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opencc-zeroApr 2024View details →

Literature review on the effect of conspecific density on animal dispersal (2000-2023)

We review empirical studies of animal dispersal in relation to conspecific density to examine the evidence for density-dependent dispersal among taxa and test whether reports of its occurrence are taxon-specific and/or biased by the methodology employed. We conducted a thorough review of the literature (2000 - 2023) and found k = 97 empirical studies of amphibians, birds, fishes, invertebrates, mammals, or reptiles that had tested for a correlation between conspecific density and animal dispersal. From each, we derived the correlation coefficient of the relationship between density and dispersal, which we z-transformed to obtain the effect size, Zr. We also extracted and compiled information on taxonomic group, sex, age, migratory behavior, experimental setup, dispersal metric, density metric, and variable type, as well as temporal and spatial scale to test their relationships with Zr using linear regressions and multilevel mixed-effect modeling.

opencc-by-4.0Nov 2024View details →

Cetaceans sighting positions from 2009 to 2021 (animal conservation)

Sighting position of the Striped dolphin (Stenella coeruleoalba), Common bottlenose dolphin (Tursiops truncatus) and Fin whale (Balaenoptera physalus) in the 2009 - 2021 period collected buy aerial line transect distance sampling. These data coupled with other from public database are linked with the Copernicus in order to fit ensemble SDMs 16 and predict their current and future potential distribution at the Mediterranean subregional scale.

opencc-by-nc-4.0Nov 2024View details →

Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells

The raw data presented in this folder corresponds to the publication # Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells Johanna E. M. Dickmann 1,2, Marjolaine Martin 1,§, Claire Lionnet 1,§, Zoe Nemec-Venza 1, Olivier Hamant 1,2 1 Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, INRAE, CNRS, UCBL1   2 Correspondence: olivier.hamant@ens-lyon.fr, johanna.dickmann@ens-lyon.fr   § Equal contribution   ORCIDs: * Johanna Dickmann: 0000-0002-0861-4440 * Zoe Nemec-Venza: 0000-0002-2346-2596 * Olivier Hamant: 0000-0001-6906-6620 Submitted to bioRxiv in November 2024   This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 521501033 to J.D. and the European Research Council (ERC-2021-AdG-101019515 “Musix” to O.H.). ## Data organization The data are organized according to the figure panels in the publication. For large experiments, the folders may contain subfolders for each experimental repeat and/or condition. For explanations on the data and the methods, please refer to the publication. All data presented here are the original raw data output of the microscopes in the CZI format, a proprietary format developed by Zeiss, encapsulating both 4D image data and metadata, i.e. acquisition settings. This format is supported by open-source software such as Fiji and Open Microscopy Environment. Refer to the README files in the subfolders for information on which exact file was used to display in the figure. ## Explanation of the file names ### Arabidopsis experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g.”PLA001”, “PRO077”) * the line of the imaged plant material (e.g. “pUBQ10-LTi6B-TdTomato”) * sometimes information on the ecotype of the line (e.g. “Col-0”) * the age of the plants (e.g. “7d” = 7 day old plants) * sometimes information on a stain added (e.g. “FM4-64_0_5ugPml” = FM4-64 dye at a final concentration of 5 ug/ml) * sometimes information on a treatment (e.g. “beforeFDA” = image taken before FDA was added; “FDA2.5ugPml” = after adding FDA at a final concentration of 2.5 ug/ml, sometimes with additional information on the time between adding the FDA and imaging, e.g. “25min”) * sometimes information on the centrifugation speed (e.g. “100g”) * sometimes information on the imaging support (e.g. “bucket” = NOA73 container, “wells” = NOA73 microwells, “coverslip”) * sometimes information on the imaging mode (“z-stack”, “t-series” = time series/timelapse, “6x” = zoom of 6 in Zen software) * the solution the sample was imaged in (“Solution A” or “A” = hyperosmotic buffer with D-mannitol, “AS” = hyperosmotic buffer with D-sorbitol) * sometimes information on experimental setup (“ON” = overnight timelapse imaging) * increasing numbers at the end of the file name indicate subsequent fields of view or positions imaged with the same settings * for Fig. 1A: information about the length of the plasmolysis (“50 min”) * for Fig. 4c,d: information on which solution the protoplasts are and have been imaged in: “A” = hyperosmotic buffer solution with 600 mM D-mannitol. “B” =  hyperosmotic buffer solution with 280 mM D-mannitol. Times indicate time between addition of new buffer and onset of imaging of the position list. * for Fig. 4e-f: the concentration of the hyperosmotic buffer solution is indicated. For the control, the number of additions of hyperosmotic buffer solution with 600 mM D-mannitol is indicated. ### Physcomitrium patens experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g. "PyP001")   * “Physco_wt” referring to Physcomitrium patens wild type * the age of the moss tissue used for protoplasting (e.g. “6d” = 6 days) * information on the stain added (e.g. “ Fm4-64_2ugPml” = FM4-64 dye at a final concentration of 2 ug/ml) * information on the imaging support (e.g. “bucket” = NOA73 container, “coverslip”) ### Maize experiments The filenames contain the following information, separated by underscores: * the date on which the experiment was performed (yyyymmdd) * the plant species (“Maize”) * sometimes information in the solution used for digestion ("A+E" = hyperosmotic buffer solution with D-mannitol) ### Bead experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g. “beads008”) * a description of the beads (“fluoresbrite1micron” = Fluoresbrite beads of a diameter of 1 um) * sometimes a short description of the protocol (e.g. “SolAwashed-2-3mLsolA” = NOA73 microwells were washed in hyperosmotic buffer with 600 mM D-mannitol 2x prior to imaging, beads were imaged in 3 ml hyperosmotic buffer solution with 600 mM D-mannitol.) * an information on the size of the field of view (e.g. “small FOV” = small field of view, i.e. one microwell with beads) * information at which approx. height of the microwell the image was taken (“TopOfWells” = close to the opening of the wells on the top) * sometimes information on the zoom of the Zen software (e.g. “7x”)

opencc-by-4.0Nov 2024View details →

Animations from "Scaling density of axion strings in terasite simulations"

Open the record for dataset details and reuse information.

opencc-by-4.0Nov 2024View details →

SUSHEAT Project Animation Video

The Project Animation Video has been developed to support the dissemination and communication activities of the SUSHEAT project. This project is funded by the European Union under Grant Agreement 101103552. The views and opinions expressed are solely those of the author(s) and do not necessarily reflect the views of the European Union or the European Climate, Infrastructure and Environment Executive Agency (CINEA). Neither the European Union nor the granting authority can be held responsible for any use that may be made of the information it contains.

opencc-by-4.0Oct 2021View details →

Animation for "Rapid Evolution of Bald Patches in a Major Solar Eruption"

Animation of Figure 1 and 4 of Lee, Sun, & Kazachenko (2020), ApJL, "Rapid Evolution of Bald Patches in a Major Solar Eruption". Animation 1. The animation (18 s, 88 frames) shows bald patch (BP) evolution from 10:49:30 UT to 13:00:00 UT. The background shows the positive (negative) polarity B_z in white (black). Vectors show B_h with foot points in the positive (negative) B_z in blue (red). The polarity inversion line (PIL) and BPs are shown by the green line and yellow/orange circles, respectively. The gray contour is for B_z = 300 G. The X9.3 flare has a GOES start, peak, and end time in soft X-ray flux at 11:53 UT, 12:02 UT, and 12:10 UT, respectively. Prior to the flare, Region 1 gradually built more BPs along the PIL. Throughout the duration of the flare and afterwards, BPs in Region 1 disintegrated. BPs in Region 2 largely remained the same and survived the flare. The large amount of pixel masking occurring in the central regions of the AR and extending into both polarities during the flare is an artifact of flare ribbons, leading to many masked pixels. It can be seen in more detail in the Animation 4. Animation 4. The animation (18 s, 88 frames) shows the flare ribbon evolution from 10:49:30 UT to 13:00:00 UT. During the onset of eruption, ribbons developed along the PIL within Region 1 and exterior to the PIL in Region 2. Prior to the flare peak, flare ribbons propagated along and separated away from the PIL covering the entirety of Region 1 and Region 2.

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Cattle- Appendix B: Excel file with all data extracted

Information on all the full-text studies that were assessed, including the reason for exclusion for those that were excluded at the full-text screening and the data extracted from the included studies, can be consulted here.  The extensive literature review was carried out by the University of Copenhagen under the contract OC/EFSA/ALPHA/2020/02 – LOT 1 (https://ted.europa.eu/udl?uri=TED:NOTICE:457654-2020:TEXT:EN:HTML)

opencc-zeroJun 2021View details →

Japanese Visual Media Graph - Anime Characters Database Ontology

This group of files represents the RDF ontology used in the Japanese Visual Media Graph for the Anime Characters Database. Included in the upload are an explanatory PDF, the ontology in the Turtle serialization, and an HTML visualization of the ontology.

Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.

Data table of egg quality parameters

opencc-zeroDec 2021View details →

The ability to disperse large seeds, rather than body mass alone, defines the importance of animals in a hyper-diverse seed dispersal network

1. Large-bodied animals play irreplaceable roles in seed dispersal, partly due to their capacity to disperse large seeds. Understanding this role at a community level has been limited by the paucity of network studies that include large vertebrates, and the almost complete absence of studies including synzoochoric dispersers. Synzoochoric dispersers can disperse seeds disproportionately large for their body size, potentially overlapping the roles of large-bodied animals. A comprehensive network, inclusive of large vertebrates and synzoochorous dispersers, is imperative to understand seed dispersal at a community level. 2. Here, we analysed the seed dispersal network of a hyper-diverse Sundaic forest in Malaysia using local ecological knowledge and including multiple forms of endozoochorous and synzoochorous dispersal. We evaluated the extent to which three disperser traits: body mass, seed-handling ability (size of the largest seed dispersed), and diet explained the importance of animals in the network. We evaluated dispersers' relative importance using four network metrics — degree of specialisation (nested rank), species strength, within-module connectivity (z-value), and between-modules connectivity (c-value). 3. We found that seed-handling ability had the biggest effect on a disperser's importance, with strong effects on three network metrics (species strength, ecological specialization, z-value) and moderate effects on connectivity between modules. Body mass was important in defining interactions within modules, and dietary differences defined the ecological specialisation of species in seed dispersal. 4. Important dispersers in our network were large-seed dispersers (e.g., rats, gibbons), large-bodied animals, in particular the Asian elephant, and animals with frugivorous diets such as hornbills. 5. Synthesis. Our work uncovers the significance of seed-handling ability in identifying pivotal seed dispersal roles in tropical rainforests. Key dispersers include large-bodied herbivores and medium-sized frugivores that could disperse large seeds by endozoochory, and smaller rodents that dispersed similar-sized seeds by synzoochory. Many of the species that emerged as particularly important for the seed dispersal network are currently threatened (e.g., the Asian elephant, gibbons, and hornbills). Their protection or reintroduction should be a top conservation priority.

Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part B)

Roundtable discussion on Fecal Microbiota Transplantation chaired by Klaus Helmann (KLIFOVET, DE). The roundtable participants enlisted below: <ul> <li>Thomas Thymann (University of Copenhagen, DK)</li> <li>Mirja Huhtinen (Orion Pharma, FI)</li> <li>Jordi Torren (European Medicines Agency, NL)</li> <li>Alexandre Thibodeau (University of Montreal, CA)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679. The video is available on YouTube: <a href="http://youtu.be/0fzARCNlDg8">https://youtu.be/0fzARCNlDg8</a> The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project. For any further questions please contact us <a href="avant@rtds-group.com">avant@rtds-group.com</a>

Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part A)

Roundtable discussion on Phage Therapy chaired by Klaus Helmann (KLIFOVET, DE). The roundtable participants enlisted below: <ul> <li>Michela Gambino (University of Copenhagen, DK)</li> <li>Frenk Smrekar (JAFRAL, SI)</li> <li>Javier Pozo Gonzalez (European Medicines Agency, NL)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679. The video is available on YouTube: <a href="http://youtu.be/ySXKKC8CGf8">https://youtu.be/ySXKKC8CGf8</a> The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project. For any further questions please contact us <a href="avant@rtds-group.com">avant@rtds-group.com</a>

opencc-by-3.0-usDec 2021View details →

Medial prefrontal cortex and anteromedial thalamus interaction regulates motivation related behavior and dopaminergic neuron activity: Animal Behavior

The excel Source DATA file contains the data described in Figures 2c, 2d, 2f, and 3b and Supplementary Figure 3b and 3c. The fiber photometry data described in Supplementary Figure 9 are found in the CSV files. The CSV file names reflect animal IDs.

Webinar on "Fighting AMR in animals: experiences and progress from the field" - WAAW 2021

During the WAAW campaign on 24 November, EU funded H2020 projects AVANT, DISARM, HealthyLivestock and ROADMAP joined forces to share experiences and progress from the field about the challenge of antimicrobial resistance in animals. Testimonials with hands-on experiences, actions and innovative solutions of livestock sector actors such as farmers, vets, pet owners and breeders on tackling AMR were demonstrated. The video is available on YouTube: <a href="http://youtu.be/S5QIQ5Wff-Y">https://youtu.be/S5QIQ5Wff-Y</a> Disclaimer: The invited speakers and the attendees of the webinar have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679. The presentations and opinions disclosed in this video are only for general information purposes and do not constitute a joint declaration on behalf of the beneficiaries of the project AVANT, DISARM, Healthy Livestock and ROADMAP. For any further questions please contact us at: <ul> <li><a href="avant@rtds-group.com">avant@rtds-group.com</a> (project AVANT),</li> <li><a href="info@disarmproject.eu">info@disarmproject.eu</a> (project DISARM),</li> <li><a href="healthylivestockproject@yahoo.com">healthylivestockproject@yahoo.com</a> (project Healthy Livestock) or</li> <li><a href="mailto:roadmap.communication@gmail.com">roadmap.communication@gmail.com</a> (project ROADMAP). </li> </ul>

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Fishes - Appendix B: Excel file with all data extracted

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Rabbits - Appendix B: Excel file with all data extracted

opencc-zeroDec 2021View details →

Data to support publication figures and animation scripts at GitHub: Modeling weather-driven long-distance dispersal of spruce budworm moths (Choristoneura fumiferana)

Long-term studies of insect populations in the North American boreal forest have shown the vital importance of long-distance dispersal to the maintenance and expansion of insect outbreaks. In this work, we extend several concepts established previously in an empirically-based dispersal flight model with recent work on the physiology and behavior of the adult eastern spruce budworm (SBW) moth, Choristoneura fumiferana (Clem.). An outbreak of defoliating SBW in Quebec, ongoing since the mid-2000s, already covers millions of hectares of forests in eastern Canada and threatens to spread into neighboring areas through annual summertime episodes of long-distance dispersal. Such flight events in favorable conditions frequently include billions of SBW moths dispersing in the warm atmospheric boundary layer, typically starting around sunset and often lasting through several hours of wind-driven transport over hundreds of kilometers. Successful SBW dispersal to possibly distant host forest areas depends acutely on the weather. Here we describe the components and results of SBW–pyATM, an open-source individual-based modeling framework developed in Python for the simulation of these weather-driven SBW dispersal events. Using seasonal SBW phenology results from BioSIM at known outbreak locations and high-resolution Weather Research and Forecasting (WRF) model output, we focus on modeling dispersal flights over two successive nights in July 2013 in southern Quebec. Our flight model closely reproduces the SBW spatial patterns and motions observed by weather surveillance radar over the St. Lawrence estuary. With SBW–pyATM we can estimate landing locations for both male and female SBW and the resulting spatial patterns of egg distribution, allowing us eventually to forecast future larval defoliation activity in new locations where immigration could help overcome local limitations on SBW populations. This information could then support forest management decisions where SBW outbreaks threaten valuable resources.

opencc-zeroJan 2022View details →

Community patch‐dynamics governs direct and indirect nutrient recycling by aggregated animals across spatial scales

Animals can have pervasive effects on ecosystems as they modify their biogeochemical and physical environments. In particular, when animals occur in high densities these effects can result in dramatic changes in the physical environment and biogeochemical hotspots or hot moments. While most research to date has focused on the direct role of animals in biogeochemical cycles, few have examined how animals indirectly influence biogeochemical cycles across scales. Freshwater mussels occur as spatially heterogeneous, dense and species-rich aggregations in many river ecosystems worldwide. Here we examined how mussel communities (1) directly influence the flux of particulate and dissolved nutrients and (2) indirectly effect the flux of N2 production, via denitrification, across a gradient of mussel biomass and differences in community composition at the patch- (0.25 m2) and stream reach-scales (60-80 m). We combined measurements of ammonia (N) and soluble reactive phosphorous (P) excretion and C, N, and P biodeposition rates for ten species with biomass and distribution estimates for seven mixed-species aggregations to quantify direct mussel contributions to biogeochemical cycling and the spatial heterogeneity of their impact. Additionally, we sampled sediments at a fine spatial scale to determine how mussel biomass and richness influence potential denitrification (indirect flux) rates at the patch- and reach-scales. We predicted that increasing mussel biomass would lead to greater direct and indirect fluxes of nutrients, manifesting in heterogeneous nutrient redistribution within and among stream reaches. We also predicted that variation in community composition would result in differential nutrient excretion and egestion stoichiometries. Our results indicate that mussel aggregations directly influence soluble and particulate nutrient fluxes with community composition, particularly phylogenetic tribe composition, controlling the stoichiometry. Mussel aggregations also indirectly influenced nutrient fluxes as greater mussel biomass and species richness resulted in higher denitrification rates as mediated by their interactions with the sediments and enhancement of nutrient availability. Our results underscore the importance of patchy communities in acting as biogeochemical control points.

opencc-by-4.0Jan 2022View details →

Dark Matter from Axion Strings with Adaptive Mesh Refinement - Supplementary Animations

Supplementary animations to the paper "Dark Matter from Axion Strings with Adaptive Mesh Refinement " (arXiv:2108.05368) <ul> <li>2D.mp4: 2D slices through our 3D simulation. A string segment piercing the 2D plane is tracked in the right two panels. Shown is the axion field, where the string core shows up as a discontinuity, as well as the radial mode.</li> <li>Axion.mp4: The evolution of the axion energy density where the string network is overlayed in yellow. The volume spans our full simulation box with periodic boundary conditions. The relative size of a Hubble volume is indicated as well by a slowly growing smaller box.</li> <li>Box.mp4: We illustrate axion radiation by focusing on a string segment. The volume shown corresponds to about 1/500th of the total simulation volume. The complex behavior of the string network can be observed with its strong influence on the axion energy density.</li> <li>Strings.mp4: The evolution of the string network is shown in yellow. The volume spans our full simulation box with periodic boundary conditions. The relative size of a Hubble volume is indicated as well by a slowly growing smaller box.</li> </ul>

Dataset supporting the article "Megapixel camera arrays for high-resolution animal tracking in multiwell plates"

IB and LF contributed equally.   This deposition contains the supporting dataset for the article: Megapixel camera arrays for high-resolution animal tracking in multiwell plates Ida Barlow, Luigi Feriani, Eleni Minga, Adam McDermott-Rouse, Thomas J O'Brien, Ziwei Liu, Maximilian Hofbauer, John R Stowers, Erik C Andersen, Siyu S Ding, André EX Brown     Acknowledgements: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 714853) and was supported by the Medical Research Council through grant MC-A658-5TY30. This work was supported by a Research Grant from HFSP (Ref.-No: RGP0001/2019). AMR was supported by a BBSRC CASE studentship part-funded by Syngenta.