cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.24222598
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: Fan-shaped body (jrc_fly-fsb-2)

description: <b>Sample:</b> Fan-shaped body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-fsb-2<b>Voxel size (nm):</b> 4 x 4 x 4 (X, Y, Z)<b>Data dimensions (µm):</b> 7.47 x 7.52 x 8.9 (X, Y, Z)<b>Imaging start date:</b> 2016-06-02<b>Imaging duration (days):</b> 6<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-fsb-2/jrc_fly-fsb-2.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-fsb-2<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>
DOI: 10.25378/janelia.24222598.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: Fan-shaped body (jrc_fly-fsb-2)

description: <b>Sample:</b> Fan-shaped body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-fsb-2<b>Voxel size (nm):</b> 4 x 4 x 4 (X, Y, Z)<b>Data dimensions (µm):</b> 7.47 x 7.52 x 8.9 (X, Y, Z)<b>Imaging start date:</b> 2016-06-02<b>Imaging duration (days):</b> 6<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-fsb-2/jrc_fly-fsb-2.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-fsb-2<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>
DOI: 10.17882/105936
title: CODE drifter observations from the DDR20 experiment in the NW Mediterranean Sea

description: In October 2020, the LaMMA Consortium carried out a field measurement campaign in the Southern Ligurian Sea (SLS) as part of the DDR20 – Drifter Demonstration and Research 2020 experiment. Organized by CMRE and supported by several EU-funded projects (SICOMAR plus, JERICO-S3, SINAPSI, and IMPACT), the campaign focused on the deployment of CODE drifters (Davis, 1985; Poulain, 1999). 
The drifters used were specifically acquired by LaMMA through the IMPACT project. Designed to monitor surface currents in the upper meter of the water column while minimizing wind influence, these were MAXO-manufactured CODE models equipped with SPOT Globalstar TRACE modules. The modules feature high-accuracy GPS receivers (&lt;10 m) and transmit position data every 5 minutes, with an estimated velocity accuracy of around 3 cm/s.
A total of 26 drifters were deployed over a few hours, arranged in a 3 km × 3 km square grid in waters about 100 meters deep (centered at Lat: 43°16′N, Lon: 10°14′E). Five were recovered within 1 to 3 days, while the rest eventually beached after drifting for several days. Drifters operating near the coast used cellular networks to transmit data, whereas those farther offshore switched to satellite communication. The resulting dataset spans from October 8 to November 8, 2020, with positions recorded at 5-minute intervals. Some gaps are present due to occasional transmission issues or device malfunctions.
This dataset supports the validation and performance analysis of HF radar measurements in coastal areas, as discussed in Doronzo et al. (2025).
 
References:
 -  Davis, R.E. (1985). Drifter observations of coastal surface currents during CODE: The method and descriptive view. Journal of Geophysical Research: Oceans, 90(C3), 4741–4755. https://doi.org/10.1029/JC090iC03p04741
 - Poulain, P.-M. (1999). Drifter observations of surface circulation in the Adriatic Sea between December 1994 and March 1996. Journal of Marine Systems, 20(1–4), 231–253. https://doi.org/10.1016/S0924-7963(98)00084-0
 - http://interreg-maritime.eu/web/impact
 - Doronzo, B.; Bendoni, M.; Taddei, S.; Boccacci, A.; Brandini, C. Validating HF Radar Current Accuracy via Lagrangian Measurements and Radar-to-Radar Comparisons in Highly Variable Surface Currents. Remote Sens. 2025, 17, 1243. https://doi.org/10.3390/rs17071243
DOI: 10.5281/zenodo.15593064
title: Filtered HF Radar Surface Current Fields from CODAR DF System – Ligurian and N. Tyrrhenian Seas (Quality-Restricted Thresholds Applied)

description: This dataset provides hourly surface current velocity fields derived from a high-frequency (HF) radar network operating at 13.5 MHz using a CODAR SeaSonde Direction Finding system. The radar network consists of three coastal stations located at Livorno (LIVO), San Vincenzo (SVIN), and Isola del Tino (TINO), covering a large portion of the Ligurian and Northern Tyrrhenian Seas.

Radial current measurements are collected on a polar grid with approximately 1.5 km radial resolution and 5° angular spacing. These radial components are then combined into total vector current fields using a least-squares method. The resulting velocities represent surface currents in the upper ~0.3 to 2.5 meters of the water column and are aggregated over 1-hour intervals centered on the cardinal hour.

The dataset has been filtered using different threshold configurations of the VART_QC (temporal variance) and MDFL_QC (median) filters, with cutoff values ranging from 0.182 to 1 m/s. These variants allow users to evaluate the impact of quality control settings on spatial coverage and data reliability.

Data are georeferenced using the WGS84 geographic coordinate system (EPSG:4326), with a spatial extent approximately between 41.5°–44.5° N and 8.5°–12.5° E. All data are stored in NetCDF-4 classic model format and conform to the CF-1.6 and Copernicus InSitu-TAC metadata conventions.

This dataset corresponds to a subset of HF radar observations recorded between October and November 2020, specifically selected for its temporal overlap with drifter deployments and for use in data validation and modeling applications.

The data are owned by the LaMMA Consortium (Consorzio LaMMA).An extended version of the HF radar dataset is available at the following link:https://thredds.hfrnode.eu:8443/thredds/NRTcurrent/HFR-LaMMA/HFR-LaMMA_catalog.html(hosted on the European HFR data-sharing server, part of the EuroGOOS HFR Task Team network).
DOI: 10.25378/janelia.24221404
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: ellipsoid body (jrc_fly-ellipsoid-body)

description: <b>Sample:</b> Ellipsoid body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-ellipsoid-body<b>Voxel size (nm):</b> 4 x 4 x 4 (X, Y, Z)<b>Data dimensions (µm): </b>7.6 x 7.3 x 9.4 (X, Y, Z)<b>Imaging start date:</b> 2016-06-08<b>Imaging duration (days):</b> 6<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-ellipsoid-body/jrc_fly-ellipsoid-body.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-ellipsoid-body<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>
DOI: 10.25378/janelia.24221404.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of Drosophila brain: ellipsoid body (jrc_fly-ellipsoid-body)

description: <b>Sample:</b> Ellipsoid body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118)<b>Sample Description:</b> Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.<b>Protocol:</b> Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.<b>Contributions:</b> Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (Yale), with post-processing by C. Shan Xu (Yale).<b>Acquisition ID:</b> jrc_fly-ellipsoid-body<b>Voxel size (nm):</b> 4 x 4 x 4 (X, Y, Z)<b>Data dimensions (µm): </b>7.6 x 7.3 x 9.4 (X, Y, Z)<b>Imaging start date:</b> 2016-06-08<b>Imaging duration (days):</b> 6<b>Landing energy (eV): </b>200<b>Imaging current (nA): </b>0.22<b>Scanning speed (MHz): </b>0.200<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_fly-ellipsoid-body/jrc_fly-ellipsoid-body.zarr/recon-2/em/<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_fly-ellipsoid-body<b>Publication: </b>Scheffer, et al., 2020; Xu et al., 2017; Xu et al., 2021<br>
DOI: 10.6084/m9.figshare.29236664
title: Supplementary Material for: Strain-specific differences in cerebellar anatomy between laboratory and wild rats

description: Introduction: Domestication and subsequent breed selection has significantly changed the phenotype of most domesticated animal species. Not only has their external appearance changed, in many species, the brain, and individual brain regions, often differ in size in domesticated strains compared with their wild ancestors. Although the majority of studies on mammals focus on cortical regions, the cerebellum often differs in relative and absolute size between domestic and wild strains, but more specific data on cell sizes and numbers are often lacking. Methods: We quantified cerebellar anatomy in two domesticated strains (Long Evans and Sprague-Dawley) and one wild-type of brown rat (Rattus norvegicus). Using unbiased stereology, we measured the total cerebellum and its layers’ volumes, as well as the number and size of Purkinje cells. Results: Long Evans rats had a larger total cerebellum volume, in both absolute and relative terms, than Sprague-Dawley and wild rats, but no other significant differences were detected. Significant differences in the absolute and relative sizes of the molecular, granule cell, and white matter layers were also found, but the differences were inconsistent among strains such as the largest values alternated between the two lab strains. The absolute number of Purkinje cells did not differ among strains, but one population of Sprague-Dawley rats and the wild rats had more Purkinje cells relative to cerebellar volume. Last, Long Evan rats had significantly smaller Purkinje cells than the other strains in both absolute and relative terms. Conclusion: Only one of the two domesticated strains differed from wild rats in cerebellar anatomy. Our results therefore demonstrate that changes in the brains of domesticated animals do not necessarily follow a universal rule; they can vary between different strains. This highlights the importance of including more than one strain in wild-domesticate comparisons in brain anatomy and avoiding the oversimplification of the effects of domestication on the brain.
DOI: 10.6084/m9.figshare.29236664.v1
title: Supplementary Material for: Strain-specific differences in cerebellar anatomy between laboratory and wild rats

description: Introduction: Domestication and subsequent breed selection has significantly changed the phenotype of most domesticated animal species. Not only has their external appearance changed, in many species, the brain, and individual brain regions, often differ in size in domesticated strains compared with their wild ancestors. Although the majority of studies on mammals focus on cortical regions, the cerebellum often differs in relative and absolute size between domestic and wild strains, but more specific data on cell sizes and numbers are often lacking. Methods: We quantified cerebellar anatomy in two domesticated strains (Long Evans and Sprague-Dawley) and one wild-type of brown rat (Rattus norvegicus). Using unbiased stereology, we measured the total cerebellum and its layers’ volumes, as well as the number and size of Purkinje cells. Results: Long Evans rats had a larger total cerebellum volume, in both absolute and relative terms, than Sprague-Dawley and wild rats, but no other significant differences were detected. Significant differences in the absolute and relative sizes of the molecular, granule cell, and white matter layers were also found, but the differences were inconsistent among strains such as the largest values alternated between the two lab strains. The absolute number of Purkinje cells did not differ among strains, but one population of Sprague-Dawley rats and the wild rats had more Purkinje cells relative to cerebellar volume. Last, Long Evan rats had significantly smaller Purkinje cells than the other strains in both absolute and relative terms. Conclusion: Only one of the two domesticated strains differed from wild rats in cerebellar anatomy. Our results therefore demonstrate that changes in the brains of domesticated animals do not necessarily follow a universal rule; they can vary between different strains. This highlights the importance of including more than one strain in wild-domesticate comparisons in brain anatomy and avoiding the oversimplification of the effects of domestication on the brain.
DOI: 10.6084/m9.figshare.29236667
title: Supplementary Material for: Malignant Hidroacanthoma Simplex: A Case Report

description: Introduction Malignant hidroacanthoma simplex (MHS) is an exceedingly rare cutaneous neoplasm with limited documented cases. This report highlights a distinctive case of MHS with prolonged clinical evolution, emphasizing its diagnostic challenges and management outcomes. Case Presentation A 64-year-old female presented with a right lumbar mass persisting for over two decades, exhibiting progressive enlargement in the past five years. Clinical examination revealed a solitary reddish-brown proliferative plaque (3.5 cm × 4.0 cm) on the right waist, characterized by irregular borders, a rough surface, and reddish-brown crusts. Histopathological findings included hyperkeratosis, irregular epidermal hyperplasia, hypertrophic stratum spinosum, and tumor cells displaying pale eosinophilic cytoplasm, vacuolated nuclei, small nucleoli, and atypical mitotic figures. Notably, tumor cells were confined to the epidermis without dermal invasion. The patient underwent local extended excision, and postoperative surveillance over 15 months demonstrated no evidence of recurrence or lymph node metastasis. Conclusion This case underscores the indolent yet locally persistent nature of MHS. Complete surgical excision remains the cornerstone of management, with favorable outcomes achievable in absence of dermal infiltration. Long-term follow-up is critical to monitor potential recurrence.
DOI: 10.6084/m9.figshare.29236667.v1
title: Supplementary Material for: Malignant Hidroacanthoma Simplex: A Case Report

description: Introduction Malignant hidroacanthoma simplex (MHS) is an exceedingly rare cutaneous neoplasm with limited documented cases. This report highlights a distinctive case of MHS with prolonged clinical evolution, emphasizing its diagnostic challenges and management outcomes. Case Presentation A 64-year-old female presented with a right lumbar mass persisting for over two decades, exhibiting progressive enlargement in the past five years. Clinical examination revealed a solitary reddish-brown proliferative plaque (3.5 cm × 4.0 cm) on the right waist, characterized by irregular borders, a rough surface, and reddish-brown crusts. Histopathological findings included hyperkeratosis, irregular epidermal hyperplasia, hypertrophic stratum spinosum, and tumor cells displaying pale eosinophilic cytoplasm, vacuolated nuclei, small nucleoli, and atypical mitotic figures. Notably, tumor cells were confined to the epidermis without dermal invasion. The patient underwent local extended excision, and postoperative surveillance over 15 months demonstrated no evidence of recurrence or lymph node metastasis. Conclusion This case underscores the indolent yet locally persistent nature of MHS. Complete surgical excision remains the cornerstone of management, with favorable outcomes achievable in absence of dermal infiltration. Long-term follow-up is critical to monitor potential recurrence.
DOI: 10.6084/m9.figshare.29236670
title: Supplementary Material for: Impact of Age on Response to Platelet-Rich Plasma Therapy

description: Although platelet-rich plasma (PRP) is a widely used treatment for androgenetic alopecia (AGA), the impact of patient age on treatment efficacy remains underexplored. This retrospective study evaluated PRP outcomes in 57 AGA patients treated at NYU Langone Health, stratified into four age cohorts. Changes in trichometric hair density and width were measured from initial to final follow-up visits. Statistical significance and linear regression testing were determined using ANOVA and Rank-Based ANCOVA, respectively. While overall changes in density and width did not differ significantly across age groups, younger patients trended toward greater density gains. Furthermore, greater baseline hair width was predictive of smaller improvements in width, and significant interactions between age and the number of PRP sessions suggested that older individuals may require a greater number of treatments to attain results comparable to those seen in younger cohorts. Additionally, improvements in hair density were positively associated with the number of adjunctive therapies, as patients who received more concurrent treatments experienced greater gains. PRP was well tolerated across all age groups. These findings highlight the potential impact of patient age on PRP efficacy, informing counseling and treatment planning.
DOI: 10.6084/m9.figshare.29236670.v1
title: Supplementary Material for: Impact of Age on Response to Platelet-Rich Plasma Therapy

description: Although platelet-rich plasma (PRP) is a widely used treatment for androgenetic alopecia (AGA), the impact of patient age on treatment efficacy remains underexplored. This retrospective study evaluated PRP outcomes in 57 AGA patients treated at NYU Langone Health, stratified into four age cohorts. Changes in trichometric hair density and width were measured from initial to final follow-up visits. Statistical significance and linear regression testing were determined using ANOVA and Rank-Based ANCOVA, respectively. While overall changes in density and width did not differ significantly across age groups, younger patients trended toward greater density gains. Furthermore, greater baseline hair width was predictive of smaller improvements in width, and significant interactions between age and the number of PRP sessions suggested that older individuals may require a greater number of treatments to attain results comparable to those seen in younger cohorts. Additionally, improvements in hair density were positively associated with the number of adjunctive therapies, as patients who received more concurrent treatments experienced greater gains. PRP was well tolerated across all age groups. These findings highlight the potential impact of patient age on PRP efficacy, informing counseling and treatment planning.