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3,484 results for “Plastic”
Input files and movie visualizations for convection models discussed in Becker and Fuchs, "Generation of evolving plate boundaries and toroidal flow from visco-plastic damage-rheology mantle convection and continents", manuscript revised for G-Cubed
<p>These input files are for the CitcomS software as available on github.com/geodynamics/citcoms and used in the version under commit 2bda530. They can be used to recreate the models discussed in Becker and Fuchs (revised manuscript submitted to G-Cubed, 11/2023), with model codes discussed and listed in Table 1 of the preprint as provided here. We also provide selected animations of the time dependence of model output, referenced to the same model names.</p>
High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences
<p><strong>Background:</strong> <i>Xanthomonas</i> <i>translucens</i> pv. <i>graminis</i> (<i>Xtg</i>) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.</p><p><strong>Results:</strong> In this study, we produced high-quality, complete genome sequences of four strains of <i>Xtg</i>, complementing the recently obtained complete genome sequence of the <i>Xtg </i>pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found in <i>Xtg </i>and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of <i>Xtg</i>. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes. </p><p><strong>Conclusion:</strong> These results suggest a high adaptability of <i>Xtg</i>, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific to <i>Xtg </i>were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of <i>Xtg</i>.</p>
Fig. 1 in What's Under a Plastic Strip? Hidden Urban Biodiversity in the Beijing Metropolitan Area, China
Fig. 1. Seasonal activity dynamics of adult Dorytomus setosus (a) and Dorytomus roelofsi (b) collected in bandshelter trap on willows in Cuihu Wetland Park, Beijing, China.
Fig. 1 in A Case ofCnestus mutilatus(Blandford) (Curculionidae: Scolytinae: Xyleborini) Females Damaging Plastic Fuel Storage Containers in Louisiana, U.S.A.
Fig. 1. Plastic gasoline storage container (23-L) with numerous holes created by female Cnestus mutilatus. White arrows indicate embedded beetles. Black arrow indicates detailed inset of holes and elytral apices of embedded beetles.
Effect of glycerol trilevulinate plasticizer on thermal and mechanical properties of PHB, PHBV, PLA, PVC and PCL polymers
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Valorization of plastic wastes into value-add biochar production through co-pyrolysis with biomass residues
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Dataset for the paper "Wedge Plasticity and a Minimalist Dynamic Rupture Model for the 2011 Mw 9.1 Tohoku-Oki Earthquake and Tsunami" in Tectonophysics
<p>This dataset contains the Fortran source codes and input files to reproduce the results in the paper "Wedge Plasticity and a Minimalist Dynamic Rupture Model for the 2011 Mw 9.1 Tohoku-Oki Earthquake and Tsunami". Sample Matlab scripts are included to visualize the results. Model results, such as final fault slip, rupture times, stress changes on fault, final surface displacements, and moment density tensors in the wedge associated with inelastic deformation, are also included as ascii files. See readme for more details.</p>
Data on heat tolerance for D latus from: Does plasticity in thermal tolerance trade off with inherent tolerance? The influence of setal tracheal gills on thermal tolerance and its plasticity in a group of European diving beetles
<h3>Dataset on heat tolerance used in the study by Verberk et al., (2018).</h3><h3>Method description</h3><p>We assessed the impact of mode of respiration on heat tolerance under different oxygen conditions in one of the 15 species: <i>D. latus</i>, the most tolerant species in our comparison, using previously described methods (<a href="https://www.sciencedirect.com/science/article/pii/S0022191017302044#b0170">Verberk and Calosi, 2012</a>, <a href="https://www.sciencedirect.com/science/article/pii/S0022191017302044#b0185">Verberk and Bilton, 2015</a>). Briefly, individuals were placed in flow-through chambers, whose water supply could be heated. For one group of animals, we used chambers where the animals were completely submerged and had no access to air, while for a second group of animals chambers were used with a small head space holding a layer of air, meaning that these animals could obtain oxygen either from the air compartment by surfacing or from the water with oxygen diffusing directly into their tracheal system <i>via</i> the setae or oxygen diffusing into their subelytral air reservoir <i>via</i> their physical gill. Individuals were left to settle for 1 h at the equilibration temperature of 10 °C, after which the temperature was ramped up at 0.25 °C min−1. The CTmax was defined as the point at which animals lost coordinated swimming, hence losing their ability to escape from the conditions that will lead to their death (<a href="https://www.sciencedirect.com/science/article/pii/S0022191017302044#b0095">Lutterschmidt and Hutchison, 1997</a>). The heating rate, endpoint and starting temperature all therefore differed from the methodology described above, meaning that the critical thermal temperatures from both methods cannot be compared directly. CTmax was assessed under <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/normoxia">normoxia</a>, <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/hypoxemia">hypoxia</a> and <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/hyperoxia">hyperoxia</a> conditions (5, 20, 60 kPa O2 respectively) and adults were assessed with and without access to air. Oxygen tension of both the water and the air in the headspace was altered to produce hypoxia and hyperoxia, as described by <a href="https://www.sciencedirect.com/science/article/pii/S0022191017302044#b0185">Verberk and Bilton (2015)</a>.</p>
Self-ion irradiation effects on nanoindentation-induced plasticity of crystalline iron: A joint experimental and computational study
<p>Set consists two folders named after the methods used to obtained the data i.e. Nanoindentation, EBSD.</p> <p><strong>→ EBSD</strong></p> <p>In EBSD folder there are 3 original image files that make up Figure 1 and Figure 3a and 3b in the paper. Below please find the description:</p> <p><em>Fig. 1</em><em>. EBSD IPF Z image of the pristine Fe sample.</em></p> <p><em>Fig. 3</em><em>. (a) EBSD map of the indentation array made within one grain with [101] orientation, (b) GND density of map of the indentation array</em></p> <p><strong>→ Nanoindentation</strong></p> <p>In Nanoindentation folder there are two folders dedicated to two different materials (pristine and ion irradiated). The name of .txt files is as follows:</p> <p>Pure_Fe_300C_5MeV_1,5mN_100x1-107131929</p> <p>where:</p> <p>Pure_Fe_300C_5MeV -> Name of the sample,</p> <p>1,5mN -> Load</p> <p>100 -> Number of repetitions</p> <p>x1 -> Number of LD curves</p> <p> </p>
Misaligned plastic and evolutionary responses of lifespan to novel carbohydrate diets
<p>Diet elicits varied effects on longevity across a wide range of animal species. For example, diets low in protein and high in carbohydrate typically extend lifespan while diets high in protein tend to reduce it. Although studies have also shown that diet-induced lifespan changes can persist through transgenerational plasticity, whether such changes lead to evolutionary shifts in lifespan remains unclear. In this study we combine experimental evolution and phenotypic plasticity assays to address this gap. Using <em>Drosophila serrata</em>, we investigated the evolutionary potential of lifespan in response to four novel diets spanning a carbohydrate-protein gradient. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments. Our results show that although lifespan evolved in response to changes in dietary carbohydrate concentration, the plastic responses for lifespan differed from the evolved responses. The direction of the evolved response (increased lifespan) observed on low carbohydrate diets was in the opposite direction to the plastic response (decreased lifespan). Our results imply that plastic responses to low carbohydrates can be maladaptive for lifespan and misaligned with the evolved responses, <span>laying the groundwork for future investigations of carbohydrate contributions to evolved and plastic effects on lifespan.</span></p>
Data from: The genomic basis of nitrogen utilization efficiency and trait plasticity to improve nutrient stress tolerance in cultivated sunflower
<p>Supplemental datafiles and raw genotype data for "The genomic basis of nitrogen utilization efficiency and trait plasticity to improve nutrient stress tolerance in cultivated sunflower" by Andries A. Temme, Kelly L. Kerr, Kristen M. Nolting, Emily L. Dittmar, Rishi R. Masalia, Alexander K. Bucksch, John M. Burke, Lisa A. Donovan. Journal of Experimental Botany 10.1093/jxb/erae025</p>
Raw data for the submitted manuscript entitled "Novel strategies for the determination of plastic additives derived from agricultural plastics in soil using ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS)"
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Supplemental Dataset S2 for Tracing Fossil-Based Plastics, Chemicals and Fertilizers Production in China
<p>Supplemental Data S2 of the article "<em><strong>Tracing Fossil-Based Plastics, Chemicals, and Fertilizers Production in China</strong></em>" presents detailed calculation data. It provides calculation data across six key areas: the division of energy and feedstock used in fossil hydrocarbons, linking primary chemicals to downstream production, tracing the carbon source, evaluating CO2 mitigation potential, and comparing emission intensities. Uncertainty ranges are indicated alongside the process-based coefficients.</p>
It's time to go - Drivers and plasticity of migration phenology in a short-distance migratory ungulate
<p>Files provided in the repository consist of two dataframes (.Rdata format) and two scripts (.R format) to perform analyses and making figures presented in the paper: "Drivers and plasticity of migration phenology in a short-distance migratory ungulate, the Alpine ibex Capra ibex" </p> <p>Abstract: </p> <p><span>Recurring events like migrations are an important part of the biological cycles of species. Understanding the factors influencing the timing of such events is crucial for determining how species face the pervasive consequences of climate change in highly seasonal environments. Relying on data from 406 GPS-collared Alpine ibex </span><span>Capra ibex</span><span> monitored across 17 populations, we investigated the environmental and individual drivers of short-distance migration in this emblematic mountain ungulate. Notably, we assessed how variations in the onset of spring and autumn affected the timing of migration and the extent to which ibex exhibited behavioral plasticity in their response. We found that vegetation phenology, including spring growth and autumn senescence, along with snow dynamics - snowmelt in spring, first snowfall in autumn - were the main drivers of the timing of migration.</span></p> <p><span>In spring, ibex migration timing was synchronized with the peak of vegetation growth, but more in males than in females. Specifically, a shift of 10 days in vegetation growth peak delayed migration by 6.4 days for males and 2.7 days for females. This led to increased differences in migration timing between sexes when the vegetation growth peak occurred early or late in the season. In addition, ibex delayed migration timing when the length of growing season was longer and when the date of snowmelt on ibex summer range occurred later. Similarly, in autumn, prolonged vegetation senescence and delayed first snowfall led to later migration.</span></p> <p><span>Overall, most of the response to inter-annual variations in vegetation and snow phenology could be explained by individual behavioral plasticity. Nonetheless, females appear to be less plastic than males in their timing of spring migration, likely due to the parturition period following migration forcing them to trade off foraging needs with predation risk. As the identified drivers of ibex migration are known to be and will continue to be largely impacted by climate change, the capacity of ibex to respond to such rapid changes could differ between sexes. </span></p> <p> </p> <p> </p>
Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum
<p>Here we provide the data for the paper "Intrinsic and synaptic determinants of receptive field plasticity in Purkinje cells of the mouse cerebellum". The dataset is saved as MAT-file (version 7.0). The source code for analysis is saved in github. Folder names indicate the contents corresponding to the specific figures in the paper.</p>
Experimental data for "The interaction between plastics and microalgae affects community assembly and nutrient availability"
<p>Dataset of the experimental data obtained for the study “The interaction between microplastics and microalgae affects community assembling and nutrient availability” (published on Communications Earth and Environment, DOI: 10.1038/s43247-024-01706-y). This include 5 different tabular files, which are listed below:</p> <p><strong>Algae growth</strong> Values of chlorophyll fluorescence (as a proxy of algal biomass growth, in arbitrary units) in all treatments between days 1 and 17 of the experiment in the 4 different replicates (shown as different columns).</p> <p><strong>Biofilm growth on plastic</strong> Measures of biofilm coverage (in % of plastic fragment's surface) via image analysis after optical microscopy and chlorophyll fluorescence via spectroscopy (after the analysis of 3 replicates per batch, relative standard deviation below 20%). Data at day 0 indicate the fragments before the incubation with the pelagic community. Data are shown for each treatment containing plastic (i.e., <em>plastic</em>, <em>biofilm</em> and <em>dispersal</em>).</p> <p><strong>Nutrient concentrations</strong> Nutrient concentration in every replicate at different days from the beginning of the experiment. Data are average values after three measure replicates (relative standard deviation below 5%). Data below LODs are shown as LOD/2.</p> <p><strong>Pelagic community composition </strong>Counting values of the different algal species from optical microscopy measurement of all treatments after 5, 8 and 15 days (average values after 3 replicates of measures (relative standard deviation below 25%). The inoculum of the pelagic community before the beginning of the experiment is also included. Species not present in the community or not detected are shown as ND.</p> <p><strong>Photosynthetic efficiency </strong>Values of photosynthetic efficiency (measured with pulse-amplitude-modulated fluorescence) in all treatments at day 5, 8 and 15 of the experiment in the 4 different replicates (shown as different columns).</p>
Single-cell Roadmap dataset "Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment" (Snabel et al.)
<p>View the temporal single-cell transcriptomics data (UMAP, PCA, Heatmaps and Violin plots) using the Shiny App interface of iSEE (<a href="https://doi.org/10.12688/f1000research.14966.1">doi:10.12688/f1000research.14966.1</a>) for easy visualization of the single-cell data described in "Single-cell roadmap of cardiac differentiation identifies roles for ZNF711 and retinoic acid in balanced epicardial and cardiomyocyte lineage commitment" (Snabel et al., bioRXiv).</p> <p>For instructions on how to use this data, please visit https://github.com/Rebecza/scRoadmap_CardiacDiffs/.</p>
FIGURE 5 Hydrolagus mirabilis Collet, 1904 in Holocephalan (Chondrichthyes) dental plates with hypermineralized dentine as a substitute for missing teeth through developmental plasticity
FIGURE 5 Hydrolagus mirabilis Collet, 1904, μCT-scans. (a) Upper dentition in oral view, including anterior dental plate with ridges on the lingual surface of the dental plate. (b) Upper dentition rendered (Avizo) showing ovoids and rods of hypermineralized dentine in the both dental plates and tritoral pads on the posterior plate. (c) Oral view, with posterior dental plate cut away to show the posterior face of the anterior dental plate and lingual ridges. (d) and (e) Anterior dental plate, cut away to show section through developing ovoids (hypermineralized), surrounding trabecular dentine, sclerotic (hypermineralized) trabecular dentine and the ridges. The double-headed arrow in (e) indicates correspondence of developing ovoids and lingual ridges. (f) Anterior and posterior dental plates in symphyseal view, with opposing plates cut away to show the symphyseal face of the anterior plate and the ridges. Numbered arrows mark different regions of the plate as in Figures 2f, 3e and 4f. Abbreviations as in previous figures
FIGURE 8 in Holocephalan (Chondrichthyes) dental plates with hypermineralized dentine as a substitute for missing teeth through developmental plasticity
FIGURE 8 Chimaera monstrosa, μCT-scans, sub-adult upper dentitions (a) from Figure 1 and (b) from Figure 3a–e, with the rod series explained as whitlockin formed to a timed order at the aboral surface in the trabecular dentine, determined by a dental epithelium, where on the lingual side ridges of the outer dentine layer form (Figure 8b, also Figures 1a, 2b and 3d–e). (a) Partially segmented upper dentition (Avizo) showing three rods of the anterior plate, 2 aligns with the rods of the posterior plate, 0 forms in the symphyseal segment of the plate, 1 and 2 along the labial ridge. (b) Anterior dental plate with five rods and a coloured overlay to explain the co-incidence of ridges with rods (0–4). Colours show the tissue types seen in a virtual section relative to the surface anatomy of the oral and lingual surfaces: whitlockin, orange; trabecular dentine, lime green; sclerotic osteodentine dentine, olive green; wear surface of the sclerotic dentine, moss green. Extent of wear surface is double arrow in Figure 7a. Abbreviations, in previous figures
FIGURE 4 Hydrolagus mirabilis Collet, 1904 in Holocephalan (Chondrichthyes) dental plates with hypermineralized dentine as a substitute for missing teeth through developmental plasticity
FIGURE 4 Hydrolagus mirabilis Collet, 1904, μCT-scans. (a) Upper dentition in oral view, including anterior dental plate with distinct ridges on the lingual surface of the dental plate. (b) Upper dentition rendered (Avizo) showing ovoids and rods of hypermineralized dentine (whitlockin) in both dental plates. Red arrowheads on the developing tritoral pad on the left side of the image showing ovoids being added to form the pad. (c) Upper dentition in oral view, with posterior dental plate cut away to show ridges on the anterior dental plate. (d) and (e) Anterior dental plate, cut away to show section through developing ovoids (hypermineralized), surrounding trabecular dentine, sclerotic (hypermineralized) trabecular dentine and the ridges. (f) Anterior and posterior dental plates in symphyseal view, with opposing plates cut away to show symphyseal face of the anterior plate and the ridges. Numbered arrows indicate different regions of the plate (as in Figures 2f and 3e). Abbreviations as in previous figures
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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.