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2,395 results for “Contrast”
LiF data pack supporting "Observation of diffraction contrast in scanning helium microscopy"
<p>All the experimental data from the paper is included in this data pack including both the images and the z scans. </p> <p>Images from the paper are presented in three different formats with filenames scan00*****:</p> <p>1) .png file which is an unprocessed image of the raw data. <br> 2) .gwy file which is an unprocessed version of the data that can be opened in Gwyddion<br> 3) .mat file which contains all the measured data that can be opened in MATLAB</p> <p>The .mat file contains the most information and requires some explanation to easily understand.<br> The data is saved in a structure named meas, the key fields are as follows:</p> <p>meas.target - A matrix of the target position for each pixel, with a column for each of the x,y coordinates<br> meas.inputs - Input parameters used in the scanning program to collect the data<br> meas.initial_pos - Position of each the three stages at the start of the scan. The 3rd coordinate is the z scan and does not change throughout the scan<br> meas.data - A vector of the measured current at each pixel in Amps<br> meas.image - A matrix that represents the acquired image</p> <p>The remaining fields are explained at the bottom of the readme.</p> <p>The z scans are saved Z*****.mat and can be opened in MATALB.<br> The key variables in the data files are:</p> <p>z_position - Raw z coordinate of the positioner in nm<br> current_z - Measured current at each point in Amps<br> m - Horizontal scan gradient (approximately 1)<br> m2 - Vertical scan gradient (approximately 0)<br> step_pos - x coordiate at z_position=0<br> step_pos_v - y coordinate at z_position=0</p> <p>The x,y position at each point in the scan can then be obtained from<br> x=step_pos + m*(z_position)<br> y=step_pos_v + m2*(z_position)</p> <p><br> The true z distance between the pinhole and the sample in nm can be calculated from z=z_position-4295000</p> <p>The included data in the pack contains:</p> <p>Images presented in the paper:<br> scan001357<br> scan001361<br> scan001398<br> scan001415</p> <p>Z000006.mat - z scan of flat region<br> Z000008.mat - z scan of heavily distorted region<br> Z0000012.mat - z scan of lightly distorted region<br> Z000013.mat - z scan of HOPG</p> <p>z_scan_movie.avi - Video illustrating how the images vary with z<br> scan001401-scan001413 - Data to produce the video</p> <p>In addition, the analysis scripts have been included for reference. <br> The scripts can be used to regnerate the figures in the paper.</p> <p><br> The remaining fields in the meas structure are:<br> meas.date_time - Start date and time of the scan<br> meas.type - Scan pattern of the image. Always raster_jump<br> meas.p1 - Unused pressure<br> meas.p2 - Unused pressure<br> meas.p3 - Unused pressure<br> meas.p_srce - Source pressure at the start of the scan<br> meas.p_diff - Differential stage pressure at the start of the scan<br> meas.p_smpl - Sample pressure at the start of the scan<br> meas.p_det - Detector pressure at the start of the scan<br> meas.N_dwell - Number of current measurements taken at each pixel<br> meas.comments - comments (unused)<br> meas.det_params - Detector parameters used in the scan<br> meas.labtemp - A vector of the labtemp at each pixel (unused)<br> meas.return_state - Error status <br> </p>
3d Virtual Patho-Histology of Lung Tissue from Covid19 Patients based on Phase Contrast X-ray Tomography
<p>X-ray phase contrast tomographys datasets of lung tissue from 6 Covid-19 patients (paraffin embedded unstained tissue), and one control tissue (healthy lung, in fixative solution). The data has been recorded as part of the Covid-19 Call for Proposals at DESY April 2020 at the GINIX instrument, beamline P10 of the PETRAIII storage ring at 8keV. Three different datasets are included in a single tar archive for each sample: (i) overview scan (up to 4mm cross section ) from stitching different tomograms, (ii) 1mm cylindrical punch, and (iii) cone-beam zoom tomogram recorded with waveguide illumination. </p> <p>voxel sizes: (i) 1.3µm, (ii) 650nm, (iii) 167nm. </p> <p>3 datasets per sample, raw format, voxel numbers given in Filename, single (32bit real)</p> <p> </p>
Flat subduction versus big mantle wedge: contrasting modes for deep hydration and overriding craton modification - Dataset
<p>This is the dataset for the paper "Flat subduction versus big mantle wedge: contrasting modes for deep hydration and overriding craton modification" that has been submitted to "Journal of Geophysical Research: Solid Earth" for publication.</p>
Data from: Assessment of tumor treatment response using active contrast encoding (ACE)-MRI: comparison with conventional DCE-MRI
<p><strong>Purpose:</strong> To investigate the validity of contrast kinetic parameter estimates from Active Contrast Encoding (ACE)-MRI against those from conventional Dynamic Contrast-Enhanced (DCE)-MRI for evaluation of tumor treatment response in mouse tumor models.</p> <p><strong>Methods:</strong> The ACE-MRI method that incorporates measurement of <em>T<sub>1</sub></em> and <em>B<sub>1</sub></em> into the enhancement curve washout region, was implemented on a 7T MRI scanner to measure tracer kinetic model parameters of 4T1 and GL261 tumors with treatment using bevacizumab and 5FU. A portion of the same ACE-MRI data was used for conventional DCE-MRI data analysis with a separately measured pre-contrast <em>T<sub>1</sub></em> map. Tracer kinetic model parameters, such as <em>K<sup>trans</sup></em> (permeability area surface product) and <em>v<sub>e</sub></em> (extracellular space volume fraction), estimated from ACE-MRI were compared with those from DCE-MRI, in terms of correlation and Bland-Altman analyses. </p> <p><strong>Results:</strong> A three-fold increase of the median <em>K<sup>trans</sup></em> by treatment was observed in the flank 4T1 tumors by both ACE-MRI and DCE-MRI. In contrast, the brain tumors did not show a significant change by the treatment in either ACE-MRI or DCE-MRI. <em>K<sup>trans</sup></em> and <em>v<sub>e</sub></em> values of the tumors from ACE-MRI were strongly correlated with those from DCE-MRI methods with correlation coefficients of 0.92 and 0.78, respectively, for the median values of 17 tumors. The Bland-Altman plot analysis showed a mean difference of -0.01 /min for <em>K<sup>trans</sup></em> with the 95% limits of agreement of -0.12 /min to 0.09 /min, and -0.05 with -0.37 to 0.26 for <em>v<sub>e</sub></em>.</p> <p><strong>Conclusion:</strong> The tracer kinetic model parameters estimated from ACE-MRI and their changes by treatment closely matched those of DCE-MRI, which suggests that ACE-MRI can be used in place of conventional DCE-MRI for tumor progression monitoring and treatment response evaluation with a reduced scan time. <br> </p>
Data from: Contrasting responses of steppe Stipa ssp. to warming and precipitation variability
Climate change, characterized by warming and precipitation variability, restricted the growth of plants in arid and semi-arid areas, and various functional traits are impacted differently. Comparing responses of functional traits to warming and precipitation variability and determining critical water threshold of dominate steppe grasses from Inner Mongolia facilitates the identification and monitoring of water stress effects. A combination of warming (ambient temperature, +1.5°C and +2.0°C) and varying precipitation (-30%, -15%, ambient, +15%, and +30%) manipulation experiments were performed on four Stipa species (S. baicalensis, S. bungeana, S. grandis, and S. breviflora) from Inner Mongolia steppe. The results showed that the functional traits of the four grasses differed in their responses to precipitation, but they shared common sensitive traits (root/shoot ratio, R/S and specific leaf area, SLA) under ambient temperature condition. Warming increased the response of the four grasses to changing precipitation, and these differences in functional traits resulted in changes to their total biomass, with leaf area, SLA and R/S making the largest contributions. Critical water thresholds of the four grasses were identified, and warming led to their higher optimum precipitation requirements. The four steppe grasses were able to adapt better to mild drought (summer precipitation decreased by 12%-28%) when warming 1.5°C rather than 2.0°C. These results indicated that if the Paris Agreement to limit global warming to 1.5°C will be accomplished, this will increase the probability for sustained viability of the Stipa steppes in the next 50-100 years.
Multi-event capture-recapture analysis in Alpine chamois reveals contrasting responses to interspecific competition, within and between populations
<p>1. Understanding components of interspecific competition has long been a major goal in ecological studies. Classical models of competition typically consider equal responses of all individuals to the density of competitors, however responses may differ both among individuals from the same population, and between populations.</p> <p>2. Based on individual long-term monitoring of two chamois populations in sympatry with red deer, we built a multi-event capture-recapture model to assess how vital rates of the smaller chamois are affected by competition from the larger red deer.</p> <p>3. In both populations, mortality and breeding probabilities of female chamois depend on age and in most cases, of breeding status the preceding year. Successful breeders always performed better the next year, indicating that some females are of high quality. In one population where there was high spatial overlap between the two species, the survival of old female chamois that were successful breeders the preceding year (high-quality) was negatively related to an index of red deer population size suggesting that they tend to skip reproduction instead of jeopardizing their own survival when the number of competitors increases. The breeding probability of young breeders (ages 2 and 3) was similarly affected by red deer population size. In contrast, in the second site with low spatial overlap between the two species, the vital rates of female chamois were not related to red deer population size.</p> <p>4. We provide evidence for population-specific responses to interspecific competition and more generally, for context-, age- and state-dependent effects of interspecific competition.</p> <p>5. Our results also suggest that the classical assumption of equal responses of all individuals to interspecific competition should be relaxed, and emphasize the need to move towards more mechanistic approaches to better understand how natural populations respond to changes in their environment.</p>
Data from: Countershading enhances camouflage by reducing prey contrast
<p>A 3D body shape is problematic for camouflage because overhead lighting produces a luminance gradient across the body's surface. Countershading, a form of patterning where animals are darkest on their uppermost surface, is thought to counteract this luminance gradient and enhance concealment, but the mechanisms of protection remain unclear. Surprisingly, no study has examined how countershading alters prey contrast, or investigated how the presence of a dorso-ventral luminance gradient affects detection under controlled viewing conditions. It has also been suggested that the direction of the dorso-ventral luminance gradient (darkest or lightest on top) may interfere with predators' abilities to resolve prey 3D shape, yet this intriguing idea has never been tested. We used live fish predators (western rainbowfish, <i>Melanotaenia australis</i>) and computer-generated prey images to compare the detectability of uniformly pigmented (i.e. non-countershaded) prey with that of optimally countershaded prey of varying contrasts against the background. Optimally countershaded prey were difficult for predators to detect, and the probability and speed of detection depended on prey luminance contrast with the background. In comparison, non-countershaded prey were always highly detectable, even though their average luminance closely matched the luminance of the background. Our findings suggest that uniformly pigmented 3D prey are highly conspicuous to predators, because overhead lighting increases luminance contrast between different body parts or between the body and the background. We found no evidence for the notion that countershading interferes with predator perception of 3D form.</p>
Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms
<p>Relationships between deep-sea invertebrates and bacterial symbionts, fueled by sulfide and methane, are well known, yet factors influencing symbiont specificity remain cryptic. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analyzed for 3 co-occurring species each of <i>Bathymodiolus</i> mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer gene was analyzed via direct and barcoded amplicon sequencing to reveal fine-scale symbiont diversity. Each of the three mussel species (<i>B. earlougheri, B. billschneideri </i>and<i> B. nancyschneideri</i>) hosted genetically-distinct thiotrophic endosymbionts, despite living nearly side-by-side in their habitat, suggesting that host identity is influential in driving symbiont specificity.<b> </b>The dominant thiotrophic symbiont of co-occurring tubeworms <i>Escarpia spicata</i> and <i>Lamellibrachia (L. barhami </i>and<i> L. donwalshi)</i>, on the other hand, was identical regardless of host species or sample location, suggesting lack of influence by either factor on symbiont selectivity in this group of animals. These findings highlight the specific, yet distinct, influences on the environmental acquisition of symbionts in two foundational invertebrates with similar lifestyles, and provide a rapid and precise method of examining symbiont identities.</p>
Data from: Contrasting effects of host identity, plant community, and local species pool on the composition and colonisation levels of arbuscular mycorrhizal fungal community in a temperate grassland
Arbuscular mycorrhizal fungi (AMF) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine effects of the surrounding plant community, of host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 weeks, and AMF in their roots were quantified. Additionally, we characterised the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMF, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonisation intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.
Data from: Experimental reduction of plant abundance changes interaction frequency of a tri-trophic micro-food web: contrasting responses of generalists and specialists
1. Species abundance is vulnerable to climate change and anthropogenic impact. Although numerous studies have examined the food web response to species loss, their response (e.g. in network topology and interaction frequency) to changes in species abundance has received little attention. 2. We experimentally reduced the abundance (by ca. 60%) of one host plant species (Saussurea nigrescens) in a tri-trophic micro-food web consisting of two common Asteraceae species (S. nigrescens and Anaphalis flavescens), their pre-dispersal seed predators (tephritid flies), and the parasitoid wasps that feed on these seed predators. 3. The neutral process hypothesis posits that network topology and interaction frequency are determined by the relative abundances of the participating species. Accordingly, we hypothesized that interaction frequency (indicated by the rate of flies infesting plants and of parasitoid wasps parasitizing flies) would decrease with decreasing abundance of host plant abundance. 4. Consistent with the neutral process hypothesis, abundance reduction significantly decreased the rate of generalist flies infesting the manipulated plant host species, but increased the rate on unmanipulated plant species. In contrast, abundance reduction significantly increased the rate of specialist flies infesting the manipulated species, but it had no demonstrable effect on the specialists on the unmanipulated plant host. 5. Moreover, abundance reduction significantly increased the rate of parasitoid wasps (as a species group) parasitizing flies in the manipulated species but decreased the rate of the unmanipulated species. These results were not attributable to neutral processes, but can be explained only by adaptive foraging theory. In addition, experimental manipulation did not shift the qualitative presence/absence of the linkages in the micro-food web, and the change in the abundance of both fly and wasp species was smaller than the abundance changes of the manipulated plant species. 6. These observations are interpreted to indicate that both neutral process and/or adaptive foraging likely contributed to food web stability in responses to changes in species abundance. Because species abundance is vulnerable to abiotic and biotic environmental changes, we suggest more research should be conducted to understand how food webs respond to climate change and anthropogenic disturbance.
Data from: Contrasting scales of local persistence between monsoonal and arid biomes in closely related, low-dispersal vertebrates
Aim: Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger-scale, late-Pleistocene changes in distributions of lizards in the Australian Arid Zone (AZ) than in the adjacent Monsoonal Tropics (MT). Location: Northern and central Australia. Taxon: Scincidae: Squamata. Methods: We sequenced ~ 2000 nuclear exons and one mitochondrial gene across the distributions of species with primarily MT or AZ distributions from three genera of lizards. Using phylogenetic analysis and population structure analyses we identified major phylogeographic lineages and then compared the spatial scale of structuring and tested for recent demographic expansions. Results: Two genera in particular, Proablepharus and Morethia, showed deeper and more geographically localised phylogeographic diversity in the MT than the AZ. In the MT, localised diversity was prevalent in the relatively mesic regions. By contrast, the AZ was characterised by widespread and often genetically uniform lineages and a higher proportion of these had signals of recent population expansion. Main conclusions: Consistent with other recent, but mostly less genetically extensive studies, our results point to deeper and more localised diversity in MT compared to AZ. In turn, this suggests higher local persistence in more mesic and topographically diverse biome through the late Quaternary climate fluctuations. For the AZ, geographically extensive range expansions have likely contributed to the low spatial turnover of this exceptionally rich lizard fauna.
DNA methylation and phenotypic data from: Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens
<p>DNA methylation can be environmentally modulated and play a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato <i>Solanum kurtzianum</i>, a close relative of the cultivated potato <i>S. tuberosum</i>. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) was assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability were positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.</p>
Contrasting signatures of introgression in North American box turtle (Terrapene spp.) contact zones
Hybridization occurs differentially across the genome in a balancing act between selection and migration. With the unprecedented resolution of contemporary sequencing technologies, selection and migration can now be effectively quantified such that researchers can identify genetic elements involved in introgression. Furthermore, genomic patterns can now be associated with ecologically relevant phenotypes, given availability of annotated reference genomes. We do so in North American box turtles (<i>Terrapene</i>) by deciphering how selection affects hybrid zones at the interface of species-boundaries and identifying genetic regions potentially under selection that may relate to thermal adaptations. Such genes may impact physiological pathways involved in temperature-dependent sex determination, immune system functioning, and hypoxia tolerance. We contrasted these patterns across inter- and intra-specific hybrid zones that differ temporally and biogeographically. We demonstrate hybridization is broadly apparent in <i>Terrapene</i>, but with observed genomic cline patterns corresponding to species boundaries at loci potentially associated with thermal adaptation. These loci display signatures of directional introgression within intra-specific boundaries, despite a genome-wide selective trend against intergrades. In contrast, outlier loci for inter-specific comparisons exhibited evidence of being under selection against hybrids. Importantly, adaptations coinciding with species-boundaries in <i>Terrapene</i> overlap with climatic boundaries and highlight the vulnerability of these terrestrial ectotherms to anthropogenic pressures.
High contrast yellow mosaic patterns are prey attractants for orb-weaving spiders
<p>Many animals improve their foraging success by producing signals that exploit the sensory biases of potential prey, but the specific properties that make these sensory traps effective remain unclear. We combine field experiments with phylogenetic comparative analyses to investigate the visual luring properties of different signal designs in web‐building spiders. Our field experiments used cardboard spider models to examine the effects of area of colour patches, colour and pattern on the foraging success of the colourful giant wood spider, <i>Nephila pilipes</i>. These experiments revealed that both the colour (yellow) and pattern (yellow and black mosaic) are essential for luring prey in a high ambient light environment. We subsequently used phylogenetic comparative analyses to demonstrate an evolutionary association between prey viewing environment and spider ventral signal among 63 species of orb‐weavers from 53 genera. Combined, our data show that (a) the colour of the bright body parts of orb‐weavers is essential for both diurnal and nocturnal prey attraction, whereas the pattern and area of colour patches are important for diurnal foraging and (b) the evolution of these visual lures is associated with the viewing environment, specifically ambient light intensity. We conclude that the effectiveness of colour luring might be a major driver of the convergent evolution of yellow mosaic patterns in phylogenetically divergent orb‐weavers. Our discoveries indicate that prey colour preferences and signal efficacy play a significant role in the evolution of visually mediated prey‐luring systems.</p>
Data from: Contrasting vulnerability of monospecific and species-diverse forests to wind and bark beetle disturbance: The role of management
<p>The published dataset contains the results of the paper titled <strong>Contrasting vulnerability of monospecific and species-diverse forests to wind and bark beetle disturbance: The role of management, in Ecology and Evolution.</strong></p> <p>Results are based on the output of the model iLand<strong> (</strong>http://iland.boku.ac.at/startpage).</p> <p>contact: Laura Dobor; dobor.laura@gmail.com</p>
The role of boundary length and adjacent patch contrast in guppy mate choice: Dataset, Matlab and R codes
<p>The presence of various combinations of adjacent colours within polymorphic species' colour pattern could have a major impact on mate choice. We studied the role of pattern geometry in predicting mate choice in guppies using boundary strength analysis (BSA). BSA estimates the visual contrast intensity between two adjacent colour patches (<i>ΔS</i>) weighted by the lengths of the boundaries between these adjacent colour patches. We measured both the chromatic (hue and saturation) and achromatic (luminance) <i>ΔS</i> for each pair of adjacent patches. For each male's colour pattern, we measured BSA as both mean (<i>mΔS</i>)<i> </i>and coefficient of variation (<i>cvΔS</i>) of all <i>ΔS</i> weighted by their corresponding boundary lengths. We also determined if specific colour patch boundaries had an impact on female preferences and whether these predicted overall male contrast (<i>mΔS</i>). We found that males with a higher <i>mΔS</i> were more attractive to females and that six boundaries containing either fuzzy black or black as one of the pair colours significantly affected female preferences, indicating that (1) females favoured highly conspicuous males and (2) melanin-based patches could be used as a signal amplifier, not only for orange but for other colours.</p>
Phase contrast mammography phantom
<p>Mammography phantom for phase-contrast simulations. For details, see our GitHub page <a href="https://github.com/ilianhaggmark/phase-contrast-phantom">here.</a></p> <p>The phantom is stored as ten separate material files (format .mat). Each file contains a matrix (type single) which is 24640 by 60160 pixels.</p> <p>Material indices:</p> <p>000 - Air<br> 001 - Adipose tissue<br> 002 - Skin tissue<br> 029 - Glandular tissue<br> 088 - Connective tissue<br> 095 - Terminal duct<br> 125 - Duct<br> 151 - Blood<br> 200 - Mass<br> 250 - Calcium oxalate<br> </p> <p>Please cite: <strong>In Silico Phase-Contrast X-Ray Imaging of Anthropomorphic Voxel-Based Phantoms</strong>, Ilian Häggmark, Kian Shaker, and Hans M. Hertz, <a href="https://doi.org/10.1109/TMI.2020.3031318">IEEE Transactions on Medical Imaging 40(2) 539-548 (2021)</a>.</p>
Contrasting biomass allocation responses across ontogeny and stress gradients reveal plant adaptations to drought and cold
How plants allocate their biomass to different organs is essential to understand plant adaptation and distribution. Overall, biomass allocation may follow fixed rules across taxa. They are also likely to exhibit substantial departure from these rules during ontogeny and in response to particular limiting factors to optimize their growth and maximize their survival. However, how plants adjust their allocation priorities depending on size and age across stress gradients remain largely unkown in wild populations. We examined ontogenetic variation in biomass allocation in Himalayan forb Potentilla pamirica across its 5250-5900 m elevation range, between populations from dry steppe, wet alpine and cold subnival zone. We tested whether biomass allocation followed optimal partitioning or fixed allometric rules using organ mass in 1019 individuals spanning 1-73 years. We found shifting biomass fractions with plant size and age, supporting the optimal partitioning theory. Young plants (<10 years) allocated similar proportions of biomass to leaves, stems, and roots, intermediate-aged plants (10-30 years) allocated more biomass to roots, while the oldest plants had 90% biomass in belowground stems. Major developmental processes including secondary thickening, branching and flowering begin 10-15 years earlier under more thermally favorable steppe conditions. Young steppe plants are larger than alpine and subnival plants, but these differences disappear in plants aged ~30, and the oldest alpine and subnival plants are larger than steppe plants. Plant age exerted significant control over biomass allocation after controlling for plant size. While in steppe plants the preference for stem biomass allocation increases with both size and age, for large alpine and subnival plants the stem prioritization decreases with age in favour of root and leaf mass fractions. We interpret the root and leaf prioritization in the oldest plants as a way to reduce carbon imbalances and the risk of frost damage to secure long life. Our analyses rejected ontogenetically fixed allometry and instead found high variation in biomass allocation depending on age, size and environment, supporting optimal partitioning theory. The uneven allocation of resources to different structures and functions during ontogenesis reflects plant adaptations to different levels of low-temperature and water stress across species elevation range.
Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems
Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.
Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads
<p><b>Premise of the study</b></p> <p>Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such trees. To investigate this possibility, we studied the genetic structures of two such species on isolated pasture trees and surrounding forest, in relation to their local abundances in different habitat types and aspects of their reproductive biology including pollen and seed dispersal agents, and looked for evidence of increased or diminished gene flow.</p> <p><b>Methods</b></p> <p>We used microsatellite markers to assess geographic patterns of genetic diversity and differentiation in two epiphytic bromeliads, <i>Catopsis nitida</i> and <i>Werauhia tonduziana,</i> in the Monteverde region of Costa Rica.</p> <p><b>Key results</b></p> <p>About 85%<sup> </sup>of the <i>F</i><sub>ST</sub> value for <i>Catopsis nitida</i> was found among pastures within regions, while for <i>Weruahia tonduziana,</i> about 80% of the <i>F</i><sub>ST </sub>value was contributed by differences between regions, indicating much more gene flow within regions, relative to <i>C. nitida</i>.</p> <p><b>Conclusions</b></p> <p>Although there was substantial genetic differentiation among epiphyte populations, those on isolated pasture trees were not substantially less diverse than those in adjacent forests, suggesting that pasture trees may serve as "stepping stones" that help these species maintain their genetic connectedness and diversity at larger geographic scales.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.