cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5sgnbn
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eugenia walkerae"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006702-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.62s58e
title: Occurrence Download

description: A dataset containing 2367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Argentina, Uruguay, Brazil)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vachellia caven"
 ]
}

 The dataset includes 2367 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006704-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/2k64p535xk
title: Use of a traction suture loop for subungual glomus tumor excision

description: Initially, the nail plate is laterally displaced with a mosquito clamp. A longitudinal incision is made in the nail matrix to expose the underlying glomus tumor. After careful dissection and exposure, the needle is inserted through the most superficial portion of the tumor to create the traction loop. Gentle upward traction is applied, providing stable exposure and facilitating dissection from its base. The procedure concludes with the closure of the nail matrix using fine absorbable sutures to preserve nail growth and reduce the risk of dystrophy.
DOI: 10.5281/zenodo.17441736
title: Processed single-cell RNA-seq data for "Evolutionarily conserved transcriptional regulators control monoaminergic neuron development"

description: Contents




Folder
Description


1_Replicate_Processed_Objects
Processed per-replicate scRNA-seq objects (post-QC, normalized, annotated).


2_Timepoint_Processed_Objects
Integrated, timepoint-specific datasets spanning 0–22 h after egg laying (AEL).


3_FullDataset_Processed_Objects
Full integrated dataset across all developmental stages with annotated cell identities.


4_MatureNeuronalDataset_Processed_Objects
Subset of mature neuronal populations used for trajectory analyses.


5_MatureNeuronalDataset_Velocity_Objects
scVelo-formatted Loom files for RNA velocity analysis.


6_MatureNeuronalDataset_CellRank_Objects
Processed CellRank outputs with fate probabilities and latent-time assignments.




---

🧩 Usage Notes



These processed objects can be loaded directly into:



R (Seurat ≥ v5.2)

Python (Scanpy / scVelo ≥ v0.3)

Refer to the Methods section of the manuscript for detailed data-processing and analysis pipelines.

For reproducibility, all analysis scripts are available at:  

🔗 https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/




---

Keywords

Drosophila • single-cell RNA-seq • embryonic neurogenesis • RNA velocity • CellRank • trajectory analysis • monoaminergic neurons • transcription factors • evolution

---

⚖️ License

This repository and dataset are made available under the **MIT License**:

Copyright (c) 2025 Clifton Lewis and contributors  

---

Citation

If you use this dataset, please cite:

> Lewis, C., et al. (2025). Evolutionarily conserved transcriptional regulators control monoaminergic neuron development. [Manuscript in preparation / published in *Journal TBD*].

---
DOI: 10.5281/zenodo.17441737
title: Processed single-cell RNA-seq data for "Evolutionarily conserved transcriptional regulators control monoaminergic neuron development"

description: Contents




Folder
Description


1_Replicate_Processed_Objects
Processed per-replicate scRNA-seq objects (post-QC, normalized, annotated).


2_Timepoint_Processed_Objects
Integrated, timepoint-specific datasets spanning 0–22 h after egg laying (AEL).


3_FullDataset_Processed_Objects
Full integrated dataset across all developmental stages with annotated cell identities.


4_MatureNeuronalDataset_Processed_Objects
Subset of mature neuronal populations used for trajectory analyses.


5_MatureNeuronalDataset_Velocity_Objects
scVelo-formatted Loom files for RNA velocity analysis.


6_MatureNeuronalDataset_CellRank_Objects
Processed CellRank outputs with fate probabilities and latent-time assignments.




---

🧩 Usage Notes



These processed objects can be loaded directly into:



R (Seurat ≥ v5.2)

Python (Scanpy / scVelo ≥ v0.3)

Refer to the Methods section of the manuscript for detailed data-processing and analysis pipelines.

For reproducibility, all analysis scripts are available at:  

🔗 https://github.com/cliftonlewis/2025_Drosophila_scRNAseq_EmbryoNeurogenesis_Monoamine/




---

Keywords

Drosophila • single-cell RNA-seq • embryonic neurogenesis • RNA velocity • CellRank • trajectory analysis • monoaminergic neurons • transcription factors • evolution

---

⚖️ License

This repository and dataset are made available under the **MIT License**:

Copyright (c) 2025 Clifton Lewis and contributors  

---

Citation

If you use this dataset, please cite:

> Lewis, C., et al. (2025). Evolutionarily conserved transcriptional regulators control monoaminergic neuron development. [Manuscript in preparation / published in *Journal TBD*].

---
DOI: 10.17632/2k64p535xk.1
title: Use of a traction suture loop for subungual glomus tumor excision

description: Initially, the nail plate is laterally displaced with a mosquito clamp. A longitudinal incision is made in the nail matrix to expose the underlying glomus tumor. After careful dissection and exposure, the needle is inserted through the most superficial portion of the tumor to create the traction loop. Gentle upward traction is applied, providing stable exposure and facilitating dissection from its base. The procedure concludes with the closure of the nail matrix using fine absorbable sutures to preserve nail growth and reduce the risk of dystrophy.
DOI: 10.17632/st6dpv4dfg.1
title: Shifts in Procedural Dermatology: Increasing Role of PAs and NPs Across Lesion Sizes and Repairs

description: Supp material for Shifts in Procedural Dermatology: Increasing Role of PAs and NPs Across Lesion Sizes and Repairs
DOI: 10.15468/dl.af78xj
title: Occurrence Download

description: A dataset containing 1435 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Corymbia henryi"
 ]
}

 The dataset includes 1435 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006703-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17474694
title: dataset to paper Maximum Likelihood Estimation for the Type I Generalized Logistic Distribution under Progressive Type II Censoring

description: It is dataset of hundred kidney transplant recipients, is founde in D.J. Hand, F. Daly, K. McConway, D. Lunn, E. Ostrowski, A Handbook of Small Data Sets, CRC Press, 1993.
DOI: 10.5281/zenodo.17474695
title: dataset to paper Maximum Likelihood Estimation for the Type I Generalized Logistic Distribution under Progressive Type II Censoring

description: It is dataset of hundred kidney transplant recipients, is founde in D.J. Hand, F. Daly, K. McConway, D. Lunn, E. Ostrowski, A Handbook of Small Data Sets, CRC Press, 1993.
DOI: 10.15468/dl.uxwvww
title: Occurrence Download

description: A dataset containing 473 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 (CAST(occurrence.taxonkey AS INTEGER) = 4263366 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 4263366 OR CAST(occurrence.kingdomkey AS INTEGER) = 4263366 OR CAST(occurrence.phylumkey AS INTEGER) = 4263366 OR CAST(occurrence.classkey AS INTEGER) = 4263366 OR CAST(occurrence.orderkey AS INTEGER) = 4263366 OR CAST(occurrence.familykey AS INTEGER) = 4263366 OR CAST(occurrence.genuskey AS INTEGER) = 4263366 OR CAST(occurrence.specieskey AS INTEGER) = 4263366)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 473 records were derived from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006678-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvan77
title: Occurrence Download

description: A dataset containing 6497556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Poland",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata",
 "Year 1970-2025"
 ]
}

 The dataset includes 6497556 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006664-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/7mrp5nkf6r
title: Religious Tolerance in Jakarta

description: Penelitian ini berjudul “Perdamaian dan Keadilan Sosial: Analisis Toleransi Antar Umat Beragama di Area Masjid Istiqlal dan Gereja Katedral”. Kajian ini berfokus pada pemahaman praktik toleransi dan kerukunan antarumat beragama di Indonesia, dengan mengambil Masjid Istiqlal dan Gereja Katedral Jakarta sebagai simbol harmoni antaragama. Hasil penelitian menunjukkan bahwa kedua tempat ibadah tersebut mencerminkan nilai-nilai perdamaian, saling menghormati, serta keadilan sosial yang dapat menjadi contoh penerapan toleransi dalam kehidupan masyarakat. Studi ini juga sejalan dengan tujuan Sustainable Development Goals (SDGs) poin ke-16, yaitu Perdamaian, Keadilan, dan Lembaga yang Kuat.
DOI: 10.17632/7mrp5nkf6r.1
title: Religious Tolerance in Jakarta

description: Penelitian ini berjudul “Perdamaian dan Keadilan Sosial: Analisis Toleransi Antar Umat Beragama di Area Masjid Istiqlal dan Gereja Katedral”. Kajian ini berfokus pada pemahaman praktik toleransi dan kerukunan antarumat beragama di Indonesia, dengan mengambil Masjid Istiqlal dan Gereja Katedral Jakarta sebagai simbol harmoni antaragama. Hasil penelitian menunjukkan bahwa kedua tempat ibadah tersebut mencerminkan nilai-nilai perdamaian, saling menghormati, serta keadilan sosial yang dapat menjadi contoh penerapan toleransi dalam kehidupan masyarakat. Studi ini juga sejalan dengan tujuan Sustainable Development Goals (SDGs) poin ke-16, yaitu Perdamaian, Keadilan, dan Lembaga yang Kuat.
DOI: 10.17632/vf5674g3wx
title: Dataset for Assessing Doppler Ultrasound in Obstetric Care Using the WHO Quality-of-Care Framework: Availability, Utilization, and Provider Knowledge in the Urban Central Region of Ghana

description: This dataset includes anonymised survey responses on Doppler ultrasound utilisation, equipment availability, and practitioner knowledge among healthcare professionals in Ghana’s Central Region.
DOI: 10.17632/vf5674g3wx.1
title: Dataset for Assessing Doppler Ultrasound in Obstetric Care Using the WHO Quality-of-Care Framework: Availability, Utilization, and Provider Knowledge in the Urban Central Region of Ghana

description: This dataset includes anonymised survey responses on Doppler ultrasound utilisation, equipment availability, and practitioner knowledge among healthcare professionals in Ghana’s Central Region.
DOI: 10.17632/hzhyds6dtb
title: Neural and Behavioral Signatures of Live and Video Demonstrations in Bimanual Interpersonal Coordination: An EEG and Kinematic Study
DOI: 10.17632/hzhyds6dtb.3
title: Neural and Behavioral Signatures of Live and Video Demonstrations in Bimanual Interpersonal Coordination: An EEG and Kinematic Study
DOI: 10.17632/jjrhrhr9vw.1
title: Association Rules Machine Learning complete intersection Calabi-Yau 5-Folds and 6-Folds

description: Associations rules for CICY5 and CICY6
DOI: 10.15468/dl.8b5qxs
title: Occurrence Download

description: A dataset containing 552 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, 0.0) eeacellcode,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, 0.0), "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.basisofrecord IN ('HUMAN_OBSERVATION', 'MATERIAL_SAMPLE', 'PRESERVED_SPECIMEN')
 AND occurrence.continent = 'EUROPE'
 AND occurrence.countrycode IN ('GB', 'IE', 'ES', 'MT', 'GR', 'PT', 'CY')
 AND occurrence.datasetkey IN ('6dce0193-6341-4eda-adcf-9d3ff9c857b0', 'b45a151e-734c-40f4-94c9-001458a2972b', 'daae5a66-7bb4-4431-ac3c-a1bf70ca3407', '3dc2a7f6-8d3a-4228-a69c-ec795028fe2f', 'e36c72ed-3b15-49f8-97fc-faaa467eb59e', '30dc001b-cd3b-49c4-83b1-e881aad9aaf2', '50c9509d-22c7-4a22-a47d-8c48425ef4a7', 'db1abc39-7b60-4103-815d-820fa37cb62b', '61313732-a660-4fdf-9cfb-0d13d4553bbe', '040c5662-da76-4782-a48e-cdea1892d14c')
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND (CAST(occurrence.taxonkey AS INTEGER) = 7579898 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 7579898 OR CAST(occurrence.kingdomkey AS INTEGER) = 7579898 OR CAST(occurrence.phylumkey AS INTEGER) = 7579898 OR CAST(occurrence.classkey AS INTEGER) = 7579898 OR CAST(occurrence.orderkey AS INTEGER) = 7579898 OR CAST(occurrence.familykey AS INTEGER) = 7579898 OR CAST(occurrence.genuskey AS INTEGER) = 7579898 OR CAST(occurrence.specieskey AS INTEGER) = 7579898)
 AND (occurrence."year" &gt;= 1901 AND occurrence."year" &lt;= 2025)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year",
 GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, 0.0)

 The dataset's 552 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006692-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/xmk4tx8bjp
title: 2025 Myers et al. Functional Analyses of Bacterial NanoRNase B Proteins. Nucleic Acids Research

description: A combination of exoribonucleases and endoribonucleases degrades RNA polymers to recycle nucleoside monophosphates. A byproduct of these reactions is the accumulation of short RNAs, 2-5 nucleotides in length. Characteristic enzymes, generally referred to as nanoRNases, specifically process short RNAs. Genes encoding nanoRNases are essential in some bacteria; therefore, it is assumed that the accumulation of short RNAs is detrimental to cells. However, the substrate preferences and enzymatic mechanisms of the known categories of nanoRNase enzymes have not been equally investigated. The NrnB category of nanoRNases has been particularly understudied. In this study, we identified bacterial NrnB homologs and discovered they can be grouped into three classes of proteins, which can be identified by their characteristic sequence features. Purified representatives of these classes of proteins revealed that they all process RNA substrates from the 3’-terminus. The presence of sequence features at the C-terminus was shown to be diagnostic for general exoribonuclease activity against long RNA substrates, whereas the absence of these C-terminal elements was correlated with proteins that preferentially acted against shorter RNA substrates. Together, these data define members of the overall NrnB family of nanoRNase proteins and identify some of their key features. 
Please contact contributing authors for any questions about raw data included in this dataset.
DOI: 10.17632/xmk4tx8bjp.1
title: 2025 Myers et al. Functional Analyses of Bacterial NanoRNase B Proteins. Nucleic Acids Research

description: A combination of exoribonucleases and endoribonucleases degrades RNA polymers to recycle nucleoside monophosphates. A byproduct of these reactions is the accumulation of short RNAs, 2-5 nucleotides in length. Characteristic enzymes, generally referred to as nanoRNases, specifically process short RNAs. Genes encoding nanoRNases are essential in some bacteria; therefore, it is assumed that the accumulation of short RNAs is detrimental to cells. However, the substrate preferences and enzymatic mechanisms of the known categories of nanoRNase enzymes have not been equally investigated. The NrnB category of nanoRNases has been particularly understudied. In this study, we identified bacterial NrnB homologs and discovered they can be grouped into three classes of proteins, which can be identified by their characteristic sequence features. Purified representatives of these classes of proteins revealed that they all process RNA substrates from the 3’-terminus. The presence of sequence features at the C-terminus was shown to be diagnostic for general exoribonuclease activity against long RNA substrates, whereas the absence of these C-terminal elements was correlated with proteins that preferentially acted against shorter RNA substrates. Together, these data define members of the overall NrnB family of nanoRNase proteins and identify some of their key features. 
Please contact contributing authors for any questions about raw data included in this dataset.
DOI: 10.15468/dl.sj2zd9
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Perlidae",
 "Country is Colombia",
 "Year is greater than or equal to 1965",
 "Year is less than or equal to 1989"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006706-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hv2jgf
title: Occurrence Download

description: A dataset containing 6932 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Corymbia citriodora"
 ]
}

 The dataset includes 6932 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006705-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17476420
title: Tone Scores of CSR Reports of European Firms

description: The data includes scores for analysing the tone used in a document. These scores were computed using the Loughran & McDonald Sentiment Word List (Loughran & McDonald, 2011; 2015). The sample comprises CSR reports from firms listed in the EUROSTOXX 600 from 2009 to 2022.

References:

Loughran, T., & McDonald, B. (2011). When Is a Liability Not a Liability? Textual Analysis, Dictionaries, and 10-Ks. The Journal of Finance, 66 (1), 35–65. https://doi.org/10.1111/j.1540- 6261.2010.01625.x

Loughran, T., & McDonald, B. (2015). The Use of Word Lists in Textual Analysis. Journal of Behavioral Finance, 16 (1), 1–11. https://doi.org/10.1080/15427560.2015.1000335
DOI: 10.5281/zenodo.17476419
title: Tone Scores of CSR Reports of European Firms

description: The data includes scores for analysing the tone used in a document. These scores were computed using the Loughran & McDonald Sentiment Word List (Loughran & McDonald, 2011; 2015). The sample comprises CSR reports from firms listed in the EUROSTOXX 600 from 2009 to 2022.

References:

Loughran, T., & McDonald, B. (2011). When Is a Liability Not a Liability? Textual Analysis, Dictionaries, and 10-Ks. The Journal of Finance, 66 (1), 35–65. https://doi.org/10.1111/j.1540- 6261.2010.01625.x

Loughran, T., & McDonald, B. (2015). The Use of Word Lists in Textual Analysis. Journal of Behavioral Finance, 16 (1), 1–11. https://doi.org/10.1080/15427560.2015.1000335
DOI: 10.15468/dl.pr3mmu
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ireland",
 "TaxonKey is Reynoutria japonica",
 "Year 2005-2005"
 ]
}

 The dataset includes 49 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006709-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13380521
title: Codes and data for the article 'Early warning signal for river-borne diseases with almost no data'

description: Codes and data for the paper "Early warning signal for river-borne diseases with almost no data" in Methods in Ecology and Evolution.

This collection includes data on the prevalence of river-borne diseases and related environmental variables.The codes are for extracting the tree structure of the river from the map and using the extended HMM model to predict the presence of contaminated samples in each part of the river.

The dataset contains the whilring disease test results of about 113 locations in the Oldman River collected in 2017 and 2018. The dataset additionally includes several environmental variables measured at 164,985 pixels of size 200m x 200m in the Oldman River. The dataset was collected and preprocessed by Alberta Environment and Parks (AEP), with contributions from Alicia Kennedy, Laurie Gallagher, Chad Sherburne, James Clayton, and Marie Veillard. The dataset is being shared with the permission of AEP.