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978 results for “Instability”
Proton Cyclotron Waves and Pickup Ion Ring Distribution Instabilities Upstream of Mars
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Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability
<p>"Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability", F. Raynaud, M. Mina, D. Tavernari and G. Ciriello</p> <p>These files are necessary to generate the supplementary table containing:</p> <p>#Sample_name #Cancer_type #Cancer_subtype #Mean_reads_per_mutations #Number_of_mutations #Number_of_altered_segments #Number_of_clones #TreeScore #Number_of_mutations_first_clone #Number_of_mutations_other_clones</p> <p>REQUIREMENTS</p> <p>Phylogenies generated by PhyloWGS (PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors](<a href="http://genomebiology.com/2015/16/1/35">http://genomebiology.com/2015/16/1/35</a>), Deshwar et al.)</p> <p>Output files from PhyloWGS for each sample:</p> <ul> <li> <p>top_k_trees which contains the best phylogenies (50 by default) with the label of each clone, the population frequency of each clone, the number of children of each clone, number of mutations in the clone, the labels of the mutations</p> </li> <li> <p>top_k_trees1, top_k_trees2, ... , top_k_treesN output file for the best k trees (50 by default)</p> </li> </ul> <p>FILES</p> <p>*Molecular data for the tumor types: CESC, UCEC, UVM, THCA, KICH, BRCA, SKCM, ACC, CRC, STAD, BLCA, LUAD, KIRP, PRAD, LIHC; has been collected in July 2015 *Molecular data for the tumor types: SARC, PAAD, MESO, LGG, GBM, DLBC, UCS, THYM, TGCT, PCPG, OV, LUSC, LAML, KIRC, HNSC, ESCA, CHOL; has been collected in 2018</p> <p>from the FireHose (<a href="https://gdac.broadinstitute.org/">https://gdac.broadinstitute.org/</a>) and cBioPortal (Cerami et al., 2012) (<a href="http://www.cbioportal.org/">http://www.cbioportal.org/</a>) data repositories for The Cancer Genome Atlas (TCGA). Only TCGA datasets publicly available at that time were used in our study.</p> <p>-Mutation files (MAF format): combined_2015_2018_MAF.maf.bz2</p> <p>-Copy number segmentation files: combined_seg_2015_2018.seg.bz2</p> <p>-analyze_public.py: Python file to generate the Supplementary Table run: python2.7 analyze_public.py</p> <p>- All input data and results from PhyloWGS: PhyloWGS_input_output.tar.bz2 </p>
Fig. 4 a in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 4 a Lateral view of the red finned Mahseer, T. tor shows hypertrophied lip structures (EU714120). b Ventral and Lateral view of head and anterior part of body of T. tor (EU714120)
Fig. 12 in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 12 Barcode gap analysis of Mahseer species as generated by Automatic Barcode Gap Discovery (Puillandre et al. 2012). Distributions of K2P distances and between each pair of specimens for the COI gene,
Fig. 8 A in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 8 A Lateral view of the Tor from River Tons (HQ609728). Ai Ventral and lateral view of head and anterior part of body of Tor from River Tons (HQ609728). B Lateral view of the Tor from River Sank. (HQ609726), Bi Lateral view of head and anterior part of body of Tor from River Sank (HQ609726)
Fig. 9 a in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 9 a Lateral view of the Tor from River Krishna (EU714115). b Ventral and lateral view of head and anterior part of body of Tor from River Krishna (EU714115)
Fig. 2 A in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 2 A Lateral view of yellow finned Mahseer, T. putitora (Hamilton) (GQ469809) and morphotypes. Ai Side ventral T. putitora (GQ469822). Aii Lateral view of head showing normal lip structure of T. putitora (GQ469822). Bi Side ventral view of morphotype I of T. putitora (GQ469815). Bii Lateral view of lips and head part showing small medium lobe in lower lip of T. putitora (GQ469815). Ci Side ventral view of morphotype II of T. putitora (GQ469824). Cii Lateral view of head showing thick lips and lower lips with thick medium lobe morphotype II of T. putitora (GQ469824)
Fig. 10 in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 10 Maximum likelihood (ML) tree developed based on Dloop sequences of mahseers. Numbers represent node supports inferred from ML bootstrap analyses (only values above 50 are shown), ML tree using Hasegawa Kishino Yano with Gamma (HKY+G); α =1.1750, I=0.2787, −lnL=1958.8831. Bootstraps estimated are derived from 500 replications
Fig. 1 Map showing major drainages and mahseer collection localities across India. 1 River Tawi, Jammu. 2 River Beas, Pong. 3 River Beas, Pathankot. 4 River Satluj, Nangal. 5 River Yamuna, Yamuna nagar. 6 River Ganga, Rishekesh. 7 River Bhagirathi. 8 River Kosi, Ramnagar. 9 River Sharda, Tanakpur. 10 River Gerua, Katarnia Ghat. 11 in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 1 Map showing major drainages and mahseer collection localities across India. 1 River Tawi, Jammu. 2 River Beas, Pong. 3 River Beas, Pathankot. 4 River Satluj, Nangal. 5 River Yamuna, Yamuna nagar. 6 River Ganga, Rishekesh. 7 River Bhagirathi. 8 River Kosi, Ramnagar. 9 River Sharda, Tanakpur. 10 River Gerua, Katarnia Ghat. 11 River Tista, Mal/Udalabadi. 12 River Jaldhaka, Bindhu. 13 River Ziyabharali, Bhlukpong. 14 River Dikrong, Doimukh. 15 River Sank, Gwalior. 16 River Tons, Chackghat. 17 River Tawa, Itarsi. 18 River Mahanadi, Sambhalpur. 19 River Krishna. 20 River Chaliyaar, Nilambur. 21 River Chalakudy, Puzha
Proton temperature anisotropy constraint associated with alpha beam instability in the solar wind
<p>Simulation data and code repository for the paper "Proton temperature anisotropy constraint associated with alpha beam instability in the solar wind". This repository contains the particle-in-cell hybrid simulation code based on CAM-CL scheme and the simulation results. The parameter files are also included in the archived tar file. Another package contains the files for the data used in the paper.</p> <p> </p>
Peptide Pool Instability of Precancerous Lesion in Rats with Model of Chronic Pancreatitis and/or Without Type 1 Diabetes Mellitus
<p><span><strong>Supplementary table 1. </strong>Data of Shapiro-Wilk (W) normality test and Homogeneity of Variance Test (Levene's F Test).</span></p> <p> </p> <p><span><strong>Supplementary table 2. </strong>Kruskal-Wallis as the overall test (H-values) and posthoc Dunn's test with Bonferroni correction. The corrected α using the Bonferroni correction method is 0.017</span></p>
Data for "Instability in supernova fallback disks and its effect on the formation of ultra long period pulsars"
<p>This dataset gives the monte-carlo simulated data used in its related article, where the folder names denote the corresponding models:</p> <ul> <li>mc_r300_ref: Using T=300K as the criteria for the disk neutralization (R_neu2), and partial instability; </li> <li>mc_r300_glo: Using T=300K as the criteria for the disk neutralization (R_neu2), and global instability;</li> <li>mc_r6500_ref: Using T=6500K as the criteria for the disk neutralization (R_neu1), and partial instability;</li> <li>mc_r6500_glo: Using T=6500K as the criteria for the disk neutralization (R_neu1), and global instability.</li> </ul> <p>Each folder contains four ".data" files, corresponding to the simulated data for different time points: 1 kyr, 10 kyr, 100 kyr and 1 Myr. These files can be easily read and used to replicate our MC results.</p> <p>Moreover, reproducing our results may require the following data columns from the files:</p> <ul> <li>"ids": "=1" represents the disk can form, while "=0" not;</li> <li>"da": "=1" represents the disk can exist, while "=0" not;</li> <li> <div>"mdisk0": the initial mass (unit: solar mass) of the fallback disk;</div> </li> <li> <div>"rf0": the initial outer radius (unit: Schwartzschild radius) of the fallback disk;</div> </li> <li> <div>"alpha0": the initial disk inclination angle of the fallback disk;</div> </li> <li> <div>"p0": the initial spin period of the neutron star;</div> </li> <li>"bns0": the initial magnetic field strength of the neutron star;</li> <li>"chi0": the initial magnetic inclination angle of the neutron star;</li> <li>"*_f": the values at the specific time point (i.e. 1 kyr, 10 kyr, 100 kyr or 1 Myr);</li> <li>"omegadot": the time derivative of spin angular velocity;</li> <li>"rin", "rco", and "rlc": the inner radius, the corotation radius and the light cylinder radius;</li> <li>"n1", "n2" and "n3": the accertion torque, the torque caused by the magnetic-disk interaction and the dipole radiation torque.</li> </ul> <p>Overall, this data repository is intended to facilitate the reproduction of the results related to the Monte Carlo simulations presented in the article: Instability in supernova fallback disks and its effect on the formation of ultra long period pulsars. If you encounter any issues while using the data, please feel free to contact us at this email: y.hr@smail.nju.edu.cn</p>
Geomagnetic field instability linked to mantle activity during the Cretaceous Normal Superchron
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Data from: Body size, developmental instability and climate change
Development is often temperature-dependent. We hypothesized smaller size and larger asymmetry with increasing temperatures. However, we also predicted associations with asymmetry to differ among traits that differ in their degree of functional importance (especially the functional wings in migratory birds were predicted to be more canalized), timing of development (skeletal (femur, tarsus and humerus) vs feather (wing and tail traits). We analyzed a large dataset of which we included species with at least 20 specimens resulting in 5533 asymmetry values in 1593 individuals from 66 species. There was a consistent significant decrease in size with temperature across all traits. Fluctuating asymmetry for wings and femur was on average lower, suggesting higher canalization, and it decreased with migration distance, while that was not the case for the other traits. Fluctuating asymmetry increased with increasing temperature for wings, but not for the other characters, where the different responses of different characters to temperature was significant. Since there was no significant three-way interaction between temperature, migration distance and character, the asymmetry-temperature response was similar in migratory and resident species. These findings imply that climate warming reduces size of all traits and decreases developmental instability of wings in birds.
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</p>
Habitat instability and oxidative stress
<p>In many animal societies, dominant individuals have priority access to resources. However, defending high rank can be costly too, especially in unstable social hierarchies where there is more intense competition. Oxidative stress has been proposed as a potential cost of social dominance but few studies have examined this cost in relation to social stability. We studied the cost of social dominance in the cichlid fish <i>Astatotilapia burtoni</i> by manipulating social stability among males in replicate naturalistic communities. We found that dominant males experienced increased plasma oxidative damage compared to subordinate males in stable hierarchies only. Subordinate males in unstable hierarchies had higher plasma oxidative damage than their stable community counterparts, but we found no effect of stability treatment for dominant males. However, dominant males tended to have lower liver total antioxidant capacity (TAC) than subordinate males in unstable hierarchies, suggesting that the cost of social dominance is higher in unstable hierarchies. There was no other effect of status in tissue (liver, gonad, muscle) and various redox markers including TAC, NADPH-oxidase activity, and DNA damage. We conclude that the stability of the social environment influences the relative cost of social dominance in a tissue and marker specific manner. </p>
A Model Instability Issue in the NCEP Global Forecast System Version 16 and Potential Solutions
<p>This dataset includes the GFSv16 model source code and the scripts and data to plot the figures for the manuscript</p> <p>" A Model Instability Issue in the NCEP Global Forecast System Version 16 and Potential Solutions" submitted to GMD</p>
Dataset from: Isolation and Phase-Space Energization Analysis of the Instabilities in Collisionless Shocks
<p>We analyze the generation of kinetic instabilities and their effect on the energiza-<br> tion of ions in non-relativistic, oblique collisionless shocks using a 3D-3V simulation<br> by dHybridR, a hybrid particle-in-cell code. At sufficiently high Mach number, quasi-<br> perpendicular and oblique shocks can experience rippling of the shock surface caused by<br> kinetic instabilities arising from free energy in the ion velocity distribution due to the<br> combination of the incoming ion beam and the population of ions reflected at the shock<br> front. To understand the role of the ripple on particle energization, we devise the new<br> instability isolation method to identify the unstable modes underlying the ripple and<br> interpret the results in terms of the governing kinetic instability. We generate velocity-<br> space signatures using the field-particle correlation technique to look at energy transfer in<br> phase space from the isolated instability driving the shock ripple, providing a viewpoint<br> on the different dynamics of distinct populations of ions in phase space. We generate<br> velocity-space signatures of the energy transfer in phase space of the isolated instability<br> driving the shock ripple using the field-particle correlation technique. Together, the<br> field-particle correlation technique and our new instability isolation method provide a<br> unique viewpoint on the different dynamics of distinct populations of ions in phase space<br> and allow us to completely characterize the energetics of the collisionless shock under<br> investigation.</p>
A new non-linear instability for scalar fields
<p>This directory contains all the necessary data, codes, and notebooks to reproduce the results of the paper titled "A new non-linear instability for scalar fields" (<a href="https://arxiv.org/abs/2107.14215">https://arxiv.org/abs/2107.14215</a>).</p> <p><br> This paper has also been published as a <em>letter </em>in Physical Review D and can be found in Volume 105, Issue 2, article id.L021304, which can be accessed at this link: <a href="https://journals.aps.org/prd/abstract/10.1103/PhysRevD.105.L021304">https://journals.aps.org/prd/abstract/10.1103/PhysRevD.105.L021304</a>. </p> <p>Directories</p> <ul> <li><strong>Codes</strong>: This directory contains different codes used to generate and post-process the simulation data, including k-evolution and Latfield2.</li> <li><strong>Simulations_data</strong>: This directory includes the data for the scalar field snapshots, information about the average of the scalar field, and power spectra.</li> <li><strong>Figure_notebooks</strong>: This directory includes Jupyter notebooks to reproduce the figures presented in the paper.</li> </ul> <p>How to Use</p> <ol> <li>Download the files to your local machine.</li> <li>Navigate to the directory where the files are saved.</li> <li>Install the necessary packages</li> <li>Navigate to the "<strong>Figure_notebooks</strong>" directory and open the Jupyter notebooks in your preferred environment.</li> <li>Run the cells in the notebooks to reproduce the figures.</li> <li>Navigate to the "codes" directory and use the appropriate code to generate and post-process the simulation data.</li> <li>Navigate to the "data" directory to access the simulation data.</li> </ol> <p><br> If you have any feedback or request feel free to email farbod.hassani@gmail.com</p>
Two-stream instability dataset from Particle-In-Cell code OSIRIS
<p>This is data of a particle-in-cell (PIC) simulation of the electrostatic two-stream instability; the PIC code used was OSIRIS [1].</p> <p>This dataset was used in [2] to demonstrate the possibility of data-driven inference of the Vlasov equation (which governs the evolution of the plasma distribution function in phase space) using sparse regression techniques [2,3].</p> <p>The details of the simulation are as follows:</p> <p>1. The simulation is in one spatial dimension and particle velocities are restricted to that same dimension (i.e. the phase space is 1D1V)</p> <p>2. The physical setup consists of two symmetrically counter-streaming populations of electrons at +/- 0.2c, where c is the speed of light; each beam has a thermal velocity of 0.04c. Each beam has equal densities, corresponding to n_0/2, where n_0 is the reference density of the simulation. There is a charge neutralizing background of immobile ions.</p> <p>3. The system size is 10c/wpe, where c/wpe is the plasma skin depth associated with the reference density n_0. The simulation domain has periodic boundary conditions.</p> <p>4. Each stream of electrons is represented by 10^4 particles per cell. Quadratic particle shapes are used.</p> <p>5. The standard Yee solver is used to advance the electromagnetic field. Particles are advanced using the relativistic Boris algorithm. The Esirkepov scheme used for the current deposit to ensure charge conservation. No current smoothing is used.</p> <p> </p> <p><strong>References:</strong></p> <p>[1] R. A. Fonseca, L. O. Silva, F. S. Tsung, V. K. Decyk, W. Lu, C. Ren, W. B. Mori, S. Deng, S. Lee, T. Katsouleas, and J. C. Adam, <em>Osiris: A three-dimensional, fully relativistic particle in cell code for modeling plasma based accelerators</em>, Lect. Notes Comput. Sci. 2331, 342 (2002).</p> <p>[2] E. P. Alves and F. Fiuza, <em>Data-driven discovery of reduced plasma physics models from fully kinetic simulations</em>, Phys. Rev. Research 4, 033192 (2022).</p>
ScienceDex guides
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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.