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(07)-Ratke2020A-DS0006 – Tribolium castaneum AGOC{Zen1'#O(LA)-mEmerald} #3 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0006 – <em>Tribolium castaneum</em> AGOC{Zen1'#O(LA)-mEmerald} #3 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
Frasnian, lateral (B1), ventral (B2), anterior (B3), posterior (B4), and dorsal (B5) views of a rounded exfoliated shell, 27.7 mm wide, 25.6 mm long, and about 14.5 mm thick. C. PUM05008, sample PY4, Panxi section, probably Middle Frasnian, lateral (C1), dorsal (C2), and ventral (C3) views of the sectioned specimen (Fig. 6). D. PUM05009, sample PY5, Panxi section, probably Middle Frasnian, ventral beak broken, showing small conjunct deltidial plates (note that true foramen (approximately dashed line) takes up only a small part at the bottom of the seen later enlarged hole). E. PUM05010, sample PY5, Panxi section, probably Middle Frasnian, posterior (E1), lateral (E2), anterior (E3), ventral (E4), and dorsal (E5) views, 26.7 mm wide, 27.7 mm long, 18.5 mm thick, adpressed ventral beak. F. PUM05011, sample GC22, Caiziyan section, Early Frasnian, dorsal view. in Early and Middle Frasnian brachiopod faunas and turnover on the South China shelf
Frasnian, lateral (B1), ventral (B2), anterior (B3), posterior (B4), and dorsal (B5) views of a rounded exfoliated shell, 27.7 mm wide, 25.6 mm long, and about 14.5 mm thick. C. PUM05008, sample PY4, Panxi section, probably Middle Frasnian, lateral (C1), dorsal (C2), and ventral (C3) views of the sectioned specimen (Fig. 6). D. PUM05009, sample PY5, Panxi section, probably Middle Frasnian, ventral beak broken, showing small conjunct deltidial plates (note that true foramen (approximately dashed line) takes up only a small part at the bottom of the seen later enlarged hole). E. PUM05010, sample PY5, Panxi section, probably Middle Frasnian, posterior (E1), lateral (E2), anterior (E3), ventral (E4), and dorsal (E5) views, 26.7 mm wide, 27.7 mm long, 18.5 mm thick, adpressed ventral beak. F. PUM05011, sample GC22, Caiziyan section, Early Frasnian, dorsal view.
Recommendations for reporting equivalent black carbon (eBC) mass concentrations based on long-term pan-European in-situ observations
<p>A reliable determination of equivalent black carbon (eBC) mass concentrations derived from filter absorption photometers (FAPs) measurements depends on the appropriate quantification of the mass absorption cross-section (MAC) for converting the absorption coefficient (babs) to eBC. This study investigates the spatial–temporal variability of the MAC obtained from simultaneous elemental carbon (EC) and babs measurements performed at 22 sites. We compared different methodologies for retrieving eBC integrating different options for calculating MAC including: locally derived, median value calculated from 22 sites, and site-specific rolling MAC. The eBC concentrations that underwent correction using these methods were identified as LeBC (local MAC), MeBC (median MAC), and ReBC (Rolling MAC) respectively. Pronounced differences (up to more than 50 %) were observed between eBC as directly provided by FAPs (NeBC; Nominal instrumental MAC) and ReBC due to the differences observed between the experimental and nominal MAC values. The median MAC was 7.8 ± 3.4 m2 g-1 from 12 aethalometers at 880 nm, and 10.6 ± 4.7 m2 g-1 from 10 MAAPs at 637 nm. The experimental MAC showed significant site and seasonal dependencies, with heterogeneous patterns between summer and winter in different regions. In addition, long-term trend analysis revealed statistically significant (s.s.) decreasing trends in EC. Interestingly, we showed that the corresponding corrected eBC trends are not independent of the way eBC is calculated due to the variability of MAC. NeBC and EC decreasing trends were consistent at sites with no significant trend in experimental MAC. Conversely, where MAC showed s.s. trend, the NeBC and EC trends were not consistent while ReBC concentration followed the same pattern as EC. These results underscore the importance of accounting for MAC variations when deriving eBC measurements from FAPs and emphasize the necessity of incorporating EC observations to constrain the uncertainty associated with eBC.</p>
Assessing Nonadiabatic Dynamics Methods in Long Timescales
<p>In this study, we employ the multiconfiguration time-dependent Hartree (MCTDH) and its multi-layer variants (ML-MCTDH), ab initio multiple spawning (AIMS), and fewest-switches surface hopping (FSSH) methodologies to simulate the excited-state dynamics of a weakly-coupled multi-dimensional (10 dimensional) Spin-Boson model Hamiltonian designed for a long timescale decay behavior. </p> <p>The pre-print of the article can be found at <a href="https://chemrxiv.org/engage/chemrxiv/article-details/66f68454cec5d6c142647b0a">https://chemrxiv.org/engage/chemrxiv/article-details/66f68454cec5d6c142647b0a</a></p> <p>MUKHERJEE S, Lassmann Y, Mattos RS, Demoulin B, Curchod BFE, Barbatti M. Assessing Nonadiabatic Dynamics Methods in Long Timescales. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-j7xxl </p> <p> </p> <p><strong>The dataset contains</strong></p> <ul> <li>MCTDH.tar.bz2 - 10 sets of text files for MCTDH simulations </li> <li>ML-MCTDH.tar.vz2 - 10 sets of text files for ML-MCTDH simulations</li> <li>DC-FSSH.tar.bz2 - HDF5 output files for 2000 independent decoherence-corrected FSSH trajectories and a Python script for Wigner Sampling initial conditions </li> <li>CSS-AIMS.tar.gz - output text files for 44 independent cannibalistic stochastic selection approach of AIMS trajectories</li> </ul>
Polished Assemblies for "GoldPolish-Target: Targeted long-read genome assembly polishing"
<p>GoldPolish-Target is a targeted genome assembly polishing tool that uses long reads. We tested GoldPolish-Target on Oxford Nanopore Technologies datasets with a human cell line (NA24385) and Drosophila melanogaster (fruit fly). Here, we provide the data for the GoldRush baseline (unpolished) assembly and the GoldPolish-Target and medaka polished assemblies of these long-read datasets.</p>
Long-range axonal projections analyses of the mouse brain
<p>Accompanying data and analyses of the article <a href="https://doi.org/10.1101/2024.10.04.616605">"Generating brain-wide connectome using synthetic axonal morphologies"</a>. The code to reproduce the figures is available at <a href="https://github.com/Remy2506/axon_projection_figures">this repository</a>.</p> <p>Main contents:</p> <ul> <li><strong>SEU_morphs.zip, peng_2021_morphs.zip, ML_morphs.zip: </strong>input morphologies from various sources (novel morphologies collected by H. Peng, Southeast University, <a href="https://www.nature.com/articles/s41586-021-03941-1">Peng et al. 2021</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754285/">Winnubst et al. 2019</a>) after <a href="https://github.com/BlueBrain/morphology-workflows"><em>morphology-workflows</em> <em>Repair</em></a> post-processing steps.</li> <li><strong>atlas</strong>: atlas of the mouse brain used (enhanced version of Allen Brain CCFv3)</li> <li><strong>out_a_p</strong>: output of the <a href="https://github.com/BlueBrain/axon-projection">axon projection</a> anaylsis and clustering on the 3601 morphologies of the dataset. <ul> <li>axon_lengths_12.csv, axon_terminals_12.csv: the lengths of axons in each subregion where they terminate, and terminals, at hierarchy level 12 from the brain hierarchy.</li> <li>clustering_output.csv: output of the GMM clustering.</li> <li>config_a_p.cfg: configuration file used to produce this analysis, with running the axonal projection code.</li> </ul> </li> <li><strong>circuit</strong>: contains files describing the circuit synthesized with Blue Brain's <em>circuit-build*.</em> <ul> <li>bioname: parameters used to synthesize the circuit (regions to synthesize, cell densities per region, location of axons to graft...).</li> <li>sonata: files that contain nodes and edges of the circuit.</li> <li>auxiliary: various cell collections from the synthesized cells, filtered by region. Cell collections are to be read with <a href="https://github.com/BlueBrain/voxcell/tree/main">Voxcell.</a></li> <li>conn_mat.h5: the connectivity matrices obtained for the case where MOp5 long-range axons were synthesized, computed with <a href="https://github.com/BlueBrain/ConnectomeUtilities/tree/main">ConnectomeUtilities.</a>Contains connectivity matrices for the synthesized LRAs, biological LRAs, and grafted local axons.</li> </ul> </li> <li><strong>local_axons</strong>: biological local axons that are grafted to the synthesized dendrites that do not have synthesized long-range axons.</li> <li><strong>synthesized_MOp5_LRAs</strong>: 1695 synthesized cells with long-range axons of the MOp5 region, in the atlas reference frame. </li> <li><strong>out_a_p_synth_MOp5</strong>: axonal projection analysis of the synthesized MOp5 axons.</li> <li><strong>synthesized_isocortex_cells</strong>: all synthesized cells of the isocortex region, except MOp5 cells. They are in h5 format, which takes less space than asc and swc. The h5 format can be read and converted for instance with <a href="https://github.com/BlueBrain/MorphIO">MorphIO</a>.</li> <li><strong>synthesized_isocortex_LRAs</strong>: 21680 synthesized cells with long-range axons of the isocortex regions for which a GMM cluster was created. </li> </ul> <p>Additional files:</p> <ul> <li>flatmap_both.nrrd: file used to generate a flat map visualization of the mouse isocortex, shown in the article.</li> <li>config_a_s.cfg: configuration file used to synthesize the long-range axons with the <a href="https://github.com/BlueBrain/axon-synthesis">axon-synthesis</a> code.</li> <li>target_pts: tufts common ancestors for the synthesized MOp5 axons.</li> <li>brain_atlas.zip: a lightweight version of the mouse brain atlas for the synthesis code example.</li> </ul> <p>*<em>These softwares might not be open-source at the time of publication of this data, but a public link will be provided as soon as they are.</em></p>
Soil and understory CO2 respiration, CH4, and N2O fluxes, tree biomass and litter, and soil carbon stock after a long-term N fertilization of a Scots pine forest in Finland
<p>Data of forest soil respiration, soil and undestory respiration, CH4, and N2O fluxes, soil temperature and volumetric water content (Data_Karstula_GHG_temp.swc.csv), continuous soil temperature and moisture data (Data_Karstula_measured_temperature_2021_2023.csv, Data_Karstula_measured_moisture_2021_2023.csv), forest biomass and litter (Data_Karstula_total_biomass_litter.csv, Data_Karstula_measured_litter_2021_2023.csv), and soil C stocks (Data_Karstula_soc.csv) from the boreal Scots pine forest site Karstula after a long-term N fertilization in Finland (62°54'43.343"N; 24°34'16.021"E).</p> <p>The dataset is used for the publication "Tupek et al. : <strong>Lower sensitivity of microbial respiration to soil moisture after long-term N fertilization increases soil carbon retention in a Scots pine forest</strong>. 2024".</p>
Linked collectors and determiners for: Daddy-long-leg giants: revision of the spider genus Artema Walckenaer, 1837 (Araneae, Pholcidae).
Natural history specimen data linked to collectors and determiners held within, "Daddy-long-leg giants: revision of the spider genus Artema Walckenaer, 1837 (Araneae, Pholcidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/4298f5cf-d85e-48fb-afe8-f12c99ad65b3">https://bionomia.net/dataset/4298f5cf-d85e-48fb-afe8-f12c99ad65b3</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4298f5cf-d85e-48fb-afe8-f12c99ad65b3">https://gbif.org/dataset/4298f5cf-d85e-48fb-afe8-f12c99ad65b3</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Notes on slender species of the long-jawed spider genus Tetragnatha (Araneae Tetragnathidae) with description of three new species.
Natural history specimen data linked to collectors and determiners held within, "Notes on slender species of the long-jawed spider genus Tetragnatha (Araneae Tetragnathidae) with description of three new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/30ae322a-ca5b-4981-9e20-acac3d0f57b7">https://bionomia.net/dataset/30ae322a-ca5b-4981-9e20-acac3d0f57b7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/30ae322a-ca5b-4981-9e20-acac3d0f57b7">https://gbif.org/dataset/30ae322a-ca5b-4981-9e20-acac3d0f57b7</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Two new European long-legged hoverfly species of the Eumerusbinominatus species subgroup (Diptera, Syrphidae).
Natural history specimen data linked to collectors and determiners held within, "Two new European long-legged hoverfly species of the Eumerusbinominatus species subgroup (Diptera, Syrphidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ec2388ec-d288-4a38-ba8f-11015339c095">https://bionomia.net/dataset/ec2388ec-d288-4a38-ba8f-11015339c095</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ec2388ec-d288-4a38-ba8f-11015339c095">https://gbif.org/dataset/ec2388ec-d288-4a38-ba8f-11015339c095</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Raphia vinifera (Arecaceae; Calamoideae): Misidentified for far too long.
Natural history specimen data linked to collectors and determiners held within, "Raphia vinifera (Arecaceae; Calamoideae): Misidentified for far too long". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e48fa103-8254-4845-be98-ed5cde6924c5">https://bionomia.net/dataset/e48fa103-8254-4845-be98-ed5cde6924c5</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e48fa103-8254-4845-be98-ed5cde6924c5">https://gbif.org/dataset/e48fa103-8254-4845-be98-ed5cde6924c5</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: The taxonomic status of Long-tailed shrews (Mammalia: genus Sorex) from Nuclear Central America.
Natural history specimen data linked to collectors and determiners held within, "The taxonomic status of Long-tailed shrews (Mammalia: genus Sorex) from Nuclear Central America". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e605eaa7-c942-4658-a155-34c3e93f1e01">https://bionomia.net/dataset/e605eaa7-c942-4658-a155-34c3e93f1e01</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e605eaa7-c942-4658-a155-34c3e93f1e01">https://gbif.org/dataset/e605eaa7-c942-4658-a155-34c3e93f1e01</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A second update to the checklist of Finnish long-legged flies (Diptera: Dolichopodidae), with a re-evaluation of the status of Hydrophorus callosoma Frey, 1915.
Natural history specimen data linked to collectors and determiners held within, "A second update to the checklist of Finnish long-legged flies (Diptera: Dolichopodidae), with a re-evaluation of the status of Hydrophorus callosoma Frey, 1915". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d30a4943-1366-49eb-b781-9429528d5929">https://bionomia.net/dataset/d30a4943-1366-49eb-b781-9429528d5929</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d30a4943-1366-49eb-b781-9429528d5929">https://gbif.org/dataset/d30a4943-1366-49eb-b781-9429528d5929</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: LOB - California State University, Long Beach Herbarium.
Natural history specimen data linked to collectors and determiners held within, "LOB - California State University, Long Beach Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b2d55172-8980-4195-9632-a186edb27d5a">https://bionomia.net/dataset/b2d55172-8980-4195-9632-a186edb27d5a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b2d55172-8980-4195-9632-a186edb27d5a">https://gbif.org/dataset/b2d55172-8980-4195-9632-a186edb27d5a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: A new species of long-legged terrestrial Terrapotamon Ng, 1986 (Crustacea: Brachyura: Potamidae) from limestone formations in Satun, southern Thailand.
Natural history specimen data linked to collectors and determiners held within, "A new species of long-legged terrestrial Terrapotamon Ng, 1986 (Crustacea: Brachyura: Potamidae) from limestone formations in Satun, southern Thailand". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/7fd40431-a108-4133-9397-7b4750b0feff">https://bionomia.net/dataset/7fd40431-a108-4133-9397-7b4750b0feff</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/7fd40431-a108-4133-9397-7b4750b0feff">https://gbif.org/dataset/7fd40431-a108-4133-9397-7b4750b0feff</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Long-term monitoring of Azorean forest arthropods: the BALA Project (1997-2022).
Natural history specimen data linked to collectors and determiners held within, "Long-term monitoring of Azorean forest arthropods: the BALA Project (1997-2022)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8a4be36d-18cd-484c-b8ce-f67194cf4bac">https://bionomia.net/dataset/8a4be36d-18cd-484c-b8ce-f67194cf4bac</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8a4be36d-18cd-484c-b8ce-f67194cf4bac">https://gbif.org/dataset/8a4be36d-18cd-484c-b8ce-f67194cf4bac</a>. Formatted as a Frictionless Data package.
Long-term biochar and soil organic carbon stability– Evidence from field experiments in Germany-ROW DATA
<p> Row data for researcher paper Long-term biochar and soil organic carbon stability– Evidence from field experiments in Germany</p>
Data products for "3D modeling of long-term slow slip events along the flat-slab segment in the Guerrero Seismic Gap, Mexico"
<p>Data products for '3D modeling of long-term slow slip events along the flat-slab segment in the Guerrero Seismic Gap, Mexico' by A. Perez-Silva, D. Li, A.-A. Gabriel and Y. Kaneko</p>
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IIB. Paratrigonidium Brunner, 1893. (A–E), Paratrigonidium nitidum Brunner, 1893: A, Male elytra membranous & harpvein only one; B, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; C, Lateral field of tegmina inmale blackish, presenting 3 parallel veins and the fourth incomplete; D, The hind femur with a feeble brownish band/stripe; E, The female ovipositor fulvous at base, darkened in the middle. Trigonidium Rambur, 1839. (F–I), Trigonidium humbertianum (Saussure, 1878): F, Anterior tibiae with tympanum on both sides; G, Fifth joint of maxillary palpi large and triangular; H, Female ovipositor curved, compressed, acute at apex; I, Male sub-genital plate feebly notched at apex.
PLATE IIA. Paratrigonidium Brunner, 1893. (A–K), Paratrigonidium nitidum Brunner, 1893: A–B, Male and female black, shining;the male with membranous elytra, while female elytra corneous, convex with plain, longitudinal veins. Vertex flattened and sloping; C, Head wide and black; antenae yellow with first joint black; D, Pronotum black, pubescent; E, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; F, Tympanum external; G, Male elytra membranous; H, The hind femurwith a feeble brownish band/stripe; I, Legs yellowish; J, Lateral field of tegmina in male blackish, presenting 3 parallel veins andthe fourth incomplete; K, The female ovipositor fulvous at base, darkened in the middle, cerci long. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IIA. Paratrigonidium Brunner, 1893. (A–K), Paratrigonidium nitidum Brunner, 1893: A–B, Male and female black, shining;the male with membranous elytra, while female elytra corneous, convex with plain, longitudinal veins. Vertex flattened and sloping; C, Head wide and black; antenae yellow with first joint black; D, Pronotum black, pubescent; E, Palpi long, yellowish, fifth joint of maxillary palpi long, feebly widening at apex; F, Tympanum external; G, Male elytra membranous; H, The hind femurwith a feeble brownish band/stripe; I, Legs yellowish; J, Lateral field of tegmina in male blackish, presenting 3 parallel veins andthe fourth incomplete; K, The female ovipositor fulvous at base, darkened in the middle, cerci long.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.