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829 results for “Evolvability”
Supplemental material: Comparing approaches for evolving high-level robot control based on behaviour repertoires
<p>Supplemental material for the paper:</p> <p>Comparing approaches for evolving high-level robot control based on behaviour repertoires<br> Jorge Gomes, Anders Lyhne Christensen</p> <p>Videos of the highest-performing solutions evolved with each method. In all videos, the schematic of the robot indicates the current wheel angles and robot speed. In the repertoire-based methods, the visualization on the bottom left indicates which primitives are being executed.</p> <p><strong>vid_evorbc_2_4_f1.12.mp4 </strong><br> Evolved by NEAT-EvoRBC. The blue cross indicates the behaviour selection vector.</p> <p><strong>vid_gp_2_2_f1.12_best.mp4</strong><br> Evolved by GP-DT. The primitives highlighted in green are the ones that exist in the decision tree.</p> <p><strong>vid_gp_8_4_f0.92_paper.mp4 </strong><br> Evolved by GP-DT. Smallest tree with fitness above 0.9. Shown in the paper.</p> <p><strong>vid_neatsub_9_5_f0.89.mp4 </strong><br> Evolved by NEAT-Subset. Only the primitives that are in the subset are shown. The numbers near each primitive indicate the activation level of the corresponding output (or maximum activation level if there are multiple outputs corresponding to the same primitive).</p> <p><strong>vid_neattr_24_f0.28.mp4 </strong><br> Evolved by NEAT-TR.</p> <p>The videos have been verified to reproduce correctly with the <strong>VLC player</strong>. But any other modern player should handle them.</p>
EditQL: A Textual Query Language for Evolving Models (Reproducibility Package)
Open the record for dataset details and reuse information.
Research data for journal article: Balancing Environmental and Economic Impacts in the rapidly evolving European EV Battery Value Chain
Open the record for dataset details and reuse information.
Figs 15–29 in Calling signal pattern vs. genitalia morphology in Planaphrodes Hamilton, 1975 (Homoptera: Auchenorrhyncha: Cicadellidae: Aphrodinae) - which trait evolves faster?
Figs 15–29. Planaphrodes spp.: 15–21 — P. bifasciatus; 22–29 — P. monticola; 15–20 and 22–28 — oscillograms of male calling signals; 21 and 29 — penis, side view; 15, 17, and 19 — male from Mytishchi District; 16, 18, and 20–21 — male from Serpukhov District (both in Moscow Oblast); 22–23, 25, 27, and 29 — male from Western Tien-Shan Mts.; 24, 26, and 28 — male from Central Tien-Shan Mts. Faster oscillograms of the parts of signals indicated as "17–20" and "25–28" are given under the same numbers. Рис. 15–29. Planaphrodes spp.: 15–21 — P. bifasciatus; 22–29 — P. monticola; 15–20, 22–28 — осциллограммы приЗывных сигналов самца; 21, 29 — пенис сбоку; 15, 17, 19 — самец иЗ МытиЩинского р-на; 16, 18, 20–21 — самец иЗ Серпуховского р-на (оба — МосковскаЯ обл.); 22–23, 25, 27, 29 — самец с Западного ТЯнь-ШанЯ; 24, 26, 28 — самец с Центрального ТЯнь-ШанЯ. Фрагменты сигналов, обоЗначенные цифрами "17–20" и "25–28", представлены на осциллограммах под такими же номерами.
Fig. 2 in Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)
Fig. 2 Subtree of Phylliroe and its closest relatives from Dendronotida s.s., Dendronotidae, Scyllaeidae, and Tethyidae. Images from life animals and histological slides. a Dendronotus venustus. b, c Dendronotus frondosus. d–f Crosslandia viridis. g–i Melibe leonina. j–l Phylliroe
Fig. 1 in Phylogenomic analysis and morphological data suggest left-right swimming behavior evolved prior to the origin of the pelagic Phylliroidae (Gastropoda: Nudibranchia)
Fig. 1 Maximum likelihood phylogeny of Cladobranchia from RAxML-NG using a concatenat- ed nucleotide matrix of 292 genes partitioned by codon position. All nodes with no support values in- dicated have 100% bootstrap support and a posterior probability of 1.0 in our analyses. The blue box indicates Dendronotida sensu stricto and the red outline shows the closest relatives to Phylliroe in our analysis (Melibe leonina, Tethyidae; Scyllaea fulva, Scyllaeidae; Dendronotus venustus, Dendronotidae), highlighted further in Fig. 2
An Empirical Study on the Impact of Refactoring Activities on Evolving Client-Used APIs
<p>Context: Refactoring is recognized as an effective practice to maintain evolving software systems. For software libraries, we study how library developers refactor their Application Programming Interfaces (APIs), especially when it impacts client users by breaking an API of the library. Objective: Our work aims to understand how clients that use a library API are affected by refactoring activities. We target popular libraries that potentially impact more library client users. Method: We distinguish between library APIs based on their client-usage (refereed to as client-used APIs) in order to understand the extent to which API breakages relate to refactorings. Our tool-based approach allows for a large-scale study across eight libraries (i.e., totaling 183 consecutive versions) with around 900 clients projects. Results: We find that library maintainers are less likely to break client-used API classes. Quantitatively, we find that refactoring activities break less than 37% of all client-used APIs. In a more qualitative analysis, we show two documented cases of where non-refactoring API breaking changes are motivated other maintenance issues (i.e., bug fix and new features) and involve more complex refactoring operations. Conclusion: Using our automated approach, we find that library developers are less likely to break APIs and tend to break client-used APIs when addressing these maintenance issues.</p>
Dataset - results of IBM of an evolving metacommunity
<p>Datasets and scripts corresponding to results of the IBM of an evolving metacommunity (https://doi.org/10.5281/zenodo.2280982) as shown in the paper: ''Regional neutrality evolves through local adaptive niche evolution" (www.pnas.org/cgi/doi/10.1073/pnas.1808615116).</p>
These arboreal ants (Cephalotes atratus) have evolved closely with the trees they live in. Photograph: Field Museum, Corrie Moreau. in The Evolution of Natural History Collections
These arboreal ants (Cephalotes atratus) have evolved closely with the trees they live in. Photograph: Field Museum, Corrie Moreau.
FIGURE 6 in Haematophagous biting midges of the extant genus Culicoides Latreille (Diptera: Ceratopogonidae) evolved during the mid-Cretaceous
FIGURE 6. Fossil Culicoides (Groganomyia) myanmaricus Szadziewski & Dominiak, sp. nov., female holotype. A—total habitus, B—head, C—flagellum, D—palpus.
FIGURE 5 in Haematophagous biting midges of the extant genus Culicoides Latreille (Diptera: Ceratopogonidae) evolved during the mid-Cretaceous
FIGURE 5. Fossil Culicoides (Groganomyia) ellenbergeri Szadziewski & Dominiak, sp. nov., female holotype. A—total habitus, B—palpus, C—flagellum.
FIGURE 4 in Haematophagous biting midges of the extant genus Culicoides Latreille (Diptera: Ceratopogonidae) evolved during the mid-Cretaceous
FIGURE 4. Fossil Culicoides (Groganomyia) burmiticus Szadziewski & Dominiak, sp. nov., female holotype. A—total habitus, B—palpus and flagellum.
FIGURE 3 in Haematophagous biting midges of the extant genus Culicoides Latreille (Diptera: Ceratopogonidae) evolved during the mid-Cretaceous
FIGURE 3. Fossil Culicoides (Groganomyia) bojarskii Szadziewski & Dominiak, sp. nov., female holotype. A—total habitus, B—head, C—flagellum.
FIGURE 2. Extant Culicoides. A–E in Haematophagous biting midges of the extant genus Culicoides Latreille (Diptera: Ceratopogonidae) evolved during the mid-Cretaceous
FIGURE 2. Extant Culicoides. A–E—male genitalia of C. (Groganomyia) cameroni Campbell & Pelham-Clinton, 1960, A—ventral aspect, B—gonocoxite and parameres, C—tergite 9, D—aedeagus, E—gonostylus; F—eye separation in male and female of C. cameroni; G—female sternite 9 of C. (subgenus?) minutissimus (Zetterstedt, 1855); H—female sternite 9 of C. (Wirthomyia) reconditus Cambell & Pelham-Clinton, 1960; I—female sternite 9 of C. (Avaritia) obsoletus (Meigen, 1818).
Single-cell transcriptome analysis reveals evolving tumor microenvironment induced by immunochemotherapy in nasopharyngeal carcinoma
<p>18 bulks and 11 single-cell RNA sequencing samples from paired before anti-PD-1 contained treatment and on treatment in patients with treatment-naive high-risk metastatic locally advanced NPCs were obtained. We aim to explore the mechanism of response heterogeneity for locally advanced NPCs underwent immunochemotherapy.</p>
Resources of "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1"
<p>Resources of the article "Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1". See https://github.com/yunlongcaolab/SARS-CoV-2-JN.1-mAbs for future updates.</p>
Data from: Do aggressive signals evolve toward higher reliability or lower costs of assessment?
It has been suggested that the evolution of signals must be a wasteful process for the signaller, aimed at the maximization of signal honesty. However, the reliability of communication depends not only on the costs paid by signallers but also on the costs paid by receivers during assessment, and less attention has been given to the interaction between these two types of costs during the evolution of signalling systems. A signaller and receiver may accept some level of signal dishonesty by choosing signals that are cheaper in terms of assessment but that are stabilized with less reliable mechanisms. I studied the potential trade-off between signal reliability and the costs of signal assessment in the corncrake (Crex crex). I found that the birds prefer signals that are less costly regarding assessment rather than more reliable. Despite the fact that the fundamental frequency of calls was a strong predictor of male size, it was ignored by receivers unless they could directly compare signal variants. My data revealed a response advantage of costly signals when comparison between calls differing with fundamental frequencies is fast and straightforward, whereas cheap signalling is preferred in natural conditions. These data might improve our understanding of the influence of receivers on signal design because they support the hypothesis that fully honest signalling systems may be prone to dishonesty based on the effects of receiver costs and be replaced by signals that are cheaper in production and reception but more susceptible to cheating.
Data from: Resource competition promotes tumour expansion in experimentally evolved cancer
Tumour progression involves a series of phenotypic changes to cancer cells, each of which presents therapeutic targets. Here, using techniques adapted from microbial experimental evolution, we investigate the evolution of tumour spreading - a precursor for metastasis and tissue invasion - in environments with varied resource supply. Evolutionary theory predicts that competition for resources within a population will select for individuals to move away from a natal site (i.e. disperse), facilitating the colonisation of unexploited resources and decreasing competition between kin. After approximately 100 generations in environments with low resource supply, we find that MCF7 breast cancer spheroids (small in vitro tumours) show increased spreading. Conversely, spreading slows compared to the ancestor where resource supply is high. Common garden experiments confirm that the evolutionary responses differ between selection lines; with lines evolved under low resource supply showing a plastic spreading phenotype. These differences in spreading behaviour between selection lines are heritable (stable across multiple generations), and show that the divergently evolved lines differ in their response to resource supply. It is possible that prolonged resource limitation itself causes a stable switch toward dispersal-like behaviour and an increased sensitivity to resource availability without the need for genetic change. Different clinical strategies may be needed depending on whether tumour progression is due to stable or plastic effects. This study highlights the effectiveness of experimental evolution approaches in cancer cell populations and demonstrates how simple model systems might enable us to observe and measure key selective drivers of clinically important traits.
Data from: Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly
Background: While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Results: Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A 2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Conclusions: Given log-scale differences in toxin abundance, which are likely correlated with biosynthetic costs, we hypothesize that as a result of natural selection, snakes optimize return on energetic investment by producing more of venom proteins that increase their fitness. Natural selection then acts on the additive genetic variance of these components, in proportion to their contributions to overall fitness. Adaptive evolution of venoms may occur most rapidly through changes in expression levels that alter fitness contributions, and thus the strength of selection acting on specific secretome components.
Data from: The evolution of a complex trait: cuticular hydrocarbons in ants evolve independent from phylogenetic constraints
Cuticular hydrocarbons (CHC) are ubiquitous and highly diverse in insects, serving as communication signal and waterproofing agent. Despite their vital function, the causes, mechanisms and constraints on CHC diversification are still poorly understood. Here, we investigated phylogenetic constraints on the evolution of CHC profiles, using a global dataset of the species-rich and chemically diverse ant genus Crematogaster. We decomposed CHC profiles into quantitative (relative abundances, chain length) and qualitative traits (presence/absence of CHC classes). A species-level phylogeny was estimated using newly generated and previously published sequences from five nuclear markers. Moreover, we reconstructed a phylogeny for the chemically diverse C. levior species group using cytochrome oxidase I. Phylogenetic signal was measured for these traits on genus and clade level and within the chemically diverse C. levior group. For most quantitative CHC traits, phylogenetic signal was low and did not differ from random expectation. This was true on the level of genus, clade and species-group, indicating that CHC traits are evolutionary labile. In contrast, the presence or absence of alkenes and alkadienes was highly conserved within the C. levior group. Hence, the presence or absence of biosynthetic pathways may be phylogenetically constrained, especially at lower taxonomic levels. Our study shows that CHC composition can evolve rapidly, allowing insects to quickly adapt their chemical profiles to external selection pressures, while the presence of biosynthetic pathways appears more constrained. However, our results stress the importance to consider the taxonomic level when investigating phylogenetic constraints.
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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.