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Evaluating the microscopic effect of brushing stone tools as a cleaning procedure [R analysis]
<p>This upload includes the following files related to the R analysis:</p> <p>- Raw data as a CSV table (brushing_v2.csv), i.e. results from the ConfoMap analysis (see <a href="https://doi.org/10.5281/zenodo.3632490">https://doi.org/10.5281/zenodo.3632490</a>)</p> <p>- RStudio project (Brushing_project.Rproj)</p> <p>- R scripts as R Markdown files (*.Rmd)</p> <p>- Output from R scripts knitted to HTML files (*.html)</p> <p>- A text file containing the version of RStudio used (RStudioVersion.txt)</p> <p> </p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Figure 1 from: Hardy H, Knapp S, Allan EL, Berger F, Dixey K, Döme B, Gagnier P-Y, Frank J, Haston EM, Holstein J, Kiel S, Marschler M, Mergen P, Phillips S, Rabinovich R, Sanchez Chillón B, Sorensen MV, Thines M, Trekels M, Vogt R, Wilson S, Wiltschke-Schrotta K (2020) SYNTHESYS+ Virtual Access - Report on the Ideas Call (October to November 2019). Research Ideas and Outcomes 6: e50354. https://doi.org/10.3897/rio.6.e50354
Figure 1 Indicative proposal flow for SYNTHESYS+ Virtual Access proposals. Blue boxes indicated proposer(s) actions/responsibilities; violet boxes VA coordinator actions/responsibilities; green boxes indicate where communication and discussion between proposers and VA coordinators will be paramount; white (no fill) boxes indicate post-proposal actions. Double-ended arrows indicate where back-and-forth will occur between proposer(s) and VA coordinator(s).
R scripts
<p>The R scripts for irrigation effects analysis.</p>
Figure 3 from: Borsch T, Stevens A-D, Häffner E, Güntsch A, Berendsohn WG, Appelhans MS, Barilaro C, Beszteri B, Blattner FR, Bossdorf O, Dalitz H, Dressler S, Duque-Thüs R, Esser H-J, Franzke A, Goetze D, Grein M, Grünert U, Hellwig F, Hentschel J, Hörandl E, Janßen T, Jürgens N, Kadereit G, Karisch T, Koch MA, Müller F, Müller J, Ober D, Porembski S, Poschlod P, Printzen C, Röser M, Sack P, Schlüter P, Schmidt M, Schnittler M, Scholler M, Schultz M, Seeber E, Simmel J, Stiller M, Thiv M, Thüs H, Tkach N, Triebel D, Warnke U, Weibulat T, Wesche K, Yurkov A, Zizka G (2020) A complete digitization of German herbaria is possible, sensible and should be started now. Research Ideas and Outcomes 6: e50675. https://doi.org/10.3897/rio.6.e50675
Figure 3 Mass throughput digitization station designed for museum objects at the Botanic Garden and Botanical Museum Berlin.
Figure 2 from: Borsch T, Stevens A-D, Häffner E, Güntsch A, Berendsohn WG, Appelhans MS, Barilaro C, Beszteri B, Blattner FR, Bossdorf O, Dalitz H, Dressler S, Duque-Thüs R, Esser H-J, Franzke A, Goetze D, Grein M, Grünert U, Hellwig F, Hentschel J, Hörandl E, Janßen T, Jürgens N, Kadereit G, Karisch T, Koch MA, Müller F, Müller J, Ober D, Porembski S, Poschlod P, Printzen C, Röser M, Sack P, Schlüter P, Schmidt M, Schnittler M, Scholler M, Schultz M, Seeber E, Simmel J, Stiller M, Thiv M, Thüs H, Tkach N, Triebel D, Warnke U, Weibulat T, Wesche K, Yurkov A, Zizka G (2020) A complete digitization of German herbaria is possible, sensible and should be started now. Research Ideas and Outcomes 6: e50675. https://doi.org/10.3897/rio.6.e50675
Figure 2 Number of digitized and non-digitized specimens held by 62 herbaria in Germany that were surveyed in 2019 (herbarium abbreviations according to Index Herbariorum).
Figure 1 from: Borsch T, Stevens A-D, Häffner E, Güntsch A, Berendsohn WG, Appelhans MS, Barilaro C, Beszteri B, Blattner FR, Bossdorf O, Dalitz H, Dressler S, Duque-Thüs R, Esser H-J, Franzke A, Goetze D, Grein M, Grünert U, Hellwig F, Hentschel J, Hörandl E, Janßen T, Jürgens N, Kadereit G, Karisch T, Koch MA, Müller F, Müller J, Ober D, Porembski S, Poschlod P, Printzen C, Röser M, Sack P, Schlüter P, Schmidt M, Schnittler M, Scholler M, Schultz M, Seeber E, Simmel J, Stiller M, Thiv M, Thüs H, Tkach N, Triebel D, Warnke U, Weibulat T, Wesche K, Yurkov A, Zizka G (2020) A complete digitization of German herbaria is possible, sensible and should be started now. Research Ideas and Outcomes 6: e50675. https://doi.org/10.3897/rio.6.e50675
Figure 1 Proportion of digitized specimens in the surveyed herbaria in Germany (left) and proportion of image and text data digitization vs. "text data only" (data) among the digitized specimens (right).
Figures 12-23 from: Yu XF, Shi R, Yang MF (2020) A new leafhopper genus of Empoascini (Hemiptera, Cicadellidae, Typhlocybinae) from China. ZooKeys 908: 39-44. https://doi.org/10.3897/zookeys.908.48316
Figures 12-23 Fanjinga digitata, sp. nov. 12 forewing 13 hindwing 14 abdominal apodemes 15 male genitalia, lateral view 16 pygofer, ventral view 17 pygofer, dorsal view 18 ventral pygofer appendage 19 aedeagus, lateral view 20 aedeagus, ventral view 21 paramere, lateral view 22 subgenital plate, lateral view 23 connective, dorsal view. Scale bars: 0.1mm.
Figures 1-11 from: Yu XF, Shi R, Yang MF (2020) A new leafhopper genus of Empoascini (Hemiptera, Cicadellidae, Typhlocybinae) from China. ZooKeys 908: 39-44. https://doi.org/10.3897/zookeys.908.48316
Figures 1-11 Fanjinga digitata, sp. nov. 1 male adult, dorsal view 2 male adult, lateral view 3 male adult, ventral view 4 head and thorax, ventrolateral view 5 head and thorax, ventral view 6 male genitalia, lateral view 7 male genitalia, dorsal view 8 male genitalia, ventral view 9 anal tube, connective and pygofer, ventral view 10 paramere, terminal part 11 aedeagus, terminal part. Scale bars: 0.5mm.
Figure 2 from: Chanthran SSD, Lim P-E, Li Y, Liao T-Y, Poong S-W, Du J, Hussein MAS, Sade A, Rumpet R, Loh K-H (2020) Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. ZooKeys 911: 139-160. https://doi.org/10.3897/zookeys.911.39222
Figure 2 Maximum likelihood haplotype tree reconstructed based on the concatenated mtDNA dataset. The bootstrap values higher than 50% are shown near the nodes.
Figure 4 from: Chanthran SSD, Lim P-E, Li Y, Liao T-Y, Poong S-W, Du J, Hussein MAS, Sade A, Rumpet R, Loh K-H (2020) Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. ZooKeys 911: 139-160. https://doi.org/10.3897/zookeys.911.39222
Figure 4 Pairwise number of difference (mismatch distribution) analysis was conducted using the constant population size model to observe the population size changes. The observed frequencies were represented by red dotted line. The frequency expected under the hypothesis of population expansion model was depicted by continuous green line. a Kuala Selangor b Kuantan c Mukah d Sandakan e Tawau f all populations.
Figure 1 from: Chanthran SSD, Lim P-E, Li Y, Liao T-Y, Poong S-W, Du J, Hussein MAS, Sade A, Rumpet R, Loh K-H (2020) Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. ZooKeys 911: 139-160. https://doi.org/10.3897/zookeys.911.39222
Figure 1 Sampling localities from East (Sandakan and Tawau, Sabah & Mukah, Sarawak) and West (Peninsula) Malaysia (Kuala Selangor, Selangor and Kuantan, Pahang).
Figure 3 from: Chanthran SSD, Lim P-E, Li Y, Liao T-Y, Poong S-W, Du J, Hussein MAS, Sade A, Rumpet R, Loh K-H (2020) Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. ZooKeys 911: 139-160. https://doi.org/10.3897/zookeys.911.39222
Figure 3 Haplotypes median-joining network corresponding to the ML tree with three observed clusters. The star-like profile observed in cluster III indicates the presence of sudden expansion.
Figures 9–11. Adult R in Observations on the natural history of Romulus globosus Knull (Coleoptera: Cerambycidae)
Figures 9–11. Adult R. globosus beetles in their pupal cells. 9–10) Females of R. globosus in their pupal cells dug out from the ground. 11) Freshly eclosed male of R. globosus in a pupal cell (apical part of elytra was damaged while removing the bark of the root).
Figures 3-7 from: Liston A, Altenhofer E, Netzberger R, Prous M (2020) Biology of two European Tenthredo species (Hymenoptera, Tenthredinidae) feeding on Gentiana. Deutsche Entomologische Zeitschrift 67(1): 13-18. https://doi.org/10.3897/dez.67.49741
Figures 3-7 Larvae of Tenthredo propinqua and scrophulariae. 3–5.Tenthredo propinqua, from Gentiana asclepiadea. Arrows indicate some of the black dorso-median markings, which on the abdomen occupy the width of a single annulet; 3. Preserved in ethanol (wax dissolved); 4. Alive, with wax coating (photographed on 11.09.2019); 5. Head, preserved in ethanol. 6, 7.Tenthredo scrophulariae larvae, on Scrophularia species. Arrows indicate some of the black dorso-median markings, which on the abdomen extend across two annulets at least in part; 6. Half-grown (photographed on 08.09.2007); 7. Nearly full-grown (photographed on 30.09.2007). Photos: A. Liston (3, 5), E. Altenhofer (4), H. Savina (6, 7).
Figures 1- 2 from: Liston A, Altenhofer E, Netzberger R, Prous M (2020) Biology of two European Tenthredo species (Hymenoptera, Tenthredinidae) feeding on Gentiana. Deutsche Entomologische Zeitschrift 67(1): 13-18. https://doi.org/10.3897/dez.67.49741
Figures 1- 2 Tenthredo atra larvae, nearly full-grown, on Gentiana asclepiadea (photographed respectively on 23.08.2019, 11.09.2019). Photos: R. Netzberger (1), E. Altenhofer (2).
R script to simulate the phenology of the box tree moth, Cydalima perspectalis
<p>This folder contains :<br> - ReadMe file with the following explanation<br> - the R script to simulate the phenology of the box tree moth (ProgR_phenology_box_tree_moth.r),<br> - the flight curve of the box tree moth in Orleans (France) in 2017 (see published dataset: https://doi.org/10.5281/zenodo.3719293 )<br> - temperature dataset (temperature.txt; col 1 = year, col 2 = month, col 3 = day, col 4 = Tmin, col 5 = Tmax)<br> - photoperiod dataset (photoperiod.txt; col 1 = year, col 2 = month, col 3 = day, col 4 = julian day, col 5 = day length in hours)<br> Note that these two former datasets are provided because they are required to make simulations.<br> Warning: since we are not allowed to redistribute the temperature and photoperiod datasets, the related files have been modified and are not those actually used in our paper in preparation.</p> <p>The R script was used in R version 3.6.1 (2019-07-05).</p> <p>To download the software R, please visit: https://www.r-project.org/</p> <p>This work was done in the frame of a regional project called INCA (grant from Région Centre Val de Loire).</p>
Figure 3 from: Carballeira R, Romay CD, Ramos A (2020) First record of a freshwater bryozoan species in Cuba: Plumatella repens (Linnaeus, 1758) (Phylactolaemata, Bryozoa). ZooKeys 918: 151-160. https://doi.org/10.3897/zookeys.918.38665
Figure 3 Geographical distribution of Plumatella species in the insular Caribbean area, indicating the new records of P. repens in Cuba (1) La Niña Bonita Reservoir and (2) Ciénaga de Zapata Swamp.
Figure 1 from: Carballeira R, Romay CD, Ramos A (2020) First record of a freshwater bryozoan species in Cuba: Plumatella repens (Linnaeus, 1758) (Phylactolaemata, Bryozoa). ZooKeys 918: 151-160. https://doi.org/10.3897/zookeys.918.38665
Figure 1 Presence of Plumatella repens (Linnaeus, 1758), in the wetlands of Cuba: A Location map of localities (1) La Niña Bonita Reservoir and (2) Ciénaga de Zapata Swamp B Aerial photograph of the La Niña Bonita Reservoir (ESRI World Imagery, ArcGIS 10.0) C Aerial photograph of the Ciénaga de Zapata Swamp (ESRI World Imagery, ArcGIS 10.0).
Figure 2 from: Carballeira R, Romay CD, Ramos A (2020) First record of a freshwater bryozoan species in Cuba: Plumatella repens (Linnaeus, 1758) (Phylactolaemata, Bryozoa). ZooKeys 918: 151-160. https://doi.org/10.3897/zookeys.918.38665
Figure 2 Plumatella repens (Linnaeus, 1758), floatoblast from La Niña Bonita Reservoir and the Ciénaga de Zapata Swamp (Cuba), SEM: A View of dorsal valve B View of ventral valve C Suture between valves is a single cord with a row of low tubercles on either side D Section of the annulus showing the connection between gas chambers, with circular pores with filiform extensions along the border. Scale bars: 50 µm (A, B); 10 µm (C); 5 µm (D).
Figure 3 from: Brincalepe Salvador R, Cavallari DC (2020) Taxonomy and distribution of enigmatic "helicoid" Polygyratia Gray, 1847 (Gastropoda, Stylommatophora). Zoosystematics and Evolution 96(1): 91-101. https://doi.org/10.3897/zse.96.51047
Figure 3 Map of Bahia state showing the known distribution of Polygyratia polygyrata. Squares: museum specimens. Circles: online records. Triangle: literature data.
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
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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.