, Ignacio
2 files · 45 GB · gzipdeclared
Trained GenFocal model checkpoints. This record contains checkpoints for GenFocal: Checkpoints for the Diffusion-based Super-Resolution model (~8.15 GiB) CHeckpoints for the Flow Matching Debiasing model (~36.45 GiB)
García Mina, Janeth Elizabeth · Rodríguez Garófalo, Napoleón Hernán · Rumbaut-Rangel, Dayron · et al.
6 files · 737 KB · docx, pdfdeclared
El objetivo de este estudio es evaluar la importancia de la inteligencia artificial (IA) en el proceso de formación académica de estudiantes de educación básica, específicamente en la enseñanza de ciencias naturales. La investigación destaca cómo la IA puede personalizar el aprendizaje, adaptándose a los estilos individuales de cada alumno, lo que resulta en una experiencia educativa más efectiva y significativa. Se utilizó un diseño cuasiexperimental con una muestra de 60 estudiantes de sexto año, distribuidos en un grupo control (30 estudiantes) que recibió instrucción tradicional y un grupo experimental (30 estudiantes) que utilizó herramientas de IA, como chatbots educativos y plataformas de aprendizaje adaptativo. Los resultados mostraron que el 70% de los estudiantes del grupo experimental alcanzaron calificaciones superiores a 8, en comparación con solo el 30% del grupo control. Este hallazgo sugiere que la implementación de herramientas de IA puede transformar la educación básica, mejorando tanto el rendimiento académico como la motivación de los estudiantes. En conclusión, el estudio resalta la necesidad de seguir investigando y desarrollando nuevas estrategias educativas que integren la IA para maximizar su potencial en la educación.
Makhado, Langanani Christinah · Raliphaswa, Ndidzulafhi Selina
9 files · 157 KB · docxdeclared
This dataset contains anonymized transcripts derived from face-to-face interviews conducted with pregnant women and breastfeeding mothers as part of the research study. The interviews were audio-recorded and transcribed verbatim to capture participants' experiences, perceptions, and insights related to the study topic. All personally identifiable information has been removed to protect participant confidentiality. The transcripts are provided to support transparency, reproducibility, and further research related to the findings reported in the associated article
Bakare, Akeem
1 files · 34 KB · gzipdeclared
Contig-ARG-Linkage Reproducible Snakemake pipeline that links antibiotic resistance genes to bacterial hosts in metagenomic data. For each sample, it assembles reads (MEGAHIT), detects ARGs (BLASTn vs MEGARes), classifies contigs (Kraken2), and joins by contig ID. Pinned envs, checksummed databases, container builds, and CI-tested on synthetic data.
Stein, Samuel
5 files · 139 MB · gzipdeclared
Raw experimental dataset accompanying the paper "Calibration-Conditioned FiLM Decoders for Low-Latency Decoding of Quantum Error Correction Evaluated on IBM Repetition-Code Experiments." This dataset contains repetition-code experiments executed on three IBM Quantum processors -- ibm_kingston, ibm_pittsburgh, and ibm_fez. It comprises 352 hardware snapshots spanning code distances d = 3, 5, 7, 9, 11, syndrome-round counts r = 1 to 11, and both the X and Z logical bases. Each snapshot runs several repetition-code chains in parallel and carries the device calibration data captured at execution time, totalling several million measurement shots. All data is provided raw, exactly as returned by the hardware -- no machine-learning processing or sparsification is applied -- and is anonymized (no IBM Runtime job identifiers are released). CONTENTS - ibm_kingston.tar.gz, ibm_pittsburgh.tar.gz, ibm_fez.tar.gz per-device archives, each unpacking to <device>/d<D>_r<R>/job_<n>/ - index.csv one row per snapshot: path, backend, d, rounds, basis, logical_states, n_chains, shots - README.md full description of the layout and field definitions Each job_<n>/ directory contains: - info.json experiment parameters (device, d, rounds, basis, states, shots, n_chains) - calibration.json the device calibration snapshot at execution time (T1, T2, gate and readout error rates, coupling map) - circuit_state0.qasm, circuit_state1.qasm transpiled circuits as executed - bitstrings.json raw per-shot measurement records for every parallel chain USAGE Because each snapshot stores its own calibration data, the per-device and per-(d, r, basis) structure used in the paper is recoverable by filtering index.csv. The same calibration is consumed by both the FiLM decoder (via its calibration-graph encoder) and the modified MWPM baseline (via its detector-graph edge weights). Github to be updated for corresponding experiments on approval. Please contact Samuel Stein (samuel.stein@pnnl.gov) if you need any information or source docs before hand.
Fontelo, Paul
1 files · 26 KB · docxdeclared
Auto-Brewery Syndrome (ABS), also known as gut fermentation syndrome, is a condition in which microbial fermentation of dietary carbohydrates generates endogenous ethanol, causing signs and symptoms of alcohol intoxication without alcohol consumption. Misdiagnosis as alcohol use disorder (AUD) is common and carries severe medical, psychosocial, legal, and forensic consequences. The objective of thus narrative review is to synthesize the clinical literature on ABS for practicing clinicians and to present the first systematic analysis of ABS susceptibility in Asian populations - including communities of Asian descent in Western countries.
Hackl, Jürgen
6 files · 132 MB · parquet, tiffdeclared
EuroFlood is an open, cloud-native index over the JRC/Copernicus CEMS-EFAS Satellite-Derived Flood Depth Maps for Europe (Betterle & Salamon, 2025; CC-BY-4.0) - ~3,280 satellite-derived observed flood-depth maps across Europe, 2015-2024. The bundle is a sparse Cloud-Optimized GeoTIFF encoding, per pixel, the set of flood events that inundated it, plus a combo_id -sorted GeoParquet dictionary and a small events table. Query by region and time via HTTP range reads (GDAL /vsicurl + DuckDB) to retrieve matching events, then fetch only the source depth rasters needed. Built with the open-source EuroFlood Python package ( pip install euroflood ).
Bojarski, Krzysztof Kamil
1 files · 66 MB · gzipdeclared
This repository contains structural models and molecular dynamics input files for complexes of cathepsins B, S, and K with three glycosaminoglycan-like ligands: naphthalene-1,3,6-trisulfonate (NTS), amide-linked bis(naphthalene disulfonate) (BNS), and suramin. Initial protein and ligand structures used for molecular docking are provided in AutoDock3 format. For each cathepsin-ligand complex, the three most populated docking clusters are included, with three representative binding poses per cluster. The repository further contains system topologies and initial coordinates for molecular dynamics simulations in AMBER format ( .parm7 and .rst7 ), ligand library files required for tleap, molecular dynamics input files, and scripts used for post-processing and analysis of the MD trajectories.
Chander, Aishwarya
2 files · 8.7 GB · gzip, zipdeclared
Analysis code and processed data for the manuscript: "Multiple myeloma and therapy reshape the bone marrow niche to durably constrain immune reconstitution and vaccine responsiveness." This repository accompanies a longitudinal multi-omic study of immune dysfunction in multiple myeloma (MM). Matched bone marrow and peripheral blood from MM patients were profiled across diagnosis, induction, autologous stem cell transplant (ASCT), and recovery, together with matched healthy donors and vaccine response subcohorts. The analyses show that the tumor imposes a compartment specific immune program; marrow-restricted metabolic, inflammatory, and cytotoxic-effector changes not mirrored in blood; and, that adaptive immune reconstitution remains impaired up to two years post-ASCT. Half of patients failed to mount IgG responses to a high dose nonadjuvanted influenza vaccine, a defect overcome by the LNP adjuvanted COVID mRNA vaccine. Contents: Single cell RNA-seq (BMMC and PBMC), flow cytometry, Olink proteomics, and MSD cytokine analysis pipelines, plus the notebooks generating all manuscript figures. Processed/derived data needed to reproduce the figures are included; raw sequencing data are deposited in GEO.
Vera, Lourdes
31 files · 4.6 MB · csv, geojson, pngdeclared
Data, analysis scripts, and derived outputs reproducing the setback analysis between occupied buildings and active oil and gas wells in Karnes County, Texas, using public data (Texas Railroad Commission well locations; FEMA/ORNL USA Structures building footprints; and U.S. Census TIGER/Line block groups and 2020-2024 American Community Survey). The pipeline runs offline in Python (geopandas) and reproduces every reported distance, summary statistic, table, and figure in the associated article. This package reproduces and updates Chapter 3 of the author's doctoral dissertation: Vera, Lourdes (2022), "Environmental Data Justice in Action: Civically Valid Air Monitoring Near Oil and Gas Extraction in the Eagle Ford Shale Play," Ph.D. dissertation, Northeastern University, Boston, MA.