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Datasets of "Influence of contrast and texture based image modifications on the performance and attention shift of U-Net models for brain tissue segmentation" Part 9 of 14
<p>This dataset is part of the work <a href="https://www.frontiersin.org/articles/10.3389/fnimg.2022.1012639/full">https://www.frontiersin.org/articles/10.3389/fnimg.2022.1012639/full</a>. This is the ninth part of 14 parts of the full dataset (9/14). It contains 3 sets of simulated T1 weighted brain volumes in 3 simulated scanning sequences of spin-echo. The parameters of simulated scanning sequences are respectively repetition time (TR) = 600ms, 700ms, 800ms, and echo time (TE) = 15ms. Under <strong>each</strong> simulated scanning sequence, there are 500 brain volumes.</p> <p>The segmentation labels for each tissue are contained in the first part which you may find at <a href="https://zenodo.org/record/7294916">https://zenodo.org/record/7294916</a></p> <p>The simulation process of this dataset involves two processes. The first is to simulate one brain under different simulated scanning sequences. For this, we use BrainWeb <a href="https://brainweb.bic.mni.mcgill.ca/cgi/bw/submit_request">https://brainweb.bic.mni.mcgill.ca/cgi/bw/submit_request</a>. In the custom setting, we use spin-echo and apply image artifact the same as the default setting of this page. The second process is to transform each simulated brain from BrainWeb to different anatomical shapes. We use Human Connectome Project (HCP) 1200 subject data <a href="https://www.humanconnectome.org/study/hcp-young-adult">https://www.humanconnectome.org/study/hcp-young-adult</a> and randomly select 500 brains as anatomical references.</p> <p>Other details of this dataset can be found at <a href="https://www.frontiersin.org/articles/10.3389/fnimg.2022.1012639/full">https://www.frontiersin.org/articles/10.3389/fnimg.2022.1012639/full</a> where the details of the data construction are discussed.</p> <p>All parts of the whole dataset can be found at:</p> <p>Part 1: <a href="https://zenodo.org/record/7294916">https://zenodo.org/record/7294916</a></p> <p>Part 2: <a href="https://zenodo.org/record/7389550">https://zenodo.org/record/7389550</a></p> <p>Part 3: <a href="https://zenodo.org/record/7390382">https://zenodo.org/record/7390382</a></p> <p>Part 4: <a href="https://zenodo.org/record/7390741">https://zenodo.org/record/7390741</a></p> <p>Part 5: <a href="https://zenodo.org/record/7391205">https://zenodo.org/record/7391205</a></p> <p>Part 6: <a href="https://zenodo.org/record/7393060">https://zenodo.org/record/7393060</a></p> <p>Part 7: <a href="https://zenodo.org/record/7393174">https://zenodo.org/record/7393174</a></p> <p>Part 8: <a href="https://zenodo.org/record/7393347">https://zenodo.org/record/7393347</a></p> <p>Part 9: <a href="https://zenodo.org/record/7394250">https://zenodo.org/record/7394250</a></p> <p>Part 10: <a href="https://zenodo.org/record/7394667">https://zenodo.org/record/7394667</a></p> <p>Part 11: <a href="https://zenodo.org/record/7394939">https://zenodo.org/record/7394939</a></p> <p>Part 12: <a href="https://zenodo.org/record/7395031">https://zenodo.org/record/7395031</a></p> <p>Part 13: <a href="https://zenodo.org/record/7395620">https://zenodo.org/record/7395620</a></p> <p>Part 14: <a href="https://zenodo.org/record/7395622">https://zenodo.org/record/7395622</a></p> <p> </p>
Testing the predictability of morphological evolution in contrasting thermal environments
<p>Gaining the ability to predict population responses to climate change is a pressing concern. Using a 'natural experiment', we show that testing for divergent evolution in wild populations from contrasting thermal environments provides a powerful approach, and likely an enhanced predictive power for responses to climate change. Specifically, we used a unique study system in Iceland, where freshwater populations of threespine sticklebacks (<em>Gasterosteus aculeatus</em>) are found in waters warmed by geothermal activity, adjacent to populations in ambient-temperature water. We focused on morphological traits across six pairs from warm and cold habitats. We found that fish from warm habitats tended to have a deeper mid-body, a sub-terminally orientated jaw, steeper craniofacial profile, and deeper caudal region relative to fish from cold habitats. Our common garden experiment showed that most of these differences were heritable. Population age did not appear to influence the magnitude or type of thermal divergence, but similar types of divergence between thermal habitats were more prevalent across allopatric than sympatric population pairs. These findings suggest that morphological divergence in response to thermal habitat, despite being relatively complex and multivariate, are predictable to a degree<a name="_Hlk345127"></a>. Our data also suggests that the potential for migration of individuals between different thermal habitats may enhance non-parallel evolution and reduce our ability to predict responses to climate change.</p>
Phase contrast images of bacteria and ground truth segmentations
<p><strong>Name</strong>: Phase contrast images of bacteria </p> <p><strong>Data type</strong>: Paired microscopy images and corresponding labels/masks used for model training, organized as recommended by the <a href="https://imagej.net/plugins/denoiseg">DenoiSeg documentation</a>.</p> <p><strong>Microscopy data type</strong>: Light microscopy (Phase Contrast)</p> <p><strong>Manual annotations</strong>: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects were left unannotated.</p> <p><strong>Microscope</strong>: Zeiss Axio Imager M2 epi-fluorescence microscope with a Zeiss Plan-Apochromat; 100x/1.4 oil DIC objective</p> <p><strong>File format</strong>: .tif (float 32-bits for phase contrast and 16-bit for mask images)</p> <p><strong>Image size</strong>: 256x256 pixels (Pixel size: 64.5 nm)</p> <p> </p> <p>Content: </p> <p>train - raw (33 files) </p> <p> - masks (33 files)</p> <p>test - raw (11 files) </p> <p> - masks (11 files)</p> <p> </p> <p>All images available in the raw folders were normalized by dividing the original images with a gaussian blurred version or the original image (200 pixels). A groovy code working within ImageJ/Fiji corresponding to this operation is as follow:</p> <pre><code class="language-java">ImagePlus normalize(ImagePlus input_image) { flatfield = (new Duplicator()).run(input_image) (new GaussianBlur()).blur(flatfield.getProcessor(), 200) return ImageCalculator.run(input_image, flatfield, "Divide create 32-bit") } import ij.ImagePlus import ij.plugin.Duplicator import ij.plugin.ImageCalculator import ij.plugin.filter.GaussianBlur</code></pre> <p> </p>
Contrasting effects of vineyard type, soil and landscape factors on ground- versus above-ground nesting bees
<p><span>1. Agricultural intensification and abandonment of traditional agricultural practices are main drivers of current insect declines. The resulting loss of feeding and nesting opportunities has led to a decrease in pollinator populations like wild bees. While the restoration of floral resources has been widely implemented in wild bee conservation, nesting resources, particularly for ground-nesting species, are barely considered.</span></p> <p><span>2. We assessed wild bee diversity in a wine-growing area in Germany in 15 study sites along a soil gradient and evaluated whether wild bees were distinctly affected by different vineyard types (vertically oriented, terraced, abandoned), local conditions (e.g. shrub and flower cover), and landscape factors in response to divergent nesting needs (above-ground vs. ground-nesting). </span></p> <p><span>3. We found that wild bees responded more strongly to the availability of nesting sites than to flower resources. While ground-nesting bees were determined by the suitability of soil aspects for nesting irrespective of vineyard management types, above-ground nesting bees profited from vineyard abandonment and shrub encroachment in vineyard fallows and were enhanced by the availability of seminatural habitats (SNH) in the surrounding landscape. In contrast, floral resource availability in managed vineyards had only marginal effects on above-ground-nesting bees.</span></p> <p><span>4. Synthesis and applications: Life history traits like nesting strategies have long been neglected in wild bee conservation approaches, but proved to be highly relevant, especially for ground-nesting bees. For this, agri-environmental schemes can no longer solely focus on the restoration of floral resources, but should equally address nesting resources. Therefore, management efforts for enhancing wild bees in vineyard landscapes should aim at complementing nesting resources for ground-nesting bees (e.g. exposed bare ground patches) and above-ground-nesting bees (e.g. woody elements, hedges) in addition to floral resources. At the landscape level, conserving heterogeneous landscapes at a mixture of actively managed vineyards and semi-natural and woody elements is significant to maintain diverse bee communities. </span></p>
Dataset for: Buckling of lipidic ultrasound contrast agents under quasi-static load
<p>Collapse of lipidic ultrasound contrast agents under high-frequency compressive load has been historically interpreted by the vanishing of surface tension. By contrast, buckling of elastic shells is known to occur when costly compressible stress is released through bending. Through quasi-static compression experiments on lipidic shells, we analyze the buckling events in the framework of classical elastic buckling theory and deduce the mechanical characteristics of these shells. They are then compared to that obtained through acoustic characterization.</p>
Data for: Hedgerows have contrasting effects on pollinators and natural enemies and limited spillover effects on apple production
<p>Agricultural intensification has resulted in a decline in insect biodiversity and threatens the provision of valuable ecosystem services. Agri-environment schemes (AESs) have been implemented in an effort to conserve biodiversity on farmland and increase agricultural sustainability, but their effectiveness can vary widely. To better determine which factors influence AES effectiveness, the relative roles of local habitat features, habitat quality, and landscape context need to be further explored. The aim of this study was to determine the most important factors influencing field margin AES effectiveness in commercial apple orchards, in terms of arthropod biodiversity conservation and ecosystem service provision. We surveyed wild bees and aphid natural enemies in field margins and apple trees in 20 orchards, ten bordered by hedgerow field margins (an AES) and ten with herbaceous field margins (no hedgerows present, not an AES). We considered field margin floral resources and the cover of semi-natural habitat in the surrounding landscape as indicators of local habitat quality and landscape context, respectively. We furthermore quantified pollination and pest control as measures of ecosystem service delivery and the relationship between arthropod communities and apple yield (initial and final fruit set) and quality. We found that hedgerow presence strongly predicted both pollinator and natural enemy communities and that these relationships were more pronounced than those with local habitat quality and landscape context. Hedgerows were negatively related to wild bee richness and abundance within the orchard, and positively related to natural enemy richness and abundance at the field margin but not within the orchard. We found no relationships between local and landscape factors and ecosystem service delivery, and no relationship between wild bee communities and apple yield, suggesting that apple is not pollen limited in our study system. There was, however, a negative relationship between natural enemy richness and initial fruit set. We conclude that annually cut hedgerows can benefit the conservation of natural enemies, but have limited arthropod-mediated private benefits for apple production, and likely need to be supplemented with additional local habitat resources for the conservation of wild bees. Our findings indicate that local habitat factors can strongly influence biodiversity regardless of landscape context, but that AESs likely need to be designed with separate biodiversity and ecosystem service targets, and specific taxonomic groups, in mind.</p>
Soil microbial relative resource limitation exhibited contrasting seasonal patterns along an elevational gradient in Yulong snow mountain
<p>1. Microbial relative resource limitations represented by enzyme stoichiometry reflect the relationship between microbial nutrient requirements and nutrient status in soil, but the issue on whether alterations in environments along elevational gradients affect the magnitude of microbial relative resource limitations remains unresolved.</p> <p>2. Here, we examined seasonal patterns in microbial relative carbon (C) and phosphorus (P) limitations indicated by vector lengths and angles using relative proportional enzymatic activities and key controlling factors along an elevational gradient in the Yulong Snow Mountain. We also analyzed the relationships between microbial metabolic processes and microclimates (i.e., soil moisture and temperature), soil properties (i.e., pH and soil texture), and microbial attributes (i.e., microbial biomass and fungal: bacterial ratio).</p> <p>3. We found that soil microbial relative C limitation decreased with increasing elevations, with lower levels observed in the dry season than in the wet season. In contrast, soil microbial relative P limitation varied significantly with elevations, with linearly increasing trends in wet seasons but unimodal trends in dry seasons. Meanwhile, we found higher relative C limitation in the coniferous forest but higher relative P limitation in the broad-leaved forest. Notably, soil microbial relative C limitation was primarily affected by the soil microenvironment (i.e., soil temperature) and substrate quantity (i.e., the ratio of soil dissolved organic C to available P), whereas soil microbial relative P limitation could be alleviated by increasing microbial relative C limitation combined with increasing soil pH. Additionally, the significant linear pattern of the C use efficacy with elevations was only observed in the wet seasons, which was directly influenced by soil microclimates and microbial relative C limitation.</p> <p>4. Overall, our results provided important information for better understanding the essential role of microbial processes in the regulation of C and P cycling in vulnerable subtropical mountain ecosystems.</p>
Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies
<p>Resource specialization and host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the general rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary time scales. We applied genome-wide SNP data obtained through low-coverage genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies collected from seven shared willow (<em>Salix</em>) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their <em>Salix</em> hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species than are most bud gallers. In contrast to bud gallers, leaf gallers also exhibit statistically significant cophylogenetic signal with their <em>Salix</em> hosts. The observed discordant patterns of resource specialization and long-term host use in two related galler groups that have radiated in parallel across a shared resource base indicate a general lack of evolutionary repeatability and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.</p>
Contrasting Responses of Surface Heat Fluxes to Tropical Deforestation
<p>2D_GSWP3*.nc are the CLM simulation outputs with GSWP3 as input forcings.</p> <p>2D_*_piControl.nc and 2D_*_deforest-globe.nc are the CMIP6 model outputs.</p> <p>Offline.m and LUMIP.m are matlab code files to reproduce figures in the article.</p> <p>nc_*.py are python code files to generate netCDF files for producing figures.</p>
Data from: Contrasting long-term trends in juvenile abundance of a widespread cold-water salmonid along a latitudinal gradient: Effects of climate, stream size and migration strategy
<p><span>A changing climate reshapes the range distribution of many organisms, and species with relatively low thermal optima, like many salmonids, are increasingly expected to face local population extinctions at lower latitudes. Understanding where and how fast these changes are happening is of pivotal importance for successful mitigation and conservation efforts.</span></p> <p><span>We used an extensive electrofishing database to explore temporal trends of brown trout juveniles (<em>Salmo</em> <em>trutta</em> L.) in 218 locations from 174 Swedish streams, over the last 30 years (1991–2020). We hypothesized that 1) declines in abundance have occurred predominately in the warmer, southern regions, while increases have occurred in the colder, northern regions, 2) larger stream sizes may partly offset negative effects of climate, and 3) migrating and resident populations are affected differently by a warming climate.</span></p> <p><span>We found that abundance of brown trout juveniles generally declined in warmer regions, especially in smaller streams (≤ 6 m wide), while the abundance increased in colder regions. In larger streams, negative effects of higher temperatures were seemingly buffered, as we found lower rates of decline or even positive trends. The rate of change (i.e. the slopes of the trends in abundance) was more pronounced towards the climate extremes and was on average zero in regions with a normal annual air temperature (average temperature over 30-year period) around 5–6 ºC. Warmer climate had stronger effects on migrating compared to resident populations, suggesting that climate-induced loss of stream connectivity could be an additional factor that hinders recruitment in anadromous populations in a changing climate.</span></p> <p><span>Considering predictions of increasing temperatures and frequency of summer droughts, management of cold-water salmonid populations should focus on conserving and restoring riparian vegetation, wetlands, climate and thermal refugia, and habitat integrity overall. Such measures may, however, not suffice for small streams at lower latitudes, unless hydrological connectivity is maintained.</span></p>
Contrasting impacts of warming and browning on periphyton
<p>We tested interactive effects of warming (+2°C) and browning on periphyton accrual and pigment composition when grown on a synthetic substrate (plastic strips) in the euphotic zone of sixteen experimental ponds. We found that increased DOC alone, or in combination with warming, resulted in a substantially enhanced biomass accrual of periphyton, illustrating that periphyton is capable of using nutrients associated with DOC, and by this may affect nutrient availability for phytoplankton. However, warming weakened the positive impact of DOC on periphyton accrual, possibly by thermal compensation inferred from altered pigment composition, and/or changes in community composition. Our results illustrate that impacts of climate change on algal growth are multiple, which could have implications for productivity and consumer resource use, especially in shallow areas in northern lakes.</p>
Hyperpolarized [15N]nitrate as a potential long lived hyperpolarized contrast agent for MRI
<p>Primary data for DOI: <a href="https://doi.org/10.1016/j.jmr.2019.01.001">10.1016/j.jmr.2019.01.001</a></p> <p>Title: Hyperpolarized [<sup>15</sup>N]nitrate as a potential long lived hyperpolarized contrast agent for MRI</p> <p>Authors: Ayelet Gamliel, Sivaranjan Uppala, Gal Sapir, Talia Harris, Atara Nardi-Schreiber, David Shaul, Jacob Sosna, J. Moshe Gomori, Rachel Katz-Brull</p> <p>Description:</p> <p>The primary datasets in this archive contain data presented in the above publication and consist of <sup>15</sup>N-NMR spectra in solutions.</p> <p>Please consult the Archive Guide.</p>
Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient
<p>Title of dataset</p> <p>Data from: Chilean bee diversity: Contrasting patterns of species and phylogenetic turnover along a large-scale ecological gradient</p> <p>Authors of dataset</p> <p>Leon Marshall<sup>1,2</sup>, John S. Ascher<sup>3</sup>, Cristian Villagra<sup>4</sup>, Amaury Beaugendre<sup>1</sup>, Valentina Herrera<sup>4</sup>, Patricia Henríquez-Piskulich<sup>4</sup>, Alejandro Vera<sup>5</sup>, Nicolas J. Vereecken<sup>1</sup></p> <ol> <li>Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/2, B 1050 Brussels, Belgium</li> <li>Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands</li> <li>Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore</li> <li>Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> <li>Departamento de Biología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Región Metropolitana, Chile</li> </ol> <p>Abstract</p> <p>Chile's isolation and varied climates have driven the evolution of a unique biodiversity with a high degree of endemism. As a result, Chile encompasses diverse environments, including the Mediterranean-type ecosystem, a global biodiversity hotspot. These environments are currently threatened by anthropogenic land use change impacting the integrity of local biomes and associated species. This area is the most intensively sampled of the country with high endemicity of native bee species. Characterising habitat requirements of bees is a pressing priority to safeguard these insects and the ecosystem services they provide. We investigated broad-scale patterns of bee (Hymenoptera: Apoidea: Anthophila) diversity using newly accessible expert-validated datasets comprising digitized specimen records from Chilean and US collections, and novel expert-validated type specimen data for the bees of Chile. We used a generalised dissimilarity modelling (GDM) approach to explore both compositional and phylogenetic β-diversity patterns across latitudinal, altitudinal, climate and habitat gradients in well-sampled bee assemblages in Central Chile. Using the GDM measures of increasing compositional and environmental dissimilarity we categorised and compared the most important drivers of these patterns and used them to classify 'wild bee ecoregions' (WBE) representing unique assemblages. Turnover of bee assemblages was explained primarily by latitudinal variation (proxy for climate) from south to north in Chile. However, temperature variations, precipitation and the presence of bare soil also significantly explained turnover in bee assemblages. In comparison, we observed less turnover in phylogenetic biodiversity corresponding to spatial gradients. We identified six de novo ecoregions (WBE), all with distinct taxa, endemic lineages, and representative species. The WBE represent distinct spatial classifications but have similarities to existing biogeographical classifications, ecosystems and bioclimatic zones. This approach establishes the baseline needed to prioritise bee species conservation efforts across this global biodiversity hotspot. We discuss the novelty of this classification considering previous biogeographical characterisations and their relevance in assessing conservation priorities for bee conservation. We argue that Chile's WBE highlight areas in need of funding for bee species surveys and description, distribution mapping and strengthening of conservation policies.</p> <p>Usage notes</p> <p>The dataset contains species occurrence data of chilean bees aggregated to a 5 x 5 km grid shapefile. The shapefile of the grid and the raster mask of the Central Chilean study area are also included. Finally, a database of type specimen data used to supplement the dataset is included here. The code for the analysis can be found at: <a href="https://github.com/lmar116/ChileanBeeDiversity">https://github.com/lmar116/ChileanBeeDiversity</a>.</p> <p>Shapefiles, rasters, CSV files and code were all loaded and analyzed using R statistics software. </p> <p>Four files are included:</p> <ol> <li>Marshall-et-al-2023_Ecosphere_DataTable_bee_grid: contains all species occurrence data used in GDM analysis, Grid column refers to cl.5km.shp.</li> <li>cl.5km.shp (and associated files): 5 x 5 km grid shapefile of the Central Chilean study area</li> <li>chile.mask.tif: raster outline of the Central Chilean study area</li> <li>Marshall-et-al-2023_Ecosphere_CentralChileTypeSpecimens.xlsx: contains type specimen data used to supplement species occurrence dataset.</li> </ol>
Contrasting Responses of Surface Heat Fluxes to Tropical Deforestation
<p>2D_*_piControl.nc and *.nc are the analyzed CMIP6 piControl experiments.</p> <p>2D_*_deforest-globe.nc are the analyzed LUMIP deforestation experiments.</p> <p>2D_GSWP3_*.nc are the analyzed CLM simulation output forced with modified GSWP3 forcings.</p> <p>Offline.m and LUMIP.m are to obtain the changes in surface heat fluxes under deforestation and plot figures.</p>
Grazing animals have contrasting effects on foliar pathogens by changing plant community characteristics
<p><span>Large herbivore grazing has substantial effects on plant community structure and ecosystem functioning, however, the impacts of grazing on plant diseases remain poorly understood. Here, we used a grazing experimentand a removal experiment manipulating plant density and litter biomass in northeast China to evaluate how large vertebrate herbivores (cattle and sheep) affect different foliar fungal diseases (biotrophs and necrotrophs). We found that cattle grazing significantly reduced pathogen load, of both biotrophs and necrotrophs, while sheep grazing increased biotrophic pathogen load, but did not affect necrotrophic pathogen load. </span><span> Mechanistically</span><span>, grazing effects were indirect and mediated by changing </span><span>plant community characteristics</span><span>. Moreover, litter biomass play an important role in affecting necrotrophs and by reducing litter build up the cattle reduced necrotrophic pathogen infection</span><span>. Our results demonstrate that </span><span>cattle and sheep grazing have</span><span> contrasting impacts on </span><span>pathogen load. This finding has important implications for improving disease management through grazing regimes in grassland systems.</span></p>
Soil fungal communities contribute to the positive diversity-productivity relationship of tree communities under contrasting water availability
<p><span>Plant diversity has often been linked to increased productivity; however, this apparent diversity-productivity relationship may rely on inter-trophic interactions such as those between plants and soil microbes. Soil fungi can create complementarity between plant species via altered plant resource partitioning, facilitation via fungal networks, or biotic feedbacks, thereby promoting plant diversity-productivity relationships. Furthermore, these relationships are likely to be context-dependent in response to resource availability. </span></p> <p><span>We used a biodiversity-ecosystem function experiment with trees exposed to high and low water availability treatments to determine the contribution of soil fungal communities to the diversity-productivity relationship in tree communities. We used amplicon sequencing of soil fungi to assess fungal richness, community composition, and richness of functional guilds. We then applied structural equation modelling to determine relationships between tree diversity, fungal communities, and tree productivity and the role of water availability in these relationships.</span></p> <p><span>Tree species richness and functional diversity both increased above-ground tree productivity and influenced soil fungal community composition. Fungal community composition had a direct impact on tree productivity and enhanced net diversity effects on productivity. Therefore, fungal communities mediated a positive, indirect effect of tree richness on productivity. While total fungal richness was not associated with tree diversity, pathogen richness decreased and mycorrhizal richness increased with tree richness. Pathogen and mycorrhizal richness had either no impact or a weak negative effect on productivity. Tree species traits strongly affected fungal communities and these changes promoted productivity. Finally, water availability greatly influenced fungal communities but did not interact with tree diversity to affect productivity; indicating possible resilience of tree communities to altered precipitation regimes and associated changes in fungal communities.</span></p> <p><span>Synthesis: Our study highlights the crucial role that fungal communities play in shaping the relationship between tree diversity, traits, and productivity, and resilience to altered water availability. </span></p>
Figure 1 in Riodinid butterfly fauna (Lepidoptera) of the Cosñipata Region, Peru: Annotated checklist, community structure, and contrast with Lycaenidae
Figure 1. Location of the Cosñipata Region (yellow box) in southeast Peru. © Amazonia Lodge.
Figure 2 in Riodinid butterfly fauna (Lepidoptera) of the Cosñipata Region, Peru: Annotated checklist, community structure, and contrast with Lycaenidae
Figure 2. The Cosñipata Valley at 1,200 m looking towards the northeast. © Loran D. Gibson.
Data and code from: Dynamics of cortical contrast adaptation predict perception of signals in noise
<p>Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.</p>
Data from: The fate of nitrogen during agricultural intensification in East Africa: nitrogen budgets in contrasting agroecosystems
<p>The intensification of agricultural systems in sub-Saharan Africa (SSA) is necessary to reduce poverty and improve food security but requires increased nutrient applications to smallholder systems. To avoid the negative consequences of intensification that result from many large-scale agricultural systems (e.g., eutrophication), we must better understand how diverse soil systems in SSA will respond to increased fertilizer applications. We tracked nitrogen (N) inputs and outputs in fertilizer trials at two maize (Zea mays)-agroecological regions of contrasting soil type. We measured maize biomass, grain yields, N leaching, and N gaseous losses from a clayey soil in Yala, Kenya, and a sandy soil in Tumbi, Tanzania, with application rates of 0, 50, 75, 100, 150, and 200 kg N ha<sup>-1</sup> yr<sup>‑1</sup> over multiple years. Using measurements of NO, N<sub>2</sub>O, NO<sub>3</sub><sup>-</sup>, biomass N, and an <sup>15</sup>N enrichment experiment, we show that N budgets in Yala were nearly always negative, meaning more N was exported in yields or lost from the system than was added in fertilizer. In Tumbi, however, N budgets were negative at lower fertilizer levels (0 and 50 kg N ha<sup>-1</sup>), but positive at higher fertilizer levels (75 and 200 kg N ha<sup>-1</sup>). At both sites, most of the N was lost through maize biomass/grain removal and N leaching (over 96% of total losses). Gas losses were a minor component of N budgets. These results highlight the importance of tailoring fertilizer recommendations to a farm's specific soil and climatic conditions. However, on these two contrasting sites, fertilizer additions at or below 50 kg N ha<sup>-1</sup> do not lead to major losses of N (via gaseous or leaching) and may be recommended at a range of sites across SSA soils in maize agroecosystems.</p>
ScienceDex guides
Understand access before you commit
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.