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226 results for “symmetry”
Learning Broken Symmetries with Resimulation and Encouraged Invariance
<p>This dataset corresponds to "Learning Broken Symmetries with Resimulation and Encouraged Invariance" (2311.05952) and is meant for use with the code at <a href="https://github.com/Edwit4/learning_broken_symmetries">https://github.com/Edwit4/learning_broken_symmetries</a>.</p>
Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
The cochlea and semicircular canals of the inner ear are vital neurosensory devices. There are associations between the anatomy of these sensorineural structures, their function, and the function of related biological systems, e.g., hearing ability, gaze stabilization, locomotor agility, and posture. The endosseous labyrinth is frequently used as a proxy to infer the performance of the hearing and vestibular systems, locomotor abilities, and ecology of extinct species. Such fossil inferences are often based on single specimens or even a single ear, representing an entire species. To address whether a single ear is representative of a population, we used geometric morphometrics to quantitatively assess the variation in shape and symmetry in a sample of endosseous labyrinths of wild turkeys Meleagris gallopavo of southern Ohio. We predicted that ears would be symmetrical both within individuals and across the sample; that labyrinth shape and size would covary; that labyrinth shape would vary with the size of the brain, measured as width of the endocranium at the cerebellum; and that labyrinths would be morphologically integrated. To test these predictions, we microCT-scanned the heads of 26 cadaveric turkeys, digitally segmented their endosseous labyrinths in Avizo, and assigned 15 manual landmarks and 20 sliding semilandmarks to each digital model. Following Procrustes alignment, we conducted an analysis of bilateral symmetry, a Procrustes regression analysis for allometry and other covariates including side and replicate, and analyses of global integration and modularity. Based on Procrustes distances, no individual's left and right ears were clearly different from each other. When comparing the ears of different specimens, statistically clear differences in shape were found in only 66 of more than 1300 contrasts. Moreover, effects of both directional and fluctuating asymmetry were very small—generally, two orders of magnitude smaller than the variance explained by individual variation. Statistical tests disagreed on whether these asymmetric effects crossed the threshold of significance, possibly due to non-isotropic variation among landmarks. Regardless, labyrinths appeared to primarily vary in shape symmetrically. Neither labyrinth size nor endocranial width was correlated with labyrinth shape, contrary to our expectations. Finally, labyrinths were found to be moderately integrated in a global sense, but four weakly separated modules—the three semicircular canals and cochlea—were recovered using a maximum-likelihood analysis. The results show that both fluctuating and directional asymmetry play a larger role in shape variation than expected—but nonetheless, endosseous labyrinths are symmetrical within individuals and at the level of the population, and their shape varies symmetrically. Thus, inferences about populations, and very possibly species, may be confidently made when only a single specimen, or even a single ear, is available for study.
Supplementary data for "Fault-tolerant quantum algorithm for symmetry-adapted perturbation theory"
<p>Supplementary data belonging to "Fault-tolerant quantum algorithm for symmetry-adapted perturbation theory".</p> <p>The data includes geometries for the molecules in the paper as well as the Hamiltonian matrix elements, orbital coefficients and overlap matrices to reproduce the data in the paper.</p>
Data supporting the publication "Quadrature nonreciprocity in bosonic networks without breaking time-reversal symmetry"
<p>Data supporting the publication "Quadrature nonreciprocity in bosonic networks without breaking time-reversal symmetry"</p>
Dataset corresponding to "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene"
<p>Data corresponding to the figures in the manuscript "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene" published in Nature Communications (2023)</p>
Supplementary data to "What are the effects of temperature on plasticity, shape symmetry and seasonal variation in freshwater benthic green microalga Micrasterias thomasiana?"
<p>The supplementary data consist of the files including the landmark coordinates of Micrasterias thomasiana semicells used for the analyses described in the manuscript submitted to Aquatic Ecology. The coordinates are presented in the TPS format.</p> <p> </p>
The symmetry-induced numerosity illusion depends on visual attention
<p>For the ST, ST-WD: each file contains a matrix called “a”. Each row of the matrix “a” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1st: Numerosity of test stimulus</li> <li>2nd: Log10 of numerosity of test stimulus divided by the standard numerosity</li> <li>3rd: Participant response (0 = standard stimulus; 1 = test stimulus)</li> <li>4th: 200</li> <li>5th: Standard numerosity </li> <li>6th: Dots size in pixels</li> <li>7th: 10</li> <li>8th: Condition (0= symmetry condition; 1= random condition)</li> <li>9th: Standard-Test order (1 = standard first; 2 = standard second)</li> <li>10th: Response time</li> <li>11th: -99</li> <li>12th: -99</li> <li>13th: -99</li> <li>14th: 0</li> </ul> <p>For the DT: each file contains a matrix called “a”. Each row of the matrix “a” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1st: Numerosity of test stimulus</li> <li>2nd: Log10 of numerosity of test stimulus divided by the standard numerosity</li> <li>3rd: Participant response (0 = standard stimulus; 1 = test stimulus)</li> <li>4th: 200</li> <li>5th: Standard numerosity </li> <li>6th: Dots size in pixels</li> <li>7th: 10</li> <li>8th: Condition (0= symmetry condition; 1= random condition)</li> <li>9th: Standard-Test order (1 = standard first; 2 = standard second)</li> <li>10th: Response time to the numerosity task</li> <li>11th: Response to the color-conjunction task (1: target; 0: no-target)</li> <li>12th: code of color-conjuction stimulus presented onscreen</li> <li>13th: Accuracy to the color-conjuction task (1:correct; 0:wrong)</li> <li>14th: 1</li> </ul>
The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea
<p>The shown folders contain the molecular dynamics simulation data, used tools, and scripts for the study of "The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea". The simulation data includes the force field and simulation setup for both AWSEM-MD and atomistic MD in OpenMM, the data analyses that are presented in the related paper, and the representative conformations from each simulation. Due to the large file size, the original trajectory files are available upon separate request.</p> <p>The tools and scripts folder includes the specific version of the AWSEM model, implemented in the LAMMPS package, and the scripts used to analyze the simulations. For detailed instructions on using AWSEM model, please refer to our Github: <a href="https://github.com/adavtyan/awsemmd/wiki">https://github.com/adavtyan/awsemmd/wiki</a>. For detailed instructions on using the LAMMPS package, please refer to <a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>. For detailed instructions on using the OpenMM package, please refer to <a href="https://openmm.org/">https://openmm.org/</a>. For any questions about using this data repository, please feel free to contact the author.</p> <p> </p> <p> </p>
Data for Local atomic stacking and symmetry in twisted graphene trilayers
<p>Data for <a href="https://arxiv.org/abs/2303.09662">Local atomic stacking and symmetry in twisted graphene trilayers</a></p> <p>Please refer to <a href="https://github.com/bediakolab/bediakolab_scripts">bediakolab_scripts</a> (relevant code in TrilayerTEM) and <a href="https://github.com/bediakolab/pyInterferometry">pyInterferometry</a>. </p> <p>key.txt contains further information regarding format and labeling of this data. </p>
Comparison of Three Surgical Techniques to Achieve Patella Symmetry During Resection
ClinicalTrials.gov study NCT01822574. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: The size, symmetry, and color saturation of a male guppy’s ornaments forecast his resistance to parasites
Open the record for dataset details and reuse information.
Data from: Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
Open the record for dataset details and reuse information.
Global distribution and evolutionary transitions of floral symmetry in angiosperms
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DNA sequences for: Synthetic control of actin polymerization and symmetry breaking in active protocells
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Complex morphologies of biogenic crystals emerge from anisotropic growth of symmetry-related facets
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The evolution of phenotypic novelty through the genetic assimilation of broken symmetry
Most animals are symmetrical; however, widespread and impressive cases occur where symmetry has been broken. Breaks in symmetry can occur as anti-symmetry, where 50% of the population have the left side enlarged and 50% the right, or through directional asymmetry where the entire population is biased either to the left or the right. Such broken symmetry represents a novel phenotype that is challenging to explain from an evolutionary perspective, given that it has ultimately evolved from a symmetrical ancestor. Here, we use artificial selection to test the hypothesis that anti-symmetry can evolve through the genetic assimilation of a developmental error that occurs in the production of an environmentally cued threshold trait. We find that anti-symmetry in the legs of the acarid mite, Rhizoglyphus echinopus, is heritable and that we are able to increase the frequency of the anti-symmetrical males through artificial selection. We find no evidence that the developmental instability of anti-symmetrical males is associated with negative fitness consequences in terms of larval viability and inbreeding depression. Our study provides empirical support for the notion that developmental errors in the production of threshold traits can be the genesis for the subsequent genetic assimilation of the phenotypic novelty that is broken symmetry.
Data from: The symmetry of children's knees is linked to their adult sprinting speed and their willingness to sprint in a long-term Jamaican study
Jamaican athletes are prominent in sprint running but the reasons for their success are not clear. Here we consider the possibility that symmetry, particularly symmetry of the legs, in Jamaican children is linked to high sprinting speed in adults. Our study population was a cohort of 288 rural children, mean age 8.2 (±1 SD = 1.7) years in 1996. Symmetry was measured in 1996 and 2006 from the fluctuating asymmetry (FA) of three lower-body traits and we constructed a lower body composite FA trait (Comp lb-FA). In 2010 we measured sprinting speed (for 90 m and 180 m races) in participants recruited from our original cohort. There were 163 untrained adults in our sample. We found: (i) high Comp lb and knee symmetry in 1996 and 2006 were linked to fast sprinting times in our 2010 runners and (ii) our sample of sprinters appears to have self-selected for greater symmetry. We conclude that high knee symmetry in childhood is linked to an ability to sprint fast in adult Jamaicans as well as a readiness to sprint.
A long tail of truth and beauty: a simple rule of pattern formation explains symmetry, complexity and beauty in the peacock's tail
<p><span>Darwin's theory of sexual selection by female choice has become a standard explanation for exaggerated sexually dimorphic traits, such as the peacock's (<i>Pavo cristatus</i>) long tail. Eyespot beauty-based female choice requires genetic variation in female preference and the number of eyespots, as well as a genetic correlation between the two. However, little genetic variation has been documented in either of these traits in natural and feral peacock populations. We examined the anatomical plan underlying feather development and discovered that eyespot feather follicles originate in alternating rows of 10/11, which uniquely determines the train's feather complexity, bilateral symmetry, and eyespot arrangement and beauty. This pattern precludes intrinsic variation in eyespot number, resulting in a fixed number of total eyespots in fully mature individuals. Since number of eyespots and tail length are independent traits and function of the age of the animal, the only variation available in these trats is also function of age. We propose an alternate, male drive, hypothesis in which females choose males based on their overall dominance (size, vigour, call, courting), and beauty of the train may (or may not) be a factor in female choice but it cannot affect the train length. This hypothesis can explain all known results. </span></p>
Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. Results: Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. Discussion: Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
Emergent symmetry in lithium molybdate (LMO)
<p>Upon cooling, condensed matter systems typically transition into states of lower symmetry. While the converse, i.e. the emergence of higher symmetry at lower temperatures, has been hypothesized, it is extremely rare. Here, we show how an unusually isotropic 25 magnetoresistance in the highly anisotropic, one-dimensional conductor Li0.9Mo6O17 (LMO), and its temperature dependence, can be interpreted as a renormalization group (RG) flow towards a so-called separatrix. This approach is equivalent to an emergent symmetry in the system. The existence of two distinct ground states – Mott insulator and superconductor – can then be traced back to two opposing RG trajectories. By establishing a direct link between quantum field theory 30 and an experimentally measurable quantity, we uncover a path through which emergent symmetry might be identified in other candidate materials.</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.