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Herbarium specimen image of Libinhania fontinalis A. G. Mill., R. Sommerer & N. Kilian, part of the collection of Botanic Garden and Botanical Museum Berlin
Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published.<br><br>Content of this deposition:<br><br>- A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values.<br>- A JPEG image file of the scanned herbarium sheet.<br>- A lossless TIFF image from which the JPEG image has been derived.
Experimental n-octanol/water Partition/Distribution Coefficients Database for Small Molecules
<p>We critically compiled experimental values of log<em>P</em><sub>N, </sub>pK<sub>a</sub>, log<em>P</em><sub>I</sub>, and log<em>D</em><sub>pH</sub> of 225 entries based on earlier literature reports. The experimental techniques of log<em>P</em><sub>N</sub> , log<em>D</em><sub>pH</sub>, and log<em>P</em><sub>I</sub> for each molecule were thoroughly revised and added to the database. The molecules were classified between acids and bases according to their functional groups and pK<sub>a</sub> values. </p> <p>If you use this database please cite our <a href="https://doi.org/10.1002/cphc.202300548">ChemPhysChem</a> paper</p>
Data set of detected atmospheric rivers, cyclones, and fronts within the region of 75°N – 82.5°N, 0°E – 30°E and at Ny-Ålesund (Svalbard) for 2017 – 2021
<p>This data set contains times when atmospheric rivers, cyclones, or fronts have been detected within the broader region of 75°N – 82.5°N, 0°E – 30°E and specifically at Ny-Ålesund, Svalbard (78.92308 °N, 11.92108 °E) for the years 2017 to 2021. To this end, the detection methods, as described in Lauer et al. (2023), have been applied to the hourly-resolved ERA5 reanalysis (Hersbach et al., 2020) data. </p> <p>Data set overview</p> <p>Each file contains the times (year, month, day, hour in UTC) when the corresponding weather system, i.e. atmospheric river, cyclone and front, has been detected within the region of 75°N – 82.5°N, 0°E – 30°E. The last column indicates if the weather system was located also over Ny-Ålesund Svalbard (78.92308 °N, 11.92108 °E). </p>
X-ray diffraction data for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
<p>X-ray diffraction dataset for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) collected at the AMX beamline (17-ID-1) at the National Synchrotron Lightsource II, Brookhaven National Laboratory, Upton, NY, USA.</p> <p>Final XDS.INP file generated by autoPROC.</p> <p>Serialized request document for vector collection from LSDC.</p> <p>KB mirrors</p> <p>Detector: EigerX9M (Si)</p> <p>Approx. photon flux at 13475eV: 4E12 ph/s</p> <p>Approx. beam size: 5 x 7 um</p>
Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains
<p>Provided are reduced trajectories (.dcd) of the MD simulations -- each trajectory has 100 ps/frame with only protein and ion atoms remaining. Each set of trajectories are accompanied by a protein structure file (.psf) which is required to visualize the trajectories in VMD. Additionally, the z-trajectories of each intracellular ion (2 ps/frame) are provided in zipped files.<br> <br> To re-create the potentials of mean force (PMF) in Yue & Haddad et al., use the scripts provided with the paper (https://github.com/reichow-lab/Yue-Haddad_et-al.JPhysiol2021):<br> <br> </p> <pre><code class="language-bash">python3 GapJ_Analysis.py "Cx46_Ace_Produc-1_POT_*"</code></pre> <ul> <li>Choose a bin size in Å (3)</li> <li>Choose an output name (Cx46_Ace)</li> <li>Choose option (M)</li> <li>Choose time (ps) / frame (2)</li> <li>Choose column from file (1)</li> <li>Choose bin<sub>min</sub>/bin<sub>max </sub>(auto)</li> </ul>
3D Archaeological Greek Pottery: MDDS-2017-0299, Attic red-figure trefoil oinochoe, Class N, The Cook Class
<p><strong>This 3D dataset is related to the publication</strong>:</p> <ul> <li>Moitinho de Almeida, V. (2023). "<a href="https://www.researchgate.net/publication/353038967_Contributions_of_3D_digital_methods_and_techniques_to_the_study_of_ancient_pottery">Contributions of 3D digital methods and techniques to the study of ancient pottery</a>". In <em>Myths, Gods, and Heroes. Greek vase collections in Portugal / Mitos, Deuses e Heróis. As coleções de vasos gregos em Portugal</em>. R. Morais, R. Centeno, D. Ferreira (eds.). Câmara Municipal de Santa Maria da Feira - Museu Convento dos Lóios; Reitoria da Universidade do Porto; Faculdade de Letras da Universidade do Porto; Imprensa da Universidade de Coimbra. Pp.269-291. (ISBN: 978-989-8183-25-5)</li> </ul> <p>3D processed dataset for object 2017-0299, from the Museu de Arqueologia D. Diogo de Sousa (MDDS) in Braga, Portugal. <strong>CC BY-NC-SA 4.0 license</strong>.</p> <p>2017-0299 is an Attic red-figure trefoil <em>oinochoe</em>, Class N, The Cook Class, dating from c. 500-475 BCE and unknown provenance (Fundação Buehler Brockhaus / Museu D. Diogo de Sousa, 2020; Morais et al., 2021).</p> <p><strong>Aims</strong>: 3D digital documentation; morphological characterization; technological and functional analysis of archaeological Greek pottery.</p> <p><strong>Data acquisition</strong>: at the Museu de História Natural e da Ciência da Universidade do Porto (MHNC-UP), with a portable non-contact structured white light scanner, Breukmann smartSCAN3D-HE, equipped with stereo colour cameras at 250 mm FOV. Additional metadata included in associated spreadsheet.<br><strong>Data processing</strong>: 29 scans aligned and merged. MDDS-2017-0299_3D01.ply: non-manifold edges, self-intersections, small components, and small tunnels in the mesh automatically fixed, noise data removed; orientation and position normalised. MDDS-2017-0299_3D01-holesFilled.ply: holes filled for calculation of material density, filling volume, and centre of mass. Mesh is not watertight (inner surface not digitised due to occlusion). Additional metadata included in associated spreadsheet.</p> <p>Access to the 2017-0299 was granted by the MDDS.</p> <p>When citing this material: please include the original inventory ID (2017-0299) reference to the physical object.</p>
REPIN population analysis in 130 Neisseria meningitidis and N. gonorrhoeae genomes
<p>This dataset is the output of RAREFAN (http://rarefan.evolbio.mpg.de/) a webserver to identify REPIN populations across an entire bacterial species. The data was created using the following command "java -jar -Xmx10g rarefan.jar neisseria/in/ neisseria/out/ Nmen_2594.fas 55 21 neisseria/in/NMAA_0235.faa neisseria.nwk 1e-80 true 1"</p> <p>All input files are located in the folder neisseria/in/, all output data is located in neisseria/out/.</p> <p>The input files include the 130 fasta formatted <em>Neisseria</em> genome files (*.fas) and a RAYT protein sequence called NMAA_0235.faa.</p> <p>The output files include the following:</p> <p>A phylogenetic tree "neisseria.nwk" of all genomes generated with andi (<a href="http://github.com/evolbioinf/andi/">http://github.com/evolbioinf/andi/</a>) and clustDist (http://guanine.evolbio.mpg.de/problemsBook/node1.html).</p> <p>A file containing the frequencies of all 21bp long sequences found in the Nmen_2594 genome: Nmen_2594.wfr</p> <p>A file containing all 21bp long sequences that occur more frequently than 55 times in the Nmen_2594 genome: Nmen_2594.overrep</p> <p>A file containing information on the RAYTs and their cooccurrence with different REPIN populations: prox.stats</p> <p>A file containing the nucleotide sequences of all NMAA_0235.faa relatives identified with BLAST+ in the <em>Neisseria </em>species: yafM_relatives.fna</p> <p>maxREPIN_[0-5] Contains the most frequent REPIN identified for each sequence type in each <em>Neisseria</em> strain.</p> <p> presAbs_[0-5].txt Contains for each strain information on the number of RAYTs, the number of REPINs, the master sequence, the number of master sequences, the entire REP/REPIN population size, the number of REPIN clusters that contain more than 10 sequences, all REPINs in the population as well as all REPINs that differ to the master sequences in at most three nucleotides.</p> <p>rayt_[strain name].tab contains location information for each identified RAYT relative for each strain. The files can be viewed with artemis.</p> <p>results.txt contains for each strain the frequency of the six identified 21bp long seeds.</p> <p>There is one folder called groupSeedSequences, which includes the data for identifying the most common 21 bp long sequences in <em>Neisseria meningitidis</em> WUE 2594. All 21bp long sequences in the genome that occur more frequently than 55 times are sorted into 6 sequence groups. These sequence groups are stored in the files Group_Nmen_2594_*.out and .out.fas. There is also a Nmen_2594_words.tab file, which contains the locations of all overrepresented 21bp long sequences in the Nmen_2594 genome. This file can be viewed in artemis (https://www.sanger.ac.uk/tool/artemis/) together with the Nmen_2594 genome file. The most common sequence in each group is used as a seed sequence to determine REPIN populations across all 130 genomes.</p> <p> </p> <p>For each genome there are six output folders (ending in _0 to _5), for each sequence group one.</p> <p>Each folder contains the following files:</p> <p>*.dd: Degree distribution of the REPIN network, where each REPIN is a node. A REPIN is connected to another REPIN if they differ in exactly one position. The degree distribution is a histogram of the number of connections of all the nodes. </p> <p>*.hist For the largest sequence cluster determined by mcl that consists of REPINs (two REPs in inverted orientation) this file contains the number of REPINs in each sequence class. Sequence class 0 is the master sequence. By definition the most common REPIN in the sequence population. Sequence class 1 contains all REPINs differing in exactly one position to the master sequence. Sequence class 2 contains REPINs differing in 2 positions etc.</p> <p>*.mcl Contains the clustering output by mcl. Each line contains the member of a cluster. Lines are sorted by cluster size.</p> <p>*.mw Contains the most common 21bp long sequence and its frequency in the genome, which is the basis for identifying first all related REP sequences and from those the REPINs formed by these REP sequences.</p> <p>*.nodes The identity and frequency of all REPINs and REP sequences for either all sequences or only for the largest sequence cluster.</p> <p>*.ss Contains REPINs and REP sequences as well as their positions in fasta format. Position information starts with the location in genome fasta file (first sequence is 0...) followed by the start and end position of the entire REPIN/REP sequence. </p> <p>*.ss.REP REP sequence information in fasta format.</p> <p>*.tab Location in tab format. Can be used to display locations of REPs and REPINs in the genome via artemis.</p> <p>*_[0-9].ss Contains REPIN/REP sequence information for each subcluster separately.</p> <p>*_[0-9].tab Contains the location of REP/REPINs for each subcluster separately for viewing in artemis.</p> <p>*allSeed.nw Contains network connections between nodes of all sequences. Can be used to view network in for example R or cytoscape together with the nodes file.</p> <p>*largestCluster.nodes Information on nodes only from the largest REPIN cluster.</p> <p>*largestCluster.ss *.ss file for the largest REPIN cluster.</p> <p>*largestCluster.tab *.tab file for the largest REPIN cluster.</p> <p>*_rayt_repin_prox.txt shows which REPIN/REP cluster is in proximity to any of the RAYT genes identified in the genome (within 200bp).</p> <p>And a subfolder that contains the complete sequences (including the variable region) for all identified REPs and REPINs.</p> <p>The dataset was generated using the following external tools:</p> <p>andi for tree building:</p> <p>B Haubold, F Klötzl, and P Pfaffelhuber. <strong>andi: fast and accurate estimation of evolutionary distances between closely related genomes.</strong> Bioinformatics, 2015 vol. 31 (8) pp. 1169-1175.</p> <p>MCL for REPIN population clustering:</p> <p>A J Enright, S Van Dongen, and C A Ouzounis. <strong>An efficient algorithm for large-scale detection of protein families.</strong> Nucleic Acids Research, 2002 vol. 30 (7) pp. 1575-1584.</p> <p>BLAST+ for identifying RAYT relatives in the different genomes:</p> <p>C Camacho, G Coulouris, V Avagyan, N Ma, J Papadopoulos, K Bealer, and T L Madden. <strong>BLAST+: architecture and applications.</strong> BMC Bioinformatics, 2009 vol. 10 (1) pp. 421-9.</p>
Dataset and codebook for the article by Gaume J, Bertholet N, McCambridge J, et al. Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial. JAMA Netw Open. 2022;5(10):e2237563. doi: 10.1001/jamanetworkopen.2022.37563
<p>Dataset and codebook for the article Gaume J, Bertholet N, McCambridge J, et al. <strong>Effect of a Novel Brief Motivational Intervention for Alcohol-Intoxicated Young Adults in the Emergency Department: A Randomized Clinical Trial</strong>. JAMA Netw Open. 2022;5(10):e2237563. doi: <a href="http://jamanetwork.com/article.aspx?doi=10.1001/jamanetworkopen.2022.37563">10.1001/jamanetworkopen.2022.37563</a></p> <p>The dataset contains all data needed to reproduce the results in the above cited article.</p> <p>Variable description and labels can be found in the codebook.</p> <p>Please refer to the published article and supplemental online content for further information about the data and the study procedures.</p>
Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"
<p>This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article. </p> <p>If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451). </p> <p>This dataset is organized in the following folders:</p> <p><strong>Snapshots_Figures_Main_Text.zip</strong>, that contains a README.txt file and:</p> <p><strong>- Figure_3</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man.</p> <p><strong>- Figure_4</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex.</p> <p>Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside <a href="https://zenodo.org/api/files/f3836540-b7b6-4820-87b3-7fa5dff7840c/Snapshots_Figures_Main_Text.zip">Snapshots_Figures_Main_Text.zip </a>for more information.</p>
Naphthalimide-Annulated [n]Helicenes: Red Circularly Polarized Light Emitters
<p>Original data to report (Abstract):<br> Two [<em>n</em>]heliceno-bis(naphthalimides) <strong>1</strong> and <strong>2</strong> (<em>n</em> = 5 and 6, respectively) where two electron-accepting naphthalimide moieties are attached at both ends of helicene core were synthesized by effective two-step strategy, and their enantiomers could be resolved by chiral stationary-phase high-performance liquid chromatography (HPLC). The single-crystal X-ray diffraction analysis of enantiopure fractions of <strong>1</strong> and <strong>2</strong> confirmed their helical structure, and together with experimental and calculated circular dichroism (CD) spectra, the absolute configuration was unambiguously assigned. Both <strong>1</strong> and <strong>2</strong> exhibit high molar extinction coefficients for the S<sub>0</sub>–S<sub>1</sub> transition and high fluorescence quantum yields (73% for <strong>1</strong> and 69% for <strong>2</strong>), both being outstanding for helicene derivatives. The red circularly polarized luminescence (CPL) emission up to 615 nm for <strong>2</strong> with CPL brightness (<em>B</em><sub>CPL</sub>) up to 66.5 M<sup>–1</sup> cm<sup>–1</sup> demonstrates its potential for applications in chiral optoelectronics. Time-dependent density functional theory (TD-DFT) calculations unambiguously showed that the large transition magnetic dipole moment |<em>m</em>| of <strong>2</strong> is responsible for its high absorbance dissymmetry (<em>g</em><sub>abs</sub>) and luminescence dissymmetry (<em>g</em><sub>lum</sub>) factor.</p>
A Simple Strategy to Eliminate Glycation Bias in the Relative Quantification of Protein N-glycosylation
<p><strong>Contents</strong></p> <p>Supplementary files for “A Simple Strategy to Eliminate Glycation Bias in the Relative Quantification of Protein <em>N</em>-glycosylation” by Esser-Skala et al (2020):</p> <ul> <li> <p><em>cafog_raw_data.tar.gz</em>: Raw data for denosumab and NISTmAb.</p> </li> <li> <p><em>cafog_source_code.zip</em>: Supplementary file 1 from the manuscript. This ZIP archive contains the source code of CAFOG.</p> </li> <li> <p><em>data.zip</em>: Supplementary file 2 from the manuscript. Files in this ZIP archive allow to reproduce all results presented in the manuscript.</p> </li> </ul> <p> </p> <p><strong>Changelog</strong></p> <ul> <li>1.1.0 – 2023-05-25 <ul> <li>added supplementary files 1 and 2 mentioned in the manuscript, since those were not published along with the manuscript</li> </ul> </li> <li>1.0.0 – 2020-01-30 <ul> <li>initial release</li> </ul> </li> </ul>
The datasets for "The Cosmos in its Infancy: JADES Galaxy Candidates at z > 8 in GOODS-S and GOODS-N"
<p>The JADES dataset of z > 8 galaxies and galaxy candidates accompanying the paper "The Cosmos in its Infancy: JADES Galaxy Candidates at z > 8 in GOODS-S and GOODS-N" (Hainline et al.). This paper was accepted in ApJ, January 2024. We also include the EAZY template set used for these fits. Please see the README files for descriptions of the datasets. </p>
Seaweed C:N:P Global Dataset
<p>Seaweed C:N:P ratios found in the peer-reviewed literature and previously unpublished data, current to 2022. </p> <p>This is the accompanying dataset for “SEAWEED BIOGEOCHEMISTRY: GLOBAL ASSESSMENT OF C:N AND C:P RATIOS AND IMPLICATIONS FOR OCEAN AFFORESTATION” (Sheppard et al., in press). Methods for collection of the dataset are found therein. </p> <p>For queries, please contact dataset creator and caretaker, Emily Sheppard. emily.sheppard@utas.edu.au </p>
Initial Conditions for ATOM-COBALT dynamic N:P model simulations in GBC paper
<p>Adjustment of standard initial conditions file for COBALT simulations to add dynamic phytoplankton P fields. </p>
Optimized stationary points on the potential energy surfaces of the N(2D) + CH2CHCN and CN + CH2CHCN reactions
<p>This Zip file contains the cartesian coordinates of optimized stationary points on the potential energy surfaces (PESs) of two reactions: N(<sup>2</sup>D) + CH<sub>2</sub>CHCN (acrylonitrile) and CN + CH<sub>2</sub>CHCN.</p> <p>The PES has been published in our article “A Theoretical Investigation of the Reactions of N(<sup>2</sup>D) and CN with Acrylonitrile and Implications for the Prebiotic Chemistry of Titan”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2022</strong>, 13378, 246-259), that can be found in https://doi.org/10.1007/978-3-031-10562-3_18 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Optimized stationary points on the potential energy surfaces of the N(2D)+ C2H4 and N(2D)+ CH2CHCN reactions
<p>This Zip file contains the cartesian coordinates of optimized stationary points on the potential energy surfaces (PESs) of two reactions: N(<sup>2</sup>D)+ C<sub>2</sub>H<sub>4</sub> and N(<sup>2</sup>D)+ CH<sub>2</sub>CHCN.</p> <p>The PESs have been published in our article “Computational Investigation of the N(<sup>2</sup>D)+ C<sub>2</sub>H<sub>4</sub> and N(<sup>2</sup>D)+ CH<sub>2</sub>CHCN Reactions: Benchmark Analysis and Implications for Titan’s Atmosphere”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2023</strong>, 14105, 705-717), that can be found in https://doi.org/10.1007/978-3-031-37108-0_45 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Sediment, C, N, and P Concentrations and Burial Rates in Three Southwestern Ohio Retention Ponds: 2006-2019
These datasets correspond to Rogers et al (2022) “Temporal patterns in sediment, carbon, and nutrient burial in ponds associated with changing agricultural tillage” published in Biogeochemistry (DOI: 10.1007/s10533-022-00916-w). We sampled three retention ponds in southwest Ohio in 2019 to compare sediment, carbon, nitrogen, and phosphorous burial rates to those calculated in 2006 to see the effect a watershed-wide shift to conservation tillage and to estimate the value of the ecosystem services these ponds provide via sequestration. Two methods were used to calculate burial rates: simple mean and spatially explicit. All datasets use simple mean except for the data set named “Spatially Explicit Sediment C N P Burial in SW OH Retention Ponds 2019”, which uses the spatially explicit method. For more information, please refer to our paper.
Soil extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Fernow Experimental Forest, WV.
Our objective was to detect possible differences in N fertilization responses of soil extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated 10 x 10 m plots in both the reference and N fertilized watersheds (N=24 plots) at the Fernow Experimental Forest, Parsons, WV. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). In addition, we measured microbial allocation to complex C degrading oxidative enzymes phenol oxidase and peroxidase. The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils during the growing season in 2017.
N cycling summary 2020-2022 of annually burned bison, cattle and ungrazed experimental watersheds on upland tallgrass prairie soils at the Konza Prairie Biological Station
Nitrogen (N) is a necessary element of soil fertility and a limiting nutrient in tallgrass prairie but grazers like bison and cattle can also recycle N. Bison and cattle impact the nitrogen (N) cycle by digesting forage that is consumed, and recycled back to the soil in a more available forms stimulating soil microbial N cycling activities. Yet we do not know how both grazers comparatively affect N cycling in tallgrass prairie. Thus, we investigated if bison cattle had similar impacts on N cycling in annually burned tallgrass prairie relative to ungrazed conditions over a 3-year period (2020-2022) at the Konza Prairie Biological Station. We took soil samples to investigate soil data: pH, soil water content, mineralized N, nitrification potential, denitrification potential and extracellular enzyme assays on upland soils of the Florence-Benfield complex soil map during the summer growing season from 2020 to 2022 on bison, cattle and ungrazed experimental watersheds at the Konza Prairie Biological Station. Soil sampling was undertaken once late in each summer growing season from 2020-2022. These years spanned a range of above-average rainfall (2020) to well below average (2021) and slightly below average (2022). We sampled along four 10-m transects, parallel to long-term plant sampling transects in each experimental watershed, in two bison grazed (N1A and N1B), two cattle grazed (C1A and C1B), and two ungrazed (1D and SpB) watersheds, all of which are burned annually.
Relyea, R. A., and N. Mills. 2001. Predator-induced stress makes the pesticide carbaryl more deadly to grey treefrog tadpoles (Hyla versicolor). PNAS 98:2491-2496.
Global declines in amphibians likely have multiple causes, including widespread pesticide use. Our knowledge of pesticide effects on amphibians is largely limited to short-term (4-d) toxicity tests conducted under highly artificial conditions to determine lethal concentrations (LC50). We found that if we used slightly longer exposure times (10–16 d), low concentrations of the pesticide carbaryl (3–4% of LC504-d) killed 10–60% of gray treefrog (Hyla versicolor) tadpoles. If predatory cues also were present, the pesticide became 2–4 times more lethal, killing 60–98% of tadpoles. Thus, under more realistic conditions of increased exposure times and predatory stress, current application rates for carbaryl can potentially devastate gray treefrog populations. Further, because predator-induced stress is ubiquitous in animals and carbaryl’s mode of action is common to many pesticides, these negative impacts may be widespread in nature.
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.