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Data from: Intra-specific differences in cognition: Bumblebee queens learn better than workers
<p><span>Species' cognitive traits are shaped by their ecology, and even within a species, cognition can </span><span><span>reflect the behavioural requirements of individuals with diffferent roles</span></span><span>. Social insects have a number of discrete roles (castes) within a colony, and thus offer a useful system to determine how ecological requirements shape cognition. Bumblebee queens are a critical point in the lifecycle of their colony, since its future success is reliant on a single individual's ability to learn about floral stimuli while finding a suitable nest site; </span><span><span>thus, one might expect particularly adept learning capabilities at this stage</span></span><span>. I compared wild </span><i><span>Bombus vosnesenskii</span></i><span> queens and workers on their ability to learn a colour association and found that queens performed better than workers. In addition, queens of another species, </span><i><span>B. insularis, </span></i><span>a cuckoo species with a different lifecycle but similar requirements at this stage, performed equally well as the non-parasitic queens. To control for differences in foraging experience, I then repeated this comparison with lab-based </span><i><span>B. impatiens</span></i><span>, and found that </span><span><span>unmated</span></span><span> queens performed better than workers. These results add to the body of work on how ecology shapes cognition and opens the door to further research in comparative cognition using wild bees.</span></p>
F in Seed-infesting chalcids of the genus Megastigmus Dalman, 1820 (Hymenoptera: Torymidae) native and introduced to the West Palearctic region: taxonomy, host specificity and distribution
F. 2. Lateral view of head, M. pictus X, ex. Larix decidua, Poland. an, anellus; clv, clava;
F in Seed-infesting chalcids of the genus Megastigmus Dalman, 1820 (Hymenoptera: Torymidae) native and introduced to the West Palearctic region: taxonomy, host specificity and distribution
F. 1. Dorsal view of body, Megastigmus amicorum W, ex. Juniperus phoenicea, Portugal.
F in Seed-infesting chalcids of the genus Megastigmus Dalman, 1820 (Hymenoptera: Torymidae) native and introduced to the West Palearctic region: taxonomy, host specificity and distribution
F. 9. Electroscan view of exserted part of ovipositor, M. pistaciae X, ex. Pistacia lentiscus,
Visualizing the organization and differentiation of the male-specific nervous system of C. elegans
<p>Image volumes and annotations for male NeuroPAL expression.</p> <p>The following image volumes were annotated by Tessa Tekieli and used by Amin Nejatbakhsh to build the male C. <em>elegans</em> atlas for:<br> "Visualizing the organization and differentiation of the male-specific nervous system of C. elegans".</p> <p>The publication is available here:<br> https://journals.biologists.com/dev/article-abstract/doi/10.1242/dev.199687/271902/Visualizing-the-organization-and-differentiation</p> <p>These image files can be viewed with the NeuroPAL ID software, available at:<br> https://www.hobertlab.org/neuropal/<br> OR<br> https://github.com/amin-nejat/CELL_ID</p> <p>This software was provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. <em>elegans</em>".<br> The publication is available here:<br> https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2</p> <p>Please cite the NeuroPAL publication when using the software.</p>
Text-fig. 5. Length-width scatter diagrams of upper molars of Sayimys giganteus from Keseköy. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 5. Length-width scatter diagrams of upper molars of Sayimys giganteus from Keseköy.
Text-fig. 4. Length-width scatter diagrams of lower molars of Sayimys giganteus from Keseköy. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 4. Length-width scatter diagrams of lower molars of Sayimys giganteus from Keseköy.
Text-fig. 2. Methods of taking measurements. in An Exceptional Large Sample Of The Early Miocene Ctenodactyline Rodent Sayimys Giganteus, Specific Variation And Taxonomic Implications
Text-fig. 2. Methods of taking measurements.
Dietary availability determines metabolic conversion of long-chain polyunsaturated fatty acids in spiders: a dual compound-specific stable isotope approach
<p>The following dataset contains fatty acid contents (in mg.g<sup>-1</sup> and in %), stable isotopes (‰), and compound specific isotopic analyses of carbon and hydrogen (‰) data for insects (terrestrial and semi-aquatic) and spiders collected around Lake Lunz (47°85'N, 15°05'E), Austria from June to September 2020. Measurements were done after storage at -80°C for 2 hours, and freeze drying (24h), followed by taxonomic identification. Analytical details can be found in "Dietary availability determines metabolic conversion of long-chain polyunsaturated fatty acids in spiders: a dual compound-specific stable isotope approach" by Mathieu-Resuge, Margaux; Pilecky, Matthias; Twining, Cornelia; Martin-Creuzburg, Dominik; Parmar, Tarn-Preet; Vitecek, Simon; Kainz, Martin. Oikos (2021), DOI: 10.1111/oik.08513</p>
Research data supporting: "Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly"
<p>This repository contains the set of data shown in the paper "<em>Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly</em>", published on <em>ACS Nano</em> (DOI: 10.1021/acsnano.1c0500).</p> <p>All the input data needed to run the simulations and get the results are organized in 5 different folders:</p> <ul> <li> <p><code>1-MinimlisticCGModel/</code></p> <p>in this folder there are the Gromacs and PLUMED input files for reproducing the minimalistic coarse-grained model shown in the article.</p> </li> <li> <p><code>2-AAandFineCGModels/</code></p> <p>the folder contains the atomistic (<code>monomerAA/</code>) and the coarse-grained Martini "wet" (<code>monomerGCWet/</code>) input files for modelling the Original monomer with one carboxyl group. The coarse-grained Martini "dry" (<code>monomerCGDry/</code>) model is reported for the Original monomer at the three different charged states.</p> </li> <li> <p><code>3-UnbiasedMD/</code></p> <p>this folder includes the Gromacs input files needed to reproduce the Unbiased simulations as shown in the article.</p> </li> <li> <p><code>4-MetaD/</code></p> <p>this folder incorporates the Gromacs and PLUMED input files necessary to reproduce both the Infrequent CG Metadynamics simulations (<code>InfrequentMetaD/</code>) and the Multiple-walker CG Metadynamics simulations (<code>MultipleWalkerMetaD/</code>)</p> </li> <li> <p><code>5-InSilico/</code></p> <p>in this folder all the files used to run the simulations about the exoliation experiments (<code>Original/</code>, <code>Type-1/</code>, <code>Type-2/</code>, <code>Type-3/</code>, <code>Type-4/</code>) are reported. Every subfolder contains all input files for the three different charged monomers (<code>Olig1-/</code>, <code>Olig2-/</code>, <code>Olig3-/</code>).</p> </li> </ul>
Association of specific biotypes in patients with Parkinson's disease and disease progression
<p><span><b>Objective </b></span></p> <p><span>To identify biotypes in newly diagnosed Parkinson's disease patients and test whether these biotypes could explain inter-individual differences in longitudinal progression. </span></p> <p><span><b>Methods</b></span></p> <p><span>In this longitudinal analysis, we use a data-driven approach clustering PD patients from the Parkinson's Progression Markers Initiative (PPMI) (n = 314, age = 61.0 ± 9.5, 34.1% female, 5 years follow-up). Voxel-level neuroanatomical features were estimated using deformation-based morphometry (DBM) of T1-weighted MRI. Voxels whose deformation values were significantly correlated (<i>P</i> < 0.01) with clinical scores (MDS-UPDRS-Parts I-III, MDS-UPDRS-total, tremor score, and postural instability and gait difficulty score) at baseline were selected. Then, these neuroanatomical features were subjected to hierarchical cluster analysis. Changes in the longitudinal progression and neuroanatomical pattern were compared between different biotypes. </span></p> <p><span><b>Results</b></span></p> <p><span>Two neuroanatomical biotypes were identified: (i) biotype 1 (n = 114) with subcortical brain volume as smaller than heathy controls; (ii) biotype 2 (n = 200) with subcortical brain volumes larger than heathy controls. Biotype 1 had more severe motor impairment, autonomic dysfunction, and very much worse REM sleep behavior disorder than biotype 2 at baseline. Although disease duration at initial visit and follow-up were similar between biotypes, PD patients with smaller subcortical brain volume had poorer prognosis, with more rapid decline in several clinical domains and in dopamine functional neuroimaging over an average of five years. </span></p> <p><span><b>Conclusion</b></span></p> <p><span>Robust neuroanatomical biotypes exist in PD with distinct clinical and neuroanatomical pattern. These biotypes can be detected at diagnosis, and predict the course of longitudinal progression, which should benefit trial design and evaluation.</span></p>
MCMC output files for: Quantitative characterization of population-wide tissue- and metabolite-specific variability in perchloroethylene toxicokinetics in male mice
<p>Quantification of inter-individual variability is a continuing challenge in risk assessment, particularly for compounds with complex metabolism and multi-organ toxicity. Toxicokinetic variability for perchloroethylene (perc) was previously characterized across three mouse strains and in one mouse strain with various degrees of liver steatosis. To further characterize the role of genetic variability in toxicokinetics of perc, we applied Bayesian population physiologically-based pharmacokinetic (PBPK) modeling to the data on perc and metabolites in blood/plasma and tissues of male mice from 45 inbred strains from the Collaborative Cross (CC) mouse population. After identifying the most influential PBPK parameters based on global sensitivity analysis, we fit the model with a hierarchical Bayesian population analysis using Markov chain Monte Carlo simulation. We found that the data from three commonly used strains were not representative of the full range of variability in perc and metabolite blood/plasma and tissue concentrations across the CC population. Using inter-strain variability as a surrogate for human inter-individual variability, we calculated dose-dependent, chemical-, and tissue-specific toxicokinetic variability factors (TKVFs) as candidate science-based replacements for the default uncertainty factor for human toxicokinetic variability of 10<sup>0.5</sup>. We found that TKVFs for glutathione conjugation metabolites of perc showed the greatest variability, often exceeding the default, whereas those for oxidative metabolites and perc itself were generally less than the default. Overall, we demonstrate how a combination of a population-based mouse model such as the CC with Bayesian population PBPK modeling can reduce uncertainty associated with toxicokinetic human variability by deriving the chemical-specific adjustment factors needed to increase accuracy and precision in quantitative risk assessment.</p>
Figure 4 from: Scholes D, Suarez A, Smith A, Johnston S, Paige K (2014) Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis. Journal of Hymenoptera Research 37: 113-126. https://doi.org/10.3897/jhr.37.6824
Figure 4 - Endopolyploidy of organs by functional system. Cycle value of organs within each functional system (abbreviations "Digest.": digestive; "Reprod.": reproductive). Shown are means ± standard error across 5 replicates of each organ within each system. Systems are presented in descending order of mean cycle value. Bars labeled with letters denote statistical groups determined by Tukey's Studentized range test (significance tested at αfamily = 0.05). Numbers above each bar indicate the number of organs that comprise each respective system.
Figure 2 from: Scholes D, Suarez A, Smith A, Johnston S, Paige K (2014) Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis. Journal of Hymenoptera Research 37: 113-126. https://doi.org/10.3897/jhr.37.6824
Figure 2 - Differences in endopolyploidy among body segments. Percentage of endopolyploid (4C, 8C, 16C, 32C, and 64C) nuclei for each body segment. Shown are means ± standard error across 5 individuals. Letters indicate significant (α = 0.05) differences among body segments. Significance was determined by analysis of arc-sine square-root transformed proportions.
Figure 1 from: Scholes D, Suarez A, Smith A, Johnston S, Paige K (2014) Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis. Journal of Hymenoptera Research 37: 113-126. https://doi.org/10.3897/jhr.37.6824
Figure 1 - Distribution of ploidy among organs. Percentage of nuclei at each of the ploidy levels observed (2C–64C) within each organ analyzed. Organs are presented by body segment in descending order of cycle value.
Figure 3 from: Scholes D, Suarez A, Smith A, Johnston S, Paige K (2014) Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis. Journal of Hymenoptera Research 37: 113-126. https://doi.org/10.3897/jhr.37.6824
Figure 3 - Cycle values for each organ analyzed within each body segment. Shown are means ± standard error across 5 replicates of each organ within each body segment. Organs are presented in descending order of mean cycle value. Bars labeled with letters denote statistical groups determined by Tukey's Studentized range test (significance tested at αfamily = 0.05).
Figure 1 from: Rakauskas R, Havelka J, Zaremba A (2013) Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp.) collected from different hosts in Europe (Hemiptera, Aphididae). ZooKeys 319: 255-267. https://doi.org/10.3897/zookeys.319.4251
Figure 1 - Maximum likelihood (ML) tree showing phylogenetic relationships among three Hyalopterus species based on partial sequences of mitochondrial COI (564 positions in final set). Numbers above branches indicate support of NJ (left) and MP (right) bootstrap test with 1000 replicates, and numbers below branches indicate support of ML (left) bootstrap test with 1000 replicates and posterior probabilities of BI analysis (right). Samples used for the discriminant analysis with a priori specified group membership followed by the construction of identification key are asterisked (*). The remaining samples were used for the post hoc classification. Sample numbers are the same as given in Table 1, together with the abbreviated symbol of respective country: BG Bulgaria, HU Hungary, LT Lithuania, RO Romania, SK Slovakia.
Figure 3 from: Rakauskas R, Havelka J, Zaremba A (2013) Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp.) collected from different hosts in Europe (Hemiptera, Aphididae). ZooKeys 319: 255-267. https://doi.org/10.3897/zookeys.319.4251
Figure 3 - Dendrogram of hierarchical cluster analysis based on 17 morphological characters (squared Mahalanobis distances) using unweighted pair-group average linkage among 29 samples of Hyalopterus. Sample numbers the same as in Table 1. ar samples from Prunus armeniaca, d Prunus domestica, du Prunus dulcis, p Prunus persica, ph Phragmites communis.
Figure 2 from: Rakauskas R, Havelka J, Zaremba A (2013) Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp.) collected from different hosts in Europe (Hemiptera, Aphididae). ZooKeys 319: 255-267. https://doi.org/10.3897/zookeys.319.4251
Figure 2 - Scatter-plot of the individual canonical scores of the first two canonical variates discriminating 21 samples of Hyalopterus collected from different host plants in five European countries (Bulgaria, Hungary, Lithuania, Romania, Slovakia).
Figure 4 from: Rakauskas R, Havelka J, Zaremba A, Bernotienė R (2014) Mitochondrial COI and morphological evidence for host specificity of the black cherry aphids Myzus cerasi (Fabricius, 1775) collected from different cherry tree species in Europe (Hemiptera, Aphididae). ZooKeys 388: 1-15. https://doi.org/10.3897/zookeys.388.7034
Figure 4 - Plot of the mean scores of the individual LDF values (number of specimens per sample is given in Table 1) plotted against the mean body length for 30 samples of Myzus cerasi (normal font in Table 1) used to evaluate effectiveness of the eventual identification key. The icons are color-coded to match the COI haplotypes. Samples cluster in accordance with winter host plant and COI haplotype (haplotype number is given in parentheses, see Table 2 for haplotype information).
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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.