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Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Jiří Gaisler, <a href="http://www.wikidata.org/entity/Q23139681">http://www.wikidata.org/entity/Q23139681</a>. Claims or attributions were made on Bionomia, <a href="https://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Data for the Article: Cross-validation of a semantic segmentation network for natural history collection specimens
<p>This deposit contains six datasets which were used for testing and validating a semantic segmentation network. The purpose was to evaluate the suitability of the segmentation network for use in the processing of images from Natural History Collections.</p>
Global Biotic Interactions: Elton Dataset Cache for Collections of National Museum of Natural History, Smithsonian Institution
<p>Global Biotic Interactions: Elton Dataset Cache for Collections of National Museum of Natural History, Smithsonian Institution</p> <p>The intended use of this archive/cache is to allow for offline-enabled access versions of existing species interaction datasets. The program "Elton" (https://doi.org/10.5281/zenodo.998263) was used to populate the content of elton-datasets.tar.gz . The same program can be used to extract information from the cache archive also. Global Biotic Interactions (https://globalbioticinteractions.org, https://doi.org/10.1016/j.ecoinf.2014.08.005) also uses these archives to create derived species interaction data archives, search indexes and APIs.</p> <p>Please note that due to size considerations, offline-enabled access to an elton dataset cache of iNaturalist interaction data has been excluded from this publications and moved into a separate Zenodo publication at https://doi.org/10.5281/zenodo.3950546 .</p> <p>Contents<br> --------</p> <p>README:<br> this file</p> <p>elton-datasets.tar.gz:<br> versioned archive with species interaction datasets</p> <p>elton-datasets.tar.sha256:<br> content signature of elton-datasets.tar</p> <p>elton-datasets.tsv:<br> list of included datasets</p> <p>elton.jar:<br> commandline program to help access the species interaction datasets</p> <p>Usage<br> -----</p> <p>To install, extract elton-datasets.tar.gz into a directory of choice using:</p> <p>tar xfz elton-dataset.tar.gz</p> <p>To use, download elton.jar included this publication and execute the following to get a list of available datasets:</p> <p>java -Xmx4G -jar elton.jar datasets</p> <p>on a system that has java v8+ installed.</p> <p>If all goes well, you should be able to regenerate the included file elton-dataset.tsv .</p> <p>For more information on how to use elton.jar, execute:</p> <p>java -jar elton.jar usage</p> <p>or visit https://github.com/globalbioticinteractions/elton for more available commands.</p> <p>Alternatively, without using Elton, you can access the data by inspecting the access.tsv files in the various directories of the datasets directory.</p> <p>When using these datasets in a publication or product, please cite the *original* data providers and publications. You can find the citations in the data.</p> <p>Included datasets:</p> <p>globalbioticinteractions/usnm National Museum of Natural History, Smithsonian Institution IPT RSS Feed https://github.com/globalbioticinteractions/usnm/archive/44794f5e68adb768de09b44692d7bd2163968563.zip 2021-11-13T03:12:33.778Z 686cacf55bbd48785d264d1bc7ff187f36a77faa92e963368f36617ab732304e 0.12.2</p> <p>Associated content ids:</p> <p>hash://sha256/a6a5c330c7e7e803ba96acafdb854e6b4d93d763a700d921cf416ec92b1521a5<br> hash://sha256/da5fde39c0048886b085b17b001b10fc69d12e259fee46e0252f0e90b0a5e988<br> hash://sha256/f7287f049bc1114619e538e42ea728dbdcaf489790f71eb1bedd55ff5396dd7f<br> hash://sha256/68bd01e004e6b0bfbde925d1f5449b8dc50f4b01ed6d3534d0a3bc01875149fd<br> hash://sha256/57901cccfa745ca64a60f5f9dfc3c2a25c0a6cd57d676cea8a60e2d605bd1828<br> hash://sha256/50cdd572f1cc66976591d9e718592681dde9e0f7139d3802738d01abd22e5729<br> hash://sha256/e176d4444d1664d486226764eeb00c5f31d7332a5ea0f5cb2947e6892e0e4e64<br> 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Fig. 1 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola
Fig. 1. – "Aspecto da embocadura do Rio Dande" [Aspect of the mouth of the River Dande] with Joaquim José da Silva (left) and José António (right). [a. "Forno da cal" [lime oven]; b. "Armazem de a-guardar" [storage]; c. "Sanzallas" [dwellings]; d. "Armazem da madeira" [timber storage]; e. "Igreja que foi dos Jesuitas" [church that was of the Jesuits]; f. "Ponta do Mussule(?)" [Mussule(?) Tip] [SILVA, J.J. (post. 1785: fig. 84); painting executed by José António] [© Arquivo Histórico dos Museus da Universidade de Lisboa]
Fig. 2 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola
Fig. 2. – Itinerary of Joaquim José da Silva in Angola from 1783 to 1810 according to TEIXEIRA (1962) in pink, SIMON (1983) in blue, and this work in red.
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
FIG. 3 in The d'Orbigny Palaeontological Collection of the National Museum of Natural History and Science, Lisbon, Portugal: Historical perspective and revision of Cretaceous Cephalopoda
FIG. 3. — Cretaceous ammonites of the d'Orbigny Collection of the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência): A-D, Neolissoceras grasianum (d'Orbigny, 1840) in ventral (A), lateral (B) and oral (C) views, and original label (D): Nº 357/Ammonites grasanus (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade S.t Julien (Hautes Alpes); E-G, Pleurohoplites (Pleurohoplites) renauxianus (d'Orbigny, 1840) in lateral (E) and ventral (F) views, and original label (G): Nº 464/Ammonites Renauxianus (d'Orb), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Mont-Blainville (Meuse); H-K, Acanthoceras rhotomagense (Brongniart, 1822) in oral (H), lateral (I) and ventral (J) views, and original label (K): Nº 463/Ammonites rhotomagensis (Lamarck), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Rouen (Seine inf.re). Scale bar: 2 cm.
FIG. 2 in The d'Orbigny Palaeontological Collection of the National Museum of Natural History and Science, Lisbon, Portugal: Historical perspective and revision of Cretaceous Cephalopoda
FIG. 2. — Cretaceous nautiloid and ammonites of the d'Orbigny Collection of the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência): A-C, Angulithes triangularis de Montfort, 1808 in oral (A) and lateral (B) views, and original label (C): Nº 459/Nautilus triangularis (Montf), Andar 20º Cenomaniense, Terreno Cretaceo, Localidade Fouras (Charente inf.re); D-G, Phylloceras (Hypophylloceras) tethys (d'Orbigny, 1840) in ventral (D), lateral (E) and oral (F) views, and original label (G): Nº 360/Ammonites Tethys (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade Arredores de [environs of] Sisteron (Basses Alpes); H-K, Ptychophylloceras (Semisulcatoceras) semisulcatum (d'Orbigny, 1840) in ventral (H), lateral (I) and oral (J) views, and original label (K): Nº 359/Ammonites semisulcatus (d'Orb), Andar 17º Neocomiense, Terreno Cretaceo, Localidade Sisteron (Basses Alpes). Scale bar: 2 cm.
Fig. 5. Baetis flaveola F.-J. Pictet, 1843 in Mayfly types and additional material (Insecta: Ephemeroptera) examined by F.-J. Pictet and A.-E. Pictet, housed in the Museums of Natural History of Geneva and Vienna
Fig. 5. Baetis flaveola F.-J. Pictet, 1843 nom. dub. (A) Syntype [?]. (B) Labels of syntype [?] 1. Scale bar: 5 mm. (C) Syntype [?] 2. Scale bar: 5 mm. (D) Labels of syntype [?] 2. Scale bar: 5 mm.
Fig. 1 in Mayfly types and additional material (Insecta: Ephemeroptera) examined by F.-J. Pictet and A.-E. Pictet, housed in the Museums of Natural History of Geneva and Vienna
Fig. 1. François-Jules Pictet de la Rive (1809-1872) in his library. Oil painting, without date or signature; attributed to a Mr Kaiser (according to an inscription on the back of the painting). Courtesy of the Fondation des Archives de la Famille Pictet, Geneva.
Fig. 3 in Joaquim José da Silva (c. 1755-1810): his life, natural history collecting activities, and involvement in the so-called first scientific expedition in the interior of Angola
Fig. 3. – Holotype of Cyphia stheno Webb at P. [Silva s.n., P00088662; © Muséum national d'Histoire naturelle, Paris]
Introduction history mediates naturalization and invasiveness of cultivated plants
<p><strong>Aim:</strong> Species characteristics and cultivation are both associated with alien plant naturalization and invasiveness. Particular species characteristics are favored for cultivation, obscuring the relationship between traits and naturalization success. We sought to better understand the drivers of naturalization and invasiveness by analyzing relationships with species characteristics and cultivation and by disentangling the direct effects of characteristics from the indirect effects mediated by cultivation.</p> <p><strong>Location:</strong> Great Britain</p> <p><strong>Time period:</strong> c. 1000–present</p> <p><strong>Major taxa studied:</strong> Seed plants</p> <p><strong>Methods:</strong> We used a comprehensive dataset of 17,396 alien plant taxa introduced to Great Britain before 1850, a country with one of the most well-documented histories of plant introductions. We integrated this with cultivation data from historical and modern records of botanic gardens and commercial nurseries and with trait data. Accounting for time since introduction, we quantified the influences of cultivation and species characteristics on present-day naturalization and invasiveness in Great Britain.</p> <p><strong>Results:</strong> Larger native range size, earlier flowering, long-lived herbaceous growth form, and outdoor cultivated habitat were all associated with naturalization. However, these relationships between characteristics and naturalization largely reflected cultivation patterns. The indirect, mediating influence of cultivation on naturalization varied among species characteristics, and was relatively strong for growth form and weak for native range size. Cultivation variables, particularly availability in present-day nurseries, best explained invasiveness, while species characteristics had weaker associations.</p> <p><strong>Main conclusions:</strong> Human influence on species introduction and cultivation is associated with increased probability of naturalization and invasiveness, and it has measurable indirect effects by biasing the distribution of species characteristics in the pool of introduced species. Accounting for human cultivation preferences is necessary to make ecological interpretations of the effects of species characteristics on invasion.</p>
Galls of Baden-Württemberg from the State Museum of Natural History Stuttgart
<p>A selection of preserved gall specimens used as a model for studying curation and digitization methods. The galls were collected in what is now the federal state of Baden-Württemberg between 1917 and 1986. Collectors include Jaap, Brielmaier, Wünsch, Möhn, Breunig, Thomas, Wunderle, and Grams. Gall forming taxa are primarily Cynipidae (Hymenoptera) and Cecidomyiidae (Diptera). Gall host plants include the genera <em>Acer, Alnus, Centaurea, Cirsium, Fagus, Filipendula, Hieracium, Quercus, Rorippa, Rosa, Rubus, Salix, Tilia, Urtica, </em>and <em>Vitis.</em></p>
Fig. 16. Lycosa piochardi Simon, 1876, natural history. A in Lycosa Latreille, 1804 (Araneae, Lycosidae) of Israel, with a note on Geolycosa Montgomery, 1904
Fig. 16. Lycosa piochardi Simon, 1876, natural history. A. Feeding on Pyrrhocoris apterus (Linnaeus, 1758), Mt. Gilboa. B. At the opening of a turretless burrow, central Negev. C. Female with egg sac, Midreshet Ben-Gurion. D. Turreted burrow sealed with silk, Midreshet Ben-Gurion. Photos by I. Armiach Steinpress.
Text-fig. 4. Lepidocarpon cone in the process of disaggregating as part of the dispersal strategy of the plants. When preserved isolated, the sporophylls are assigned to the fossil-genus Lepidostrobophyllum. Refigured from Thomas (1981). Grovesend Formation (upper Asrturian – lower Moscovian), Kilmersdon Tip, Radstock Coalfield, UK; Natural History Museum (London) specimen V.60431. in Naming Of Parts: The Use Of Fossil-Taxa In Palaeobotany
Text-fig. 4. Lepidocarpon cone in the process of disaggregating as part of the dispersal strategy of the plants. When preserved isolated, the sporophylls are assigned to the fossil-genus Lepidostrobophyllum. Refigured from Thomas (1981). Grovesend Formation (upper Asrturian – lower Moscovian), Kilmersdon Tip, Radstock Coalfield, UK; Natural History Museum (London) specimen V.60431.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Gotfred Kvifte, <a href="http://www.wikidata.org/entity/Q5587748">http://www.wikidata.org/entity/Q5587748</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Gunnar Soot, <a href="http://www.wikidata.org/entity/Q124540283">http://www.wikidata.org/entity/Q124540283</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Wilhelm Ramm, <a href="http://www.wikidata.org/entity/Q97570173">http://www.wikidata.org/entity/Q97570173</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Oddkjell Bosheim, <a href="http://www.wikidata.org/entity/Q125291661">http://www.wikidata.org/entity/Q125291661</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Joseph Lauterer, <a href="http://www.wikidata.org/entity/Q1707480">http://www.wikidata.org/entity/Q1707480</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
ScienceDex guides
Understand access before you commit
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.