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10,735 results for “dependability”
Data from: Effects of impulsive noise on marine mammals: investigating range-dependent risk
Concerns exist about the impacts of underwater noise on marine mammals. These include auditory damage, which is a significant risk for marine mammals exposed to impulsive sounds such as explosions, pile-driving, and seismic airguns. Currently, impact assessments use different risk criteria for impulsive and non-impulsive sounds (e.g. ships, drilling). However, as impulsive sounds dissipate through the environment, they potentially lose hazardous features (e.g. sudden onset) and become non-impulsive at some distance from the source. Despite management implications, a lack of data on range-dependent characteristics currently limits their inclusion in impact assessments. We address this using acoustic recordings of seismic airguns and pile-driving to quantify range-dependency in impulsive characteristics using four criteria: (i) rise time <25 ms; (ii) quotient of peak pressure and pulse duration >5,000 Pa.s-1; (iii) duration <1 s; (iv) crest factor >15 dB. We demonstrate that some characteristics changed markedly within ranges of ~10 km, and that the mean probability of exceeding criteria (i) and (ii) was <0.5 at ranges >3.5 km. In contrast, the mean probability of exceeding criteria (iii) remained >0.5 up to ~37.0 km, and the mean probability of exceeding criteria (iii) remained <0.5 throughout the range. These results suggest that a proportion of the recorded signals should be defined as impulsive based on each of the criteria, and that some of the criteria change markedly as a result of propagation. However, the impulsive nature of a sound is likely to be a complex interaction of all these criteria, and many other unrelated parameters such as duty cycle, recovery periods, and sound levels will also strongly affect the risk of hearing damage. We recommend future auditory damage studies and impact assessments explicitly consider the ranges at which sounds may lose some of their potentially hazardous characteristics.
Dependability Benchmarking of soft-core processors at different levels of design representation: MC8051, AVR and Microblaze as a case study
<p>The dataset contains the results of fault injection experiments carried out for dependability benchmarking of three soft-core processors (MC8051, AVR, Microblaze) at three design representation levels:</p> <ol> <li>Register-transfer level (RTL) HDL model;</li> <li>Implementation-level HDL model (defined in the basis of Xilinx simprim library);</li> <li>Level of FPGA prototype (Xilinx Zynq XC7Z020);</li> </ol> <p>Fault injection experiments have been carried out by means of DAVOS toolkit (<a href="https://github.com/IlyaTuzov/DAVOS">https://github.com/IlyaTuzov/DAVOS</a>). </p> <p>Installation guide is attached (readme.pdf in the package root directory).</p> <p> </p>
Data from: Temperature-dependent development and survival of an invasive genotype of wheat curl mite, Aceria tosichella
<p><strong>Filename: Development.xlsx</strong></p> <p>Variables:</p> <p>1. id_spec - specimen ID<br> 2. temp - temperature of incubation<br> 3. trial - replication ID<br> 4. larv - number of days needed to reach larva stage <br> 5. q_larv - number of days needed to reach quiescent larva stage <br> 6. nymph - number of days needed to reach nymph stage <br> 7. q_nymph - number of days needed to reach quiescent nymph stage <br> 8. adult - number of days needed to reach adult stage <br> 9. egg - number of days needed to oviposit egg of next generation </p> <p><strong>Filename: Survival.xlsx</strong></p> <p>Variables:</p> <p>1. id_spec - specimen ID<br> 2. temp - temperature of incubation<br> 3. time - number of days when individual was observed alive<br> 4. stage - developmental stage which individual reached before death<br> 5. sex - sex of an individual (F - female; M - male; NA - unknown)<br> 6. status - 0 - censored observation; 1 - observed event of death</p>
Bayesian regional flood frequency analysis with GEV hierarchical models under spatial dependency structures (code and dataset)
<p>The provided material contains the dataset and the models' code used in the article named “Bayesian regional flood frequency analysis with GEV hierarchical models under spatial dependency structures”.</p>
Simulation data and scripts for DEM simulation of stress- and orientation-dependent rock permeability
<p>Data set- contains all the raw data required to replicate the plots in the main article;</p> <p>Codes- contains the codes which are needed to run a Darcy flow test on the DEM model. The codes for the generation of both isotropic model and the anisotropic model are also provided in this .zip file. Also enclosed is a ReadMe.txt file detailing the procedures for the simulations. </p>
The association between tumor mutational burden and prognosis is dependent on treatment context
<p>This dataset has been used to analyze the association between high tumour mutational burden and survival in immunotherapy-treated and non–immunotherapy-treated patients with cancer. The dataset contains clinical and genomic data for 10,233 patients with 17 cancer types.</p>
Individual simulation results of "New insight into the frequency-dependent megathrust rupture from dynamic simulations"
<p>The model settings and results of individual simulations in the work "New insight into the frequency-dependent megathrust rupture from dynamic simulations" by Yin and Denolle.</p>
VEGFA dependent endothelial lumen formation in scaffold-free tissue engineering: a hybrid in vitro and in silico approach to improve vascularization of tissue: Spheroid simulation data
<p>Vascularization is a tightly regulated process involving a complex interplay of multiple bio-signaling events. Among these events, lumen formation is a crucial rate-limiting step in successful anastomosis of tissue engineered constructs in a host. We have developed scaffold-free endothelial-fibroblast based constructs with preformed microvessel networks that are a promising approach to rapid host-implant anastomosis. However, rapid formation of a continuous endothelial lumen within the microvessels remains elusive. We propose that pretreatment of these constructs with vascular endothelial growth factor A, a potent proangiogenic molecule, can improve large caliber lumen formation within constructs during <i>in vitro</i> self-assembly.</p> <p>Here, we present a hybrid <i>in vitro </i>and <i>in silico </i>approach to evaluating endothelial-fibroblast spheroid self-assembly and the effects of VEGF-A on lumen formation. Our VEGF-A dosing experiments ultimately demonstrated that our endothelial cells responded to VEGF-A by increased clustering tendency and hollow lumen formation. This behavior was coincident with an increase in polarization markers as well as a time and dose dependent increase in diameter of lumens. We used these observations to develop a simulation model using the Cellular Potts framework, a modeling framework that is well-adapted to tissue self-assembly. The model explores how changes in interfacial energy costs between cell types in our model as well as changes in basic cell parameters such as response to VEGF-A, growth and proliferation can alter dynamics of lumen formation within a construct. From our model, we ran a series of simulated experiments to generate tissues with an optimal distribution of large caliber vessels. Our analysis of the resulting regression model identified several statistically significant modifiable factors that could be mapped back to potential spheroid pretreatment strategies. These strategies could augment VEGF-mediated lumen formation and provide rationale for alterations in the design of our constructs.</p>
An Extended Viscoacoustic Wave Equation for Frequency-dependent Wavefields Modeling in Viscoacoustic Media
<p>An excel file containing the velocity of three viscoacoustic media (velocity.xlsx);</p> <p>A mat file containing the wavefields of viscoacoustic media (model_viscoacoustic.mat);</p> <p>A mat file containing the wavefields of acoustic media (model_acoustic.mat);</p> <p>A mat file containing the wavefields of viscoacoustic media with changed dispersion parameters (model_diffusion.mat);</p> <p>A mat file containing the wavefields of viscoacoustic media with changed viscous parameters (model_viscous.mat);</p>
Data from: Genetic consequences of post-glacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus
How does range expansion affect genetic diversity in species with different ecologies, and do different types of genetic markers lead to different conclusions? We addressed these questions by assessing the genetic consequences of post-glacial range expansion using mitochondrial DNA (mtDNA) and nuclear restriction site associated DNA (RAD) sequencing in two congeneric and co-distributed rodents with different ecological characteristics: the desert kangaroo rat (Dipodomys deserti), a sand specialist, and the Merriam's kangaroo rat (D. merriami), a substrate generalist. For each species, we compared genetic variation between populations that retained stable distributions throughout glacial periods and those inferred to have expanded since the last glacial maximum. Our results suggest that expanded populations of both species experienced a loss of private mtDNA haplotypes and differentiation among populations, as well as a loss of nuclear SNP private alleles and polymorphism. However, only D. deserti experienced a loss of nucleotide diversity (both mtDNA and nuclear) and nuclear heterozygosity. For all indices of diversity and differentiation that showed reduced values in the expanded areas, D. deserti populations experienced a greater degree of loss than did D. merriami populations. Additionally, patterns of loss in genetic diversity in expanded populations were substantially less extreme (by two orders of magnitude in some cases) for nuclear SNPs in both species compared to that observed for mitochondrial data. Our results demonstrate that ecological characteristics may play a role in determining genetic variation associated with range expansions, yet mtDNA diversity loss is not necessarily accompanied by a matched magnitude of loss in nuclear diversity.
Data from: Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae)
Background: Tropical rainforests (TRFs) harbour almost half of the world's vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth's major TRF regions remains poorly understood. Here we investigate the evolutionary processes shaping continental species richness disparities of the pantropical, epiphytic and mostly TRF-dwelling orchid genus Bulbophyllum (c. 1,948 spp. in total; Asia-Pacific region: c. 1,564 spp.; Madagascar: 210; Africa: 80; Neotropics: 94) using diversification analyses based on a time-calibrated molecular phylogeny, coupled with ecological niche modelling (ENM) of geographic distributions under present and past (Last Glacial Maximum) conditions. Results: Our results suggest an early-to-late Miocene scenario of 'out-of-Asia-Pacific' origin and progressive, dispersal-mediated diversification in Madagascar, Africa and the Neotropics, respectively. Species richness disparities amongst these four TRF lineages are best explained by a time-for-speciation effect rather than differences in net diversification or diversity-dependent diversification due to present or past spatial-bioclimatic limits. All four lineages of experienced dramatic range expansions during the LGM, which conflicts with the common notion that TRFs mostly fragmented/contracted during glacial periods. Conclusions: Most species of at least the Madagascan, African and Neotropical lineages originated during the Quaternary. Their diversification under high species turnover (i.e. high rates of speciation and extinction) might relate to climate-induced range fluctuations during this time period combined with various intrinsic features commonly invoked to foster rapid population turnover in tropical orchids (e.g., epiphytism, specialization on pollinators and mycorrhizal fungi, dispersal by wind). Further (e.g., phylogenomic and ecological) research within each Bulbophyllum lineage but also other pantropical TRF taxa is required to provide a better understanding of how evolutionary processes as well as past and current environmental conditions drive tropical biodiversity and account for regional differences in species richness patterns on a global scale.
Data from: Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell‐to‐cell variability in signal strength and cellular response. Here, we screened 1,141 non‐essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4. We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane‐localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule‐dependent signal stabilization might also operate throughout metazoans.
Data from: Among-sibling differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank
We investigated whether among-sibling differences in the phenotypes of juvenile fish were systematically related to the position in the egg mass where each individual developed during oogenesis. We sampled eggs from the front, middle and rear thirds of the egg mass in female brown trout of known dominance rank. In the resulting juveniles, we then measured traits that are related to individual fitness: body size, social status and standard metabolic rate (SMR). When controlling for differences among females in mean egg size, siblings from dominant mothers were initially larger (and had a lower mass-corrected SMR) if they developed from eggs at the rear of the egg mass. However, heterogeneity in the size of siblings from different positions in the egg mass diminished in lower ranking females. Location of the egg within the egg mass also affected the social dominance of the resulting juvenile fish, although the direction of this effect varied with developmental age. This study provides the first evidence of a systematic basis for among-sibling differences in the phenotypes of offspring in a highly fecund organism.
Data from: Human foveal cone photoreceptor topography and its dependence on eye length
We provide the first measures of foveal cone density as a function of axial length in living eyes and discuss the physical and visual implications of our findings. We used a new generation Adaptive Optics Scanning Laser Ophthalmoscope to image cones at and near the fovea in 28 eyes of 16 subjects. Cone density and other metrics were computed in units of visual angle and linear retinal units. The foveal cone mosaic in longer eyes is expanded at the fovea, but not in proportion to eye length. Despite retinal stretching (decrease in cones/mm2), myopes generally have a higher angular sampling density (increase in cones/deg2) in and around the fovea compared to emmetropes, offering the potential for better visual acuity. Reports of deficits in best-corrected foveal vision in myopes compared to emmetropes cannot be explained by increased spacing between photoreceptors caused by retinal stretching during myopic progression.
Data from: Beyond thermal performance curves: modeling time-dependent effects of thermal stress on ectotherm growth rates
Thermal performance curves have been widely used to model the ecological responses of ectotherms to variable thermal environments and climate change. Such models ignore the effects of time dependence—the temporal pattern and duration of temperature exposure—on performance. We developed and solved a simple mathematical model for growth rate of ectotherms, combining thermal performance curves for ingestion rate with the temporal dynamics of gene expression and protein production in response to high temperatures to predict temporal patterns of growth rate in constant and diurnally fluctuating temperatures. We used the model to explore the effects of heat shock proteins on larval growth rates of Manduca sexta. The model correctly captures two empirical patterns for larval growth rate: first, maximal growth rate and optimal temperature decline with increasing duration of temperature exposure; second, mean growth rates decline with time in diurnally fluctuating temperatures at higher mean temperatures. These qualitative results apply broadly to cases where proteins or other molecules produced in response to high temperatures reduce growth rates. We discuss some of the critical assumptions and predictions of the model and suggest potential extensions and alternatives. Incorporating time-dependent effects will be essential for making more realistic predictions about the physiological and ecological consequences of temperature fluctuations and climate change.
Data from: Experimental evidence of frequency-dependent selection on group behaviour
Evolutionary ecologists often seek to identify the mechanisms maintaining intraspecific variation. In social animals, whole groups can exhibit between-group differences in their collective traits. We examined whether negative frequency-dependent selection (i.e., a rare-type advantage) could help to maintain between-group variation. We engineered neighborhoods of social spider colonies bearing bold or shy foraging phenotypes and monitored their fecundity in situ. We found that bold colonies enjoyed a rare-type advantage that is lost as the frequency of bold colonies in a neighborhood increases. The success of shy colonies was not frequency-dependent. These dynamics appear driven by a foraging advantage of bold colonies that is lost in bold neighborhoods because prey become scarce, and shy colonies perform better than bold colonies under low-resource conditions. Thus, to understand selection on collective traits, it is insufficient to examine groups in isolation. One must consider the phenotypic environment in which groups reside and compete.
Data from: Drought legacies are dependent on water table depth, wood anatomy, and drought timing across the eastern U.S.
Severe droughts can impart long-lasting legacies on forest ecosystems through lagged effects that hinder tree recovery and suppress whole-forest carbon uptake. However, the local climatic and edaphic factors that interact to affect drought legacies in temperate forests remain unknown. Here, we pair a dataset of 143 tree ring chronologies across the mesic forests of the eastern U.S. with historical climate and local soil properties. We found legacy effects to be widespread, the magnitude of which increased markedly in diffuse porous species, sites with deep water tables, and in response to late-season droughts (August – September). Using an ensemble of downscaled climate projections, we additionally show that our sites are projected to drastically increase in water deficit and drought frequency by the end of the century, potentially increasing the size of legacy effects by up to 65% and acting as a significant process shaping forest composition, carbon uptake, and mortality.
Data from: Local adaptation when competition depends on phenotypic similarity
Recent work incorporating demographic–genetic interactions indicates the importance of population size, gene flow, and selection in influencing local adaptation. This work typically assumes that density-dependent survival affects individuals equally, but individuals in natural population rarely compete equally. Among-individual differences in resource use generate stronger competition between more similar phenotypes (frequency-dependent competition) but it remains unclear how this additional form of selection changes the interactions between population size, gene flow, and local stabilizing selection. Here, we integrate migration–selection dynamics with frequency-dependent competition. We developed a coupled demographic-quantitative genetic model consisting of two patches connected by dispersal and subject to local stabilizing selection and competition. Our model shows that frequency-dependent competition slightly increases local adaptation, greatly increases genetic variance within patches, and reduces the amount that migration depresses population size, despite the increased genetic variance load. The effects of frequency-dependence depend on the strength of divergent selection, trait heritability, and when mortality occurs in the life cycle in relation to migration and reproduction. Essentially, frequency-dependent competition reduces the density-dependent interactions between migrants and residents, the extent to which depends on how different and common immigrants are compared to residents. Our results add new dynamics that illustrate how competition can alter the effects of gene flow and divergent selection on local adaptation and population carrying capacities.
Data from: Size-dependent mortality and competition interactively shape community diversity
Body size is recognized as a major factor in evolutionary processes mediating sympatric diversification and community structuring. Life-history types with distinct body sizes can result from two fundamental mechanisms, size-dependent competition and size-dependent mortality. While previous theoretical studies investigated these two processes in separation, the model analyzed here allows both selective forces to affect body-size evolution interactively. Here we show for the first time that in the presence of size-dependent competition, size-dependent mortality can give rise to multiple, coexisting size morphs representing the final outcomes of evolution. Moreover, our results demonstrate that interactions between size-dependent competition and mortality can create characteristic abrupt changes in size structure and non-monotonic patterns of biological diversity along continuous and monotonic environmental gradients. We find that the two selective forces differentially affect the body-size ratios of coexisting morphs: size-dependent competition results in small and relatively constant ratios, whereas size-dependent mortality can open niches for morphs that greatly differ in body size. We show that these differential effects result in characteristic distributions of size ratios across communities, which we suggest can help detect the concurrent action and relative influence of size-dependent competition and mortality in nature.
Microstructural heterogeneity in rate-dependent plasticity of multiphase titanium alloys
<p>This datasheet contains original data for figures 8 and 9 in the paper. If readers need further information, please feel free to contact: zhen.zhang@imperial.ac.uk</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.