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34,973 results for “Morphological”
Demography and Morphology of Ericaceous Species on a Sand Plain in Montague MA 1994-1996
The study was a demographic analysis of Gaultheria procumbens conducted on the Montague Sand Plain. It compared the demographic parameters of above-ground stems between plowed and unplowed areas within scrub oak and hardwood sites. Past land use can have long-term effects on plant species distributional patterns if alterations in resources and environmental conditions have persistent effects on population demography ("environmental change") and/or if plants are intrinsically limited in their colonisation ability ("historical factors"). We evaluated the role of environmental alteration versus historical factors in controlling distributional patterns in Gaultheria procumbens (L.), a woody, clonal, understorey species with a pronounced restriction to areas that have never been ploughed and near absence from adjoining areas that were ploughed in the 19th century. The demographic study was conducted in scrub oak and hardwood plant communities on an extensive sand plain where it was possible to control for the effect of variation in environment prior to land use.
Nitrogen Deposition and Pitcher Plant Morphology in Massachusetts and Vermont 1998-1999
Atmospheric transport and deposition of nutrients, especially nitrogen, is a global environmental problem with well-documented consequences for ecosystem dynamics. However, monitoring nitrogen deposition is relatively expensive, monitoring stations are widely spaced, and estimates and predicted impacts of nitrogen deposition are currently derived from spatial modeling and interpolation of limited data. Bogs are nutrient-poor ecosystems that are especially sensitive to increasing nutrient input, and carnivorous plants, which are characteristic of these widespread ecosystem types, may be especially sensitive indicators of N deposition. Botanical carnivory is thought to have evolved in nutrient-poor and well-lit habitats such as bogs because the marginal benefits accruing from carnivory exceed the marginal photosynthetic costs associated with the maintenance of carnivorous organs. However, the production of carnivorous organs can be a phenotypically plastic trait. The northern pitcher plant, Sarracenia purpurea, produces leaves specialized for prey capture and nutrient uptake (pitchers) and leaves that are more efficient at photosynthesis (phyllodia). We hypothesized that relative allocation to these two types of leaves reflects ambient nitrogen availability. We manipulated nutrient availability to plants with leaf enrichment and whole-plot fertilization experiments. Increased nitrogen, but not phosphorus, reduced production of pitchers relative to phyllodia; this result provided empirical support for the cost–benefit model of the evolution of botanical carnivory. Because this phenotypic shift in leaf production occurs in ecological time, our results suggest that S. purpurea could be a reliable and inexpensive biological indicator of nitrogen deposition rates. This suggestion is supported by field observations across a geographic gradient of nitrogen deposition.
Red knot occurrence, prey density, island morphology, and climate change in the Virginia Barrier Islands (2009-2023)
Global climate change is reshaping dynamic coastal ecosystems, with uncertain consequences for migratory shorebirds such as the federally threatened red knot (Calidris canutus rufa) that rely on coastal staging sites during migration. Understanding how sea-level rise and changing climate drivers affect red knot foraging ecology is critical for informing conservation and management at coastal staging sites. We integrated long-term biological, geomorphological, and climatological data to examine the direct and indirect pathways influencing red knots and their prey at intertidal foraging sites on the Virginia Barrier Islands during spring migration (May 21 - 28, 2009-2023). Using piecewise structural equation modeling, we tested hypothesized two causal networks linking 1) red knot occurrence and 2) densities of their main invertebrate prey to habitat characteristics, island morphology, geomorphic change, and climate drivers of ecosystem change. Red knots were indirectly affected by geomorphic change and climate drivers through bottom-up effects on invertebrate communities mediated by island morphology. Accelerated shoreline change narrowed islands, reducing invertebrate density and richness and indirectly decreasing red knot occurrence. Storms interacted with global climate oscillations to drive erosion or accretion of beaches, with variable effects on invertebrate density and red knot occurrence. Invertebrate responses were taxon-specific: shoreline change directly increased blue mussel density but indirectly reduced coquina clam and crustacean densities by narrowing island width, while storms impacts on crustacean density were mediated by beach width. Our findings suggest that accelerated ecosystem change under future climate scenarios may alter foraging conditions for red knots and other migratory shorebirds in the Virginia Barrier Islands, with broader implications for long-term population resilience.
Dataset of "Tuning the morphology and energy levels in organic solar cells with metal- organic framework nanosheets"
<p>Metal-organic framework nanosheets (MONs) have proved themselves to be useful<br>additives for enhancing the performance of a variety of thin film solar cell devices. However,<br>to date only isolated examples have been reported. In this work we take advantage of the<br>modular structure of MONs in order to resolve the effect of their different structural and<br>optoelectronic features on the performance of organic photovoltaic (OPV) devices. Three<br>different MONs were synthesized using different combinations of two porphyrin-based ligands<br>meso-tetracarboxyphenyl porphyrin (TCPP) or tetrapyridyl-porphyrin (TPyP) with either zinc<br>and/or copper ions and the effect of their addition to polythiophene-fullerene (P3HT-PCBM)<br>OPV devices was investigated. The power conversion efficiency (PCE) of devices was found to<br>approximately double with the addition of MONs of Zn2(ZnTCPP), but was unchanged with<br>the addition of Cu2(ZnTPyP) and halved upon the addition of Cu2(CuTCPP) compared to<br>devices without nanosheets. Our analysis indicates that there are three different mechanisms<br>by which MONs can influence the photoactive layer – light absorption, energy level alignment,<br>and morphological changes. Analysis of external quantum efficiency, UV-vis photoelectron<br>spectroscopy data found that MONs have similar effects on light absorption and energy level<br>alignment. However, atomic force and Raman microscopy studies revealed that the nanosheet<br>thickness and lateral size are crucial parameters in enabling the MONs to act as beneficial<br>additives resulting in an improvement of the OPV device performance. We anticipate this<br>study will aid in the design of MONs and other 2D materials for future use in other light<br>harvesting and emitting devices.</p>
Point locations for spatial and morphological analyses of barchans in swarms
<div>This dataset contains the long-lat coordinates of seven points on ~6000 barchans located in six swarms.</div> <div> </div> <div>Four of the locations are on Earth (three in the Tarfaya region of the Western Sahara, one in Mauritania).</div> <div>The other two swarms are from high latitudes of the northern hemisphere of Mars.</div> <div> </div> <div>In each location between 850 and 1112 barchans were measured.</div> <div> </div> <div>The measurements were carried out manually by Dominic T Robson and Andreas CW Baas according to the method described in</div> <div>Robson, D. T., Annibale, A., & Baas, A. C.W. (2022). Reproducing size distributions of swarms of barchan dunes on Mars and Earth using a mean-field model. Physica A: Statistical Mechanics and its Applications, 606, 128042.</div> <div> </div> <div>The included metadata file lists the copyrights and dates (DD/MM/YYYY) for the imagery used, all imagery was accessed through Google Earth. </div> <div> </div> <div>The metadata file also includes descriptions of the format of the data. The data themselves are provided in separate comma delimited files for each location. Only the bedforms identified as barchans are included although other bedforms in the locations were also measured (see Robson et al. Physica A (2022)).</div> <div> </div> <div>Using the seven points recorded for each dune it is possible to calculate:</div> <div>Body length</div> <div>Total length</div> <div>Horn lengths</div> <div>Total width</div> <div>Horn-to-horn width</div> <div>Port flank width</div> <div>Starboard flank width</div> <div>Slipface length</div> <div>Dune orientation</div> <div> </div> <div>The area of the polygons formed by the points also provides an estimate for the basal area of the dune though it is not a perfect match.</div> <div> </div> <div>We hope that these data will be of use to those seeking to study the morphology, size, asymmetry, and spatial distribution of barchans in swarms.</div> <div> </div> <div>Dominic T Robson and Andreas CW Baas.</div>
Dataset: Electrolyte-dependent deposition morphology on magnesium metal utilizing MeMgCl, Mg[B(hfip)4]2 and Mg(HMDS)2–2AlCl3 electrolytes
<p>This is a collection featuring the data generated and used within the paper: 'Electrolyte-dependent deposition morphology on magnesium metal utilizing MeMgCl, Mg[B(hfip)4]2 and Mg(HMDS)2–2AlCl3 electrolytes'. The deposition behavior of two state-of-the-art electrolytes, magnesium tetrakis(hexafluoroisopropyloxy)borate (Mg[B(hfip)~4~]~2~) in dimethoxyethane (DME) and magnesium bis(hexamethyldisilazide) with two equivalents of aluminum chloride (Mg(HMDS)~2~-2AlCl~3~) in tetrahydrofuran (THF) was investigated. Using symmetric flooded magnesium-magnesium cells with different electrolyte concentrations and current densities the deposition process was monitored optically in-situ by a video microscope. The depositions were characterized by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX) and compared to depositions from methylmagnesium chloride (MeMgCl) in THF, known for its dendritic growth. In this work, MeMgCl showed unidirectional growth and for the harshest applied conditions, mossy depositions, but no branching dendrites as reported in previous literature. Mg[B(hfip)~4~]~2~ and Mg(HMDS)~2~-2AlCl~3~ did not show the formation of dendrites or a dendrite preform but also did not result in a desired smooth layer but in spherical depositions. For the Mg[B(hfip)~4~]~2~ electrolyte, the influence of magnesium borohydride (Mg(BH~4~)~2~) as an additive was additionally tested resulting in a more planar growth.</p>
Thalassia leaf morphology and productivity measurements from arbitrary plots located in a Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay (FCE) from March 2000 to April 2001
Thalassia leaf morphology and productivity were measured from six arbitrary 200 cm2 plots within a Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay.
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.
Controlling the Dewetting Morphologies of Thin Liquid Films by Switchable Substrates
<p>Data and scripts for the creation of the data used in the publication: "Controlling the dewetting morphologies of thin liquid films by switchable substrates" in Phys. Rev. Fluids.</p>
Morphometric data from: Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae: Thomisidae) in Europe
<p>Here we provide the complete set of files used by <a href="https://doi.org/10.3897/zookeys.1078.64116">Urfer et al. (2021</a>, see References section below for the complete citation of the publication) for the morphometric and the molecular analysis. In particular, we provide the following documents:</p> <p><br> PART 1: MORPHOMETRIC ANALYSIS</p> <p>- 1_Synema_data_multiple_imputation_mice.R: R-script used for replacing NAs.</p> <p>- 1_Synema_data_NA_imputed.csv: Dataset with raw values (in millimeters) of all 28 specimens used for the morphometric analysis. Each specimen was measured 4 times. NAs replaced using the R-script "Synema_multiple_imputation_mice.R" above. This is the datafile used for all morphometric analyses.</p> <p>- 1_Synema_data_with_NA.csv: Dataset with raw values (in millimeters) of all 28 specimens. Each specimen was measured 4 times. NAs not replaced.<br> <br> - 1_Synema_Reliability.R: R-script for calculating reliability.<br> <br> - 1_Synema_Reliability_supplementary_figure.pdf: Results of reliability analysis presented in a bar plot.</p> <p>- 1_Synema_Reliability_supplementary_table.txt: Results of reliability analysis presented in a table.<br> <br> - 1_Synema_Shape_PCA_and_PCA_Ratio_Spectrum.R: R-script for calculating the shape PCA and the PCA Ratio Spectrum of the first shape PC. You may get the necessary MRA source script from http://doi.org/10.5281/zenodo.4250142<br> <br> - Synema_globosum_AR9379_PV.jpg, Synema_globosum_AR9379_PV.jpg, Synema_globosum_AR9379_PV.jpg, etc.: Photographs taken with a LEICA M205 C stere-omicroscope.</p> <p> 1. Numbers after AR_ refer to the inventory number of the specimens in the Natural History Musuem Bern (NMBE). The specimen number was also used in the data file.<br> 2. The photo named "Synema_globosum_AR9163_with_measurements" shows the position of the measurements. Otherwise, the measurements are not indicated in the raw photos.</p> <p><br> Example image Character name Definition<br> Synema_globosum_AR9163_with_measurements cym.l Cymbium lenght Distance of the anterior margin to the tip of the cymbium<br> Synema_globosum_AR9163_with_measurements cym.b Cymbium breadth widest breadth of the cymbium<br> Synema_globosum_AR9163_with_measurements bul.b Bulb breadth widest breadth of the genital bulbus<br> Synema_globosum_AR9163_with_measurements tib.b Tibia breadth breadth of the tibia base at the patella joint</p>
Supplementary Materials for 'Measuring and assessing indeterminacy and variation in the morphology-syntax distinction'
<p><strong>Supplementary materials for the article 'Measuring and assessing indeterminacy and variation in the morphology-syntax distinction' in <em>Linguistic Typology </em>(Vol. and No. TBD).</strong></p> <p>Abstract:</p> <p>We provide a discussion of some of the challenges in using statistical methods to investigate the morphology-syntax distinction cross-linguistically. The paper is structured around three problems related to the morphology-syntax distinction; (i) the boundary strength problem; (ii) the composition problem; (iii) the architectural problem.<br> The boundary strength problem refers to the possibility that languages vary in terms of how distinct morphology and syntax are or the degree to which morphology is autonomous. The composition problem refers to the possibility that languages vary in terms of how they distinguish morphology and syntax: what types of properties distinguish the two systems. The architecture problem refers to the possibility that languages vary in terms of whether a global distinction between morphology and syntax is motivated at all and the possibility that languages might partition phenomena in different ways.<br> This paper is concerned with providing an overarching review of the methodological problems involved in addressing these three issues. We illustrate the problems using three statistical methods: correlation matrices, random forests with different choices for the dependent variable, and hierarchical clustering with validation techniques.</p> <p> </p> <p>Overview of materials:</p> <ul> <li>SM1: csv with the data</li> <li>SM2: code and pdf for generating the correlation matrices</li> <li>SM3: code and pdf for the random forest analyses</li> <li>SM4: code and pdf for the clustering and cluster validation analyses</li> </ul>
Experimental data for 'Scaling laws for coastal overwash morphology'
<p>This dataset contains the experimental data described in Lazarus, ED (2016) Scaling laws for coastal overwash morphology, <em>Geophysical Research Letters</em>, 43, 12113–12119, <a href="https://doi.org/10.1002/2016GL071213">https://doi.org/10.1002/2016GL071213</a>.</p> <p>The physical experiments that produced these data were conducted at St Anthony Falls Laboratory (University of Minnesota, USA) in December 2014. The experiments were conducted in a 3 x 5 x 0.6 m tank filled with well-sorted coarse river sand. The tank and the experimental trials are detailed in Text S1 of the Supporting Information for Lazarus (2016): <a href="https://agupubs.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2F2016GL071213&file=grl55284-sup-0001-SI.pdf">https://agupubs.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2F2016GL071213&file=grl55284-sup-0001-SI.pdf</a></p> <p>This dataset consists of two *.csv files:</p> <ul> <li>'...THROATS.csv' – morphometric data for <strong>erosional</strong> (throat) features in the experimental barrier</li> <li>'...WASHOVER.csv' – morphometric data for <strong>depositional</strong> (washover) features on the back-barrier floodplain</li> </ul> <p>Both files have the same general column headings: feature width (in the alongshore dimension) [m], feature length (in the cross-shore dimension) [m], feature area [m<sup>2</sup>], feature volume [m<sup>3</sup>], alongshore spacing (centroid-to-centroid distance to neighbouring feature) [m], and real alongshore position [m].</p> <p>All features were formed along an initially geometrically uniform (topographically homogenous) trapezoidal barrier under inundation-type forcing (denoted in 'forcing' column). These data report the compiled results of three experimental trials (denoted in 'trial' column).</p> <p>Note that these data are also available as part of the Supporting Information for Lazarus (2016), but the format in which they were originally uploaded is not conducive to straightforward integration into open-source analysis. Publishing them here, in this tidier format, is an effort to rectify that.</p>
Merging Morphological and Genetic Evidence to assess hybridization in Eurasian Late Pleistocene hominins
<pre>Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive one. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent paleogenomic work shows that gene flow between distinct lineages (e.g., Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the Late Pleistocene, likely contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of Late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridisation signals differentially. We urge further studies of the phenotype in order to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA. </pre>
Data, scripts, and R Notebook for Carneiro et al 2023. Flight performance and wing morphology in the bat Carollia perspicillata: biophysical models and energetics. Integrative Zoology DOI:10.1111/1749-4877.12707
<p>Files provided as supporting information for the paper by Carneiro et al. 2023. Flight performance and wing morphology in the bat <em>Carollia perspicillata</em>: biophysical models and energetics. Integrative Zoology. DOI:10.1111/1749-4877.12707</p> <p>File descriptions</p> <p>ArmTA.txt - Temperature and surface areas for arms of <em>C. perspicillata</em> after flight experiment<br> BodyTA.txt - Temperature and surface areas for body of <em>C. perspicillata</em> after flight experiment<br> HeadTA.txt - Temperature and surface areas for head of <em>C. perspicillata</em> after flight experiment<br> WingTA.txt - Temperature and surface areas for wings (patagium) of <em>C. perspicillata</em> after flight experiment<br> WingMorph.txt - Morphological variables measured in the body and wings of <em>C. perspicillata</em><br> HeatLoss.R - Function to estimate heat loss (Qt)<br> PowFlight.R - Function to estimate minimum power required to fly<br> Script-HeatLoss-FlightPerformance.R - R script with set of analyses performed<br> SupportingInformationFile.docx - R notebook with set of analyses performed, word format<br> SupportingInformationFile.nb.html - R notebook with set of analyses performed, html format<br> SupportingInformationFile.Rmd - R notebook with set of analyses performed (R markdown)</p> <p>For the R scripts (Script-HeatLoss-FlightPerformance.R) and notebook (<br> SupportingInformationFile.Rmd) to work and be compiled, all files need to be copied to the same folder.</p>
Data set: Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes
<h1>Repository for "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes"</h1> <p>---</p> <p>These data scripts were used to perform analyses included in the research paper "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes" </p> <p>Main questions for the study:</p> <p>1. What are the main axes of morphological variation?<br>2. Does variation in morphology among species correlate with their current environments? <br>3. Are lineages that occupy ecologically similar habitats morphologically convergent? <br>4. Is speciation predominantly allopatric or sympatric? <br>5. Do sister species have greater morphological and ecological niche overlap than expected relative to non-sister species pairs?</p> <h2>## Data structure</h2> <p>Contents in the data folder is archived as a zip and can be downloaded from Zenodo (for all versions see https://zenodo.org/doi/10.5281/zenodo.10397830). Once you unzip the zipped files, you will see three folders and some files that are no in any folders. </p> <p>/data/ - files that were manually created and the phylogeny</p> <p>/data/script_generated_data/ - A combination of processed data needed to run the analyses </p> <p>/data/dorsal/ - photographs of the head from the dorsal view. These photos were used for digitising landmarks and semilandmarks. </p> <p>/data/worldclim2_30s/ - cropped and merged annual temperature from WorldClim2 (Fick and Hijmans 2017), soil bulk density from <a href="https://esoil.io/TERNLandscapes/Public/Pages/SLGA/GetData.html">Soil and Landscape Grid of Australia</a>, and Global Aridity Index from Zomer et al. (2022). <br><br>/DREaD/ - contains some files required to replicate DREaD analysis</p> <h2>## Code/Software</h2> <p>All scripts can be run using open source software. Scripts should be run in order to create necessary files that will be saved in /data/script_generated_data/ for further scripts. R is required to run R scripts (.R).</p> <h3>### /Code</h3> <p> - utility/*.R - scripts for custom functions. These are sourced in other scripts.<br> - DREaD/*.R - scripts associated with DREaD analyses<br> - 00_linear_measurement_shaperatio.R - script used to account for sexual dimorphism and calculate conventional PCA. Addresses Q1.<br> - 01_model_fitting.R - script used to address Q2 and plot visualisations.<br> - 02_convergence.R - this script calculates Ct1-4 and C5 scores. Addresses Q3.<br> - 02_convergence_model_fitting.R - this script evaluates fit of different evolutionary models to traits. Addresses Q3.<br> - 02_convergence_test_simulations.R - simulation studies to show that our phylogeny has sufficient power to detect convergence.<br> - 03_niche_enmtools_bias_account.R - calculates ecological niche models (ENMs) for each species using MAXENT. Runs Age-Overlap Correlation tests for geography and ENMs. Partially addresses Q4.<br> - 03_DREaD_Blindsnakes_AS.R - script to run DREaD analysis. <br> - 03_morpho_niche_overlap_plots.R - Runs Age-Overlap Correlation tests for body shape and snout shape. Plots AOCs. Partially addresses Q4. <br> - 04_pairwise_distance_test.R - Binomial tests between sister and non-sister pairs for ENMs and Geographic Range. Partially addresses Q5<br> - 04_morpho_pairwise.R - Binomial tests between sister and non-sister pairs for body shape and snout shape. Partially addresses Q5</p> <h2>## Contact</h2> <p>Should you have questions about these scripts or would like to request raw data, please do not hesitate to contact Sarin Tiatragul (contact information can be found in the paper) or on Github (https://github.com/stiatragul/blindsnakemorphoevo)</p> <h2>## References</h2> <p><a name="ref-fickWorldClim2017"></a>Fick, S. E., and R. J. Hijmans. 2017. <a href="https://doi.org/10.1002/joc.5086">WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas</a>. International Journal of Climatology 37:4302–4315.</p> <p><a name="ref-zomerVersion2022"></a>Zomer, R. J., J. Xu, and A. Trabucco. 2022. <a href="https://doi.org/10.1038/s41597-022-01493-1">Version 3 of the global aridity index and potential evapotranspiration database</a>. Scientific Data 9:409.</p>
Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data
<p>The applicability domain of machine learning models trained on structural fingerprints for the prediction of biological endpoints is often limited by the lack of diversity of chemical space of the training data. In this work, we developed “similarity-based merger models” which combined the output of individual models trained on cell morphology (based on Cell Painting) and chemical structure (based on chemical fingerprints) and the structural and morphological similarities of the test compounds to training compounds. We applied these similarity-based merger models using logistic equations to weigh individual features and predicted assay hit calls of 177 assays from ChEMBL, PubChem and the Broad Institute, where the required Cell Painting annotations were available. We found that the similarity-based merger models outperformed other models with an additional 20% assays (79 out of 177 assays) with an AUC>0.70 compared with 65 out of 177 assays using structural models and 50 out of 177 assays using Cell Painting models. Our results demonstrate that similarity-based merger models combining structure and cell morphology models can more accurately predict a wide range of biological assay outcomes and expand the applicability domain by better extrapolating to new structural and morphology spaces.</p>
Supplementary data: Agro-morphological and molecular characterization reveal deep insights in promising genetic diversity and marker-trait associations in Fagopyrum esculentum and F. tataricum
<p>Our study focuses on the global/European buckwheat germplasm collected as part of the ECOBREDD project. The potential of this highly diverse collection for organic buckwheat breeding was evaluated at two complementary levels: phenotypic and genetic. Here, we characterized the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species <em>Fagopyrum esculentum</em> and <em>F. tataricum</em> (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers (Simple Sequence Repeats) (see publication and info sheet of the data).</p>
Density-dependent effects of exotic brook trout on aquatic communities in mountain lakes revealed by environmental DNA and morphological taxonomy
Invasion of non-native fishes threatens freshwater biodiversity worldwide. Yet, detailed estimates of population demography for invasive species, that estimate population size and body size of the invasive species, are rarely integrated in evaluating aquatic community responses. Our study capitalized on detailed brook trout population demographic data collected for a replicated whole lake ecosystem experiment involving experimental harvesting of exotic brook trout in nine mountain lakes. We applied environmental DNA (eDNA) metabarcoding and morphological taxonomy to examine the response of crustacean zooplankton and macroinvertebrate communities to gradients in brook trout effective density and lake elevation. Density-dependent effects of brook trout on crustacean zooplankton and macroinvertebrate communities were detected even decades after their first introductions (between 1926 and 1980). However, they were moderated by environmental factors such as elevation, lake maximum depth and dissolved organic carbon. Elevation was important in structuring crustacean zooplankton and macroinvertebrate community composition. While there were differences in explanatory variables when describing communities characterized by eDNA metabarcoding and morphological taxonomy, the principal environmental factors that structured the communities were similar. Our paper highlights persisting density-dependent impacts of exotic trout on invertebrate communities even decades after first introduction, and it considers the conservation implications for lake restoration.
What the heart wants: adaptive significance of cordate leaf morphology in Arnica (Asteraceae)
We studied how the leaf inclination of basal leaves of two species, heartleaf arnica (Arnica cordifolia Hook.) and broadleaf arnica (Arnica latifolia Bong.) varied with canopy cover in the Greater Yellowstone Ecosystem, Wyoming, USA in July and August, 2022. Basal leaves of heartleaf arnica possess cordate leaf bases while those of broadleaf arnica do not, leading to potential biomechanical limitations of the latter to persist in shaded forest understories. Leaf inclination was measured as the angle (degrees) between the petiole and leaf planes of basal leaves for each species; cordateness was measured as the ratio of leaf length on either side of the petiole insertion point in basal leaves of heartleaf arnica. Data collection are complete.
Morphological and nutritional characteristics of Gambel's Quail, Callipepla gambelii, in the greater Phoenix metropolitan area, Arizona (July-September 2015)
Gambel's Quail, Callipepla gambelii, are gregarious birds commonly found in the southwestern deserts of the United States and Northwestern Mexico. With expanding urbanization, these birds are often found in exurban and suburban areas where they have access to food sources that may differ from those used by birds living in rural-urban fringes. To investigate this question, we compared the morphology and nutritional physiology of quail sampled at sites varying with respect to land use and cover. We hypothesized that quail living in urbanized areas have access to a greater variety of food sources and to more stable food resources, and so are in better body condition, than quail residing in less urbanized areas. We sampled birds at locations in the Phoenix, Arizona (USA) area, that vary with respect to land use and cover types. Birds were weighed and we measured their body length and chest circumference. A blood sample was collected from the jugular vein of each individual for analysis of plasma glucose, total proteins, triglycerides, and free glycerol using commercially available kits. Consistent with our hypothesis, birds living in more urbanized environments were longer, and they had larger chest circumferences and greater circulating triglyceride concentrations than birds living in less developed areas, suggesting greater access to lipid-rich foods. In addition, the abundance of grass at the sampling sites was associated positively with plasma protein concentrations but negatively with plasma free glycerol levels. Areas with more grass may provide birds with less dietary fats than the diet of urban birds, resulting in the breakdown of triglycerides into free glycerol. These findings are the first to demonstrate an association between urbanization and the morphology and nutritional physiology of Gambel's Quail.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.