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1,368 results for “Proximity”
RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity
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Forest bat activity declines with increasing wind speed in the proximity of operating wind turbines
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Data from: Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants
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Data from: Proximity to seabird colonies and water availability shape moss distributions in Antarctica
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Data from: Network structure and the optimisation of proximity-based association criteria
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Carotenoid- but not melanin-based plumage coloration is negatively related to metal exposure and proximity to the road in an urban songbird
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Forest cover and proximity decrease herbivory and increase crop yield via enhanced natural enemies in soybean fields
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Data from: Prey colonization in freshwater landscapes can be stimulated or inhibited by the proximity of remote predators
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BES bird survey habitat features. This is a collection of the habitat features for the BES bird sampling points. Features include number of houses, proximity to trees, shrubs, grass, annuals, and other vegetation and physical features.
This dataset is associated with BES Bird Monitoring Bird Monitoring Project: ================= The BES Bird Monitoring Project is a breeding bird survey designed to find out what birds are found in the breeding season in Baltimore and where. Our monitoring efforts will show associations among block group socioeconomic variables, land cover, land use, and habitat features with breeding bird abundance, to provide information for land managers on possible consequences of land use changes on bird communities. A distinguishing feature of the bird monitoring at BES LTER, relative to other urban bird work, is the capacity for long-term monitoring of features at multiple scales through links to other parts of the project. Different processes influence habitat for birds at different scales, e.g. ongoing household level human decision-making at lot scale vs. block or neighborhood scale abandonment/re-development. Our project seeks to understand how these processes impact bird occurrence, abundance, and composition differ at the lot, block and neighborhood scale. The data consists of four major elements, Sites, Surveys, Taxalist, and Birds. Sites records the sites and their characteristics. Surveys describe the actual outings or sampling sessions. They describe the weather, the temperature, the sites visited. Taxalist provides the integration of speciaies abbreviations and common names, and Birds describes the actual sightings, linking to the other three tables. Attribute information: Here are the fields Surveys: site_id FK->Sites[site_id] survey_id survey_date time_start time_end observer wind_speed wind_dir air_temp temp_units cloud_cover notes Sites: site_id park_code park_district park_name point_code point_location park_acreage Taxalist: species_id common_name Birds: survey_id FK->surveys[survey_id] site_id FK->surveys[site_id] species_id FK->taxalist[species_id] distance bird_count notes seen heard direction time_class
Data from: When to stay and when to leave? Proximate causes of dispersal in an endangered social carnivore
<p>1. Reliable estimates of birth, death, emigration, and immigration rates are fundamental to understanding and predicting the dynamics of wild populations and, consequently, inform appropriate management actions. However, when individuals disappear from a focal population, inference on their fate is often challenging.</p> <p><br> 2. Here we used 30 years of individual-based mark-recapture data from a population of free-ranging African wild dogs (Lycaon pictus) in Botswana and a suite of individual, social, and environmental predictors to investigate factors affecting the decision to emigrate from the pack. We subsequently used this information to assign an emigration probability to those individuals that were no longer sighted within their pack (i.e. missing individuals).</p> <p>3. Natal dispersal (i.e. emigration from the natal pack) showed seasonal patterns with female dispersal peaking prior to the mating season and male dispersal peaking at the beginning of the wet season. For both sexes, natal dispersal rate increased in the absence of unrelated individuals of the opposite sex in the pack. Male natal dispersal decreased with increasing number of pups in the pack and increased in larger packs. Female natal dispersal decreased with increasing number of pups in larger packs, but increased with increasing number of pups in smaller packs. Individuals of both sexes were less likely to exhibit secondary dispersal (i.e. emigration from a pack other than the natal pack) if they were dominant and if many pups were present in the pack.</p> <p>4. Our models predicted that 18% and 25% of missing females and males, respectively, had likely dispersed from the natal pack, rather than having died. A misclassification of this order of magnitude between dispersal and mortality can have far-reaching consequences in the evaluation and prediction of population dynamics and persistence, and potentially mislead conservation actions.</p> <p>5. Our study showed that the decision to disperse is context-dependent and that the effect of individual, social, and environmental predictors differs between males and females and between natal and secondary dispersal related to different direct and indirect fitness consequences. Furthermore, we demonstrated how a thorough understanding of the proximate causes of dispersal can be used to assign a dispersal probability to missing individuals. Knowledge of causes of dispersal can then be used within an integrated framework to more reliably estimate mortality rates.</p>
Habitat selection of foraging male Great Snipes on floodplain meadows: importance of proximity to the lek, vegetation cover and bare ground
<p>Drainage of wetlands and agricultural intensification has resulted in serious biodiversity loss in Europe, not least in grasslands. Consequently, many meadow birds have drastically declined, and the habitats they select for breeding currently rely on land management. However, the selection of habitats maintained by agriculture may contribute to reduced fitness and thus remain maladaptive for individuals, which makes conservation challenging. An understanding of the relationships between species' habitat selection, food supply and land management in the context of species' behaviour is therefore crucial for conservation. Lowland populations of Great Snipe Gallinago media are currently declining at a moderate rate, causing a conservation concern. We examined the daytime site selection (assumed as foraging sites) and food supply of radiotracked Great Snipe males breeding on a floodplain in NE Poland. Foraging sites were classified at micro- and macro-scale levels using the logistic regression in a use–availability design. On the microscale level, males selected moderate sward height and density, and a large amount of bare ground patches, and the importance of these increased as the breeding season progressed. On the macro-scale level, these conditions were associated with (1) meadows mown twice per season and grazed thereafter (associated with the most abundant food resources – earthworms) and (2) extensively managed pastures, suggesting the importance of grazing. Abandoned or late-mown meadows under agri-environmental schemes (AES) were avoided by foraging males. However, parcels with delayed mowing offer safe breeding sites for females nesting close to leks, unlike land-use types preferred by foraging males, which may act as an ecological trap. Effective conservation of Great Snipes on floodplain meadows requires precisely targeted AES schemes that will provide a mosaic of intensive and extensive land-use patches in the vicinity of identified leks.</p>
RNAseq raw counts FLCN positive vs. FLCN negative renal proximal tubular epithelial cells (RPTEC)
<p>Germline inactivating mutations in Folliculin (FLCN) cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanisms by which FLCN prevents kidney cancer remain unknown. Here we show that deleting FLCN activates TFE3, upregulating its downstream E-box genes in human renal tubular epithelial cells (RPTEC/TERT1), including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, deletion of FLCN or its binding partners FNIP1/FNIP2 also induces interferon response genes, but independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence the immune response. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.</p>
Data from: Love the one you're with: proximity determines paternity success in the barnacle Tetraclita rubescens
A species' mating system sets limits on the strength of sexual selection. Sexual selection is widespread in dioecious species, but is less well documented in hermaphrodites, and may be less important. We used four highly polymorphic microsatellite markers to assign paternity to broods of the hermaphroditic eastern Pacific volcano barnacle Tetraclita rubescens. These data were used to describe the species' mating system and to examine factors affecting male reproductive success. Tetraclita can sire broods over distances of 11.2 cm, but proximity to the sperm recipient had a highly significant effect on the probability of siring success. There was no effect of body size or the mass of male reproductive tissues on siring success. Broods showed relatively low frequencies of multiple paternity; even at high densities, 75% of broods had only one father. High frequencies of single-paternity broods imply either that this species does not compete via sperm displacement, or that sperm displacement is extremely effective, potentially explaining the lack of a positive relationship between male investment and paternity. In addition, there was low variance in siring success among individuals, suggesting a lack of strong sexual selection on male traits. Low variance among sires and the strong effect of proximity are likely driven by the unusual biology of a sessile copulating species.
Data from: Effects of undergrowth removal and edge proximity on ground beetles and vascular plants in urban boreal forests
Urban forests are regularly managed for human safety and aesthetic reasons, but they are crucial habitat for many species. Removals of undergrowth occur commonly in these forests, yet the ecological consequences of these operations are poorly understood. We sampled ground beetles (Coleoptera, Carabidae) and vascular plants along 20-m edge gradients in Finnish urban forests, in five stands treated 0.5−2.5 years earlier with undergrowth removal and in five untreated stands. We hypothesized that undergrowth removal and edge proximity would benefit opportunistic and open-habitat species, whereas shady-habitat species would be affected negatively. (1) Regarding carabids, diversity and evenness indices, open-habitat species and Carabus nemoralis responded positively, and forest species, Leistus terminatus and Pterostichus oblongopunctatus responded negatively, to the undergrowth removal. Regarding plants, generalists, Maianthemum bifolium, Rubus saxatilis and Sorbus aucuparia responded positively, and forest species, Geranium sylvaticum, Oxalis acetocella and Vaccinium myrtillus responded negatively, to the undergrowth removal. (2) Edge proximity had little effect on both plants and carabids. However, open-habitat carabids were less abundant and less speciose, and the plants Oxalis acetocella, Trientalis europaea and Rubus saxatilis had higher cover, 10−20 m from than right at the edge. (3) Plant (but not carabid) community responded to the undergrowth removal but not to the edge proximity. While managing urban forests, we recommend an avoidance of undergrowth removals at sites that host rare or threatened forest-associated flora and fauna.
Data from: Proximity to roads disrupts rodents' contributions to seed dispersal services and subsequent recruitment dynamics
1. Seed dispersal and subsequent recruitment dynamics play a crucially important role in regulating species coexistence and structuring tree diversity in diverse forests. Wildlife, which can dually shape the tree recruitment process by simultaneously functioning as natural enemies and seed dispersers, are undergoing widespread changes in population and behaviour due to the detrimental effects of expanding global road networks. However, the impact of these changes on recruitment dynamics through the alteration of seed dispersal processes remains understudied. 2. Here, we assessed how roads affect animal-mediated recruitment dynamics from the seed to adult stages of trees using a ubiquitous vertebrate-seed model: rodents and acorns. To quantify the degree to which proximity to a road alters seed dispersal and regulates subsequent recruitment dynamics, we conducted seed dispersal and predation experiments, and investigated the natural recruitment of a dominant tree species (Quercus aliena) from September 2009 to July 2012 in a subtropical forest of central China. 3. Roads caused a decreased seed dispersal distance and increasing larder hoarding, demonstrating a weakened contribution of rodents to seed dispersal services. These patterns were stronger in the masting year than in the non-masting year. Correspondingly, seedlings, saplings, and adult trees had higher densities near roads than far from roads. Near roads, recruit transition rates (i.e., seedling-to-sapling and sapling-to-juvenile) were low, and the influential strength of conspecific adult density was weakened over these recruit transitions, indicating that space limitation and lottery competition, not conspecific negative density-dependent effects, approximately determined the near-road recruitment process. Furthermore, most adults near roads were young, and their ages matched the road ages. 4. Synthesis. Roads diminished animal-mediated seed dispersal services and disrupted subsequent recruitment dynamics in Q. aliena populations, thus weakening the key process promoting diversity in forest ecosystems. Given that these animal-regulated roles in recruitment dynamics are widespread stabilizing forces for tree coexistence, our findings suggest that the ubiquity of roads and their continued expansion will contribute to the increase in forests dominated by a relatively low number of species. Consequently, the growing expansion of road networks will ultimately cause profound changes in community composition and structure across diverse forests worldwide.
Data from: Longleaf pine proximity effects on air temperatures and hardwood top-kill from prescribed fire
Background Regulation of the dominance of sprouting understory hardwoods is a common objective for prescribed fire in open-canopy longleaf pine woodland of the southeastern USA. Nevertheless, little is known about the influence of individual pines on fire and hardwood mortality. We studied growing-season fires in stem-mapped stands in southwest Georgia USA which displayed large variation in structure due to cutting treatments applied 7 yr earlier. We measured air temperature and heating duration, and measured post-fire sprouting behavior of four guilds of understory hardwoods: mesic oaks, upland oaks, xeric oaks, and fleshy-fruited hardwoods. Mean air temperature (i.e., of flames, buoyant plume and smoldering combustion) and heating duration (time over 60°C) were analyzed with respect to fuel-bed conditions and neighboring tree density. Hardwood top-kill was analyzed with respect to neighboring tree density and hardwood height. Results Size of and distance to longleaf pines strongly affected time over 60°C, which increased linearly from a mean of 87 s to a mean of 234 s across a gradient of pine basal area from 0 to 30 m2 ha-1. Mean air temperature during prescribed fire was unaffected by pine density but increased linearly from a mean of 114°C to a mean of 148°C across a gradient of wiregrass cover from 0 to 100%. Neighborhood models showed that time over 60°C during the burns was longest at the base of pines and decreased by two-thirds at 3.3 m distance. Pines affected hardwood top-kill probability at a similar scale, the effect at 4.4 m decreasing by two-thirds compared to at the base of the pine. The four hardwood guilds were readily top-killed when ≤ 1 m tall, but at 2 m height upland and xeric oaks had become more resistant to top-kill than mesic oaks or fleshy fruited broadleaved trees. Conclusions The influence of individual pine trees on heating duration and top-kill power of prescribed fire drops by ⅔ of maximum within 3 to 4 m of a tree, compared to a maximum at the base of the tree. Neighborhood models provide a method to estimate tree effects on prescribed fire heating duration and top-kill probability, and thus a way of predicting stand structures that provide ecological benefits of openings while remaining below thresholds that trigger vigorous hardwood response.
Data from: Cough frequency during treatment associated with baseline cavitary volume and proximity to the airway in pulmonary TB
Background: Cough frequency, and its duration, is a lab-free biomarker that can be used in low-resource settings and has been associated with transmission and treatment response. Radiological characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has never been studied. Methods: We analyzed 41 human immunodeficiency virus-negative adults with culture-confirmed, drug-susceptible pulmonary tuberculosis throughout treatment. Cough recordings were based on the Cayetano Cough Monitor and sputum samples were evaluated using microscopic-observation drug susceptibility broth culture, among culture-positive samples bacillary burden was assessed by time to positivity. Computerized tomography scans were analyzed by a U.S. board-certified radiologist and an automated-computer algorithm. The algorithm evaluates cavity volume and cavitary proximity to the airway. Computerized tomography scans were taken within one month of treatment initiation. We compared small cavities (≤7-mL) versus large cavities (>7-mL) and cavities located closer to (≤10-mm) and farther (>10-mm) from the airway to cough frequency and cough cessation until treatment day 62. Results: Cough frequency during treatment was two-fold higher in participants with large cavity volumes (Rate Ratio [RR]=1.98, p=0.01) and cavities located closer to the airway (RR=2.44, p=0.001). Comparably, cough ceased three times faster in smaller cavities (adjusted hazard ratio [HR]=2.89, p=0.06) and those farther from the airway (adjusted HR=3.61, p=0.02). Similar results are found for bacillary burden and culture conversion during treatment. Conclusions: Cough frequency during treatment is greater and lasts for longer in patients with larger cavities, especially those closer to the airway.
Data from: Projected population proximity indices (30km) for 2005, 2030 & 2050
This data package includes nine population proximity index layers for 2005, 2030 and 2050, for rural, urban and total populations. The layers are distributed as 1km GeoTIFFs and GeoJPGss at 1km. The aim of these layers is to describe the population which may be likely to visit a specific locality where access is determined by Euclidean distance. By using the layers alongside other geographic datasets relating to disease risk it may help identify where people may come into contact with a disease. Human population layers are often used in models to identify risk areas where humans and viruses interact, however most pathogens are not restricted to areas of human habitation: many are found in lesser populated areas such as forests. This dataset will help identify less populated areas that may well still receive high visitor numbers. The layers have been projected to 2030 and 2050 to enable projections of human/disease interfaces in the medium-term which are required to inform policy makers at country and continental level. Urban and rural populations have been separated into individual layers as in some cases it is useful to distinguish between the behaviour and associated risks attributed to the different population segments. There may be a different risk of contacting diseases in rural habitats for rural workers than for than urban visitors.
Data from: Denning habits of free-ranging dogs reveal preference for human proximity
Dens are crucial in the early development of many mammals, making den site selection an important component of parental care in such species. Resource availability and shelter from predators primarily govern den selection. Species inhabiting human-dominated landscapes typically den away from human disturbance, often shifting dens to avoid humans during the early life of their young. Domesticated dogs have evolved in human proximity over centuries, being bred and reared in human homes for generations. While pets rely on their owners for shelter and care, free-ranging dogs roam uncared, and typically whelp in dens. We conducted a study on 148 free-ranging dog dens in India to understand their denning habits. Distance from resources influenced den choice, but anthropogenic disturbance did not. Dens were found in areas of high human activity, and begging from humans was preferred over scavenging. A study on 15 pregnant females revealed that females actively searched for denning sites, rejecting several intermediate ones before selecting the final den. We propose that the obvious preference of dogs for denning close to humans is a behavioural adaptation that helps them to survive in the urban landscape, in spite of the high human induced mortality during the early life of pups.
Data from: Compositional turnover and ecological changes related to the waxing and waning of glaciers during the Late Paleozoic ice age in ice-proximal regions (Pennsylvanian, western Argentina)
The late Paleozoic ice age (LPIA) had a profound effect on the biota. Despite much research having been focused on paleotropical regions or global-scale analyses, regional ecological changes have seldom been studied in ice-proximal basins. Here, I study the compositional turnover and diversity structure across the main Carboniferous glacial event recorded in western Argentina and the subsequent nonglacial interval. Brachiopod and bivalve data from western Argentina suggest that the transition from glacial to nonglacial climates caused major compositional changes. Turnover, however, was not uniform across the bathymetric gradient, being higher in deep environments. Because extirpation was concentrated in brachiopods, but immigration was similar in both clades, the taxonomic structure of the region was significantly modified. Although regional hierarchical diversity structure and occupancy distributions remained stable, dissecting the analysis in brachiopods and bivalves underscores that both clades had different responses to climate change. Brachiopods, on the one hand, show stability in the diversity structure and a very slight decrease in occupancies of intermediate genera, while bivalves show an important rise in diversity, both at the environment and regional scale, and an increase in genera with intermediate occupancies. The bathymetric diversity gradient was also modified from hump shaped with maximum diversity in the deep subtidal to a linear gradient with maximum values toward the offshore. However, relative compositional differences within environments remained stable, with maximum values at intermediate depths both in glacial and nonglacial intervals. Moreover, local-scale coexistence between brachiopods and bivalves changed in the nonglacial interval, showing significant segregation, which indicates relevant modifications in community assembly dynamics. Results from western Argentina highlight the magnitude of regional-scale ecological changes during the LPIA in ice-proximal regions, suggesting that the waxing and waning of glaciers was able to cause regional taxonomic turnover and medium-scale ecological changes even during intervals of relative macroevolutionary quiescence.
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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.