cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.weww4c
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ligiidae",
 "Year 2005-2007",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 251 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046095-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.awd57f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odonata",
 "Geometry POLYGON ((51.4741 -10.5904, 51.6872 -10.0924, 51.464 -9.7, 51.5346 -9.2212, 51.4094 -8.8834, 51.0293 -8.7096, 50.2991 -9.0646, 50.2456 -9.492, 50.6261 -9.8954, 50.5382 -10.1732, 50.6846 -10.5267, 51.1274 -10.7274, 51.4741 -10.5904))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046100-250811113504898/datasets/export for details.
DOI: 10.15468/dl.a8z89k
title: Occurrence Download

description: A dataset containing 1599 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pilocarpus spicatus"
 ]
}

 The dataset includes 1599 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046097-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16947883
title: Facility-Level, process-based CO2 emissions inventory of China's petrochemical plants

description: CO2 emission inventory of China's petrochemcial plants, distinguishing variations in energy consumption, feedstock types, product categories, production processes, technologies, electricity carbon intensity, and interconnected product chains
DOI: 10.15468/dl.yhahrm
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 39 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046098-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n73jt7
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 48 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046099-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fvxg66
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 84 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046101-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyp4te
title: Occurrence Download

description: A dataset containing 725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ligiidae",
 "Year 2011-2013",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 725 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046102-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvxnrg
title: Occurrence Download

description: A dataset containing 1727 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ligiidae",
 "Year 2017-2019",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1727 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046103-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spjqf2
title: Occurrence Download

description: A dataset containing 130847 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is World distribution of the aquatic Oligochaeta"
 ]
}

 The dataset includes 130847 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046081-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygcpum
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex depressa transsilvanica"
 ]
}

 The dataset includes 173 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046104-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ts4c7s
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odonata",
 "Geometry POLYGON ((53.2221 -7.3094, 53.175 -6.9401, 52.2917 -6.9401, 52.2873 -7.3844, 52.5484 -7.6243, 53.0196 -7.576, 53.2221 -7.3094))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046105-250811113504898/datasets/export for details.
DOI: 10.15468/dl.9uvm26
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tylidae",
 "Year 1999-2001",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046106-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16948787
title: Test data for Galaxy IUC SnapATAC2  tool

description:  Test data for Galaxy IUC SnapATAC2  tool.  The data is based on published 10x human  PBMC 500 scATAC-seq data. The data was filtered for chromosome 21 only.
DOI: 10.15468/dl.cfptqx
title: Occurrence Download

description: A dataset containing 646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 646 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046108-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t2894e
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Canada",
 "HasCoordinate is true"
 ]
}

 The dataset includes 86 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046109-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34711/inptdat.942
title: Modelling studies of arcs of short length between copper electrodes: Dataset

description: The data correspond to the results of modelling studies of DC electric arcs at a current of 2 A in air with admixture of copper metal vapour. Experimental findings are used to adjust input parametrs of the model in order to achieve a good match. The simulations are performed strating with a discharge burning with a minimum gap length of 30 µm for a physical time of 11 ms. Then, the separation of the electrodes is followed for further 51 ms and the discharge gap is increased up to 3 mm. The comparision of experimental and modelling data is based on the measured arc voltage. Variations of the discharge radius during the contact opening, the field enhancement factor, and the molar fraction of copper metal vaopur show the sensitivity of the computed arc voltage.
DOI: 10.15468/dl.7z3bpv
title: Occurrence Download

description: A dataset containing 585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lioconcha castrensis"
 ]
}

 The dataset includes 585 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046110-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v863yr
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tylidae",
 "Year 2011-2013",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 47 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046114-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ea7ndd
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tylidae",
 "Year 2005-2007",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046111-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17863/cam.116518
title: Research data supporting publication "Optical Control of Single Atom Dynamics in Plasmonic Nanogaps"

description: Figure 1: (E) 633 nm laser irradiation intensity over the course of a typical write-read experiment (note y-scale). (F) Corresponding SERS time scans for (E). Initial ‘check’ scan collected at 5 μW μm-2 with 8 s integration time per spectrum, ‘write’ at 3 mW μm-2 for 170 ms irradiation time, ‘read’ at 10 μW μm-2 every 4 s (further scans in Fig. S1). Figure 2: Picocavity writing and reading dynamics vs laser power density. (A) Empirical cumulative density distribution functions (ECDF) of picocavity write time distributions along with exponential CDF fits (F_W=1-e^(-Γ_W t)) for 1 mW μm-2 and 5 mW μm-2 incident laser power densities (dashed). Shaded regions denote 95% confidence intervals. (B) Histogram of picocavity write times at 1mW μm-2 write intensity, with exponential probability distribution function (dashed line, f_W=Γ_W e^(-Γ_W t)) derived from the ECDF in (A). (C) Picocavity write rate Γ_W vs laser intensity with fit to Eq.(1) model assuming 1 eV activation barrier (28); ◼ marks critical intensity I_c. Error bars derived from CDF least squares fits are too small to be seen. (D) Percentage of picocavities that survive for 200 s vs read illumination intensity (at write intensity 3 mW μm-2). Upper and lower limit survival percentages extracted from criteria detailed in Methods and Supplementary Note S1. (E) Picocavity % survival during read vs laser intensity in the preceding write (read intensity 40 μW μm-2). Error bars in (D-E) are derived from binomial distribution variance. Figure 3: (A) 785 nm excitation SERS spectra resulting from a write-read-erase experiment with a 20 h storage period at the read stage. Only the final write spectrum is shown. All spectra are normalised to the 290 cm-1 nanocavity peak and smoothed with a 3rd order 5 pt Savitzky-Golay filter. (C-E) 633 nm excitation SERS spectra resulting from write-read experiments on three example picocavities over the course of a week, with increasing periods of dark storage between read spectra. Only the final write spectra (red) are shown. (F) 633 nm excitation SERS spectra resulting from read experiments on a control NPoM with no prior write stage, over the course of 76 h. All spectra in (C-F) are normalised to the 1050 cm-1 nanocavity peak and smoothed with a 3rd order 11 pt Savitzky-Golay filter. Figure 4: (A) Example histogram of picocavity state evolution times, with exponential probability distribution (dashed line, f_S=Γ_S e^(-Γ_S t)) derived from fitting 80 μW μm-2 ECDF in (B). (B) Example ECDFs of picocavity state evolution time distributions along with exponential CDF fits (F_S=1-e^(-Γ_S t)). Shaded regions denote 95% confidence intervals. (C) Picocavity state change rate Γ_S dependence on laser intensity (line is guide to eye). Error bars are derived from the CDF least squares fits. Figure 5B: Migration energy of the adatom and surface area of the pit in (A) vs simulation trajectory over time.
DOI: 10.15468/dl.ww2bz3
title: Occurrence Download

description: A dataset containing 130847 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is World distribution of the aquatic Oligochaeta"
 ]
}

 The dataset includes 130847 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046096-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15857384
title: 2013, 2016, 2017, 2021 and 2023 pooled multi-site female sex worker respondent-driven sampling data in Zimbabwe
DOI: 10.5281/zenodo.15857385
title: 2013, 2016, 2017, 2021 and 2023 pooled multi-site female sex worker respondent-driven sampling data in Zimbabwe
DOI: 10.15468/dl.8ks7an
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Cuba",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046112-250811113504898/datasets/export for details.
DOI: 10.15468/dl.af6zvw
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tylidae",
 "Year 2017-2019",
 "Continent is Europe",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 25 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046115-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16029014
title: Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital

description: # Additional file 4 — Code & Data package (DOI-ready)

**Recommended deposition:** Zenodo (DataCite DOI) or OSF (DataCite/Crossref DOI).  **Title (Zenodo):** Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital”  **Creators:** Hamiyet Büşra Gündoğdu, et al.  **Description:** Reproducible materials accompanying the manuscript. Includes Python script, machine-readable raw counts (Table 3 / Table 4), and a conda environment to reproduce the figures and statistics (Fisher’s exact tests, BH-FDR).  **Keywords:** Pseudomonas aeruginosa; CRPA; carbapenem resistance; exoT; exoY; PFGE; Fisher’s exact test; FDR; BH; EUCAST; reproducible research  **Version:** 1.0 (2025-08-26)**Funding:** [Recep Tayyip Erdoğan University] Scientific Research Projects Coordination Unit (BAP), grant [TTU-2020-1191]

## ContentsSee `Additional_file_4_manifest.csv` for file sizes and SHA256 checksums.

- `reproduce_analysis_corrected.py` — analysis/plot script- `table3_counts.csv` — gene-prevalence counts- `table4_counts_corrected.csv` — exoT/exoY vs antibiotic counts- `environment.yml` — conda environment spec

## How to reproduce```bashconda env create -f environment.ymlconda activate crpa_analysispython reproduce_analysis_corrected.py```Figures S1–S2 (q-value plots) will be generated as PNG/PDF.

## Licensing- **Data (CSV):** CC BY 4.0 recommended.  - **Code (Python):** MIT recommended.  If you prefer a single-license deposition on Zenodo, select **CC BY 4.0** and also include `LICENSE-MIT.txt` inside the archive for code-level permission. This README clarifies the dual intent.

## Suggested citation (will update after DOI is minted)Gündoğdu HB, Rakıcı E, Ejder N, Çopur Çiçek A, Özgümüş OB. (2025). Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital” (Version 1.0) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.16029015

## ContactCorresponding author: Osman Birol Özgümüş — [ozgumus.ob@erdogan.edu.tr]
DOI: 10.5281/zenodo.16029015
title: Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital

description: # Additional file 4 — Code & Data package (DOI-ready)

**Recommended deposition:** Zenodo (DataCite DOI) or OSF (DataCite/Crossref DOI).  **Title (Zenodo):** Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital”  **Creators:** Hamiyet Büşra Gündoğdu, et al.  **Description:** Reproducible materials accompanying the manuscript. Includes Python script, machine-readable raw counts (Table 3 / Table 4), and a conda environment to reproduce the figures and statistics (Fisher’s exact tests, BH-FDR).  **Keywords:** Pseudomonas aeruginosa; CRPA; carbapenem resistance; exoT; exoY; PFGE; Fisher’s exact test; FDR; BH; EUCAST; reproducible research  **Version:** 1.0 (2025-08-26)**Funding:** [Recep Tayyip Erdoğan University] Scientific Research Projects Coordination Unit (BAP), grant [TTU-2020-1191]

## ContentsSee `Additional_file_4_manifest.csv` for file sizes and SHA256 checksums.

- `reproduce_analysis_corrected.py` — analysis/plot script- `table3_counts.csv` — gene-prevalence counts- `table4_counts_corrected.csv` — exoT/exoY vs antibiotic counts- `environment.yml` — conda environment spec

## How to reproduce```bashconda env create -f environment.ymlconda activate crpa_analysispython reproduce_analysis_corrected.py```Figures S1–S2 (q-value plots) will be generated as PNG/PDF.

## Licensing- **Data (CSV):** CC BY 4.0 recommended.  - **Code (Python):** MIT recommended.  If you prefer a single-license deposition on Zenodo, select **CC BY 4.0** and also include `LICENSE-MIT.txt` inside the archive for code-level permission. This README clarifies the dual intent.

## Suggested citation (will update after DOI is minted)Gündoğdu HB, Rakıcı E, Ejder N, Çopur Çiçek A, Özgümüş OB. (2025). Code and data for “Genotypic and Phenotypic Landscape of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Respiratory and Non-Respiratory Samples in a Tertiary Hospital” (Version 1.0) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.16029015

## ContactCorresponding author: Osman Birol Özgümüş — [ozgumus.ob@erdogan.edu.tr]
DOI: 10.15468/dl.72nb3s
title: Occurrence Download

description: A dataset containing 988748 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Podiceps cristatus, Fulica atra, Cygnus olor, Acrocephalus arundinaceus, Acrocephalus scirpaceus, Acrocephalus arundinaceus, Aythya fuligula, Remiz pendulinus, Spatula clypeata, Mareca strepera strepera, Anser anser)",
 "Year is one of (2020, 2021, 2022, 2023, 2024)",
 "DecimalLatitude is greater than or equal to 47.53364139636112",
 "DecimalLatitude is less than or equal to 54.8769089978912",
 "DecimalLongitude is greater than or equal to 6.033629",
 "DecimalLongitude is less than or equal to 15.037743",
 "Year is not null",
 "HasCoordinate is TRUE",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE",
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)"
 ]
}

 The dataset includes 988748 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046059-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wwqps
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odonata",
 "Geometry POLYGON ((37.7662 19.7333, 37.7663 20.0599, 37.1382 20.0599, 37.1382 11.0599, 44.3186 11.0599, 44.0798 11.2595, 43.8495 11.8222, 43.8305 12.54, 43.3858 13.2657, 41.2508 15.1278, 41.3523 15.6631, 41.1413 16.086, 40.7405 16.3725, 40.5343 16.9022, 39.5387 17.0726, 39.1348 18.0388, 39.3493 18.6268, 39.116 19.1892, 38.3245 19.7041, 37.7662 19.7333))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)"
 ]
}

 The dataset includes 190 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046116-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kyhkcv
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyracantha coccinea",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046118-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3rs72v
title: Occurrence Download

description: A dataset containing 2732 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Araucaria angustifolia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2732 records from 127 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046117-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.