cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6945366
title: Sim2real flower detection towards automated Calendula harvesting

description: This dataset serves as supplementary material for the research paper titled '<em>Sim2real flower detection towards automated Calendula harvesting</em>', which was published in the October 2023 issue of Biosystems Engineering. Within this upload, you will find a collection of both authentic and computer-generated images featuring Calendula (<em>Calendula officinalis L.</em>) flowers. Additionally, we have included the resources and original data utilized in generating the synthetic images. This dataset proves instrumental in demonstrating the successful transference of a deep neural network from simulation to real-world applications. The contents of this upload includes: Original RGB and depth images of Calendula flowers captured in a natural flower field, complete with bounding box annotations. The test data employed in our experiments. Unedited RGB images that were used in the photogrammetry pipeline. Three-dimensional models representing Calendula flowers. The resulting dataset of synthetic images. The synthetic dataset follows the Synthetic Optimized Labeled Objects (SOLO) Dataset Schema, as defined in the Unity Perception package. For completeness, the data scheme is also included in the upload. For more comprehensive details regarding this dataset and its associated metadata, we invite you to consult the published article in Biosystems Engineering, available at the following link: https://doi.org/10.1016/j.biosystemseng.2023.08.016.
DOI: 10.5281/zenodo.6945367
title: Sim2real flower detection towards automated Calendula harvesting

description: This dataset serves as supplementary material for the research paper titled '<em>Sim2real flower detection towards automated Calendula harvesting</em>', which was published in the October 2023 issue of Biosystems Engineering. Within this upload, you will find a collection of both authentic and computer-generated images featuring Calendula (<em>Calendula officinalis L.</em>) flowers. Additionally, we have included the resources and original data utilized in generating the synthetic images. This dataset proves instrumental in demonstrating the successful transference of a deep neural network from simulation to real-world applications. The contents of this upload includes: Original RGB and depth images of Calendula flowers captured in a natural flower field, complete with bounding box annotations. The test data employed in our experiments. Unedited RGB images that were used in the photogrammetry pipeline. Three-dimensional models representing Calendula flowers. The resulting dataset of synthetic images. The synthetic dataset follows the Synthetic Optimized Labeled Objects (SOLO) Dataset Schema, as defined in the Unity Perception package. For completeness, the data scheme is also included in the upload. For more comprehensive details regarding this dataset and its associated metadata, we invite you to consult the published article in Biosystems Engineering, available at the following link: https://doi.org/10.1016/j.biosystemseng.2023.08.016.
DOI: 10.5281/zenodo.8273493
title: Dataset for 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions'

description: Raw data and scripts to produce figures and tables from the article 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions.'
DOI: 10.5281/zenodo.8273494
title: Dataset for 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions'

description: Raw data and scripts to produce figures and tables from the article 'Optimized strategies for the quantum-state preparation of single trapped nitrogen molecular ions.'
DOI: 10.5281/zenodo.8338254
title: Phantom measurement data for 'Configuration-based electrical properties tomography', Iyyakkunnel et al. (2021)

description: This dataset contains the phantom bSSFP measurement data used in the published article Iyyakkunnel et al., 'Configuration-based electrical properties tomography', Magn Reson Med. 2021;85:1855–1864 (doi: 10.1002/mrm.28542). The acquisitions were made with a 3 T MRI system (Magnetom Prisma; Siemens Healthcare, Erlangen, Germany) using a dual-tuned 1H/23Na quadrature head coil for transmission and reception (Rapid Biomedical, Rimpar, Germany).<br> The data includes the magnitude and phase measurements for eight phase-cycled scans (in dicom (.dcm) format). The RF phase increment for the phase cycled scans corresponds to 0°, 45°, 90°, 135°, 180°, 225°, 270° and 315°. For further measurement details, please refer to the mentioned original article.
description: {"references": ["Iyyakkunnel, Santhosh et al., Condiguration-based electrical properties tomography, Magn Reson Med. 2021;85:1855\u20131864, doi: 10.1002/mrm.28542"]}
DOI: 10.5281/zenodo.8338255
title: Phantom measurement data for 'Configuration-based electrical properties tomography', Iyyakkunnel et al. (2021)

description: This dataset contains the phantom bSSFP measurement data used in the published article Iyyakkunnel et al., 'Configuration-based electrical properties tomography', Magn Reson Med. 2021;85:1855–1864 (doi: 10.1002/mrm.28542). The acquisitions were made with a 3 T MRI system (Magnetom Prisma; Siemens Healthcare, Erlangen, Germany) using a dual-tuned 1H/23Na quadrature head coil for transmission and reception (Rapid Biomedical, Rimpar, Germany).<br> The data includes the magnitude and phase measurements for eight phase-cycled scans (in dicom (.dcm) format). The RF phase increment for the phase cycled scans corresponds to 0°, 45°, 90°, 135°, 180°, 225°, 270° and 315°. For further measurement details, please refer to the mentioned original article.
description: {"references": ["Iyyakkunnel, Santhosh et al., Condiguration-based electrical properties tomography, Magn Reson Med. 2021;85:1855\u20131864, doi: 10.1002/mrm.28542"]}
DOI: 10.6084/m9.figshare.22811384.v3
title: Guppy and M. picta repeats_annotation

description: 1. The <em>Poecilia reticulata</em> files are in the folder “Guppy repeats_annotation”. The dataset was produced using RepeatModeler2 (Flynn<em> et al.</em> 2020) to generate an initial comprehensive set of candidate TE families in the male reference genome assembly (Fraser<em> et al.</em> 2020). RepeatMasker (Smit<em> et al.</em> http:// repeatmasker.org) was used to make a library of consensus sequences from the RepeatModeler2 analysis plus Teleostei repeats from Repbase (https://www.girinst.org/repbase/). A filtered list of candidates was created and manually annotated following the procedures and criteria described by Goubert<em> et al.</em> (2022). RepeatMasker was then run again to find and annotate repeat copies throughout the male reference genome. There are two files, as follows. consensus_library.fa (consensus TE library from RepeatModeler) guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result) 2. <em>Micropoecilia picta</em><br> This folder contains files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly. Files with .out and .gff suffixes are included for the whole genome and for just chromosome 12, the sex chromosome. The folder “RM_54167.FriNov121514092021” includes the consensus sequences produced by RepeatModeler. <strong>References</strong> Flynn, J. M., R. Hubley, C. Goubert, J. Rosen, A. G. Clark<em> et al.</em>, 2020 RepeatModeler2: automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117<strong>:</strong> 9451-9457. doi: 10.1073/pnas.1921046117 Fraser, B. A., J. R. Whiting, J. R. Paris, C. J. Weadick, P. J. Parsons<em> et al.</em>, 2020 Improved reference genome uncovers novel sex-linked regions in the guppy (<em>Poecilia reticulata)</em>. Genome Biology and Evolution 12<strong>:</strong> 1789–1805. doi: 10.1093/gbe/evaa187 Goubert, C., R. J. Craig, A. F. Bilat, V. Peona, A. A. Vogan<em> et al.</em>, 2022 A beginner's guide to manual curation of transposable elements. Mob DNA 13<strong>:</strong> 7. doi: 10.1186/s13100-021-00259-7 Smit, A., R. Hubley and P. Green, 2013-2015 RepeatMasker Open-4.0
DOI: 10.5281/zenodo.8403262
title: Dataset related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists"

description: This record contains new data related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists". Osteoarthritis (OA) is characterized by an abundance of inflammatory M1-like macrophages damaging local tissues. The search of new potential drugs for OA suffers from the lack of appropriate methods of long-lasting inflammation. Here we developed and characterized an <em>in vitro</em> protocol of long-lasting culture of primary human monocyte-derived macrophages differentiated with a combination of M-CSF+GM-CSF that optimally supported long-cultured macrophages (LC-Mfs) for up to 15 days, unlike their single use. Macrophages repeatedly stimulated for 15 days with the TLR2 ligand Pam3CSK4 (LCS-Mfs), showed sustained levels over time of IL-6, CCL2 and CXCL8, inflammatory mediators that were also detected in the synovial fluids of OA patients. Furthermore, macrophages isolated from the synovia of two OA patients showed an expression profile of inflammation-related genes similar to that of LCS-Mfs, validating our protocol as a model of chronically activated inflammatory macrophages. Next, to confirm that these LCS-Mfs could be modulated by anti-inflammatory compounds, we employed Dexamethasone and/or Celecoxib, two drugs widely used in OA treatment, that significantly inhibited the production of inflammatory mediators. This easy-to-use in vitro protocol of long-lasting inflammation with primary human macrophages could be useful for the screening of new compounds to improve the therapy of inflammatory disorders.
DOI: 10.5281/zenodo.8403261
title: Dataset related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists"

description: This record contains new data related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists". Osteoarthritis (OA) is characterized by an abundance of inflammatory M1-like macrophages damaging local tissues. The search of new potential drugs for OA suffers from the lack of appropriate methods of long-lasting inflammation. Here we developed and characterized an <em>in vitro</em> protocol of long-lasting culture of primary human monocyte-derived macrophages differentiated with a combination of M-CSF+GM-CSF that optimally supported long-cultured macrophages (LC-Mfs) for up to 15 days, unlike their single use. Macrophages repeatedly stimulated for 15 days with the TLR2 ligand Pam3CSK4 (LCS-Mfs), showed sustained levels over time of IL-6, CCL2 and CXCL8, inflammatory mediators that were also detected in the synovial fluids of OA patients. Furthermore, macrophages isolated from the synovia of two OA patients showed an expression profile of inflammation-related genes similar to that of LCS-Mfs, validating our protocol as a model of chronically activated inflammatory macrophages. Next, to confirm that these LCS-Mfs could be modulated by anti-inflammatory compounds, we employed Dexamethasone and/or Celecoxib, two drugs widely used in OA treatment, that significantly inhibited the production of inflammatory mediators. This easy-to-use in vitro protocol of long-lasting inflammation with primary human macrophages could be useful for the screening of new compounds to improve the therapy of inflammatory disorders.
DOI: 10.5281/zenodo.8402615
title: Experimental recordings of cross-flow vortex-induced vibrations on slender free-clamped ends cylinder and cylinder with a pair of branches in constant uniform flow for different reduced velocities.

description: Dataset of the experiments done on a cylinder (N=0) and a coral model (N=1) 3D-printed with SLS out of TPE material. Cross-flow VIV are recorder with a GoPro in a test section of a water tunnel for different reduced velocities (Ur). This was made for our publication "Modelling vortex-induced vibrations of branched structures by coupling a 3D-corotational frame finite element formulation with wake-oscillators" in the Journal of Fluids and Structures.
DOI: 10.5281/zenodo.8402614
title: Experimental recordings of cross-flow vortex-induced vibrations on slender free-clamped ends cylinder and cylinder with a pair of branches in constant uniform flow for different reduced velocities.

description: Dataset of the experiments done on a cylinder (N=0) and a coral model (N=1) 3D-printed with SLS out of TPE material. Cross-flow VIV are recorder with a GoPro in a test section of a water tunnel for different reduced velocities (Ur). This was made for our publication "Modelling vortex-induced vibrations of branched structures by coupling a 3D-corotational frame finite element formulation with wake-oscillators" in the Journal of Fluids and Structures.
DOI: 10.25345/c59k4639v
title: MassIVE MSV000093016 - Cell Free Biosynthesis of Peptide Natural Products
title: A library of peptide natural product macrocycles are synthesized via cell-free methods.
DOI: 10.5281/zenodo.8403145
title: Dataset related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists"

description: This record contains new data related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists". Osteoarthritis (OA) is characterized by an abundance of inflammatory M1-like macrophages damaging local tissues. The search of new potential drugs for OA suffers from the lack of appropriate methods of long-lasting inflammation. Here we developed and characterized an <em>in vitro</em> protocol of long-lasting culture of primary human monocyte-derived macrophages differentiated with a combination of M-CSF+GM-CSF that optimally supported long-cultured macrophages (LC-Mfs) for up to 15 days, unlike their single use. Macrophages repeatedly stimulated for 15 days with the TLR2 ligand Pam3CSK4 (LCS-Mfs), showed sustained levels over time of IL-6, CCL2 and CXCL8, inflammatory mediators that were also detected in the synovial fluids of OA patients. Furthermore, macrophages isolated from the synovia of two OA patients showed an expression profile of inflammation-related genes similar to that of LCS-Mfs, validating our protocol as a model of chronically activated inflammatory macrophages. Next, to confirm that these LCS-Mfs could be modulated by anti-inflammatory compounds, we employed Dexamethasone and/or Celecoxib, two drugs widely used in OA treatment, that significantly inhibited the production of inflammatory mediators. This easy-to-use in vitro protocol of long-lasting inflammation with primary human macrophages could be useful for the screening of new compounds to improve the therapy of inflammatory disorders.
DOI: 10.5281/zenodo.8403146
title: Dataset related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists"

description: This record contains new data related to article "An in vitro model for osteoarthritis using long-cultured inflammatory human macrophages repeatedly stimulated with TLR agonists". Osteoarthritis (OA) is characterized by an abundance of inflammatory M1-like macrophages damaging local tissues. The search of new potential drugs for OA suffers from the lack of appropriate methods of long-lasting inflammation. Here we developed and characterized an <em>in vitro</em> protocol of long-lasting culture of primary human monocyte-derived macrophages differentiated with a combination of M-CSF+GM-CSF that optimally supported long-cultured macrophages (LC-Mfs) for up to 15 days, unlike their single use. Macrophages repeatedly stimulated for 15 days with the TLR2 ligand Pam3CSK4 (LCS-Mfs), showed sustained levels over time of IL-6, CCL2 and CXCL8, inflammatory mediators that were also detected in the synovial fluids of OA patients. Furthermore, macrophages isolated from the synovia of two OA patients showed an expression profile of inflammation-related genes similar to that of LCS-Mfs, validating our protocol as a model of chronically activated inflammatory macrophages. Next, to confirm that these LCS-Mfs could be modulated by anti-inflammatory compounds, we employed Dexamethasone and/or Celecoxib, two drugs widely used in OA treatment, that significantly inhibited the production of inflammatory mediators. This easy-to-use in vitro protocol of long-lasting inflammation with primary human macrophages could be useful for the screening of new compounds to improve the therapy of inflammatory disorders.
DOI: 10.7910/dvn/p2pioh
title: Replication Data for: The Referendum Campaign Finance Regulation Index: Comparing Political Finance Regimes for Referendum Campaigns in Europe

description: Dataset with referendum political finance regimes in Europe
DOI: 10.5281/zenodo.8403292
title: SciExpeM - 10.5281/zenodo.8403292

description: Issayev, Gani; Giri, Binod Raj, 0000-0001-9812-4455; Elbaz, Ayman M.; Shrestha, Krishna Prasad, 0000-0001-5672-7354; Mauss, Fabian, 0000-0002-6305-8213; Roberts, William L.; Farooq, Aamir - Renewable Energy, 2022, (181), 1353-1370
DOI: 10.5281/zenodo.8403291
title: SciExpeM - 10.5281/zenodo.8403292

description: Issayev, Gani; Giri, Binod Raj, 0000-0001-9812-4455; Elbaz, Ayman M.; Shrestha, Krishna Prasad, 0000-0001-5672-7354; Mauss, Fabian, 0000-0002-6305-8213; Roberts, William L.; Farooq, Aamir - Renewable Energy, 2022, (181), 1353-1370
DOI: 10.7284/152036
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise MGL2204 using a Hawaii UHDAS instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152067
title: Expendable Probe data collected during research cruise MGL2204 using a Sippican MK21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152033
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL2204 using a CCTech C-Nav 2000 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152059
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL2204 using a CCTech C-Nav 3050 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152034
title: Gravimeter data collected during research cruise MGL2204 using a Bell BGM-3 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152032
title: Gyrocompass data collected during research cruise MGL2204 using a Kongsberg Simrad GC80 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152035
title: INS (Inertial Navigation System) data collected during research cruise MGL2204 using a Applanix POS/MV-320 V3 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152064
title: INS (Inertial Navigation System) data collected during research cruise MGL2204 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152030
title: Magnetometer data collected during research cruise MGL2204 using a Geometrics G-882 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152063
title: Meteorological Station data collected during research cruise MGL2204 using a Vaisala WXT520 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152065
title: Multibeam Echosounder data collected during research cruise MGL2204 using a Kongsberg EM122 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152066
title: Multibeam Echosounder data collected during research cruise MGL2204 using a Kongsberg EM122 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152031
title: Singlebeam Echosounder data collected during research cruise MGL2204 using a Knudsen 3260 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152060
title: Speedlog data collected during research cruise MGL2204 using a Furuno DS-80 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152062
title: SSV (Sound Speed Velocimeter) data collected during research cruise MGL2204 using a AML MicroSV instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152061
title: TSG (Thermosalinograph) data collected during research cruise MGL2204 using a SeaBird SBE-45 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153583
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise MGL2214 using a Hawaii UHDAS instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153600
title: Expendable Probe data collected during research cruise MGL2214 using a Sippican MK21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153582
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL2214 using a CCTech C-Nav 2000 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153592
title: GNSS (Global Navigation Satellite System) data collected during research cruise MGL2214 using a CCTech C-Nav 3050 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153581
title: Gyrocompass data collected during research cruise MGL2214 using a Kongsberg Simrad GC80 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153597
title: INS (Inertial Navigation System) data collected during research cruise MGL2214 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153596
title: Meteorological Station data collected during research cruise MGL2214 using a Vaisala WXT520 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/153598
title: Multibeam Echosounder data collected during research cruise MGL2214 using a Kongsberg EM122 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition