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33 results for “Urban morphology”
Modeling the effects of lake morphology on chloride retention and salt-driven stratification in two urban lakes in St. Paul, MN
Road salt inputs have caused widespread salinization of urban lakes in northern temperate regions. Watershed characteristics are known to be important drivers of lake chloride concentrations, but there has been less focus on how lake morphometry influences seasonal and interannual dynamics in lake chloride, and how these chloride levels may alter mixing in the water column. We analyzed chloride retention for two urban lakes (Como Lake and Lake McCarrons) in Saint Paul, Minnesota, that are in adjacent watersheds and have similar surface areas, but differ in depth and water residence time. Summer chloride concentrations were negatively related to total summer precipitation for Como Lake (maximum depth 2.2 m), but the relationship was less strong for Lake McCarrons (maximum depth 7.6 m). We used a zero-dimensional model to simulate chloride dynamics in both lakes and tracked the fate of chloride over time. In Como Lake, the mass of chloride in the lake turns over within three years, whereas chloride inputs are retained for >10 years in Lake McCarrons. We then used a one-dimensional hydrodynamic lake model (GLM-AED) to examine how lake depth affects how current chloride loading rates alter lake mixing. Salt inputs significantly extended the duration of summer stratification for simulated lakes with depths of 8 m or more, and salt inputs increased the number of days of hypoxia and anoxia across all depths. These results underscore the importance of considering lake morphometry in understanding the effects of salt inputs on lake ecosystems.
Deep Learning based Urban Morphology for City-scale Environmental Modeling
<p>The WRF simulations were performed using the Weather Research and Forecasting (WRF) model, version 4.2.1. The three nested domains are centered over Chicago, USA, with a spatial resolution of 9, 3, and 1 km for the outermost, middle, and innermost domains. The model was implemented with 42 pressure levels, with the first model level located at 21.2 m and the first 1 km vertical height containing 11 model levels. The initial and boundary conditions are taken from the National Centers for Environmental Prediction (NCEP) Final Reanalysis dataset at 1 degree spatial and 6-hourly temporal resolution.</p><p>The physics components include the WRF single moment 6 class for microphysics, Dudhia for shortwave, the Rapid Radiative Transfer Model for longwave radiation parameterizations, Bougeault for the planetary boundary layer, Noah for the land surface model, Building Environment Parametrization (BEP) for the urban model, and Grell for the cumulus scheme (only for the outermost domain of 9 km spatial resolution). The LCZs of Chicago, USA, are generated using the crowd-sourcing method. The training dataset, created manually, is obtained from the WUDAPT portal, and random forest classification is applied to Landsat 8 imagery to derive the LCZs for the desired region. The simulations are performed from 1/Jul/2018 00:00 to 7/Jul/2018 06:00, where the first 6 hours are discarded as spin-up time.</p><p>The Digital Synthetic City (DSC) of Chicago, USA, uses satellite imagery and global-scale population and elevation data as input to the automatic method for producing a statistically similar and synthetic city-scale 3D urban model as output.</p><p>The Control simulations use National Land Cover Database land use/land cover with NUDAPT parameters, the three default WRF urban classes, and corresponding UCPs; the WUDAPT uses the MODIS classes with additional urban LCZs and UCPs from Brousse et al. (2016), and the DSC uses the WUDAPT classes with UCPs generated from DSC method.</p><p>The dataset contains:</p><p>1. Output from DSC in Shapefile.</p><p>2. WRF model output for the third domain (1 km) spatial resolution domain for (a) NUDAPT or Control (b) WUDAPT or LCZs (c) DSC</p>
Fig. 2a, b in Morphological, ecological and toxicological aspects of Raphidiopsis raciborskii (Cyanobacteria) in a eutrophic urban subtropical lake in southern Brazil
Fig. 2a, b. Bar graphs indicating the relative percentages of different phytoplankton groups in the lake inflow (a) and outflow (b), sampled every month from November 2009 to November 2010.
Fig. 6 in Morphological, ecological and toxicological aspects of Raphidiopsis raciborskii (Cyanobacteria) in a eutrophic urban subtropical lake in southern Brazil
Fig. 6. Principal Component Analysis (PCA) ordination of the sampling units (P1) = water inflow and (P2) = water outflow, and of the physical and chemical variables analyzed. The sampling units are listed by month abbreviated as follows: Jan = January; Feb = February; Mar = March; Apr = April; May = May; Jun = June; Jul = July; Aug = August; Sept = September; Oct = October; Nov = November; Dec = December. T = Temperature; Transp = Transparency; Cond = Conductivity; DO = Dissolved oxygen; NH4 = Ammonium; OM = Organic material.
Fig. 4a-c in Morphological, ecological and toxicological aspects of Raphidiopsis raciborskii (Cyanobacteria) in a eutrophic urban subtropical lake in southern Brazil
Fig. 4a-c. Photomicrographs of Raphidiopsis raciborskii bloom from the studied lake demonstrating: a. general aspect of the bloom; c. part of a trichome with a heterocyte and an akinete; c. part of a trichome with only an akinete. Bars =10µm.
Fig. 1 in Morphological, ecological and toxicological aspects of Raphidiopsis raciborskii (Cyanobacteria) in a eutrophic urban subtropical lake in southern Brazil
Fig. 1. Map of the studied lake, showing the two sampling sites (I = water inflow and O = water outflow).
Data and R code for The Finer Points of Urban Adaptation: Intraspecific Variation in Lizard Claw Morphology (2020; Biological Journal of the Linnean Society)
<p>This zip file contains all data (tps files, Rdata, csv) and annotated R script to conduct all analyses presented in Falvey et al. (2020, BJLS), which examines claw morphology in 5 species of anole lizards using geometric morphometrics.</p>
GLobAl building MOrphology dataset for URban climate modelling
<p>GLobAl building MOrphology dataset for URban climate modelling (GLAMOUR) offers the building footprint and height files at the resolution of 100 m in global urban centers.</p> <ul> <li>the `BH_100m` contains the building height files where each file is named as `BH_{lon_start}_{lon_end}_{lat_start}_{lat_end}.tif`.</li> <li>the `BF_100m` contains the building footprint files where each file is named as `BF_{lon_start}_{lon_end}_{lat_start}_{lat_end}.tif`.</li> </ul> <p>Here `lon_start`, `lon_end`, `lat_start`, `lat_end` denote the starting and ending positions of the longitude and latitude of target mapping areas.</p> <p>To avoid possible confusion, it should be clarified that the 'building footprint' in GLAMOUR represents the 'building surface fraction', i.e., the ratio of building plan area to total plan area.</p> <p> </p> <p>We also offer the snapshot of source code used for the generation of the GLAMOUR dataset including:</p> <ul> <li>`GC_ROI_def.py` defines regions of interest (ROI) used in the mapping of the GLAMOUR dataset.</li> <li>`GC_user_download.py` retrieves satellite images including Sentinel-1/2, NASADEM and Copernicus DEM from Google Earth Engine and exports them into Google Cloud Storage.</li> <li>`GC_master_pred.py` downloads exported data records from Google Cloud Storage and then performs the estimation of building footprint and height using Tensorflow-based models.</li> <li>`GC_postprocess.py` performs postprocessing on initial estimations by pixel masking with the World Settlement Footprint layer for 2019 (WSF2019).</li> <li>`GC_postprocess_agg.py` aggregates masked patches into larger tiles contained in the GLAMOUR dataset.</li> </ul>
Data from: Evolutionary change in flight-to-light response in urban moths comes with changes in wing morphology
<p>Moths and other insects are attracted by artificial light sources. This flight-to-light behaviour disrupts their general activity focused on finding essential habitat resources, such as mating partners, and increases predation risk. It thus has substantial fitness costs. In illuminated urban areas, spindle ermine moths <em>Yponomeuta cagnagella</em> were reported to have evolved a reduced flight-to-light response. Yet, the specific mechanism remained unknown, and was hypothesized to involve either changes in visual perception or general flight ability or overall mobility traits. Here, we test whether spindle ermine moths from urban and rural populations—with known differences in flight-to-light response—differ in flight-related morphological traits. Urban individuals were found to have on average smaller wings than rural moths, which in turn correlated with a lower probability of being attracted to an artificial light source. Our finding supports the reduced mobility hypothesis, which states that reduced mobility in urban areas is associated with specific morphological changes in the flight apparatus.</p>
Machine Learning Framework for High-Resolution Air Temperature Downscaling Using LiDAR-Derived Urban Morphological Features
<p>This dataset supports the study titled <em>"Machine Learning Framework for High-Resolution Air Temperature Downscaling Using LiDAR-Derived Urban Morphological Features"</em>, published in <em>Urban Climate</em> (<a href="https://doi.org/10.1016/j.uclim.2024.102102" target="_new" rel="noopener">DOI: 10.1016/j.uclim.2024.102102</a>).</p> <p> </p> <p><strong>Content Overview:</strong></p> <ul> <li> <p><strong>Building Label Data for Footprint Detection</strong>:</p> <ul> <li><em>Amsterdam_BDG_Label.rar</em></li> <li><em>MiamiDade_BDG_Label.rar</em></li> </ul> <p>These are the label datasets used for training the building detection segmentation models. They have been instrumental in accurately detecting building footprints in Amsterdam.</p> </li> <li> <p><strong>Amsterdam_3D_Buildings.rar</strong>: CityGML file of 3D building models for Amsterdam, derived from LiDAR data and U-Net3+ model.</p> </li> </ul> <ul> <li> <p><strong>Morphological Features.rar</strong>: Contains urban morphological features (in raster format) extracted from LiDAR data used in the study.</p> </li> <li> <p><strong>Training and Test Data for Air Temperature Estimation</strong>:</p> <ul> <li><em>Train_Test_AvgTemp_Amsterdam.rar</em></li> <li><em>Train_Test_MaxTemp_Amsterdam.rar</em></li> <li><em>Train_Test_MinTemp_Amsterdam.rar</em></li> </ul> <p>This dataset includes training and testing data for estimating air temperatures in three scenarios: average daily temperature, minimum daily temperature, and maximum daily temperature for the city of Amsterdam.</p> </li> </ul>
Southeast US Urban Convective Morphological Statistical Tests
<p>Dataset to accompany the publication "Weakly Forced Thunderstorms in the Southeast U.S. are Stronger Near Urban Areas" in <em>Geophysical Research Letters</em> by Paul Miller and Neil Debbage. The file contains the urban versus non-urban mean values for 31 cities in the Southeast US for the following variables: initiation time (decimal hours since 1200 UTC), duration (min), total lifetime thunderstorm pixels, maximum composite reflectivity (dBZ), maximum number of thunderstorm pixels during any single volume scan, maximum pixel ratio. T statistics and p values for the urban vs non-urban t-tests are also provided. More information can be found in the associated manuscript.</p>
Data from: Linking locomotor performance to morphological shifts in urban lizards
Open the record for dataset details and reuse information.
Data from: Evolutionary change in flight-to-light response in urban moths comes with changes in wing morphology
Open the record for dataset details and reuse information.
Data from: Skull morphology diverges between urban and rural populations of red foxes mirroring patterns of domestication and macroevolution
<p class="western"><span><span><span>Human activity is drastically altering the habitat use of natural populations. This has been documented as a driver of phenotypic divergence in a number of wild animal populations. Here we show that urban and rural populations of red foxes (<i>Vulpes vulpes</i>) from London and surrounding boroughs are divergent in skull traits. These changes are primarily found to be involved with snout length, with urban individuals tending to have shorter and wider muzzles relative to rural individuals, smaller braincases, and reduced sexual dimorphism. Changes were widespread and related to muscle attachment sites and thus are likely driven by differing biomechanical demands of feeding or cognition between habitats. Through extensive sampling of the genus <i>Vulpes</i>, we found no support for phylogenetic effects on skull morphology, but patterns of divergence found between urban and rural habitats in <i>V. vulpes</i> quantitatively aligned with macroevolutionary divergence between species. The patterns of skull divergence between urban and rural habitats matched the description of morphological changes that can occur during domestication. Specifically, urban populations of foxes show variation consistent with 'domestication syndrome'. Therefore, we suggest that occurrences of phenotypic divergence in relation to human activity, while interesting themselves, also have the potential to inform us of the conditions and mechanisms that could initiate domestication. Finally, this also suggests that patterns of domestication may be developmentally biased toward larger patterns of interspecific divergence. </span></span></span></p>
Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration
<p>The dataset (including videos) are uploaded to support the research study <strong>Bed morphology adjustment under the impact of a near-bank emergent model vegetation patch: implications for urban channel restoration</strong> </p>
Data from: Morphological clines and weak drift along an urbanization gradient in the butterfly, Pieris rapae
Urban areas are increasing globally, providing opportunities for biodiversity researchers to study the process in which species become established in novel, highly disturbed habitats. This ecological process can be understood through analyses of morphological and genetic variation, which can shed light on patterns of neutral and adaptive evolution. Previous studies have shown that urban populations often diverge genetically from non-urban source populations. This could occur due to neutral genetic drift, but an alternative is that selection could lead to allele frequency changes in urban populations. The development of genome scan methods provides an opportunity to investigate these outcomes from samples of genetic variation taken along an urbanization gradient. Here we examine morphological variation in wing size and diversity at neutral amplified fragment length polymorphisms in the butterfly Pieris rapae L. (Lepidoptera, Pieridae) sampled from the center to the periphery of Marseille. We utilize established and novel environmental correlation approaches to scan genetic variation for evidence of selection. We find significant morphological differences in urban populations, as well as weak genetic structure and decreased genetic diversity in urban versus non-urban sites. However, environmental correlation tests provide little support for selection in our dataset. Our comparison of different methods and allele frequency clines suggests that loci identified as significant are false positives. Although there is some indication that selection may be acting on wing size in urban butterflies, genetic analyses suggest P. rapae are undergoing neutral drift.
Supplementary material 1 from: Ang Y, Rajaratnam G, Su KFY, Meier R (2017) Hidden in the urban parks of New York City: Themira lohmanus, a new species of Sepsidae described based on morphology, DNA sequences, mating behavior, and reproductive isolation (Sepsidae, Diptera). ZooKeys 698: 95-111. https://doi.org/10.3897/zookeys.698.13411
Aligned COI sequences for Themira putris, T. biloba, and Themira 'biloba-like' (i.e., T. lohmanus n. sp.) specimens : Data type: Fasta file
Figure 2 in The morphological and molecular analyses of a new South American urban tardigrade offer new insights on the biological meaning of the Macrobiotus hufelandi group of species (Tardigrada: Macrobiotidae)
Figure 2. Macrobiotus kristenseni sp. nov. (A) Claws of the hind pair of legs; (B) claws of the hind legs and cuticular dots on the external surface of the leg (arrow); (C) cuticular "pores" (arrow) in the body cuticle; (D) drawing of the claws of the hind legs; (E) claws of the second pair of legs; (F) claws of a hind leg. A–C: scanning electron micrographs; E, F: holotype (phase contrast). Scale bars: A–C = 5 µm; E, F = 10 µm.
Figure 5 in The morphological and molecular analyses of a new South American urban tardigrade offer new insights on the biological meaning of the Macrobiotus hufelandi group of species (Tardigrada: Macrobiotidae)
Figure 5. Macrobiotus kristenseni sp. nov. (A) Egg; (B) egg processes with filamentous matter developing from their tips (arrows); (C, D) egg processes with annulated surface (arrow) and filamentous matter developing from their tips (arrow head). A–D: scanning electron micrographs. Scale bars: A = 10 µm; B–D = 2 µm.
Figure 4 in The morphological and molecular analyses of a new South American urban tardigrade offer new insights on the biological meaning of the Macrobiotus hufelandi group of species (Tardigrada: Macrobiotidae)
Figure 4. Macrobiotus kristenseni sp. nov. (A) Embryonated eggs; (B) egg surface with small rounded meshes (arrow) bearing elongated conical processes; (C) egg with embryo buccopharyngeal apparatus in development (arrow); (D) egg processes with filamentous matter developing from their tips (arrow). A–D: phase contrast. Scale bars: A–C = 20 µm; D = 5 µm.
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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.