cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31430122
title: Piperine inhibits biofilm formation in co-cultures of <i>Pseudomonas aeruginosa</i> and <i>Staphylococcus aureus</i>

description: Polymicrobial biofilms of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> pose serious clinical challenges due to their persistence, metabolic adaptability, and antibiotic tolerance. The present study investigated the ability of these two bacteria to co-exist and form mixed-species biofilms and evaluated the antibiofilm potential of piperine, a plant-derived alkaloid from <i>Piper nigrum</i>. Co-existence of <i>S. aureus</i> and <i>P. aeruginosa</i> was confirmed by enumeration of colony-forming units, growth kinetics, cross-streaking, metabolic fingerprinting, Gini coefficient analysis, and antibiotic susceptibility. Sub-minimum inhibitory concentrations of piperine significantly inhibited mixed-species biofilm formation, as demonstrated by biochemical, microbiological and microscopic analysis. Piperine treatment led to noticeable reductions in biofilm biomass, exopolysaccharide content, total protein content, metabolic activity and extracellular DNA. Mechanistic investigations revealed that piperine impaired biofilm-forming determinants by reducing cellular co-aggregation and cell surface hydrophobicity, inducing intracellular reactive oxygen species (ROS) accumulation, and increasing membrane permeability. Significantly, piperine effectively disrupted pre-established mixed-species biofilms, and its antibiofilm efficacy was further validated in a catheter model, highlighting its relevance against device-associated infections. Collectively, these findings demonstrate that piperine inhibits and disintegrates <i>S. aureus</i>-<i>P. aeruginosa</i> biofilms through diverse mechanisms, positioning it as a promising phytochemical for managing biofilm-associated infections.
DOI: 10.6084/m9.figshare.31430122.v1
title: Piperine inhibits biofilm formation in co-cultures of <i>Pseudomonas aeruginosa</i> and <i>Staphylococcus aureus</i>

description: Polymicrobial biofilms of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> pose serious clinical challenges due to their persistence, metabolic adaptability, and antibiotic tolerance. The present study investigated the ability of these two bacteria to co-exist and form mixed-species biofilms and evaluated the antibiofilm potential of piperine, a plant-derived alkaloid from <i>Piper nigrum</i>. Co-existence of <i>S. aureus</i> and <i>P. aeruginosa</i> was confirmed by enumeration of colony-forming units, growth kinetics, cross-streaking, metabolic fingerprinting, Gini coefficient analysis, and antibiotic susceptibility. Sub-minimum inhibitory concentrations of piperine significantly inhibited mixed-species biofilm formation, as demonstrated by biochemical, microbiological and microscopic analysis. Piperine treatment led to noticeable reductions in biofilm biomass, exopolysaccharide content, total protein content, metabolic activity and extracellular DNA. Mechanistic investigations revealed that piperine impaired biofilm-forming determinants by reducing cellular co-aggregation and cell surface hydrophobicity, inducing intracellular reactive oxygen species (ROS) accumulation, and increasing membrane permeability. Significantly, piperine effectively disrupted pre-established mixed-species biofilms, and its antibiofilm efficacy was further validated in a catheter model, highlighting its relevance against device-associated infections. Collectively, these findings demonstrate that piperine inhibits and disintegrates <i>S. aureus</i>-<i>P. aeruginosa</i> biofilms through diverse mechanisms, positioning it as a promising phytochemical for managing biofilm-associated infections.
DOI: 10.15468/dl.cw3bmc
title: Occurrence Download

description: A dataset containing 1381 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.9203 36.12219,42.61796 36.12219,42.61796 48.07032,3.9203 48.07032,3.9203 36.12219))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Podarcis siculus campestris"
 ]
}

 The dataset includes 1381 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001807-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c6r3sj
title: Occurrence Download

description: A dataset containing 511 records in GBIF matching the query:

SELECT
 GBIF_ISEA3HCode(
 8, 
 decimalLatitude,
 decimalLongitude,
 COALESCE(coordinateUncertaintyInMeters, 1000)
 ) AS geogrid_id,
 CASE 
 WHEN classKey IN ('359') THEN 'Mammals'
 WHEN classKey IN ('212') THEN 'Birds'
 WHEN familyKey IN ('1103', '1104', '494', '495', '1105', '496', '497', '1106', '498', '499', '1107', '537', '538', '1153', '547', '1162', '548', '549', '550', '1163', '1164', '1165', '1166', '1167', '1305', '1067', '1306', '1307', '1308', '1068', '1069', '587', '1310', '588', '589', '1311', '1312', '1313', '590', '708', '890', '774', '889', '773', '772', '888', '765', '879') THEN 'Bony Fish'
 WHEN classKey IN ('131') THEN 'Amphibians'
 WHEN classKey IN ('216') THEN 'Insects'
 WHEN classKey IN ('11418114', '11569602', '11592253', '11493978') THEN 'Reptiles'
 WHEN phylumKey IN ('52') THEN 'Molluscs'
 WHEN classKey IN ('367') THEN 'Arachnids'
 WHEN classKey IN ('220', '196') THEN 'Flowering Plants'
 WHEN classKey IN ('194', '244', '228', '282') THEN 'Gymnosperms'
 WHEN orderKey IN ('392') THEN 'Ferns'
 WHEN phylumKey IN ('35') THEN 'Mosses'
 WHEN phylumKey IN ('95') THEN 'Sac Fungi'
 WHEN phylumKey IN ('34') THEN 'Basidiomycota'
 END AS taxonomic_group,
 COUNT(DISTINCT speciesKey) AS species_count
FROM occurrence
WHERE countryCode = 'BW'
 AND hasCoordinate = TRUE
 AND hasGeospatialIssues = FALSE
 AND coordinateUncertaintyInMeters &lt;= 2000
 AND occurrenceStatus = 'PRESENT'
 AND speciesKey IS NOT NULL
 AND basisOfRecord != 'FOSSIL_SPECIMEN'
 AND taxonRank = 'SPECIES'
 AND (
 classKey IN ('359', '212', '131', '216', '11418114', '11569602', '11592253', '11493978', '367', '220', '196', '194', '244', '228', '282')
 OR familyKey IN ('1103', '1104', '494', '495', '1105', '496', '497', '1106', '498', '499', '1107', '537', '538', '1153', '547', '1162', '548', '549', '550', '1163', '1164', '1165', '1166', '1167', '1305', '1067', '1306', '1307', '1308', '1068', '1069', '587', '1310', '588', '589', '1311', '1312', '1313', '590', '708', '890', '774', '889', '773', '772', '888', '765', '879')
 OR phylumKey IN ('52', '35', '95', '34')
 OR orderKey IN ('392')
 )
GROUP BY geogrid_id, taxonomic_group;


 The dataset's 511 records were derived from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001785-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4t6hgy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Dischistodus pseudochrysopoecilus"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001809-260226173443078/datasets/export for details.
DOI: 10.25740/cv694yk7414
title: OmicVerse: An Agent-Enabled Unified Framework for Bulk, Single-Cell, and Spatial Transcriptomics Data Analysis

description: Recent advances in bulk, single-cell, and spatial transcriptomics have transformed biological discovery, yet fragmented tools hinder cross-modal integration. OmicVerse is a unified Python framework linking bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomics through a standardized API and data model. It supports preprocessing, gene selection, cell type annotation, trajectory inference, batch correction, spatial mapping, and bulk-to-single-cell deconvolution with GPU–CPU acceleration. A novel Agent-based architecture enables adaptive analysis: dynamically benchmarking algorithms, optimizing pipelines, and integrating foundation models (e.g., scGPT, Geneformer, CellPLM) for embeddings, annotation, and conversational workflows. OmicVerse further offers publication-ready visualization, MOFA+ multi-omics integration, and pathway enrichment. This protocol guides installation, configuration, and execution from raw data to integrative, AI-augmented analyses, establishing a scalable standard for reproducible, cross-modal transcriptomics.
DOI: 10.18150/xsfpv6
title: Datasets presented in "Light-adapted flicker optoretinograms captured with a spatio-temporal optical coherence-tomography (STOC-T) system"

description: This repository contains the datasets used in the main publication. The data are provided as .mat files and as native MATLAB figure files (.fig), enabling direct access to and extraction of the datasets of interest.
DOI: 10.5281/zenodo.18621222
title: Data for unpublished Paper
DOI: 10.5281/zenodo.18621221
title: Data for unpublished Paper
DOI: 10.48366/r1586703
title: Nutritional Composition of Ebobolo

description: This comparison describes the nutritional composition of Ebobolo, a commonly consumed food in Cameroon. It presents the nutritional composition in terms of Iron, Zinc, Copper, Magnesium, Phytate.
DOI: 10.5281/zenodo.18800297
title: Pantelleria noise test measurements
title: pantelleria noise test measurements

description: This dataset presents seismic noise measurements collected within the Panta Rei project, which was conducted to assess site feasibility, including logistical accessibility, LTE (Long Term Evolution) signal coverage for data transmission, and the identification of possible local noise sources. The dataset contains ambient noise recordings covering the period from September 2023 to October 2025 for station TST10.
DOI: 10.5281/zenodo.18800438
title: THE PROBLEM OF MORAL CHOICE IN F.M. DOSTOEVSKY'S NOVEL THE BROTHERS KARAMAZOV

description: The article is devoted to the study of the problem of moral choice in Fyodor Dostoevsky’s novel The Brothers Karamazov—the writer’s culminating work, in which his ethical concept is revealed with the greatest completeness. The paper analyzes how, through the destinies of the main characters—Dmitri, Ivan, Alexei Karamazov, and Smerdyakov—Dostoevsky explores the fundamental questions of human existence: the correlation between freedom and responsibility, faith and disbelief, good and evil. Special attention is paid to the philosophical core of the novel—“The Legend of the Grand Inquisitor,” in which the problem of moral choice acquires a universal and historiosophical dimension. The article examines Dostoevsky’s key idea of “universal responsibility”—the ontological guilt of each person before everyone—and repentance as a path to moral purification and personal transformation.
DOI: 10.5281/zenodo.18800296
title: Pantelleria noise test measurements
title: pantelleria noise test measurements

description: This dataset presents seismic noise measurements collected within the Panta Rei project, which was conducted to assess site feasibility, including logistical accessibility, LTE (Long Term Evolution) signal coverage for data transmission, and the identification of possible local noise sources. The dataset contains ambient noise recordings covering the period from September 2023 to October 2025 for station TST10.
DOI: 10.5281/zenodo.18800437
title: THE PROBLEM OF MORAL CHOICE IN F.M. DOSTOEVSKY'S NOVEL THE BROTHERS KARAMAZOV

description: The article is devoted to the study of the problem of moral choice in Fyodor Dostoevsky’s novel The Brothers Karamazov—the writer’s culminating work, in which his ethical concept is revealed with the greatest completeness. The paper analyzes how, through the destinies of the main characters—Dmitri, Ivan, Alexei Karamazov, and Smerdyakov—Dostoevsky explores the fundamental questions of human existence: the correlation between freedom and responsibility, faith and disbelief, good and evil. Special attention is paid to the philosophical core of the novel—“The Legend of the Grand Inquisitor,” in which the problem of moral choice acquires a universal and historiosophical dimension. The article examines Dostoevsky’s key idea of “universal responsibility”—the ontological guilt of each person before everyone—and repentance as a path to moral purification and personal transformation.
DOI: 10.5281/zenodo.18800090
title: Dataset and workflow for Flushing Ratio Calculation

description: Dataset and workflow for Flushing Ratio Calculation

This Zenodo record provides a complete, citable package for computing the Flushing Ratio (FR) from RGB imagery, including:



a snapshot of the analysis/processing code (mirroring the GitHub repository structure), and

the image data used in the study.


Flushing Ratio (FR) is defined as FR = BA/RA, where:- BA (Budburst Area) is the area of flushing (light-green) tissues,- RA (Ramet Area) is the area of the entire visible crown/ramet.BA and RA masks are obtained using CNN-based instance segmentation (YOLOv11) and subsequently used to compute FR and derived traits for downstream analyses.

Contents



code: snapshot of https://github.com/jirkachuchl/flushing-ratio (scripts/notebooks for data processing and statistical/genetic analyses)

data:



original_images - RGB image data used for training/validation and/or FR extraction

data - data obtained from images used for statistical analysis



weights: Notebook for model training and trained Yolo11 instance segmentation model for 2 classes:



norway-spruce

spruce-bud



testing_folder: folder includes the full set of intermediate artifacts produced by the pipeline, as well as the README.md file with description of the shortest way to the loading and running the weights

Fig_1.png: graphical workflow

README.md: Introduction to each folder, summary


Citation

Please cite this Zenodo record (DOI) when using the code and/or the dataset.
DOI: 10.5281/zenodo.18679042
title: Dataset and workflow for Flushing Ratio Calculation

description: Dataset and workflow for Flushing Ratio Calculation

This Zenodo record provides a complete, citable package for computing the Flushing Ratio (FR) from RGB imagery, including:



a snapshot of the analysis/processing code (mirroring the GitHub repository structure), and

the image data used in the study.


Flushing Ratio (FR) is defined as FR = BA/RA, where:- BA (Budburst Area) is the area of flushing (light-green) tissues,- RA (Ramet Area) is the area of the entire visible crown/ramet.BA and RA masks are obtained using CNN-based instance segmentation (YOLOv11) and subsequently used to compute FR and derived traits for downstream analyses.

Contents



code: snapshot of https://github.com/jirkachuchl/flushing-ratio (scripts/notebooks for data processing and statistical/genetic analyses)

data:



original_images - RGB image data used for training/validation and/or FR extraction

data - data obtained from images used for statistical analysis



weights: Notebook for model training and trained Yolo11 instance segmentation model for 2 classes:



norway-spruce

spruce-bud



testing_folder: folder includes the full set of intermediate artifacts produced by the pipeline, as well as the README.md file with description of the shortest way to the loading and running the weights

Fig_1.png: graphical workflow

README.md: Introduction to each folder, summary


Citation

Please cite this Zenodo record (DOI) when using the code and/or the dataset.
DOI: 10.15468/dl.rdz4qz
title: Occurrence Download

description: A dataset containing 485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Castilleja fissifolia",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 485 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001810-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x7xwzv
title: Occurrence Download

description: A dataset containing 316 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence)",
 "Country is one of (Tanzania, United Republic of, Kenya)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tragelaphus scriptus",
 "Year 2023-2026"
 ]
}

 The dataset includes 316 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001814-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5wyh6t
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "Geometry POLYGON ((105.610544 14.999999, 179.999961 14.999999, 179.999961 65.08290100000001, 105.610544 65.08290100000001, 105.610544 14.999999))",
 "TaxonKey is Ephippus orbis"
 ]
}

 The dataset includes 70 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001813-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdfwaw
title: Occurrence Download

description: A dataset containing 1641338561 records in GBIF matching the query:
SELECT
 issue,
 gbifid,
 specieskey specieskey,
 decimallatitude decimallatitude,
 decimallongitude decimallongitude
FROM
 occurrence
WHERE
 occurrence.datasetkey = '4fa7b334-ce0d-4e88-aaae-2e0c138d049e'
 AND occurrence.basisofrecord = 'HUMAN_OBSERVATION'
 AND occurrence.license IN ('CC_BY_4_0', 'CC0_1_0')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND occurrence.decimallatitude IS NOT NULL
 AND occurrence.decimallongitude IS NOT NULL
 AND occurrence.specieskey IS NOT NULL
 AND occurrence.phylum = 'Chordata'
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence."year" &gt;= 2010
 AND occurrence."year" &lt;= 2100

 The dataset's 1641338561 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001757-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpjfzm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001798-260226173443078/datasets/export for details.
DOI: 10.15468/dl.wgnt36
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.29_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phrynocephalus vlangalii"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001818-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m3y6qp
title: Occurrence Download

description: A dataset containing 182 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is MONICEPH - Monitoring cephalopods during whale watching activity in the Azores"
 ]
}

 The dataset includes 182 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001819-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.82hvfm
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Huperzia crassa",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 542 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001820-260226173443078/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5287/ora-kq0ojzynd
title: Dataset for “Single-molecule quantification of RNA modifications using a probabilistic framework”

description: This dataset supports the study “Path Signatures Enable Model‑Free Mapping of RNA Modifications” (arXiv:2511.08855v1), authored by Maud Lemercier, Paola Arrubarrena, Salvatore Di Giorgio, Julia Brettschneider, Thomas Cass, Isabel S. Naarmann‑de Vries, Anastasia Papavasiliou, Alessia Ruggieri, Irem Tellioglu, Chia Ching Wu, F. Nina Papavasiliou, and Terry Lyons. The dataset contains raw and processed single‑molecule measurements used to develop and validate a model‑free, signature‑based approach for detecting RNA modifications. It is provided as a compressed archive () together with a checksum file (). The archive includes molecule‑level data from mouse, dengue virus, and E. coli, as well as IVT controls and native RNA measurements. The file hierarchy is as follows: BM_mouse-chr10_mettl3koP2E224hLPS-g_M-sup-I-m6A-I-m6A.sorted_chr10.bam.txt BM_mouse-chr10_ctr2-24hLPS-g_M-sup-I-m6A.sorted_chr10.bam.txt Bm_mouse-chr10-IVT_ctr1-24hLPS-g_IVT-sup-I-m6A.sorted_chr10.bam.txt Dengue_Data/ 20241002_DENV_IVT_gRNA.txt.gz 20241029_DENV_gRNA-pA_oligo.txt.gz IVT.txt.gz Native_sfRNA.txt.gz Ecoli_Data/ Native_rRNa_1623.txt.gz IVT_rRNa_1623.txt.gz Due to the size and structure of the dataset, the files will be delivered to the Oxford Research Archive (ORA) on a physical hard drive for secure ingestion into ORA DeepData. A README file has been uploaded as the required placeholder for this Symplectic Elements deposit.