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12,662 results for “linking”
Unveiling the link between Phytoplankton Molecular Physiology and Biogeochemical Cycling via Genome-Scale Modeling
<p>Data used for the manuscript "Unveiling the link between Phytoplankton Molecular Physiology and Biogeochemical Cycling via Genome-Scale Modeling"</p>
Extreme events in Indian Monsoon linked to Global warming scenario during Bølling–Allerød
<p>Stable Oxygen isotope data from stalagmite samples of Kailash cave, Central India, during the Bølling-Allerød warmth </p>
Singing strategies are linked to perch use on foraging territories in heart-nosed bats
<p>These data include the GPS data of 14 VHF telemetry tracked heart-nosed bats (<em>Cardioderma cor</em>) and associated singing behavior collected during the long dry season (May to October) in Tanzania. These data were used to establish that singing occurs on nighttime foraging areas, and that foraging areas are exclusive and repeatedly used, supporting the hypothesis that <em>C. cor</em> maintain individualistic foraging territories with singing. Times and locations of singing are included in the data set and linked to the GPS waypoints of perches individuals used repeatedly during then 4-6 nights of tracking. GPS data is organized by list of separate waypoints and whether they were used for singing. Furthermore, individuals sit in trees and sing for long stretches of time, and thus these durations were subsampled into 2 minute intervals and associated with the perch location to create a dateset of points for Kernal Density Estimates. Times and perch locations for KDE, including associated singing behavior, are also included. Finally, singing duration of each individual is broken down by perch, night, and hour. Of the 14 tracked individuals, 13 are male (one of which stopped singing soon after tracking commenced) and one is a nonsinging female. </p>
Mediobasal hypothalamic FKBP51 acts as a molecular switch linking autophagy to whole-body metabolism - Dataset IC
<p>Raw data associated to the following publication: “Mediobasal hypothalamic FKBP51 acts as a molecular switch linking autophagy to whole-body metabolism".</p> <p><em>The stress-responsive FKBP51 controls body weight gain by regulating the balance between autophagy and mTOR signaling. We identified FKBP51 as a central nexus for the recruitment of the LKB1/AMPK complex to WIPI4 and TSC2 to WIPI3, thereby regulating the balance between autophagy and mTOR signaling in response to metabolic challenges. MBH FKBP51 dose-dependently regulates autophagy both in the brain as well as in peripheral metabolic tissues. Consequently, deletion of MBH FKBP51 strongly induces obesity, while its overexpression protects against high-fat diet (HFD) induced obesity.</em></p> <p>IC data in Thermo RAW data format; 2nd of 2 datasets.</p>
Mediobasal hypothalamic FKBP51 acts as a molecular switch linking autophagy to whole-body metabolism - Dataset Bz
<p>Raw data associated to the following publication: “Mediobasal hypothalamic FKBP51 acts as a molecular switch linking autophagy to whole-body metabolism".</p> <p><em>The stress-responsive FKBP51 controls body weight gain by regulating the balance between autophagy and mTOR signaling. We identified FKBP51 as a central nexus for the recruitment of the LKB1/AMPK complex to WIPI4 and TSC2 to WIPI3, thereby regulating the balance between autophagy and mTOR signaling in response to metabolic challenges. MBH FKBP51 dose-dependently regulates autophagy both in the brain as well as in peripheral metabolic tissues. Consequently, deletion of MBH FKBP51 strongly induces obesity, while its overexpression protects against high-fat diet (HFD) induced obesity.</em></p> <p>Bz data in Thermo RAW data format; 1 of 2 datasets.</p>
Social media articles dataset - article titles and links
<p>This dataset contains the raw results of topic mapping presented at ngi.https://ngitopics.delabapps.eu. </p> <p>The dataset includes the title and link to the collected article, as well as the location on the map. </p> <p>There is a separate dataset for each analysed map: six umbrella topics + 6 regions</p> <p>For details on data collection and methodology see: https://ngitopics.delabapps.eu/report.pdf and https://ngitopics.delabapps.eu/report_multilanguage.pdf</p> <p> </p> <p> </p>
Links between boreal forest management, soil fungal communities and belowground carbon sequestration
<p>Forest management has a potential to alter belowground carbon storage. However, the underlying mechanisms, and the relative importance of carbon input and decomposition in regulation of soil carbon dynamics are poorly understood.</p> <p>We examined whether interactive effects of forest fertilization and thinning on carbon stocks in the topsoil of boreal forests were linked to changes in fungal community composition, biomass, and enzyme activities, in a long-term fertilization and thinning experiment distributed across 29 Pinus sylvestris forests along a 1300 km latitudinal transect in Sweden.</p> <p>Nitrogen fertilization increased fungal biomass, particularly towards the north and mainly by promoting root associated Ascomycetes, but the response was moderated by thinning. Fungal biomass correlated positively with carbon stocks in the organic topsoil. However, ectomycorrhizal Cortinarius species were reduced in abundance by fertilization and correlated negatively with carbon stocks.</p> <p>Plausibly, increased soil carbon stocks after fertilization are linked to increased input of carbon in the form of root-associated mycelium combined with loss of ectomycorrhizal decomposers within the genus Cortinarius. These fungal responses to fertilization may mediate a natural climate solution by promoting carbon sequestration in the organic topsoil, but the effect of fertilization may also be undesired from a biodiversity perspective.</p>
Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C
<p><i>Telopea speciosissima, </i>the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for <i>T. speciosissima</i>. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs 'Complete'. We present a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering scaffolds, which combines read depths, <i>k</i>-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2<i>n</i> = 22). Genome annotation predicted 40,158<code> </code>protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated <i>CYCLOIDEA </i>(<i>CYC</i>)<i> </i>genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 'Duplicated' BUSCO genes using a new tool, DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level <i>T. speciosissima</i> reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.</p>
Linking habitat interactions and biodiversity within seascapes - Dataset
<p>This dataset supports the article: </p> <p>Bugnot AB, Dafforn KA, Coleman RA, Ramsdale M, Gibbeson JT, Erickson K, Vila-Concejo A, Figueira WF, Gribben PE<span>. </span>Linking habitat interactions and biodiversity within seascapes. Ecosphere </p>
Hematopoietic Tumors in a Mouse Model of X-linked Chronic Granulomatous Disease after Lentiviral Vector-Mediated Gene Therapy
<p>Chronic granulomatous disease (CGD) is a rare inherited disorder due to loss-of-function mutations in genes encoding the NADPH oxidase subunits. Hematopoietic stem and progenitor cell (HSPC) gene therapy (GT) using regulated lentiviral vectors (LVs) has emerged as a promising therapeutic option for CGD patients. We performed non-clinical Good Laboratory Practice (GLP) and laboratory-grade studies to assess the safety and genotoxicity of LV targeting myeloid specific Gp91phox expression in X-linked chronic granulomatous disease (XCGD) mice. We found persistence of gene-corrected cells for up to 1 year, restoration of Gp91phox expression and NADPH oxidase activity in XCGD phagocytes, and reduced tissue inflammation after LV-mediated HSPC GT.<br> Although most of the mice showed no hematological or biochemical toxicity, a small subset of XCGD GT mice developed<br> T cell lymphoblastic lymphoma (2.94%) and myeloid leukemia (5.88%). No hematological malignancies were identified in C57BL/6 mice transplanted with transduced XCGD HSPCs. Integration pattern analysis revealed an oligoclonal composition with rare dominant clones harboring vector insertions near oncogenes in mice with tumors. Collectively, our data support the long-term efficacy of LV-mediated HSPC GT in XCGD mice and provide a safety warning because the chronic inflammatory XCGD background may contribute to oncogenesis.</p>
Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules - Data
<p>This repository contains the performance data used in the paper "Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules".</p> <p>The configurations run are in 'dt_run_confs.csv', and each other csv-file corresponds the the AUC values of one of these configurations.</p> <p>The script used to generate the full performance data is included in 'generate.py', and the processing using IOHanalyzer is shown in 'script.R' </p>
Dataset used in the study "Residential buildings real estate values linked to summer surface thermal anomaly patterns and urban features: the Florence (Italy) case study."
<p>This dataset repository includes eight raster layers (Reference System EPSG:3035 - ETRS89-extended / LAEA Europe), used in the study "Residential buildings real estate values linked to summer surface thermal anomaly patterns and urban features: the Florence (Italy) case study", and obtained by the adaptation of analyses carried out by previous studies (Morabito et al., 2021; Guerri et al., 2021; 2022).</p> <p>Further information regarding the source, study period, and horizontal resolution is available in the attached text file. </p> <p> </p> <p><strong><em>References</em></strong></p> <p>Guerri, G., Crisci, A., Congedo, L., Munafò, M., Morabito, M., <strong>2022</strong>. A functional seasonal thermal hot-spot classification: Focus on industrial sites. Science of The Total Environment 806, 151383.<a href="http://https://doi.org/10.1016/j.scitotenv.2021.151383"> https://doi.org/10.1016/j.scitotenv.2021.151383</a>.</p> <p>Guerri, G., Crisci, A., Messeri, A., Congedo, L., Munafò, M., Morabito, M., <strong>2021</strong>. Thermal Summer Diurnal Hot-Spot Analysis: The Role of Local Urban Features Layers. Remote Sensing 13, 538. <a href="https://doi.org/10.3390/rs13030538">https://doi.org/10.3390/rs13030538</a>.</p> <p>Morabito, M., Crisci, A., Guerri, G., Messeri, A., Congedo, L., Munafò, M., <strong>2021</strong>. Surface Urban Heat Islands in Italian Metropolitan Cities: Tree Cover and Impervious Surface Influences. Science of The Total Environment 751, 142334. <a href="https://doi.org/10.1016/j.scitotenv.2020.142334">https://doi.org/10.1016/j.scitotenv.2020.142334</a>.</p>
Nest architecture is linked with ecological success in songbirds
<p>Nests are essential constructions that directly determine fitness, yet their structure can vary substantially across bird species. While there is evidence supporting a link between nest architecture and the habitat a species occupies, we still ignore what ecological and evolutionary processes are linked to different nest types. Using information on 3175 species of songbirds, we show that – after controlling for latitude and body size – species that build domed nests (i.e., nests with a roof) have smaller ranges, are less likely to colonise urban environments and have potentially higher extinction rates compared to species with open and cavity nests. Domed nests could be a costly specialisation, and we show these nests take more time to be built, which could restrict breeding opportunities. These diverse strands of evidence suggest that transition from domed to open nests in passerines could represent an important evolutionary innovation behind the success of the largest bird radiation.</p>
Demographic, physiological, and genetic factors linked to poleward range expansion along the shoreline of China
<p><span>Distribution </span><span>range expansion is one of the most significant consequences of climate change in the Anthropocene. During range expansion, the former biogeographic barrier can be broken and then a new biogeographic pattern might appear. A comprehensive study, including demographic pattern, physiological performance and genetic features, is crucial for understanding how the expanding population occupies and survives in the new habitat, within which it formerly did not occur. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod </span><span><em>Nerita yoldii</em>, which has extended its northern limit by ~200 km into areas that are warming up faster than the historical distribution over the former biogeographic break of the Yangtze River Estuary (YRE) during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modeling analysis revealed that the new marginal populations experienced strong genetic bottlenecks followed by recent demographic expansion. Successful expansion that overcomes the founder effect (reduced genetic variation) might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Our study also reveals a fast loss of </span><span>transcriptional</span><span> plasticity in the new marginal populations, potentially contributing to local adaptation. These results suggest a new biogeographic pattern for the snail <em>N. yoldii</em> has formed with the occurrence of demographic, physiologic and genetic changes, and emphasize the roles of adaptation of marginal populations during distribution range expansion.</span></p>
Fig. 2 in Formation Of Inter-Species Links In Ungulates In The Azov-Syvash National Nature Park
Fig. 2. Change in relationship of numbers of the hoof-animals in the Azov-Syvash NNP.
Data from: Neuron numbers link innovativeness with both absolute and relative brain size in birds
<p>A long-standing issue in biology is whether the intelligence of animals can be predicted by absolute or relative brain size. However, progress has been hampered by an insufficient understanding of how neuron numbers shape internal brain organization and cognitive performance. Based on estimations of neuron numbers for 111 bird species, we show here that the number of neurons in the pallial telencephalon is positively associated with a major expression of intelligence: innovation propensity. The number of pallial neurons, in turn, is greater in brains that are larger in both absolute and relative terms, and positively co-varies with longer post-hatching development periods. Thus, our analyses show that neuron numbers link cognitive performance to both absolute and relative brain size through developmental adjustments. These findings help unify neuro-anatomical measures at multiple levels, reconciling contradictory views over the biological significance of brain expansion. The results also highlight the value of a life history perspective to advance our understanding of the evolutionary bases of the connections between brain and cognition.</p>
Linking agri-environment scheme habitat area, predation and the abundance of chick invertebrate prey to the nesting success of a declining farmland bird
<p>Across Europe, farmland bird populations have continued to decline since the 1970s owing to the intensification of farming practices. Studies of such declines have tended to focus specifically on either the impacts of habitats (nesting and foraging), nest predators or prey availability on bird demographics. The study presented here provides new insights into the relative effects of each of these factors on Yellowhammer nest survival. The Yellowhammer was selected for this study as it is a UK red-listed bird species whose population is in decline across much of Europe. We use a long-term dataset of 147 nests, monitored between 1995 and 2007, to provide an insight into how Yellowhammer nest survival is influenced by nesting habitat (nest concealment and nest height), foraging habitats (habitat coverage within 100 m of nests), the removal of nest predators (Magpie Pica pica abundance as an inverse measure of avian predator removal through gamekeeping) and food availability (measured with a D-vac invertebrate suction sampler). Our results indicated that Yellowhammer hatching success was negatively related to the coverage of spring agri-environment scheme habitats, a group which represents invertebrate-rich agri-environment habitats, but hatching success increased with nest height. Fledging success was positively related to the coverage of the seed-rich habitat Wild Bird Seed mixture. The farm-level abundance of Yellowhammer chick-food invertebrates declined over the study period. Our results highlight the importance of simultaneously considering multiple agents that shape avian breeding success, i.e. their ability to produce offspring, to inform conservation management. Our key finding for land managers relates to the positive relationship between the proportion seed rich foraging habitat within the Yellowhammer's average foraging range and Yellowhammer fledging success, which shows that a habitat intended primarily to provide winter food resources is also important to breeding birds. Chick food abundance in this habitat was, however, similar to broadleaf and cereal crops. We recommend that this habitat should be provided near to potential Yellowhammer nesting sites and adjacent to invertebrate-rich agri-environment scheme habitats such as beetle banks and conservation headlands to further boost invertebrate resources for a declining farmland bird.</p>
Variation in developmental rates is not linked to environmental unpredictability in annual killifishes
<p>Comparative evidence suggests that adaptive plasticity may evolve as a response to predictable environmental variation. However, less attention has been placed on unpredictable environmental variation, which is considered to affect evolutionary trajectories by increasing phenotypic variation (or bet-hedging). Here, we examine the occurrence of bet-hedging in egg developmental rates in seven species of annual killifish that originate from a gradient of variation in precipitation rates, under three treatment incubation temperatures (21°C, 23°C, and 25°C). In the wild, these species survive regular and seasonal habitat desiccation, as dormant eggs buried in the soil. At the onset of the rainy season embryos must be sufficiently developed in order to hatch and complete their life-cycle. We found substantial differences among species in both the mean and variation of egg development rates, as well as species-specific plastic responses to incubation temperature. Yet, there was no clear relationship between variation in egg development time and variation in precipitation rate (environmental predictability). The exact cause of these differences therefore remains enigmatic, possibly depending on differences in other natural environmental conditions in addition to precipitation predictability. Hence, if species-specific variances are adaptive, the relationship between development and variation in precipitation is complex and does not diverge in accordance with simple linear relationships.</p>
Linking land-use and land-cover transitions to their ecological impact in the Amazon
<p>Authors: Cássio Alencar Nunes, Erika Berenguer, Filipe França, Joice Ferreira, Alexander C. Lees, Julio Louzada, Emma J. Sayer, Ricardo Solar, Charlotte C. Smith, Luiz E. O. C. Aragão, Danielle de Lima Braga, Plinio Camargo, Carlos Eduardo Pellegrino Cerri, Raimundo Cosme, Mariana Durigan, Nárgila Moura, Victor Hugo Fonseca Oliveira, Carla Ribas, Fernando Vaz-de-Mello, Ima Vieira, Ronald Zanetti, Jos Barlow</p> <p>Code repository for the paper: Nunes et al. Linking land-use and land-cover transitions to their ecological in the Amazon. Proceedings of the National Academy of Sciences. 2022. In this repository we included codes and data that we used to run the all the analyses presented in the paper.</p>
Linking variation in planktonic primary production to coral reef fish growth and condition
<p class="MsoNormal"><span>Within low nutrient tropical oceans, islands and atolls with higher primary production support higher reef fish biomass and reef organism abundance. External energy subsidies can be delivered onto reefs via a range of physical mechanisms. However, the influence of spatial variation in primary production on reef fish growth and condition is largely unknown. It is not yet clear how variability in food delivery onto a reef interacts with reef depth and slope, and affects reef fish productivity. </span><span>Here we test the hypothesis that with increased proximity to deep-water oceanic allochthonous nutrient sources, or at sites where transportation of these water bodies onto reefs is facilitated by shallower reef slopes, parameters of fish growth and condition will be higher, and this pattern will be further emphasised in areas naturally higher in primary production. Contrary to expectations, we found no association between fish growth rate and sites with higher mean chlorophyll values. There were no differences in </span><span>δ</span><sup><span>15</span></sup><span>N or</span><span> δ</span><sup><span>13</span></sup><span>C values in fish collected at greater depths across reefs, suggesting a homogeneous primary production resource. However, the relationship between fish condition and primary production was influenced by depth of collection, driven by higher fish condition at shallow depths within a study site which is a 'hotspot' of primary production. Carbon </span><span>δ</span><sup><span>13</span></sup><span>C values were depleted at sites with increasing primary production, and this trend was reversed by an interactive effect with shallower reef slopes. </span><span>Our results indicate that deep-water ocean nutrient influences did not </span><span>translate into observable increases in overall population growth in </span><span>planktivorous </span><em><span>Chromis fieldi </span></em><span>with</span><span>in the </span><span>10–17.5 m</span><span> </span><span>depth range, but show the importance of site specific variation in hydrodynamics and reef physical characteristics influencing fish carbon isotopic composition and condition. </span></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.