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849 results for “linear”
Data for "Calculation of permanent magnet arrangements for stellarators: A linear least-squares method"
<p>Data associated with the paper "Calculation of permanent magnet arrangements for stellarators: A linear least-squares method"</p>
Efficient weighting methods for genomic best linear unbiased prediction (BLUP) adaption to the genetic architectures of quantitative traits
<p><a name="_Hlk19877414"></a>Genomic best linear unbiased prediction (GBLUP) assumes equal variance for all marker effects, which is suitable for traits that conform to the infinitesimal model. For traits controlled by major genes, Bayesian methods with shrinkage priors or genome-wide association study (GWAS) methods can be used to identify <a name="_Hlk24974556">causal variants</a> effectively. The information from Bayesian/GWAS methods can be used to construct the weighted genomic relationship matrix (<b>G</b>). However, it remains unclear which methods perform best for traits varying in genetic architecture. Therefore, we developed several methods to <a name="_Hlk23592218">optimize</a> the performance of weighted GBLUP and compare them with other available methods using simulated and real datasets. First, two types of methods (marker effects with local-shrinkage or normal prior) were used to obtain test statistics and estimates for each marker effect. Second, three weighted <b>G</b> matrices were constructed based on the marker information from the first step: (1) the genomic-feature weighted <b>G</b> (GFWG), (2) the estimated marker-variance weighted <b>G</b> (EVWG), and (3) the absolute value of estimated marker-effect weighted <b>G</b> (AEWG). Following the above process, six different weighted GBLUP methods (local-shrinkage/normal prior GF/EV/AE-WGBLUP) were proposed for genomic prediction. Analyses with both simulated and real data demonstrated that these options offer flexibility for optimizing the weighted GBLUP for traits with a broad spectrum of genetic architectures. The advantage of weighting methods over GBLUP in terms of accuracy were trait dependent, ranging from 14.8% to marginal for simulated traits and from 44% to marginal for real traits. Local-shrinkage prior EVWGBLUP is superior for traits mainly controlled by loci of large effect. Normal prior AEWGBLUP performs well for traits mainly controlled by loci of moderate effect. For traits controlled by some loci with large effects (<a name="_Hlk49869847">explain 25%~50% genetic variance</a>) and a range of loci with small effects, GFWGBLUP has advantages. In conclusion, the optimal weighted GBLUP method for genomic selection should take both the genetic architecture and number of QTLs of traits into consideration carefully.</p>
Data for Automated Mechanism Generation Using Linear Scaling Relationships and Sensitivity Analyses applied to Catalytic Partial Oxidation of Methane
<p>Data, scripts, and plots for the preprint and article titled '<i>Automated Mechanism Generation Using Linear Scaling Relationships and Sensitivity Analyses applied to Catalytic Partial Oxidation of Methane</i>'</p>
Data from: Testing the thermal limits: Non-linear reaction norms drive disparate thermal acclimation responses in Drosophila melanogaster
Critical thermal limits are important ecological parameters for studying thermal biology and for modelling species' distributions under current and changing climatic conditions (including predicting the risk of extinction for species from future warming). However, estimates of the critical thermal limits are biased by the choice of assay and assay conditions, which differ among studies. Furthermore, estimates of the potential for phenotypic plasticity (thermal acclimation) to buffer against future warming are usually based on single assay conditions and (usually linear) extrapolation from a few acclimation temperatures. We produced high resolution estimates of adult acclimation capacity for upper tolerance limits at different assay conditions (ramping rates and knock-down temperatures) using CTmax (dynamic) and knock-down (static) thermal assays in the model species Drosophila melanogaster. We found the reaction norms to be highly dependent on assay conditions. We confirmed that progressively lower ramping rates or higher knock-down temperatures led to overall lower tolerance estimates. More surprisingly, extended assays (lower ramping rates or lower knock-down temperatures) also led to increasingly non-linear reaction norms for upper thermal tolerance across adult acclimation temperatures. Our results suggest that the magnitude (capacity) and direction (beneficial or detrimental) of acclimation responses are highly sensitive to assay conditions. The results offer a framework for comparison of acclimation responses between different assay conditions and a potential for explaining disparate acclimation capacity theories. We advocate cautious interpretation of acclimation capacities and careful consideration of assay conditions, which should represent realistic environmental conditions based on species' ecological niches.
Nanoscale Crystal Grain Characterization via Linear Polarization X-ray Ptychography: Raw data
<p>File Description:</p> <p>energy_rot1.dat, energy_rot2.dat</p> <p>List of energies that were taken in the spectroscopy scans of two sample orientations. Unit is KeV.</p> <p> </p> <p>P5_rot1_amp.tif, P5_rot2_amp.tif:</p> <p>Tiff stacks of absorption images of the sample scanned across Vanadium K-edge at two perpendicular orientations relative to beam polarization. Pixel values are in range of [0,20000], which equal [Normalized transmission]*20000.</p> <p> </p> <p>P5_rot1_phase.tif, P5_rot2_phase.tif:</p> <p>Tiff stacks of phase images of the sample scanned across Vanadium K-edge at two perpendicular orientations relative to beam polarization. Pixel values equal [Real part of refractive index(Delta)]*[Factor]*10000, the factor is given in separate files.</p> <p> </p> <p>delta_factor_rot1.dat, delta_factor_rot2.dat</p> <p>List of factors to calculate delta values from phase images for each energy. The factor has no unit.</p>
Sync and Render Video and Audio Clips in a Non-Linear Video Editor
<p>In this instructional video, one can learn how to use a non-linear video editor (in this case, Adobe Premiere CC) to synchronise multi-cam (2D and 360-degree) and multi-mic footage recorded simultaneously in a single event and render each track with the same IN and OUT points. The motivation for doing this is to make sure the all the recordings of an event will play synchronously in the relevant qualitative research software, such as <em>DOTE</em> (Distributed Open Transcription Environment) and <em>AVA360VR</em> (Annotate, Visualise, Analyse 360 video on VR).</p>
Near-optimal robust bilevel linear instances
<p>This repository contains the bilevel instances used in the paper Near-Optimal Robust Bilevel Optimization (https://arxiv.org/abs/1908.04040). They come in four groups, small, medium, large and mips instances, with different numbers of variables and constraints as described in the paper.</p> <p>The MIPS instances are constructed from the MIPS/RANDOM instances from https://coral.ise.lehigh.edu/data-sets/bilevel-instances/</p> <p>The /data folder contains instances in JLD format, the DataReader folder contains a Julia project for reading the data.</p>
FIGURES 1–5. Trichoptera larvae and linear regression. Figure 1, Ithytrichia lamellaris Eaton 1873, fifth instar larva with case. Figure 2, Hydropsyche tabacarui Botosaneanu 1960 in Tools for instar determination of European caddisfly larvae (Insecta: Trichoptera)
FIGURES 1–5. Trichoptera larvae and linear regression. Figure 1, Ithytrichia lamellaris Eaton 1873, fifth instar larva with case. Figure 2, Hydropsyche tabacarui Botosaneanu 1960, fifth instar larva, abdominal segments VI–IX (white ovals = pupal gill buds). Figure 3, Athripsodes longispinosus paleochora (Malicky 1972), fifth instar larva, head, right anterolateral (arrow = subocular ecdysial line). Figure 4, Halesus rubricollis (Pictet 1834), first instar larva, pronotum, dorsal (white numerals refer to setal positions; arrows indicate pits). Scale bars: 0.5 mm in Figs. 1 and 3, 1 mm in Fig. 2, 0.1 mm in Fig. 4. Figure 5, linear regression (with 95% confidence bands) of forewing length versus final instar head width, based on pooled data of 451 European Trichoptera species across all families, showing the regression equation, the coefficient of determination, and the probability level for the relationship.
Non-linear variation in clinging performance with surface roughness in geckos
<p>Understanding the challenges faced by organisms moving within their environment is essential to comprehending the evolution of locomotor morphology and habitat use. Geckos have developed adhesive toe pads that enable exploitation of a wide range of microhabitats. These toe pads, and their adhesive mechanisms, have typically been studied using a range of artificial substrates, usually significantly smoother than those available in nature. Although these studies have been fundamental in understanding the mechanisms of attachment in geckos, it is unclear whether gecko attachment simply gradually declines with increased roughness as some researchers have suggested, or whether the interaction between the gekkotan adhesive system and surface roughness produces non-linear relationships. To understand ecological challenges faced in their natural habitats, it is essential to use test surfaces that are more like surfaces used by geckos in nature. We tested gecko shear force (i.e., frictional force) generation as a measure of clinging performance on three artificial substrates. We selected substrates that exhibit microtopographies with peak-to-valley heights similar to those of substrates used in nature, to investigate performance on a range of surfaces smooth (glass), and fine-grained (fine sandpaper) to rough (coarse sandpaper). We found that shear force did not decline monotonically with roughness, but varied non-linearly among substrates. Clinging performance was greater on glass and coarse sandpaper than on fine sandpaper, and clinging performance was not significantly different between glass and coarse sandpaper. Our results demonstrate that performance on different substrates varies, probably depending on the underlying mechanisms of the adhesive apparatus in geckos.</p>
Data from: Moving beyond linear food chains: trait-mediated indirect interactions in a rocky intertidal food web
In simple, linear food chains, top predators can have positive indirect effects on basal resources by causing changes in the traits (e.g. behaviour, feeding rates) of intermediate consumers. Although less is known about trait-mediated indirect interactions (TMIIs) in more complex food webs, it has been suggested that such complexity dampens trophic cascades. We examined TMIIs between a predatory crab (Carcinus maenas) and two ecologically important basal resources, fucoid algae (Ascophyllum nodosum) and barnacles (Semibalanus balanoides), which are consumed by herbivorous (Littorina littorea) and carnivorous (Nucella lapillus) snails, respectively. Because crab predation risk suppresses snail feeding rates, we hypothesized that crabs would also shape direct and indirect interactions among the multiple consumers and resources. We found that the magnitude of TMIIs between the crab and each resource depended on the suite of intermediate consumers present in the food web. Carnivorous snails (Nucella) transmitted TMIIs between crabs and barnacles. However, crab–algae TMIIs were transmitted by both herbivorous (Littorina) and carnivorous (Nucella) snails, and these TMIIs were additive. By causing Nucella to consume fewer barnacles, crab predation risk allowed fucoids that had settled on or between barnacles to remain in the community. Hence, positive interactions between barnacles and algae caused crab–algae TMIIs to be strongest when both consumers were present. Studies of TMIIs in more realistic, reticulate food webs will be necessary for a more complete understanding of how predation risk shapes community dynamics.
Data from: Corridors or risk? movement along, and use of, linear features vary predictably among large mammal predator and prey species
<p>1. Space-use behaviour reflects trade-offs in meeting ecological needs and can have consequences for individual survival and population demographics. The mechanisms underlying space-use can be understood by simultaneously evaluating habitat selection and movement patterns, and fine-resolution locational data are increasing our ability to do so. 2. We use high-resolution location data and an integrated step-selection analysis to evaluate caribou, moose, bear, and wolf habitat selection and movement behavior in response to anthropogenic habitat modification, though caribou data were limited. Space-use response to anthropogenic linear features (LFs) by predators and prey are hypothesized to increase predator hunting efficiency and are thus believed to be a leading factor in woodland caribou declines in western Canada. 3. We found that all species moved faster while on LFs. Wolves and bears were also attracted towards LFs, whereas prey species avoided them. Predators and prey responded less strongly and consistently to natural features such as streams, rivers and lakeshores. These findings are consistent with the hypothesis that LFs facilitate predator movement and increase hunting efficiency, while prey perceive such features as risky. 4. Understanding the behavioural mechanisms underlying space-use patterns is important in understanding how future land-use may impact predator-prey interactions. Explicitly linking behaviour to fitness and demography will be important to fully understand the implications of management strategies.</p>
Data from: A new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed models
Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics mostly uses landscape resistance surfaces and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of resistance surfaces is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix resistance surfaces were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between landscape predictor variables and genetic distances was then assessed following a mixed modeling approach to account for the non-independence of values in distance matrices. Subsequently, predictor variables were selected making use of the R_β^2 statistic. We applied LCTA and the mixed model approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis and showed that LCTA not only outperforms existing methods in a statistical way, but also provides more information about the migration ecology of the focal species. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed.
Data from: Body mass estimates of an exceptionally complete Stegosaurus (Ornithischia: Thyreophora): comparing volumetric and linear bivariate mass estimation methods
Body mass is a key biological variable, but difficult to assess from fossils. Various techniques exist for estimating body mass from skeletal parameters, but few studies have compared outputs from different methods. Here, we apply several mass estimation methods to an exceptionally complete skeleton of the dinosaur Stegosaurus. Applying a volumetric convex-hulling technique to a digital model of Stegosaurus, we estimate a mass of 1560 kg (95% prediction interval 1082–2256 kg) for this individual. By contrast, bivariate equations based on limb dimensions predict values between 2355 and 3751 kg and require implausible amounts of soft tissue and/or high body densities. When corrected for ontogenetic scaling, however, volumetric and linear equations are brought into close agreement. Our results raise concerns regarding the application of predictive equations to extinct taxa with no living analogues in terms of overall morphology and highlight the sensitivity of bivariate predictive equations to the ontogenetic status of the specimen. We emphasize the significance of rare, complete fossil skeletons in validating widely applied mass estimation equations based on incomplete skeletal material and stress the importance of accurately determining specimen age prior to further analyses.
Data from: Slip-spring simulations of different constraint release environments for linear polymer chains
The constraint release(CR) mechanism has important effects on polymer relaxation and the chains will show different relaxation behavior in conditions of monodisperse, bidisperse and other topological environments. By comparing relaxation data of linear PI chains dissolved in very long matrix and monodisperse melts, Matsumiya et al. showed that CR mechanism accelerates both dielectric and viscoelastic relaxation[Matsumiya et al., 2013,46, 6067]. In this work, the experimental data reported by Matsumiya et al. are reproduced using the single slip-spring model(SSp) and the CR accelerating effects are validated by simulations. A variant of SSp with each entanglement assigning a characteristic lifetime is also proposed to simulate various CR environment flexibly. Using this lifetime version SSp model, the correct relaxation function can be obtained with equal numbers of entanglements destructions by CR and reptation/Contour length fluctuation(CLF) for monodisperse melts. Good agreement with published experiment data is also obtained for bidisperse melts, which validates the ability to correctly describe the CR environment of the lifetime version model.
Data from: Compensatory selection for roads over natural linear features by wolves in northern Ontario: implications for caribou conservation
Woodland caribou (Rangifer tarandus caribou) in Ontario are a threatened species that have experienced a substantial retraction of their historic range. Part of their decline has been attributed to increasing densities of anthropogenic linear features such as trails, roads, railways, and hydro lines. These features have been shown to increase the search efficiency and kill rate of wolves. However, it is unclear whether selection for anthropogenic linear features is additive or compensatory to selection for natural (water) linear features which may also be used for travel. We studied the selection of water and anthropogenic linear features by 52 resident wolves (Canis lupus x lycaon) over four years across three study areas in northern Ontario that varied in degrees of forestry activity and human disturbance. We used Euclidean distance-based resource selection functions (mixed-effects logistic regression) at the seasonal range scale with random coefficients for distance to water linear features, primary/secondary roads/railways, and hydro lines, and tertiary roads to estimate the strength of selection for each linear feature and for several habitat types, while accounting for availability of each feature. Next, we investigated the trade-off between selection for anthropogenic and water linear features. Wolves selected both anthropogenic and water linear features; selection for anthropogenic features was stronger than for water during the rendezvous season. Selection for anthropogenic linear features increased with increasing density of these features on the landscape, while selection for natural linear features declined, indicating compensatory selection of anthropogenic linear features. These results have implications for woodland caribou conservation. Prey encounter rates between wolves and caribou seem to be strongly influenced by increasing linear feature densities. This behavioral mechanism - a compensatory functional response to anthropogenic linear feature density resulting in decreased use of natural travel corridors - has negative consequences for the viability of woodland caribou.
Data from: Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname
To achieve maximum efficacy, taxonomic studies that seek to distinguish amongst species must first account for allometric shape variation within species. Two recently developed software packages (SMATR and MorphoJ) offer regression-based allometric approaches that are notable for their statistical power and ease of use and that may prove highly useful to taxonomists working with linear or geometric morphometric data. We investigate species delimitation of the slender-bodied fishes in the Leporinus cylindriformis group using these programs and demonstrate the utility of the allometric corrections that they provide. Without allometric correction, many pairs of species are difficult to distinguish on the basis of morphometrics, but once regressions are used to account for marked allometric variation within species, most of the recognized species in this group can be readily distinguished with linear or geometric morphometrics, particularly using variation in the depth of the body. Both approaches returned congruent patterns of separation amongst putative species, but the geometric approach in MorphoJ distinguished amongst four more pairs of species than did the linear approach in SMATR and appears to provide slightly more statistical power. Based on distinctive morphometrics, meristics, and coloration, a highly elongate species of Leporinus from the Suriname, Corantijn, and Coppename rivers of Suriname is described herein as a new species, Leporinus apollo sp. nov. The unique L. cylindriformis holotype from Porto de Moz, Brazil differs in morphology, meristics, and pigmentation from specimens commonly referred to that species from the main basin of the Amazon; the latter specimens may represent an additional undescribed species. The L. cylindriformis holotype itself may represent a rare species or a specimen collected at the edge of its native range. Measurements of the holotype and paratype of Leporinus niceforoi, which were collected in the Amazonian slope of Colombia, differ substantially from similarly pigmented and putatively conspecific specimens from Amazonian portions of Ecuador and Peru. Recently collected specimens from Colombia are needed to determine whether the observed morphometric variation encompassed by the current concept of L. niceforoi indicates a morphocline within a single species, suggests the presence of multiple cryptic species, or results from shrinkage of the types. In all these cases, linear or geometric morphometric data can reliably differentiate amongst species, but only after one accounts for allometric shape variation. The new SMATR and MorphoJ software packages both offer easy and effective approaches to such allometrically informed taxonomy, and may prove useful to any systematist working on taxa that change shape as they grow.
Materials for "Induced Polarization of Clayey Rocks and Soils: Non-Linear Complex Conductivity Models"
<p>These files are for the work "Induced Polarization of Clayey Rocks and Soils: Non-Linear Complex Conductivity Models" that is submitted to Journal of Geophysical Research: Solid Earth.</p><p>They include two parts of Experiments and Simulations, details of each part being explained in the Readme.txt therein. </p><p>Through these materials, models and results presented in this work can be independently validated by readers.</p>
Linear programs used for testing
<p>Linear programs used for benchmarking results presented in section 4</p> <p>Hardware/Software used: Text editor/spreadsheet</p> <p>Data format: Tab-separated values (*.teau files); text files (eq-*)</p> <p>Source: Randomly generated</p> <p>Number of samples: 6</p> <p>Size per sample: 5x5 to 288x202</p>
FIGURE 2. Landmarks used for obtain the linear measurements, 1 in Two new species of the genus Xenotoca Hubbs and Turner, 1939 (Teleostei, Goodeidae) from central-western Mexico
FIGURE 2. Landmarks used for obtain the linear measurements, 1 to 9 standard length (SL); 1 to 5 head length (HL); 4 to 17 head high (HH); 1 to 2 preorbital length (PrOL); 3 to 5 postorbital length (POL); 2 to 3 eye diameter (ED); 8 to 11 body least depth (BLD); 13 to 14 pelvic-anal fin distance (PAD); 14 to 6 pelvic-dorsal fin distance (PDD); 14 to 15 pelvic-pectoral fin distance (PPD); 6 to 13 dorsal-anal fin distance (DAD); 6 to 12 dorsal fin origin to anal fin posterior extent distance (DOAE); 7 to 13 dorsal fin posterior extent to anal fin origin distance (DEAO); 7 to 9 end of dorsal fin-hypural plate distance (EDHP); 9 to 12 end of the anal fin-hypural plate distance (EAHP); 6 to 7 dorsal fin base length (DFL); 12 to 13 anal fin base length (AFL); 15 to 16 pectoral fin base length (PFL); 10 to 12 caudal peduncle length (CPL).
Global Observation-based LInear Vorticity Vertical Velocities (OLIV3) over isopycnal levels
<p>Observation-based Linear Vorticity Vertical Velocities (OLIV3) estimates from observation-based geostrophic velocities within the global themocline during the 1993-2019 period at annual frequency.</p> <p>The beta-plane geostrophic OLIV3 fields are computed following the Indefinite depth-integrated geostrophic linear vorticity balance methodology described in <em>Cortés-Morales and Lazar, 2024, </em><em>Diego Cortés Morales, 2023 [thesis] and Cortés-Morales et al., (submitted) </em>applied to the ARMOR3D [<em>Mulet et al., 2013; https://data.marine.copernicus.eu/product/MULTIOBS_GLO_PHY_TSUV_3D_MYNRT_015_012</em>] geostrophic meridional velocities. The boundary condition used is the Ekman pumping vertical velocities computed from ERA5 wind stress [DOI: 10.24381/cds.f17050d7]. The velocity field is quality-flagged based on the relative error and interannual correlation coefficient between w_g and w_tot in an OGCM perfect model test (<em>Cortés-Morales et al., (submitted)</em>).</p> <p>----------------------------------------------------------------------------------------</p> <p>Geographical coverage: Global Ocean</p> <p>Grid and horizontal spatial resolution: Evenly spaced 0.25º grid</p> <p>Vertical levels: 71 levels from sigma level 21 to 28.17 kg/m^3.</p> <p>Temporal resolution: Annual (1993-2019)</p> <p>-----------------------------------------------------------------------------------------</p> <p>Variables:</p> <p>lon (2D): Longitude</p> <p>lat (2D): Latitude</p> <p>isolev (1D): Isopycnal level</p> <p>time (1D): Year</p> <p>w_oliv3(4D): Beta-plane geostrophic vertical velocities</p> <p>h_depth (4D): Depth isopycnal surfaces</p> <p>flag_time_var (3D): Flag based on correlation coeffcient between geostrophic and total vertical velocties from OGCM</p> <p>flag_time_mean (3D): flag based on relative error between geostrophic and total vertical velocties from OGCM</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.