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9,882 results for “Scale”
Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.
<p>This database contains the coordinates of individuals of <em>Aechmea mariae-reginae</em> and <em>Werauhia ampla</em> in phorophytic trees and the genotypes for 8 microsatellite loci.</p>
Data and R scripts for "Allometric scaling of hyporheic respiration across basins in the Pacific Northwest USA" submission (Release L1)
<p>This repository holds data and scripts used for the analyses presented in a manuscript entitled "Allometric scaling of hyporheic respiration across basins in the Pacific Northwest United States" in revision in JGR Biogeosciences.</p>
First insights into the scale of invasions in African marine protected areas: leveraging global databases and crowdsourced data
<p>This dataset stems from the paper "First insights into the scale of invasions in African marine protected areas: leveraging global databases and crowdsourced data". Additional data is provided as supplementary material and is associated with the manuscript. </p>
Microbiological characterization data from full scale CS#3 DWDN
<p>Microbiology measurements on the network and tanks.</p> <p>Laboratory LIMS database and flow-cytometry sensor database.</p> <p>Provide water quality microbiological measurements based on the planned monitoring schedule. Schedule tailored to SafeCREW project needs plus CAT usual legal water sampling.</p>
Online water quality monitoring data from full scale CS#3 DWDN for the DBP prediction model
<p>Online water quality data though the drinking water distribution network. More than 1 year of data.</p> <p>SCADA data source.</p> <p>Provide water quality of the whole system at selected locations.</p>
Online hydraulic data from full scale CS#3 DWDN for model calibration
<p>Online hydraulic data including hydraulic model for the full distribution network. More than one full year of data.</p> <p>SCADA data source.</p> <p>Provide knowledge of the water distribution network and how the water moves in the system.</p>
Green quantitative spectrofluorimetric analysis of rupatadine and montelukast at nanogram scale using direct and synchronous techniques
<p>Two green sensitive spectrofluorimetric methods at nanogram scale were investigated for the determination of rupatadine fumarate (RUP) [method I] and its binary mixture with montelukast (MKT) [method II]. Method I is concerned with measuring the native fluorescence of RUP in presence of 0.10 M H2SO4 and 0.10 % w/v sodium dodecyl sulfate at 455 nm after excitation at 277 nm. The linearity range of the first method was 0.20-2.00 µg/mL with detection and quantitation limits of 11.00 ng/mL and 36.00 ng/mL, respectively. The second method includes the concurrent estimation of RUP and MKT in their co-formulated tablet preparation by applying first derivative synchronous spectrofluorimetric technique. The derivative intensities were measured for the two drugs in aqueous solution containing Mcllvaine's buffer pH 2.60 at fixed wavelength difference (Δλ) of 140 nm. Each drug was estimated at the zero contribution of the other. For RUP, the intensity was measured at 261 nm while MKT was quantitated at 371 nm. The method was linear over the range of 0.10-4.00 µg/mL and 0.20-1.60 µg/mL with limits of detection 4.00 and 5.00 ng/mL and limits of quantitation 13.38 and 15.00 ng/mL for RUP and MKT, respectively. The method was extended to determine the two analytes in laboratory-prepared mixtures and combined tablets. Validation of the two methods was performed according the official recommendations of the International Council of Harmonization (ICH). Statistical interpretation of data revealed that our results were in good agreement with the comparison method. Moreover, the greenness of the methods has been assessed and confirmed by applying three different reported assessment tools.</p>
Data from: Urbanization affects oak–pathogen interactions across spatial scales
<p>The world is rapidly urbanizing, thereby transforming natural landscapes and changing the abundance and distribution of organisms. However, insights into the effects of urbanization on species interactions, and plant-pathogen interactions in particular, are lacking. We investigated the effects of urbanization on powdery mildew infection on <i>Quercus robur</i> at continental and within-city scales. At the continental scale, we compared infection levels between urban and rural areas of different-sized cities in Europe, and investigated whether plant traits, climatic variables and CO<sub>2 </sub>emissions mediated the effect of urbanization on infection levels. Within one large city (Stockholm, Sweden), we further explored whether local habitat features and spatial connectivity influenced infection levels during multiple years. At the continental scale, infection severity was consistently higher on trees in urban than rural areas, with some indication that temperature mediated this effect. Within Stockholm city, temperature had no effect, while local accumulation of leaf litter negatively affected powdery mildew incidence in one out of three years, and more connected trees had lower infection levels. This study is the first to describe the effects of urbanization on plant-pathogen interactions both within and among cities, and to uncover the potential mechanisms behind the observed patterns at each scale.</p>
FIGURE 2 in A checklist of the scale insects (Hemiptera: Coccomorpha) of Kenya, with some new combinations
FIGURE 2. Paracoccus sativus (James, 1936) comb. n., adult female, modified from De Lotto (1957b: 227, Fig. 22), © The Trustees of the Natural History Museum, London, U.K.
FIGURE 1 in A checklist of the scale insects (Hemiptera: Coccomorpha) of Kenya, with some new combinations
FIGURE 1. Trionymus glomerulus (De Lotto) comb. n., adult female, modified from De Lotto (1961a: Plate 25), © The Trustees of the Natural History Museum, London, U.K.
FIGURE 3 in A checklist of the scale insects (Hemiptera: Coccomorpha) of Kenya, with some new combinations
FIGURE 3. Nipaecoccus masakensis (James) comb. n. adult female, modified from De Lotto (1957b: 199, Fig. 7), © The Trustees of the Natural History Museum, London, U.K.
FIGURE 4 in A checklist of the scale insects (Hemiptera: Coccomorpha) of Kenya, with some new combinations
FIGURE 4. Paracoccus commiphorae (De Lotto) comb. n. adult female, modified from De Lotto (1961a: Plate 42), © The Trustees of the Natural History Museum, London, U.K.
Data and code for "Hydrogen-driven Surface Segregation in Pd-alloys from Atomic Scale Simulations"
<p>This record contains data and scripts pertaining to the publication "Hydrogen-driven Surface Segregation in Pd-alloys from Atomic Scale Simulations".</p>
Genotyping validates the efficacy of photographic identification in a capture-mark-recapture study based on the head scale patterns of the prairie lizard (Sceloporus consobrinus)
Population studies often incorporate capture-mark-recapture (CMR) techniques to gather information on long-term biological and demographic characteristics. A fundamental requirement for CMR studies is that an individual must be uniquely and permanently marked to ensure reliable reidentification throughout its lifespan. Photographic identification involving automated photographic identification software has become a popular and efficient non-invasive method for identifying individuals based on natural markings. However, few studies have a) robustly assessed the performance of automated programs by using a double-marking system or b) determined their efficacy for long-term studies by incorporating multi-year data. Here, we evaluated the performance of the program Interactive Individual Identification System (I<sup>3</sup>S) by cross-validating photographic identifications based on the head scale pattern of the prairie lizard (<i>Sceloporus consobrinus</i>) with individual microsatellite genotyping (N=863). Further, we assessed the efficacy of the program to identify individuals over time by comparing error rates between within-year and between-year recaptures. Recaptured lizards were correctly identified by I<sup>3</sup>S in 94.1% of cases. We estimated a false rejection rate (FRR) of 5.9% and a false acceptance rate (FAR) of 0%. By using I<sup>3</sup>S we correctly identified 97.8% of within-year recaptures (FRR=2.2%; FAR=0%) and 91.1% of between-year recaptures (FRR=8.9%; FAR=0%). Misidentifications were primarily due to poor photo quality (N=4). However, two misidentifications were caused by indistinct scale configuration due to scale damage (N=1) and ontogenetic changes in head scalation between capture events (N=1). We conclude that automated photographic identification based on head scale patterns is a reliable and accurate method for identifying individuals over time. Because many lizard or reptilian species possess variable head squamation, this method has potential for successful application in many species.
Data for: Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota
<p>Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat-forming species can potentially influence the genetic diversity of large numbers of co-distributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of co-colonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance-related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two co-distributed species, one of which is an epibiotic amphipod and the other a subtidal macroalga, show few if any genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post-uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, co-demographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events likely facilitated by macroalgal rafting. These results highlight that high-resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.</p>
FIGURE. Differences of Adiantum japonicum and A. pedatum. A–C, G–I, M–O: A. japonicum; D–F, J–L, P–R: A. pedatum. A, D. rhizome; B, E. stipe; C, F. scales of stipe; G, J. pinna at apex; H, K. pinnules; I. L. Direction of leaf branching; M-R. spore. Photo credit: Ting Zhao. in Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan
FIGURE. Differences of Adiantum japonicum and A. pedatum. A–C, G–I, M–O: A. japonicum; D–F, J–L, P–R: A. pedatum. A, D. rhizome; B, E. stipe; C, F. scales of stipe; G, J. pinna at apex; H, K. pinnules; I. L. Direction of leaf branching; M-R. spore. Photo credit: Ting Zhao.
Impacts of growth form and phylogenetic relatedness on seed germination: a large-scale analysis of a subtropical regional flora
<p>Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25ºC; daily alternating 25/15ºC for each 12 h). Germination was low with a skewed distribution (mean = 38.9% at 25ºC, and 43.3% at 25/15ºC). One fifth of the species had low (<10%) and slow (4–30d) germination, and only a few (8%) species had a high (>80%) and rapid (1.2–6.6d) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.</p>
Does Coding in Pythonic Zen Peak Performance? Preliminary Experiments of Nine Pythonic Idioms at Scale
<p><strong>Link to pre-print: </strong><a href="https://arxiv.org/abs/2203.14484">https://arxiv.org/abs/2203.14484</a><br> <br> <strong>How to run</strong></p> <ol> <li>Extract <strong>pythonnic_performance.zip </strong>and move into the extracted directory.</li> <li>Execute <strong>install.sh</strong> to install required dependencies.</li> <li>Execute <strong>run.sh </strong>to start the experiment.</li> <li>Execute <strong>python statistic.py </strong>to perform the statistical test and show data statistics.</li> </ol> <p>Note that files in <strong>submitted_output</strong> are our experimental results shown in the paper.</p> <p><br> <strong>Abstract</strong></p> <p>In field of data science, and for academics in general, the Python programming language is a popular choice, mainly because of its libraries for storing, manipulating, and gaining insight from data.<br> Evidence includes the versatile set of machine learning, data visualization, and manipulation packages used for the ever-growing size of available data.<br> The <em>Zen of Python</em> is a set of guiding design principles that developers use to write acceptable and elegant Python code.<br> Most principles revolve around simplicity.<br> However, as the need to compute on large amounts of data, performance has become a necessity for the Python programmer.</p> <p>The new idea in this paper is to empirically confirm whether writing the Pythonic way peaks performance at scale.<br> As a starting point, we conduct a set of preliminary experiments to evaluate nine Pythonic code examples by comparing the performance of both Pythonic and Non-Pythonic code snippets.<br> Our results reveal that writing in Pythonic idioms may save memory and time.<br> We show that incorporating list comprehension, generator expression, zip, and itertools.zip\_longest can save up to 7,000 MB and 32.25 seconds.<br> The results open more questions on how they could be utilized in a real-world setting.</p>
A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs (Recorded Talk)
<p>This entry contains the recording of the presentation that was presented at the 2020 Intelligent Systems for Molecular Biology as part of the Bio-Ontologies COSI (https://www.iscb.org/ismb2020).</p>
Data related to "Near-bed sediment transport during offshore bar migration in large-scale experiments"
<p>Abstract: </p> <p>This paper presents novel insights into hydrodynamics and sediment fluxes in large-scale laboratory experiments with bi-chromatic wave groups on a relatively steep initial slope (1:15). An Acoustic Concentration and Velocity Profiler provided detailed information of velocity and sand concentration near the bed from shoaling up to the outer breaking zone including suspended sediment and sheet flow transport. The morphological evolution was characterized by offshore migration of the outer breaker bar. Decomposition of the total net transport revealed a balance of onshore-directed, short wave-related and offshore-directed, current-related net transport. The short wave-related transport mainly occurred as bedload over small vertical extents. It was linked to characteristic intrawave sheet flow layer expansions during short wave crests. The current-related transport rate featured lower maximum flux magnitudes but occurred over larger vertical extents. As a result, it was larger than the short wave-related transport rate in all but one cross-shore position, driving the bar's offshore migration. Net flux magnitudes of the infragravity component were comparatively low but played a non-negligible role for total net transport rate in certain cross-shore positions. Net infragravity flux profiles sometimes featured opposing directions over the vertical. The fluxes were linked to a standing infragravity wave pattern and to the correlation of the short wave envelope, controlling suspension, with the infragravity wave velocity.</p> <p>About the data:</p> <p>The data on beach profile (from mechanical profiler), velocity (from ACVP and ADV), sand concentration (from ACVP and OBS) and water surface elevation (from RWG, AWG and PT) measurements is given in .mat (MATLAB) files.</p> <p>The folder “Beach Profiles” contains the measurements from the mechanical profiler before and after each test. To save time, only the morphologically active section of the profiles was measured. Additionally, the folder contains the initial profiles at the start of a sequence (after application of the benchmark waves). Here the full profile was measured.</p> <p>The structure “MobFrame” contains the absolute cross-shore position of the mobile frame (from which detailed measurements were taken) in the considered tests.</p> <p>The folder “ACVP” contains structures with ensemble-averaged velocity and concentration measurements in vertical reference to the undisturbed bed level or a few bins below it (zeta0-coordinate system) sampled at 50.5051Hz. For better interpretation of the measurements, it also features the ensemble-averaged intrawave instantaneous erosion depth (bed elevation) and the upper limit of the sheet flow layer.</p> <p>The folder “ADV” contains structures with the ensemble-averaged ADV data of each test sampled at 100Hz. Apart from the velocity components of each ADV it contains the vertical elevation of each ADV with respect to the ACVP transceiver. The ADV measurements were not subject to the same vertical referencing procedure that was described in the paper for the near-bed ACVP measurements and a more or less constant distance to the bed was assumed.</p> <p>The folder “OBS” contains structures with the ensemble-averaged OBS data of each test sampled at 40Hz. Apart from the concentration measurements it contains the vertical elevation of the OBSs with respect to the ACVP transceiver.</p> <p>The folder “ETA” contains structures with the ensemble-averaged water surface elevation measurements in many different absolute cross-shore locations in the flume sampled at 40Hz.</p> <p>For visualizing the near-bed concentration data, which may not be as trivial as visualizing the rest of the data, an example of MATLAB code is given:</p> <p>%S=ACVP_xx; %to choose which ACVP file you want to look into<br> con=S.c;<br> con(con<1)=1; %to cater for the cells where the logarithm is not defined<br> xphase=linspace(0,1,length(S.solbed)).*ones(size(S.c,2),size(S.c,1));<br> figure; hold on; box on; <br> [C,h]=contourf(xphase,S.z,log10(transpose(con)),[0:0.1:3]); <br> cbh=colorbar; caxis([0 3]); <br> set(h,'edgecolor','none'); <br> tt=get(cbh,'Title'); set(tt,'String','$^{10}log(c)$ $[kg/m^3]$','Interpreter','Latex');<br> plot(xphase(1,:),S.solbed,'k','Linewidth',1.5);<br> plot(xphase(1,:),S.solflo,'r','Linewidth',1.5);<br> xlabel('$t/T_r$','Interpreter','Latex')<br> ylabel('$\zeta_0$ $[m]$','Interpreter','Latex')<br> set(gca,'Fontsize',18)</p> <p> </p> <p> </p>
ScienceDex guides
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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.