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978 results for “instabilities”
Data from: A new trophic specialization buffers a top predator against climate-driven resource instability
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Pulsational pair-instability supernovae in very close binaries
<p>Models of pulsational pair-instability supernovae arising from the evolution of metal poor helium stars. These simulations have been made with the MESA software instrument for stellar evolution, and are used in the paper <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...882...36M/abstract">"Pulsational pair-instability supernovae in very close binaries"</a>. Data includes machine-readable tables, both history and profile files from the simulations, as well as the terminal output and a movie for each. All MESA output files have been post-processed to reduce their size. All the code used to process the MESA simulations and produce figures is provided in a jupyter-notebook.</p> <p>WARNING: Simulations were done using a development MESA version (11123) rather than an official release. </p> <p>List of files:</p> <p>- template.tar.xz: MESA work folder to reproduce the simulations.</p> <p>- xxx_xx.tar.xz: Each of these files contains stellar profiles at different moments of evolution for one simulation.</p> <p>- histories.tar.xz: MESA history files for each simulation, containing the time evolution of quantities that are single-valued at each moment in time.</p> <p>- preSN.tar.xz: profiles for stars before the onset of pulsations (see paper for definition).</p> <p>- movies.tar: Movies for all simulations, produced using MESAs pgstar.</p> <p>- terminal_output.tar.xz: Terminal output from the simulations.</p> <p>- masses_table.txt: Machine readable version of Table 1 in the paper.</p> <p>- pulse_tables.tar.xz: machine readable tables containing mass lost, time, and kinetic energy of each pulse.</p> <p>- notebook.tar.xz: jupyter-notebook plus complementary files used to post-process the data and produce Figures.</p> <p>This version of the files has an updated notebook.tar.xz to produce the figures in the published version of the paper.</p>
Data from: Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells
<p>CSV files of whole-Genome Knockout Screens for Proliferation and Tumorigenic Growth. The data is retrieved from:</p> <p>Title: "Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells"</p> <p>DOI: https://doi.org/10.1016/j.celrep.2020.03.029</p> <p>The excel sheet with data shown in figure 1B is converted to CSV files.</p>
Extreme developmental instability is associated with the pea aphid wing plasticity
A key focus of evolutionary developmental biology is on how phenotypic diversity is generated. In particular, both plasticity and developmental instability can contribute to phenotypic variation among genetically identical individuals, but the interactions between the two phenomena and their general fitness impacts are unclear. We discovered a striking example of asymmetry in pea aphids: the presence of wings on one side and the complete or partial absence of wings on the opposite side. We used this asymmetric phenotype to study the connection between plasticity, developmental instability, and fitness. We found that this asymmetry equally affects both sides and thus is a developmental instability; is present in some genetically unique lines but not others and thus has a genetic basis; and has intermediate levels of fecundity, and thus does not necessarily have negative fitness consequences. We conclude that this dramatic asymmetry may arise from incomplete switching between developmental targets, linking plasticity and developmental instability. We posit that what we have observed may be a more widespread phenomenon, occurring across species that routinely produce distinct, alternative phenotypes.
Data from: Plasticity via feedback reduces the cost of developmental instability
<p><span>Costs of plasticity are thought to have important physiological and evolutionary consequences. A commonly predicted cost to plasticity is that plastic genotypes are likely to suffer from developmental instability. Adaptive plasticity requires that the developing organism can in some way sense what environment it is in or how well it is performing in that environment. These two information pathways—an "environmental signal" or a "performance signal" that indicates how well a developing phenotype matches the optimum in the current environment—can differ in their consequences for the organism and its evolution. Here, we consider how developmental instability might emerge as a side-effect of these two distinct mechanisms. Because a performance cue allows a regulatory feedback loop connecting a trait to a feedback signal, we hypothesized that plastic genotypes using a performance signal would be more developmentally robust compared to those using a purely environmental signal. Using a numerical model of a network of gene interactions, we show that plasticity comes at a cost of developmental instability when the plastic response is mediated via an environmental signal, but not when it is mediated via a performance signal. We also show that a performance signal mechanism can evolve even in a constant environment, leading to genotypes pre-adapted for plasticity to novel environments even in populations without a history of environmental heterogeneity.</span></p>
Stratified shear instabilities in diurnal warm layers: datasets
<p>Datasets associated with the paper "Stratified shear instabilities in diurnal warm layers" by Hughes, Moum, Shroyer, and Smyth.</p> <p>Full details in the README PDF</p>
Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?
<p>Pathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. <span>To address</span> biological complexity below the species level<span>, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr <i>Salvelinus namaycush</i> ecotypes in Rush Lake, USA. </span>A rapid phenotypic shift in body and head shape was found within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (ages 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing changes in growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.</p>
Particle-in-cell Simulation of the Neutrino Fast Flavor Instability
<p>1D_fiducial.tgz contains the input parameters and simulation output data from the fiducial simulation. Each timestamp with output data is stored in a plt* directory.</p> <p>scripts.tgz contains the data reduction and plotting scripts used in the paper. We require yt to read the data with our scripts.</p> <p>inputs.tgz contains input files for each of the simulations in the paper. The test problem inputs (MSW, bipolar, homogeneous FFI, inhomogeneous FFI) are part of the test suite in Emu.</p> <p>Simulations are run using the version of Emu (v1.1) at http://doi.org/10.5281/zenodo.4423166 or https://github.com/AMReX-Astro/Emu.</p>
Coupling Lattice Instabilities Across the Interface in Ultrathin Oxide Heterostructures
<p>Dataset corresponding to the publication 'Coupling Lattice Instabilities Across the Interface in Ultrathin Oxide Heterostructures' (ACS Materials Letters, 2020, 2, 4, 389-394), available open access at <a href="https://doi.org/10.1021/acsmaterialslett.9b00540">https://doi.org/10.1021/acsmaterialslett.9b00540</a></p>
Data from: Isolation by instability: historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene-flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability", highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.
Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
<p><span><span><span><span><span><span><span><span><span><span><span>The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. Here, we explain this association by elucidating a mutational cascade, downstream of <a>th</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>e single cell division error of chromosome bridge formation, that rapidly generates extreme genomic complexity. We show that actomyosin forces are required for initial bridge breakage and mutagenesis, following which chromothripsis accumulates with aberrant interphase replication of bridge DNA. This is then followed by an unexpected burst of DNA replication in the next mitosis, generating extensive DNA damage. During this second cell division, broken bridge chromosomes frequently mis-segregate and form micronuclei, promoting additional chromothripsis. We <a>fu</a></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>rther show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.</span></span></span></span></span></span></span></span></span></span></span></p>
Cyclic tensile-compressive tests on thin concrete boundary elements with a single layer of reinforcement prone to out-of-plane instability
<p>The growing need for residential housing in Latin American countries has led to the construction of reinforced concrete buildings with wall thicknesses as low as 8-10 cm. Such walls have typically only a single layer of vertical rebars and are therefore particularly susceptible to out-of-plane failure. To investigate the response of the corresponding wall boundary elements, twelve reinforced concrete columns with a single layer of vertical rebars were tested under tension-compression cycles. The objective of this test series was to gain insights into parameters triggering wall instability and out-of-plane failure. The experimental tests investigate the effect of thickness, reinforcement ratio, and eccentricity of the longitudinal rebars with respect to the element axis. This paper summarises the results of the test campaign. The specimen response is analysed at the global and local level, and the influence of the crack pattern on the out-of-plane response of the column and the conditions leading to out-of-plane failure are described. Furthermore, the differences between members with a single layer of vertical rebars to members with two layers are discussed. The influence on the response of the parameters analysed in the experimental campaign is addressed, showing that section with small thickness and large reinforcement content are more prone to out-of-plane failures. Finally, the predictions of existing models are compared to the new experimental data. The entire data set is publically available.</p>
Entropy Poduction in a Box: Analysis of Instabilities in Confined Hydrothermal Systems
<p>This data set was generated using the numerical tool SHEMAT suite. All relevant input and output files are given here for the scenarios discussed in our manuscript: (1) onset of convection, varying box geometry for (2) homogeneous models, and (3) heterogeneous models.</p> <p>Additionally, some Matlab files show how the simulation results are analyses d in terms of the entropy production.</p>
Dark Matter Annihilation and Pair Instability Supernovae
<p>Reproduction package for the paper "Dark Matter Annihilation and Pair Instability Supernovae".</p>
Data from: Friction and instability of glaucophane gouges at blueschist temperatures support abundance of intermediate-depth earthquakes
<p>Fluid release from the hydraulically-confined dehydration of blueschist minerals may significantly elevate fluid pressures and concomitantly reduce effective stresses. This is a viable mechanism to explain brittle failure and frictional instability, and it is a possible explanation for intermediate-depth earthquakes in cold subduction zones. We examine this hypothesis for glaucophane – a key index mineral for blueschist facies – at lower confining stresses where behavior is poorly understood. We conduct laboratory shear tests on glaucophane gouge at temperatures of 100–500<em>℃</em> and effective normal stresses of 50–200 <em>MPa</em>, to explore the controls of temperature, stresses and excess pore fluid pressures on fault friction. Frictional strength of glaucophane gouge at representative temperatures and stresses is ~0.70 and insensitive to temperature with a slight increase in friction coefficient at lower effective stresses. Elevating temperature promotes a transition from velocity-strengthening to mild velocity-weakening behavior, indicating the destabilizing effect of high-temperature downdip in subduction zones. Reducing effective normal stress or concomitantly elevating pore fluid pressure, potentially sourced from dehydration reactions, further strengthens the velocity-weakening response and would be manifest as moderate-sized earthquakes. This observed instability at higher temperatures or lower stresses is indexed with and accompanied by denser distributions of strongly- to moderately-localized shears in the microstructures – congruent with the observed mechanical response. Our results support the potential for enhanced unstable sliding of glaucophane gouges at lower effective stresses and at blueschist facies temperatures - and have significant implications for understanding the abundance of intermediate-depth earthquakes apparent in cold subduction zones.</p>
Chaos in Inhomogeneous Neutrino Fast Flavor Instability
<p>Data from paper "Chaos in inhomogeneos fast flavor instability".</p> <p>Dense neutrino gases exhibit complex flavor oscillations due to coherent forward scattering among neutrinos. The potentially chaotic nature of these oscillations challenges the prediction of neutrino flavor transformations in simulations. By studying small flavor perturbations in a small region within a NSM and a simplified neutrino distribution, we observe chaotic paths in the flavor state space, making micro-scale neutrino flavor changes unpredictable. However, this chaos has minimal impact on the stability of the domain-averaged neutrino density matrix, indicating that despite exponential errors, domain-averaged quantities remain reliable.</p> <p>For information regarding the data read the "information.txt" files in "nsm.tar.gz" and "fiducial.tar.gz".</p>
Whistler waves and two-stream instabilities at non-stationary quasi-perpendicular collisionless shocks
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Data for: Viral receptor-binding protein evolves new function through mutations that cause trimer instability and functional heterogeneity
<p>When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that non-native, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor binding protein (RBP) during host-range evolution. We studied the properties of the RBP of bacteriophage before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.</p>
Chromosomal instability degrades developmental phenotypes essential for anti-GD2 immunotherapy outcomes in high-risk neuroblastoma
<p>Childhood Cancer Data Initiative (CCDI)<br>dbGaP Study Accession: phs002431</p>
Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability
<p>This repository contains the data used to generate the figures in paper: Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.