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4,753 results for “SHAPE”
Processed Data of "Selective laser melting of a Fe-Si-Cr-B-C-based complex-shaped amorphous soft-magnetic electric motor rotor with record dimensions"
<p>This data set includes the processed data of the pubblication. ABSTRACT: A record large amorphous rotor bearing an intricate 3D-geometry is produced through additive manufacturing via selecting laser melting using a powder of a traditional bulk metallic glass-forming composition of the Fe-Si-Cr-B-C system. Not only does this technique overcome the technical limitations characteristic of casting processes for amorphous alloys, but the possibility to print complex 3D geometries is expected to greatly facilitate the channeling of the magnetic flux, when such component is used as a rotor in an electric machine. The as-built part is characterized in comparison to the powder material as well as as-spun ribbons using a wide range of complementary techniques, including synchrotron x-ray diffraction, calorimetry, electron microscopy as well as room temperature ferromagnetic and hardness testing. The built part has extraordinarily high values of hardness (877 HV) and remarkable high magnetic susceptibility (9.17). This latter feature leads to a better magnetic response in the presence of an external magnetic field evidenced by a faster approach to saturation. The coercivity is small (0.51 kA/M) and the magnetic saturation relatively high (1.29 T). In addition, a large anisotropic effect on the magnetization reaction in connection with the partial crystallization in the melt pool areas is investigated experimentally.</p>
SHAPE datasets from manuscript: Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1
<p>Normalized SHAPE reactivity for the MALT1 M1 minigene RNA constructs (wildtype, variant 1, and variant 2) reported in the manuscript titled 'Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of <em>MALT1'</em> .</p> <p> </p>
Acaulescence promotes speciation and shapes the distribution patterns of palms in Neotropical seasonally dry habitats
<p>Rainforests have been a source of lineages to open and seasonally dry habitats throughout Angiosperm evolution, especially in the Neotropics. However, the underlying mechanisms that allow such shifts remain poorly understood at large spatial scales. Here, we test whether acaulescence (an underground stem or a very short stem concealed in the ground) has affected the colonization and speciation in Neotropical seasonally dry habitats by <span>cocosoid palms</span> (Cocoseae). Acaulescent species maintain their growth underground, which increases their chances of survival from prolonged seasonal dry season and frequent fires. We use an integrative approach based on trait‐dependent diversification models, phylogenetic comparative methods, and ecological niche models. We found that shifts towards acaulescent growth form were accompanied by evolutionary transitions to seasonally dry habitats. Acaulescent lineages had higher speciation rates than non-acaulescent ones.<i> </i>However, the interaction between acaulescence and seasonally dry habitats had no significant effect on Cocoseae speciation rates. Acaulescent palms are primarily distributed in Neotropical seasonally dry habitats and non-acaulescent palms are concentrated in Amazonian rainforests. Our results suggest that an underground stem, with high carbohydrate and water storage capacity, is a preadaptation by which rainforest lineages were able to colonize and diversify in new fire-prone, increasingly seasonal and drier adaptive zones. The projected global expansion of dry seasonal habitats requires an understanding of how drought-avoidance functional traits evolve and how they are linked to seasonally dry habitats. Our results are, thus, a step forward in determining plant response mechanisms to drier and seasonal conditions.</p>
Simulation outputs used in "Individual variation in dispersal, and its sources, shape the fate of pushed vs. pulled range expansions"
<p>Simulation outputs used in "Individual variation in dispersal, and its sources, shape the fate of pushed vs. pulled range expansions" (by Maxime Dahirel, Chloé Guicharnaud and Elodie Vercken)</p> <p>This is a copy for archiving purposes of the saved outputs from a NetLogo simulation model of range expansions, used in the analyses described in the following GitHub repository: https://github.com/mdahirel/pushed-pulled-2020-heritability-IBM (Zenodo archive: https://doi.org/10.5281/zenodo.5830993)</p> <p>This .csv file is the final output of the "generate_simulations" code in that repo, and feeds into in the "analyse_simulations" and "supplementary" codes. It is meant to be copied in the NetLogo_output folder of the aforementioned repo after download, in case one:</p> <p>- wants to check our analysis code</p> <p>- and does not want/ have time to re-run the simulations from scratch</p> <p>For any other information, including on the contents of the csv, please see the aforementioned repository</p> <p> </p>
TransProteus, Predicting 3D shapes, masks, and properties of materials, liquids, and objects inside transparent containers from images
<p>We present TransProteus, a dataset, for predicting the 3D structure and properties of materials, liquids, and objects inside transparent vessels from a single image without prior knowledge of the image source and camera parameters. Manipulating materials in transparent containers is essential in many fields and depends heavily on vision. This work supplies a new procedurally generated dataset consisting of 50k images of liquids and solid objects inside transparent containers. The image annotations include 3D models and material properties (color/transparency/roughness...) for the vessel and its content. The synthetic (CGI) part of the dataset was procedurally generated using 13k different objects, 500 different environments (HDRI), and 1450 material textures (PBR) combined with simulated liquids and procedurally generated vessels. In addition, we supply 104 real-world images of objects inside transparent vessels with depth maps of both the vessel and its content.</p> <p>Note that there are two files here:</p> <p><a href="https://zenodo.org/api/files/12b013ca-36be-4156-afd4-c93b5fa22093/Tansproteus_SimulatedLiquids2_New_No_Shift.7z">Transproteus_SimulatedLiquids2_New_No_Shift.7z</a></p> <p>and</p> <p><br> <a href="https://zenodo.org/api/files/2b833de0-4007-4682-ad5b-5e08bd63597e/TranProteus2.7z?versionId=f16e7126-8750-41f7-99e6-d35ca60399cc">TranProteus2.7z </a>, contain subset of the virtual CGI data set.</p> <p>https://zenodo.org/api/files/12b013ca-36be-4156-afd4-c93b5fa22093/Tansproteus_SimulatedLiquids2_New_No_Shift.7z</p> <p><a href="https://zenodo.org/api/files/2b833de0-4007-4682-ad5b-5e08bd63597e/TransProteus_RealSense_RealPhotos.7z">TransProteus_RealSense_RealPhotos.7z </a>: Contain real-world photos scanned with real sense with depth map of both the vessel and its content</p> <p>See ReadMe file in side the downloaded files for more details</p> <p>The full dataset (>100gb) can be found here:</p> <p><a href="https://e.pcloud.link/publink/show?code=kZfx55Zx1GOrl4aUwXDrifAHUPSt7QUAIfV">https://e.pcloud.link/publink/show?code=kZfx55Zx1GOrl4aUwXDrifAHUPSt7QUAIfV</a></p> <p>https://<a href="http://icedrive.net/1/6cZbP5dkNG">icedrive.net/1/6cZbP5dkNG</a></p> <p>See: <a href="https://arxiv.org/pdf/2109.07577.pdf"> https://arxiv.org/pdf/2109.07577.pdf</a> for more details</p> <p><strong><a href="https://zenodo.org/record/4736111#.YVOAx3tE1H4">**This dataset is complementary to LabPics dataset with 8k real images of materials in vessels in chemistry labs, medical labs, and other settings. The LabPics dataset can be downloaded from here:</a></strong></p> <p><strong><a href="https://zenodo.org/record/4736111#.YVOAx3tE1H4">https://zenodo.org/record/4736111#.YVOAx3tE1H4</a></strong></p> <p> </p> <p><strong>************************************************************************************</strong></p> <p><a href="https://zenodo.org/api/files/12b013ca-36be-4156-afd4-c93b5fa22093/Tansproteus_SimulatedLiquids2_New_No_Shift.7z">Transproteus_SimulatedLiquids2_New_No_Shift.7z </a>and <a href="https://zenodo.org/api/files/2b833de0-4007-4682-ad5b-5e08bd63597e/TranProteus2.7z?versionId=f16e7126-8750-41f7-99e6-d35ca60399cc">TranProteus2.7z</a></p> <p>The two folders contain relatively similar data styles.<br> The data in No_Shift contain images that were generated with no camera shift in the camera paramters. If you try to predict 3d model from an image as a depth map, this is easier to use (Otherwise, you need to adapt the image using the shift). For all other purposes, both folders are the same, and you can use either or both. In addition, a real image dataset for testing is given in the RealSense file.</p> <p> </p> <p> </p> <p> </p>
Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island
<p>Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai`i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.</p>
Experimental assessment of the mixing quality in a circular cross-sectional t-shaped mixer for the precipitation of sparingly soluble compounds
<p>Precipitation processes have been successfully proved to be a feasible route to extract high-value products from wastes. However, reactive crystallization is characterized by fast kinetics, especially when highly concentrated solutions are used or sparingly soluble compounds precipitate, thus requiring a fast mixing of the reactants. In this context, T-shaped mixers have been extensively investigated both experimentally and numerically as a mean to achieve a rapid reactants homogenization. Many research efforts have been focused on the analysis of rectangular cross-sectional T-shaped mixers, while less attention has been devoted to the study of circular cross-sectional ones. In the present work, mixing times in a 3 mm circular cross-sectional T-shaped mixer have been optically estimated by exploiting the extremely fast neutralization reaction between sodium hydroxide and hydrochloric acid solutions. Reynolds numbers ranging between 1,000 and 6,000 were investigated. Mixing phenomena were (i) captured by detecting the colour change of a pH indicator by means of a high frame rate camera and (ii) quantified by a suitable image analysis technique. The assessed mixing times were found in accordance with available data in the literature.</p>
Local adaptation and archaic introgression shape global diversity at human structural variant loci
<p>Supporting data associated with the manuscript "Local adaptation and archaic introgression shape global diversity at human structural variant loci". These include:</p> <ul> <li>structural variant genotypes (Paragraph; <a href="https://github.com/Illumina/paragraph">https://github.com/Illumina/paragraph</a>)</li> <li>eQTL mapping results (fastqtl permutation pass; see <a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a> for column descriptions)</li> <li>eQTL fine-mapping results (CAVIAR; see <a href="http://genetics.cs.ucla.edu/caviar/index.html">http://genetics.cs.ucla.edu/caviar/index.html</a>)</li> <li>structural variant selection scan results (Ohana; <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</li> </ul> <p>Description of files in this directory:</p> <p><strong>Structural variant genotypes</strong></p> <p><code>SVs_paragraphFormat.vcf.gz</code> - merged long-read structural variant calls</p> <p><code>SVs_1KGP_pgGTs.vcf.gz</code> - genotypes for 1000 Genomes samples in VCF format</p> <p><strong>eQTL mapping results</strong></p> <p><code>fastqtl_out.txt</code> - results from fastQTL permutation pass; see <a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a> for column descriptions</p> <p><code>caviar_out.txt</code> - results from fine-mapping SNPs and SVs at significant SV eQTL loci with CAVIAR. Description of columns:</p> <ul> <li>query_sv: SV that was a significant eQTL and underwent fine-mapping</li> <li>gene_id: gene exhibiting an expression association with the query_sv</li> <li>var_id: variant (SNV or SV) that was tested for expression association with the above gene in the fine-mapping analysis</li> <li>var_in_credible_causal_set: Boolean variable denoting whether the above variant is in the 95% credible causal set</li> <li>prob_in_pcausal_set: the amount that this variant contributes to 95% credible causal set</li> <li>causal_post_prob: the posterior probability that the variant is causal in the expression association</li> </ul> <p><strong>Structural variant selection scan results</strong></p> <p><code>chr21_pruned_50_Q.matrix</code> - admixture proportion matrix (generated by Ohana; <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</p> <p><code>chr21_pruned_50_F.matrix</code> - matrix of inferred ancestral allele frequencies (generated by Ohana)</p> <p><code>chr21_pruned_50_C.matrix</code> - matrix of ancestry component covariances (generated by Ohana) Entries of the matrix can be modified to produce "selection hypothesis" matrices where allele frequencies are allowed to vary in one ancestry component (<a href="https://github.com/jade-cheng/ohana/wiki/Population-or-ancestry-specific-selection-scan">https://github.com/jade-cheng/ohana/wiki/Population-or-ancestry-specific-selection-scan</a>).</p> <p><code>selscan_50_k8_p*.txt.gz</code> - raw output of Ohana selscan (see <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</p> <p><code>selscan_res.txt.gz</code> - Ohana selection scan results. These results have been filtered to exclude SVs that have low genotyping rates (<50% of samples), violate Hardy-Weinberg equilibrium expectations (excess of heterozygotes) in more than half of populations, or have extreme global log likelihood estimate (LLE) values. Description of columns:</p> <ul> <li>ID: SV ID</li> <li>#CHROM: SV chromosome</li> <li>POS: SV start position</li> <li>SVLEN: SV length (negative for deletions)</li> <li>step: number of steps needed to interpolate between genome-wide and selection hypothesis models</li> <li>lle_ratio: likelihood ratio statistic (LRS) of the genome-wide vs. selection hypothesis model</li> <li>global-lle: log likelihood of the genome-wide model</li> <li>local-lle: log likelihood of the selection hypothesis model</li> <li>f-pop0: inferred allele frequency in ancestry component 0</li> <li>f-pop1: inferred allele frequency in ancestry component 1</li> <li>f-pop2: inferred allele frequency in ancestry component 2</li> <li>f-pop3: inferred allele frequency in ancestry component 3</li> <li>f-pop4: inferred allele frequency in ancestry component 4</li> <li>f-pop5: inferred allele frequency in ancestry component 5</li> <li>f-pop6: inferred allele frequency in ancestry component 6</li> <li>f-pop7: inferred allele frequency in ancestry component 7</li> <li>ancestry_component: ancestry component tested by the selection hypothesis model. Note that we have added 1 to the ancestry component numbers to match the terminology used in paper (which orders the components from 1-8 rather than 0-7 for interpretability)</li> <li>snp_perc: SV's percentile in the LRS distribution for frequency-matched SNPs</li> <li>p_nominal: nominal p-value calculated from the likelihood ratio</li> <li>p_adj: adjusted p-value calculated from the likelihood ratio</li> </ul> <p> </p>
Analysis of the alveolar shape in 3D
<p>Compressed version of the GitLab Repository containing the original data for the research article "Analysis of the alveolar shape in 3D".</p> <p>Link to the repository on GitLab: https://gitlab.com/AReimelt/analysis-of-the-alveolar-shape-in-3d</p>
Data from: Global plant-frugivore trait matching is shaped by climate and biogeographic history
<p>Species interactions are influenced by the trait structure of local multi-trophic communities. However, it remains unclear whether mutualistic interactions, in particular, can drive trait patterns at the global scale, where climatic constraints and biogeographic processes gain importance. Here we evaluate global relationships between traits of frugivorous birds and palms (<em>Arecaceae</em>), and how these relationships are affected, directly or indirectly, by assemblage richness, climate and biogeographic history. We leverage a new and expanded gape size dataset for nearly all avian frugivores, and find a positive relationship between gape size and fruit size, that is, trait matching, which is influenced indirectly by palm richness and climate. We also uncover a latitudinal gradient in trait matching strength, which increases towards the tropics and varies among zoogeographic realms. Taken together, our results suggest trophic interactions have consistent influences on trait structure, but that abiotic, biogeographic and richness effects also play important, though sometimes indirect, roles in shaping the functional biogeography of mutualisms.</p>
Dataset for Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria
<p>This repository hosts data for the paper entitled: "<em>Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria</em>" by Samuel Bickel and Dani Or.</p> <p>The following files are provided:</p> <p><strong>Microcosm experiment:</strong></p> <p>- Fluorescence microscopy images of the microcosm experiment (*.tif)</p> <p>- Code used for extracting cell locations from images (image_analysis.py)</p> <p><strong>Global model estimates from the bacterial interactions heuristic model:</strong></p> <p>- Maps of estimated cell density and proportion of biomass associated with anoxic cell clusters (*.nc)</p> <p> </p>
Supplementary material: Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules
<p><strong>Supplementary material to the manuscript <em>"Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules"</em> by Terry Mullins, Evangelos T. Karamatskos, Joss Wiese, Jolijn Onvlee, Arnaud Rouzée, Andrey Yachmenev, Sebastian Trippel, and Jochen Küpper, <em>Nat Commun</em> 13, 1431 (2022). <a href="https://doi.org/10.1038/s41467-022-28951-z">https://doi.org/10.1038/s41467-022-28951-z</a>, arXiv: <a href="https://arxiv.org/abs/2009.08157">2009.08157 </a></strong></p> <ul> <li> <em><strong>simulations_part.z*</strong> </em>is split zip archive containing simulations data for indole molecule, such as files with rotational probability density distributions computed at different times <span class="math-tex">\(t=0..1500\)</span> ps during the laser pulse and field-free evolution, and example python scripts for data retrieval.</li> <li><strong><em>rawdata_part.z*</em></strong> is split zip archive containing raw experimental data.</li> <li><strong><em>analysis_scripts.zip</em></strong> is zip archive containing experimental analysis codes.</li> </ul> <p><strong>The <em>simulations_part.zip</em> contains the following files and folders:</strong></p> <ul> <li><em><strong>prob_density_euler_angles</strong></em> contains files <em>rotdens_av_<time>.gz</em> with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times <time>, ranging from the beginning of the alignment laser pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Calculations of probability density distributions were done using <a href="https://github.com/CFEL-CMI/richmol">Richmol</a> program.<br> The gzipped ASCII data files <em>rotdens_av_<time>.gz</em> contain in columns the values of the Euler angles <span class="math-tex">\(\phi,\theta,\chi\)</span> followed by the normalized probability density value.</li> <li><em><strong>prob_density_atoms_xyz</strong></em> contains files <em>monte_carlo_av_<time>.h5</em> with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times <time>, ranging from the beginning of the alignment pulse at <span class="math-tex">\(t=0\)</span> up to <span class="math-tex">\(t=1500\)</span> ps with a time step of 1 ps.<br> Structure of <em>monte_carlo_av_<time>.h5</em> HDF5 files:<br> Key Description<br> ----- ----------------<br> 'C10' - Cartesian coordinates of carbon atom no. 10<br> 'C11' - Cartesian coordinates of carbon atom no. 11<br> 'C12' - ...<br> 'C14' - ...<br> 'C3' - ...<br> 'C6' - ...<br> 'C7' - ...<br> 'C9' - ...<br> 'N4' - ...<br> 'H1-C3' - Cartesian coordinates of a vector pointing from carbon atom no. 3 to hydrogen atom no. 1<br> 'H13-C11' - ...<br> 'H15-C12' - ...<br> 'H16-C14' - ...<br> 'H2-N4' - ...<br> 'H5-C7' - ...<br> 'H8-C9' - ...<br> 'ref_vectors' - reference molecular-frame Cartesian coordinates of all atoms<br> 'x' - coordinates of the x-axis of Principal Axes of Inertia Frame<br> 'y' - coordinates of the y-axis of Principal Axes of Inertia Frame<br> 'z' - coordinates of the z-axis of Principal Axes of Inertia Frame<br> 'pol_x' - coordinates of the x-axis of Principal Axes of Polarizability Frame<br> 'pol_y' - coordinates of the y-axis of Principal Axes of Polarizability Frame<br> 'pol_z' - coordinates of the z-axis of Principal Axes of Polarizability Frame</li> <li><em><strong>indole_deflected_states.txt</strong></em> ASCII file contains initial populations of rotational states of indole in the deflected beam.<br> The following data is arranged in columns: <em>m, J</em>, <em>id</em>, <em>energy</em>, <em>normalized population</em>. The <em>J</em> and <em>m</em> are rotational quantum numbers of the total angular momentum and its <em>Z</em>-projection, the <em>id</em> number refers to the state's index in file <em>indole_energies_j0_j20.txt</em> listing rotational states of indole.</li> <li><em><strong>indole_data.py</strong></em> Python module provides basic functions to extract information from HDF5 data files <em>monte_carlo_av_<time>.h5</em>. It can also be used to compute alignment and orientation.</li> <li><em><strong>example_cos.py</strong></em> and <em><strong>example_dens.py</strong></em> Python scripts that demonstrate how to use <em>indole_data.py</em> module for computing and plotting alignment traces and a 2D projection of the probability density distribution, respectively.</li> <li><em><strong>monte_carlo.py</strong></em> Python script that was used to compute through Monte-Carlo sampling probability density distributions for Cartesian positions of atoms in indole (<em>monte_carlo_av_<time>.h5</em> files) using probability density distribution functions in Euler angles (outputs of Richmol program <em>rotdens_av_<time>.gz</em>).</li> </ul> <p><strong>The <em>analysis_scripts.zip</em> contains the following files and folders:</strong></p> <ul> <li><strong><em>H_Plus</em></strong> folder contains codes relevant for the analysis of H<sup>+</sup> ion data. <ul> <li><strong><em>analyse_full_alignment_scans.m</em></strong>: subtracts background and combines delay scan data sets together, takes account of errors.</li> <li><em><strong>calculate_resamped_df.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> to calculate the frequency sampling.</li> <li><em><strong>unique_mean.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> when combining data sets. Combines non-unique data points into a single data point.</li> </ul> </li> <li><em><strong>C_Plus2</strong></em> folder contains codes for the analysis of C<sup>2+</sup> ion data. The file descriptions are identical to those in the <em>H_Plus</em> directory.</li> <li><em><strong>intensity/calculate_intensity.m</strong></em>: calculates peak intensity of the laser pulse from measured parameters as well as statistical error.</li> <li><em><strong>intensity/compare_exp_sim.m</strong></em>: fits experimental and theoretical tomography and delay-dependent 2D projection values.</li> <li><em><strong>intensity/nir2hdf5_kHz.py</strong></em>: converts raw data files (from <em>rawdata_part.z*</em> archive<em>)</em> into hdf5 files.</li> </ul>
Fig. 4 in Shape Analysis Of Otoliths Of The Round Goby, Neogobius Melanostomus (Gobiiformes, Gobiidae), From The Black Sea Basin
Fig. 4. Dendrogram for Euclidian distances between otolith contours of round goby (n = 786) from nine sampling areas, sampled during three years of study. Stippled line represents five clusters representing pairs of similar sampling sites. It shows that similarity of the sampling sites does not follow the pattern of their allocation chain along the coast of the Black sea visible in fig. 1.
Fig. 1 in Shape Analysis Of Otoliths Of The Round Goby, Neogobius Melanostomus (Gobiiformes, Gobiidae), From The Black Sea Basin
Fig. 1. Map of the study area with sampling localities: 1 — Lake Yalpuh; 2 — Snake Island; 3 — Dniester Estuary; 4 — Gulf of Odesa; 5 — Khadzhibey Estuary; 6 — Tylihul Estuary; 7 — Dnipro-Bug Estuary; 8 — Dzharylhach Bay; 9 — Obytichna Bay of the Sea of Azov.
Data and code from: Geomorphological processes shape plant community traits in the Arctic
<p><strong>Aim</strong></p> <p>Geomorphological processes profoundly affect plant establishment and distributions, but their influence on functional traits is insufficiently understood. Here, we unveil trait-geomorphology relationships in Arctic plant communities.</p> <p> </p> <p><strong>Location</strong></p> <p>High-Arctic Svalbard, low-Arctic Greenland, and sub-Arctic Fennoscandia.</p> <p> </p> <p><strong>Time period</strong></p> <p>2011-2018</p> <p> </p> <p><strong>Major taxa studied</strong></p> <p>Vascular plants</p> <p> </p> <p><strong>Methods</strong></p> <p>We collected field-quantified data on vegetation, geomorphological processes, microclimate, and soil properties from 5280 plots and 200 species across the three Arctic regions. We combined these data with database trait records to relate local plant community trait composition to dominant geomorphological processes of the Arctic, namely cryoturbation, deflation, fluvial processes, and solifluction. We investigated the relationship between plant functional traits and geomorphological processes using hierarchical generalised additive modelling.</p> <p> </p> <p><strong>Results</strong></p> <p>Our results demonstrate that community-level traits are related to geomorphological processes, with cryoturbation most strongly influencing both structural and leaf economic traits. These results were consistent across regions, suggesting a coherent biome-level trait response to geomorphological processes.</p> <p> </p> <p><strong>Main conclusions</strong></p> <p>The results indicate that geomorphological processes shape plant community traits in the Arctic. We provide empirical evidence for the existence of generalisable relationships between plant functional traits and geomorphological processes. The results indicate that the relationships are consistent across these three distinct tundra regions and that geomorphological processes should be considered in future investigations of functional traits.</p> <p> </p> <p>Kemppinen, Niittynen, Happonen, le Roux, Aalto, Hjort, Maliniemi, Karjalainen, Rautakoski & Luoto. Provisionally accepted. Geomorphological processes shape plant community traits in the Arctic. Global Ecology and Biogeography.</p> <p>These are the data and code from Kemppinen et al. (Provisionally accepted).</p>
Data from 'Fast-growing species shape the evolution of reef corals'
<p>Datasets and scripts generated and/or analysed in the paper 'Fast-growing species shape the evolution of reef corals', published in Nature Communications. More details can be found in the README file.</p>
Fig. 2 in Shape Analysis Of Otoliths Of The Round Goby, Neogobius Melanostomus (Gobiiformes, Gobiidae), From The Black Sea Basin
Fig. 2. Basic morphometric characters used for the shape description of the round goby otoliths. At the internal surface: 1 — dorsal part; 2 — ventral part; 3 — anterior margin; 4 — posterior margin; 5 — rostrum; 6 — pararostrum; 7 — acoustic groove.
Fig. 3 in Shape Analysis Of Otoliths Of The Round Goby, Neogobius Melanostomus (Gobiiformes, Gobiidae), From The Black Sea Basin
Fig. 3. The visualized reconstruction of the round goby otolith contour features predicated upon the first six Principal components (see Material and method for details).
Data and Rscripts from: An integrated experimental and mathematical approach to inferring the role of food exploitation and interference interactions in shaping life history
<p><span>Intraspecific interactions can occur through many ways but the mechanisms can be broadly categorized as food exploitation and interference interactions. Identifying how intraspecific interactions impact life history is crucial to accurately predict how population density and structure influence dynamics. However, disentangling the effects of interference interactions from exploitation using experiments, is challenging for most biological systems.</span></p> <p><span>Here we propose an approach that combines experiments with modeling to infer the pathways of intraspecific interactions in a system. First, a consumer-resource model is built without intraspecific interactions. Then, the model is parameterized by fitting it to life-history data from a first experiment in which food abundance was varied. Next, hypothesized scenarios of intraspecific interactions are incorporated into the model which is then used to predict life histories with increasing competitor density. Lastly, model predictions are compared against data from a second experiment which raised groups of competitors of different densities. This comparison allows us to infer the role of interference and exploitation in shaping life history.</span></p> <p><span>We demonstrated the approach using the smaller tea tortrix <em>Adoxophyes honmai</em> across a range of temperature. We investigated five scenarios of interactions that included exploitation and three pathways for interference through some effects either on energetics to represent changes in ingestion or activity, or on mortality to model deadly interactions, or on mortality and ingestion to model cannibalism.</span></p> <p><span>Overall, intraspecific interactions in tea tortrix are best explained by a high level of deadly interactions along with some level of interference that acts on energy such as escaping and blocking access to food. Deadly interactions increase with temperature while interference that acts on energy is strongest close to the optimal temperature for reproduction. Interestingly, exploitation is more important than interference at low competitor density.</span></p> <p><span>The combination of mathematical modeling and experimentation allowed us to mechanistically characterize the intraspecific interactions in tea tortrix in a way that is readily incorporated into population-level mathematical models. The primary value of this approach, however, is that it can be applied to a much wider range of taxa than is possible with pure experimental approaches. </span></p>
Social polyandry shapes sperm morphology
<p>Sexual selection is a major driver of trait variation, and the intensity of male competition for mating opportunities has been linked with sperm size across diverse taxa. Mating competition among females may also shape the evolution of sperm traits, but the interplay between female-female competition and male-male competition on sperm morphology is not well understood. We evaluated variation in sperm morphology in two species with socially polyandrous mating systems, in which females compete to mate with multiple males. Northern jacanas (<em>Jacana spinosa</em>) and wattled jacanas (<em>J. jacana</em>) vary in their degree of polyandry and sexual dimorphism, suggesting species differences in the intensity of sexual selection. We compared mean and variance in sperm head, midpiece, and tail length between species and breeding stages, because these measures have been associated with the intensity of sperm competition. We found that the species with greater polyandry, northern jacana, has sperm with longer midpieces and tails, as well as marginally lower intra-ejaculate variation in tail length. Intra-ejaculate variation was also significantly lower in copulating males than in incubating males, suggesting flexibility in sperm production as males cycle between breeding stages. Our results indicate that stronger female-female competition for mating opportunities may also shape more intense male-male competition by selecting for longer and less variable sperm traits. These findings extend frameworks developed in socially monogamous species to reveal that sperm competition may be an important evolutionary force layered atop female-female competition for mates.</p>
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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.