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1,067 results for “perturbation”
The origin and diversification of pteropods predate past perturbations in the Earth's carbon cycle
<p>This study examines the taxonomy of pteropods and their divergence time using phylogenomics by incorporating 21 new species and new fossil evidence. In agreement with traditional taxonomy, we recovered the first molecular support for a division between sea butterflies (Thecosomata) and sea angels (Gymnosomata). Molecular dating demonstrated that these two lineages diverged in the early Cretaceous, and that all main pteropod clades, including shelled, partially-shelled and unshelled groups, diverged in the mid to late Cretaceous. This datasets includes the following files: </p> <ul> <li>'pteropods_May18_s7.cali': fossil calibrations used for molecular dating </li> <li>'Concat-Ptero200.phy.gz': reduced alignment with 200 marker genes showing highest support</li> <li>'Concat-Ptero040317.phy.gz': main alignment of 2654 marker genes </li> <li>'OMA-alis.tgz': individual alignments for each marker gene</li> <li>'Ptero200_PBcatgtr.tgz': phylobayes run files on the reduced 200 genes dataset</li> <li>'Ptero040317_examl.tgz': examl run files on the main 2654 markers alignment</li> <li>'pteropods_May18_s7_cir_sb_bd.tgz'z: phylobayes molecular dating run with log-normal model </li> <li>'pteropods_May18_s7_ugam_sb_bd.tgz': phylobayes molecular dating run with UGALM model </li> </ul>
Perturbation drives changing metapopulation dynamics in a top marine predator
Metapopulation theory assumes a balance between local decays/extinctions and local growth/new colonisations. Here we investigate whether recent population declines across part of the UK harbour seal range represent normal metapopulation dynamics or are indicative of perturbations potentially threatening the metapopulation viability, using 20 years of population trends, location tracking data ( n = 380), and UK-wide, multi-generational population genetic data ( n = 269). First, we use microsatellite data to show that two genetic groups previously identified are distinct metapopulations: northern and southern. Then, we characterize the northern metapopulation dynamics in two different periods, before and after the start of regional declines (pre-/peri-perturbation). We identify source–sink dynamics across the northern metapopulation, with two putative source populations apparently supporting three likely sink populations, and a recent metapopulation-wide disruption of migration coincident with the perturbation. The northern metapopulation appears to be in decay, highlighting that changes in local populations can lead to radical alterations in the overall metapopulation's persistence and dynamics.
Atmospheric responses to partial SST perturbations simulated by MIROC5 and 6
<p>Ogura, T. and Webb, M. J., Positive low cloud feedback primarily caused by increasing longwave radiation from the sea surface in climate models.</p> <p>Files in netCDF format contain data from Figs.1-4 and Figs. S1-S6 in the above manuscript.</p> <p>All data are monthly climatology.</p> <p>Any queries please contact Tomoo Ogura ogura@nies.go.jp</p>
Data from: Genetic perturbation of key central metabolic genes extends life span in Drosophila and affects response to dietary restriction
There is a connection between nutrient inputs, energy-sensing pathways, lifespan variation and aging. Despite the role of metabolic enzymes in energy homeostasis and their metabolites as nutrient signals, little is known about how their gene expression impacts lifespan. In this report, we use P-element mutagenesis in Drosophila to study the effect on lifespan of reductions in expression of seven central metabolic enzymes, and contrast the effects on normal diet and dietary restriction. The major observation is that for five of seven genes, the reduction of gene expression extends lifespan on one or both diets. Two genes are involved in redox balance, and we observe that lower activity genotypes significantly extend lifespan. The hexokinases also show extension of lifespan with reduced gene activity. Since both affect the ATP/ADP ratio, this connects with the role of AMP-activated protein kinase as an energy sensor in regulating lifespan and mediating caloric restriction. These genes possess significant expression variation in natural populations, and our experimental genotypes span this level of natural activity variation. Our studies link the readout of energy state with the perturbation of the genes of central metabolism and demonstrate their effect on lifespan.
Data from: Quantifying human mobility perturbation and resilience in Hurricane Sandy
Human mobility is influenced by environmental change and natural disasters. Researchers have used trip distance distribution, radius of gyration of movements, and individuals' visited locations to understand and capture human mobility patterns and trajectories. However, our knowledge of human movements during natural disasters is limited owing to both a lack of empirical data and the low precision of available data. Here, we studied human mobility using high-resolution movement data from individuals in New York City during and for several days after Hurricane Sandy in 2012. We found the human movements followed truncated power-law distributions during and after Hurricane Sandy, although the β value was noticeably larger during the first 24 hours after the storm struck. Also, we examined two parameters: the center of mass and the radius of gyration of each individual's movements. We found that their values during perturbation states and steady states are highly correlated, suggesting human mobility data obtained in steady states can possibly predict the perturbation state. Our results demonstrate that human movement trajectories experienced significant perturbations during hurricanes, but also exhibited high resilience. We expect the study will stimulate future research on the perturbation and inherent resilience of human mobility under the influence of hurricanes. For example, mobility patterns in coastal urban areas could be examined as hurricanes approach, gain or dissipate in strength, and as the path of the storm changes. Understanding nuances of human mobility under the influence of such disasters will enable more effective evacuation, emergency response planning and development of strategies and policies to reduce fatality, injury, and economic loss.
Data from: Selection at the Esterase-2 locus of Drosophila buzzatii? Perturbation-reperturbation experiments
Apparent selection affecting starch gel electrophoretic alleles at the Esterase-2 locus of Drosophila buzzatii has been detected in laboratory and natural populations. Perturbation-reperturbation of allele frequencies in replicated laboratory populations attempts to test direct selective effects at the locus versus effects of linked loci. Sequential gel electrophoresis has identified more alleles within starch classes, and three of these alleles (within the a, b and c starch alleles) were used in cage population experiments. Allele a/1.00/1.00/1.00 was set up in 10 replicate populations with allele c/1.00/1.00/1.00, and in an independent 10 replicate populations with allele b/0.99/1.01/1.00. For each set, three reperturbations were done. Replicate populations generally showed similar patterns of allele frequency change and clear directionality: effects of selection, not drift. However, four populations deviated from their replicates, indicating dissipation of linkage disequilibrium. Estimates of pre-adult viability in the F2 of pair-wise crosses among 12 sequential gel electrophoretic alleles showed very variable modes of inheritance and relative viability fitnesses. Together with the diversity of patterns of allele frequency change in the cage populations, these results suggest a gene complex, with selection acting on an interacting set of loci which may include Esterase-2.
Data from: Predicting species' vulnerability in a massively perturbed system: the fishes of Lake Turkana, Kenya
Background and Trophic Diversity Study: Lake Turkana is an understudied desert lake shared by Kenya and Ethiopia. This system is at the precipice of large-scale changes in ecological function due to climate change and economic development along its major inflowing river, the Omo River. To anticipate response by the fish community to these changes, we quantified trophic diversity for seven ecological disparate species (Alestes baremose, Hydrocynus forskalli, Labeo horie, Lates niloticus, Oreochromis niloticus, Synodontis schall, and Tilapia zillii) using stable isotopes. Based on their marked morphological differentiation, we postulated that dietary niches of these species would be similar in size but show little overlap. The degree of trophic diversity varied greatly among the species studied, refuting our hypothesis regarding dietary niche size. Oreochromis niloticus and L. niloticus had the highest trophic diversity and significantly larger dietary niches than T. zillii, A. baremose and H. forskalli. Low overlap among the dietary niches of the seven species, with the exception of the synodontid catfish S. schall, is consistent with our second hypothesis. Predicting Species' Vulnerability: Breeding vulnerability was highest among those species with the lowest trophic diversity. We predict that in suffering two strikes against them, A. baremose, H. forskalli, T. zillii, and L. horie will be most affected by the highly altered Lake Turkana ecosystem and that O. niloticus, L. niloticus and S. schall will be least affected. Low vulnerability among O. niloticus and L. niloticus is promising for the future of the lake's fishery, but the third most important fishery species (L. horie) will be highly vulnerable to impending ecosystem change. T. zillii should be treated as separate from O. niloticus in the fishery given higher sensitivity and a different ecological role. We see potential for expansion of the fishery for S. schall but don't recommend the development of a fishery for A. baremose and H. forskalli.
Data from: Spatially heterogeneous perturbations homogenize the regulation of insect herbivores
Anthropogenic influences on resources and consumers can affect food web regulation, with impacts on trophic structure and ecosystem processes. Identifying how these impacts unfold is challenging because alterations to one or both resources and consumers can similarly transform community structure, especially for intermediate consumers. To date, empirical testing of perturbations on trophic regulation has been limited by the difficulty in separating the direct effect of perturbations on species composition and diversity from those unfolding indirectly via altered feeding pathways. Moreover, disentangling the independent and interactive impacts of covarying stressors that characterize human-altered systems has been an ongoing analytical challenge. We used a large-scale metacommunity experiment in grasslands to test how resource inputs, stand perturbation, and spatial factors affect regulation of insect herbivores in tritrophic grassland food webs. Using path-model comparisons, we observed significant simplification of food web regulation on insect herbivores, shifting from mixed predator-resource regulation in unaltered mainland areas to strictly resource-based regulation with landscape perturbation and fragmentation. Most changes were attributed to homogenization of plant community caused by landscape fragmentation and the deterministic influence of eutrophication that reduced among-patch beta diversity. This led to a simplified food web dominated by fewer but more abundant herbivore taxa. Our work implies that anthropogenic perturbation relating to resources and spatial isolation can transform the regulation of food web diversity, structure, and function.
Data from: Environmental perturbation, grazing pressure and soil wetness jointly drive mountain tundra toward divergent alternative states
1. Plant communities are structured by complex interactions between multiple factors, which veil our understanding of the effects of environmental changes on communities and ecosystems. Besides the relative role of biotic and abiotic factors as community-structuring processes, addressing how they jointly affect the ecological resilience and resistance of plant communities is crucial to understand better the long-term response of communities facing global changes. 2. Here, we used the results from a long-term (23 years) perturbation experiment set up in Fennoscandian mountain tundra to test these mechanisms. The experiment consisted of a transplantation of twenty blocks of Vaccinium myrtillus heath vegetation including upper soil layer from a lower elevation tundra heath habitat to a snowbed habitat 150 m higher in elevation where V. myrtillus lies at its upper limit. In the snowbed with contrasting levels of soil wetness, half of the transplanted blocks were protected from mammalian herbivores. 3. Our results revealed that in addition to the important role of environmental conditions as a structuring force, the joint effects of multiple drivers resulted in divergent patterns in both plant functional composition and species diversity among transplanted communities. Under environmental perturbation (i.e. transplantation to snowbed), the heath vegetation was altered by grazing pressure that reduced the cover of shrubs (especially V. myrtillus). In grazed dry snowbed, a species rich community with high functional type evenness and diversity developed. Reversely, in dry exclosures, V. myrtillus gained high dominance associated with only few graminoids and forbs. In wet snowbed conditions, shrubs tended to decline both in grazed plots and exclosures whereas bryophytes attained high abundance. Grazing promoted species richness while soil waterlogging tended to promote among-plot heterogeneity (β-diversity) which was highest in wet exclosures. 4. Synthesis Our long-term experiment reveals that environmental perturbation, grazing and soil wetness exhibit joint effects that induce divergent trajectories of tundra plant communities. We suggest that a strong environmental perturbation triggers mountain tundra heath community to move away from its equilibrium state. The outcome of this shift depends on the interplay between grazing pressure and soil wetness that drive tundra plant communities toward divergent alternative states.
Data from: Biogeographical scenarios modulate seagrass resistance to small-scale perturbations
1. Seagrasses constitute a key coastal habitat worldwide, but are are exposed to multiple perturbations. Understanding elements affecting seagrass resistance to disturbances is critical for conservation. Distinct biogeographical scenarios are intrinsically linked with varying ecological and evolution backgrounds shaped across millennia. 2. We addressed whether the resistance (change in shoot abundances) and performance (change in leaf morphology and growth) of the seagrass Cymodocea nodosa to a local stressor, light reduction, varied across three regions (Southeast Iberia, the Balearic Sea and the Canaries) within the temperate northern Atlantic realm. We hypothesized that distinct biogeographical scenarios, in terms of distinct ecological/environmental conditions and genetic diversity of meadows, would affect seagrass resistance and performance, with flow-on effects on associated epifauna. The same experiments, in terms of shading intensities, timing and duration, were replicated at three seagrass meadows within each region. 3. Results demonstrated inter-regional variation in the resistance and performance of C. nodosa. Under moderate and high shading, shoot abundance was abruptly decreased, relative to controls, in the Canaries with concurrent, but less accentuated, changes in leaf morphology and no changes in growth. In the other two regions, however, moderate and high shading had a negligible effect on shoot abundance, leaf morphology and growth. Shading had no overall effect over the total abundance and assemblage structure of epifauna; these faunal attributes, however, varied between regions. Low seagrass resistance at the Canaries is linked with the peripheral distribution of the species there, favoring isolation and decreased genetic diversity. 4. Synthesis. Different biogeographical scenarios shape seagrass resistance to local perturbations. From a conservation perspective, if resistance differs among biogeographical scenarios, universal conservation rules for seagrasses are challenging.
Ground magnetic perturbation due to external ionospheric current for a solar minimum and maximum year
The ground magnetic perturbations are calculated using the 3D ionospheric current system based on a stand-alone electrodynamo module using the neutral winds, ionospheric conductivities and high latitude potential from the Thermosphere-Ionosphere-Electrodynamics GCM (TIEGCM). The TIEGCM is driven at its 97 km lower boundary by 27 day averaged diurnal perturbations from a Thermosphere-Ionosphere-Mesosphere-Electrodynamics GCM (TIMEGCM) simulation using MERRA reanalysis data at the 30km TIMEGCM boundary. For details of the TIEGCM simulation please see Maute (2017). Effects of gravity and plasma pressure gradient driven ionospheric currents are included. At high latitude the Heelis ion convection is employed driven by 3-hourly Kp values. Two TIEGCM simulations are conducted, one for the solar minimum year 2009 and one for the solar maximum year 2002 by using the corresponding F10.7 and Kp values for that year. The lower boundary of TIEGCM, which simulates year 2009 conditions, was not changed for the 2002 simulation, since the 2002 simulation was used to derived dominant ionospheric current patterns and not to study the evolution of the current system. The data set is associated with the manuscript "Modeling Diurnal Variation Magnetic Fields due to Ionospheric Currents" by G. Egbert, P Alken, A. Maute and H. Zhang submitted to Geophysical Journal International.
Ground magnetic perturbations associated with "Ultra-Fast Kelvin Wave (UFKW) Variations in the Surface Magnetic Field"
<p>The data set is based on the thermosphere-ionosphere-electrodynamics general circulation model (TIEGCM) simulation results and a post-processing 3D ionospheric current and magnetic perturbation calculation, which is used in the publication "Ultra-Fast Kelvin Wave (UFKW) Variations in the Surface Magnetic Field" by Forbes et al. Focus is on an eastward-propagating ultra-fast Kelvin wave (UFKW) packet with periods between 2-4 days and zonal wavenumber s = -1 during DOY 266-281, 2009. Two sets of simulations are provided with different lower boundary (97km) conditions: 1. forced by daily and zonal mean (S0) 2. forced by S0 and 2-7days with s=-1 perturbations with the planetary wave amplitudes increased by a factor of 1.5. For these simulations the solar flux and geomagnetic forcing is held constant. Hourly output is provided of the neutral wind, neutral temperature, and ground magnetic perturbations.</p>
CLM5 Perturbed Parameter Ensembles
<p>These data are the results of parameter sensitivity simulations and multiple perturbed parameter ensembles (PPE) with the Community Land Model, version 5 (CLM5). These simulations form the basis of a publication documenting a machine learning approach to studying parameter uncertainty in CLM5.</p> <p>The parameter sensitivity simulations include thirty-four CLM5 biophysical parameters perturbed one at a time to their minimum and maximum values, as well as a control simulation with default parameter values. The output files are labeled by the parameter name with "_min" or "_max" to denote simulation type, where each file includes 5 years of monthly output. The simulation with default parameter values includes 30 years of monthly output, labeled "CLM_control".</p> <p>The PPE simulations include six of the aforementioned parameters perturbed simultaneously. We use Latin Hypercube (LHC) sampling to generate 100 unique parameter sets for the top six parameters identified by the sensitivity simulations. There are two 100-member PPEs with present-day climate forcing conditions, but each uses a different LHC sampling. The output files are labeled "PPE_x" and "PPE_v2_x" with the ensemble member x from 1 to 100. There is also a simulation with default parameter values labeled "PPE_control". Again each file includes 5 years of monthly output.</p> <p>We test optimized parameter values with CLM, the results of which are labeled "CLM_test_calibration", and this file also includes 5 years of monthly output.</p>
Snow-Induced Perturbations in Nitrous Acid (HONO) Levels: Insights into Heterogeneous Reactions During Wintertime in Mid-Latitude Regions
<ol> <li>Variations in HONO, PM2.5, NO2, and HONO/NO2 concentrations data</li> <li>Time series data of pollutants</li> </ol>
MME-only models trained with lightly perturbed data for JAMES paper "Machine-learned uncertainty quantification is not magic"
<p>This tar file contains all 100 trained models in the MME-only ensemble from Experiment 2 (i.e., those trained with lightly perturbed data). To read one of the models into Python, you can use the method neural_net.read_model in the ml4rt library.</p>
MME/CRPS models trained with lightly perturbed data for JAMES paper "Machine-learned uncertainty quantification is not magic"
<p>This tar file contains all 100 trained models in the MME/CRPS ensemble from Experiment 2 (i.e., those trained with lightly perturbed data). To pare the ensemble down to 50 models, we randomly select 50. To read one of the models into Python, you can use the method neural_net.read_model in the ml4rt library.</p>
Phonons from Density-Functional Perturbation Theory using the All-Electron Full-Potential Linearized Augmented Plane-Wave Method FLEUR
<p>The archive files contain the input and result files for the corresponding publication in IOP Electronic Structure - Technical Notes, as well as a short python script to plot them.</p>
Negative Stain Electron Microscopy Datasets for alphaB-crystallin NT-IXI perturbed mutants in fibrillar and cage-like morphologies
<p>Negative stain datasets for alphaB-crystallin NT-AXA mutant. Contains two datasets, one for the fibrillar morphology (93 micorgraphs) and another for the cage-like morphology (119 micrographs)</p> <p>Images were taken on a Thermo Fisher Tecnai T-12 microscope equipped with a BM-Eagle detector at a calibrated pixel size of 4.37<span>Å/px</span></p>
Data for Numerical Simulation of Tornado-like Vortices Induced by Small-Scale Cyclostrophic Wind Perturbations
Open the record for dataset details and reuse information.
Simulated geomagnetic perturbation data at several geomagnetic observatories for 23 July 2012 event
<p>The data file incudes the simulated geomagentic perturbations data at 29 geomagnetic observatories for a super solarstorm event on 23 July 2012. The geomagnetic perturbations are calculated by the Space Weather Modeling Framework (SWMF).</p> <p> </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.