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12,662 results for “linking”
Data for Linking Experimental and Ab-initio Thermochemistry of Adsorbates with a Generalized Thermochemical Hierarchy
<p>Data and scripts for the preprint "Linking Experimental and Ab-initio Thermochemistry of Adsorbates with a Generalized Thermochemical Hierarchy".</p>
Interaction matters: Bottom-up driver interdependencies alter the projected response of phytoplankton communities to climate change, links to model results
<p>This dataset provides the output of ten model simulations with the global ocean biogeochemical model FESOM-REcoM necessary to reproduce the findings of Seifert et al. (2023). In addition to information on the mesh, the dataset contains 5-year means of global phytoplankton biomass, chlorophyll, net primary production, growth rates, limitations, carbonate system parameters (dissolved inorganic carbon, CO2 partial pressure, total alkalinity), temperature, photosynthetically active radiation, and mixed layer depths.</p> <p>File names refer to the figures in the paper where the respective data are used. See “readme” for detailed information on the dataset and separate files.</p>
Bird breeding season linked to sunshine hours in a marginally seasonal equatorial climate
<p><span>The timing of reproduction is a fundamental aspect of life history, yet the breeding seasons of most birds of the world, i.e., those in the tropics, remain poorly understood. Here we use more than 3,000 mist-netting records and 300,000 citizen scientist observations collected over six years to characterize the nesting, incubation, fledging, and juvenile stages of the breeding season on Singapore Island in Southeast Asia's equatorial rainforest zone. The breeding season was compared with climate variables and food availability to identify possible proximate and ultimate causes. Breeding was seasonal and began just after the rainiest months of the year, when insect abundance was highest and when masting events were most likely to occur. While true photoperiod varied little throughout the year, overcast weather in November–December and sunnier weather in February–March caused average daily sunshine to increase by several hours at the onset of the breeding season in all six years. Our data suggest that subjective daily sunshine hours, which correlate with photoperiod at higher latitudes but not in the tropics, may be the actual proximate trigger of breeding activity in most of the world's birds.</span></p>
Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm
<p class="MsoNormal"><span><span><span><span><span><span><span>Adaptive evolution following colonization </span></span></span></span></span></span></span><span><span><span><span><span>can affect the impact of invasive species.</span></span></span></span></span><span><span><span> <span>The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. </span><span><span>The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. </span></span>Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographic factors explained a similar proportion of the genetic variation across all populations compared to climatic factors. However, when the two population groups were analyzed separately, environmental factors explained more of the variation than geographic factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.</span></span></span></p>
Unsere Konservatorin Isabelle Zürcher zeigt einige Kästen unserer Sammlung (links). Renato Joos und Erich Streit bei der Revision unserer vorbildlich organisierten Bibliothek (rechts). (Fotos Armin Coray) in Entomologische Gesellschaft Basel (EGB)
Unsere Konservatorin Isabelle Zürcher zeigt einige Kästen unserer Sammlung (links). Renato Joos und Erich Streit bei der Revision unserer vorbildlich organisierten Bibliothek (rechts). (Fotos Armin Coray)
Die Autobahnbrücke über die Limmat durchschneidet die Dietiker Auen, die zu Fuss erkundet werden können (links). Auf Informationstafeln (oben), die Auskunft über Entwicklung und Schutz- ziele des Auengebiets geben, sind die für das Publikum offenen Wege eingezeichnet. (Fotos Hansruedi Wildermuth) in SAGLS-Exkursion 2018 in die Limmat-Auen
Die Autobahnbrücke über die Limmat durchschneidet die Dietiker Auen, die zu Fuss erkundet werden können (links). Auf Informationstafeln (oben), die Auskunft über Entwicklung und Schutz- ziele des Auengebiets geben, sind die für das Publikum offenen Wege eingezeichnet. (Fotos Hansruedi Wildermuth)
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Visualizing phage infection
<p>We staged infections at four multiplicities of infection (MOI 0, 0.01, 0.1, and 1), and took snapshots every ten minutes over a 40-minute period. We designed FISH probes targeting the non-coding strand of the <em>gp34</em> gene, which encodes a tail fiber protein and quantified cells with 5 or more MGE spots, less than 5 spots, and no spots</p>
Josef Reinhofer, Oskar Oester und Joseph Schlier (von links) auf gemeinsa- mer Exkursion auf Stock bei Kandersteg. Selbst im Hochgebirge wird nicht auf die Krawatte verzich- tet. Aufnahme um 1935. (Foto Archiv EVB) in Entomologischer Verein Bern (Evb)
Josef Reinhofer, Oskar Oester und Joseph Schlier (von links) auf gemeinsa- mer Exkursion auf Stock bei Kandersteg. Selbst im Hochgebirge wird nicht auf die Krawatte verzich- tet. Aufnahme um 1935. (Foto Archiv EVB)
Rainfall maps from commercial microwave link data for Ouagadougou, Burkina Faso
<p>Rainfall maps from commercial microwave link data for Ouagadougou, Burkina Faso, accompanying a submission to <em>Journal of Hydrometeorology </em>(<em>JHM</em>) are store in <em>CML_rainfall_maps_Ougadougou.nc</em> . The generation of these rainfall maps is described in the manuscript.</p> <p>The data are stored in a netCDF file with the dimensions <em>x</em>, <em>y</em> and <em>time</em>, <em>longitude</em> and <em>latitude</em> values defining the grid, and the variable <em>rain_rate </em>holding the rainfall maps.</p> <ul> <li>The dataset covers the area over Ouagadougou (longitude: -1.61 to -1.415 and latitude: 12.27 to 12.45) in a regular space grid of 72x79 with 0.55 km grid size.</li> <li>The temporal resolution is 5 minutes for the period from 2020-06-29 to 2020-10-10 <em> </em></li> </ul> <p>As supplementary material an animation (<em>Animation_2020_08_21.mp4</em>) showcases two rainfall events from 18:30 to 21:00 UTC on 2020-08-21.</p>
pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle
<p>This file contains the original data underpinning the following study:</p> <p>The chloroquine resistance transporter, PfCRT, of the human malaria parasite <em>Plasmodium falciparum </em>displays a strong pH-sensitivity in the weakly acidic range. Consequently, PfCRT operates only at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs that interfere with heme detoxification. Despite structural information, the molecular mechanism by which PfCRT senses pH changes has remained unclear. Here we show, by alanine-scanning mutagenesis and functional transport studies, that E207 plays a critical role in pH sensing. The E207A mutant displayed a pH-insensitive transport activity, while preserving drug substrate specificity. Replacement of E207 by Asp or His, but not by any other proteinogenic amino acid, reconstituted pH sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can simultaneously accept both protons and chloroquine in a partial non-competitive manner, with increasing proton concentrations reducing the drug transport activity. Molecular dynamics simulations of the open-to-vacuole, the occluded and the open-to-cytosol conformation of PfCRT revealed a drastic relocation of E207 from a peripheral to an engaged location during the transport cycle, resulting in E207 forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor for interactions accelerating progression through the transport cycle and that the pH sensing is a by-product of this function.</p>
Figure 5 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia
Figure 5. Raised first and second dorsal fins of P. variabilis with characteristic pigmentation (© M. Iqbal).
Figure 4 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia
Figure 4. Ventral view of P. variabilis showing pelvic fins with frenum and the inner rays fused at their base (© M. Iqbal).
Figure 1 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia
Figure 1. Distribution of Periophthalmus variabilis, circles indicate previous records, triangle represents most recent record in southern Sumatra, Sugihan estuary, 02°55'41.8''S; 104°45'51.6''E.
Figure 2 in Linking a gap, First record of dusky-gilled mudskipper Periophthalmus variabilis Eggert, 1935 (Perciformes: Gobiidae) in southern Sumatra, Indonesia
Figure 2. Location at Sugihan estuary in southern Sumatra where P. variabilis was found (© M. Iqbal).
Data from: Predictive links between petal color and pigment quantities in natural Penstemon hybrids
<p class="MsoNormal">Flowers have evolved remarkable diversity in petal color, in large part due to pollinator-mediated selection. This diversity arises from specialized metabolic pathways that generate conspicuous pigments. Despite the clear link between flower color and floral pigment production, studies determining predictive relationships between pigmentation and petal color are currently lacking. In this study, we analyze a dataset consisting of hundreds of natural <em>Penstemon</em> hybrids that exhibit variation in flower color, including blue, purple, pink, and red. For each individual hybrid, we measured anthocyanin pigment content and petal spectral reflectance. We found that floral pigment quantities are correlated with hue, chroma, and brightness as calculated from petal spectral reflectance data: hue is related to the relative amounts of delphinidin vs. pelargonidin pigmentation, whereas brightness and chroma are correlated with the total anthocyanin pigmentation. We used a partial least squares regression approach to identify predictive relationships between pigment production and petal reflectance. We find that pigment quantity data provide robust predictions of petal reflectance, confirming a pervasive assumption that differences in pigmentation should predictably influence flower color. Moreover, we find that reflectance data enables accurate inferences of pigment quantities, where the full reflectance spectra provide much more accurate inference of pigment quantities than spectral attributes (brightness, chroma, and hue). Our predictive framework provides readily interpretable model coefficients relating spectral attributes of petal reflectance to underlying pigment quantities. These relationships represent key links between genetic changes affecting anthocyanin production and ecological functions of petal coloration.</p>
Widespread changes in Southern Ocean phytoplankton blooms linked to climate drivers
<p>Bloom phenology metrics calculated from OC-CCI v6.0 data. Dataset forms part of a publication in Nature Climate Change.</p>
Linking up Bell beakers in the Iberian Peninsula: Supplementary Material
<p>Many studies in complexity theory employ agent-based models whose interactions can be expressed as networks. In such models, the pattern of interactions between actors is crucial, and the network topology that emerges from the raw data can be characterized through many metrics. There is one tool that has been previously employed in Archaeology studies and has the potential to deal with networks in social contexts at different scales of analysis: social network analysis (SNA). This discipline has been applied successfully in wide range of archaeological problems, providing valuable insights and a different perspective. It also could be useful to provide quantification to concepts associated with social complexity, such as robustness, resilience, and edge-of-chaos threshold. In this work, we will propose some methodologic possibilities to approximate some of these concepts through SNA. In order to illustrate the process, we will present a case study from the Copper Age in the Iberian Peninsula: Bell beaker phase.</p>
Fig. 47. Begonia hirtella Link. A. Habit. B. Stipule. C. Leaf, adaxial surface. D. Leaf, abaxial surface. E. Inflorescence. F. Staminate flower, side view. G. Staminate flower, front view. H in The genus Begonia (Begoniaceae) in Peru
Fig. 47. Begonia hirtella Link. A. Habit. B. Stipule. C. Leaf, adaxial surface. D. Leaf, abaxial surface. E. Inflorescence. F. Staminate flower, side view. G. Staminate flower, front view. H. Tepal of staminate flower. I. Androecium, side view. J. Pistillate flower, side view. K. Pistillate flower, front view. L. Cross section of ovary. M. Developing fruit, side view. N. Pistils, side view. O. Smallest tepal of pistillate flower. P. Largest tepal of pistillate flower. Q. Bracteole. All photographs taken by D.A. Purvis from a glasshouse weed in the living collections of the Royal Botanic Garden Edinburgh.
Supplementary dataset for "Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking"
<p>The supplementary dataset for the paper "Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking". We include the splits for cora, citeseer, and pubmed, the hard negative samples, and the node2vec embeddings. We also include a jupyter file <em>read_data.ipynb</em> to show how to read the non-txt file.</p> <ul> <li>heart_test_samples.npy, heart_valid_samples.npy: the heard negative samples</li> <li>*-n2v-embedding.pt: node2vec embeddings</li> <li>test_samples_index.pt, valid_samples_index.pt: the node index of the selected samples in ogbl-ppa under HeaRT</li> <li>gnn_feature: the input feature of cora, citeseer, pubmed</li> </ul> <p>More details for our code and how to use the dataset are on the code repository: https://github.com/Juanhui28/HeaRT .</p>
Supplementary Files and Data of 'Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond'
<p> Live birth (viviparity) has arisen repeatedly and independently among animals. We sequenced the genome and transcriptome of the viviparous Pacific beetle-mimic cockroach and performed comparative analyses with two other viviparous insect lineages, tsetse flies and aphids, to unravel the basis underlying the transition to viviparity in insects. We identified pathways undergoing adaptive evolution for insects, involved in uro-genital remodeling, tracheal system, heart development, and nutrient metabolism. Transcriptomic analysis in the cockroach and tsetse viviparity reveals that uterine remodeling and nutrient production are increased and the immune response is altered during pregnancy, facilitating structural and physiological changes to accommodate and nourish the progeny. These patterns of convergent evolution of viviparity among insects, together with similar adaptive mechanisms identified among vertebrates, highlight that the transition to viviparity requires changes in uro-genital remodeling, enhanced tracheal and heart development (corresponding to angiogenesis in vertebrates), nutrient metabolism, and shifted immunity in all animal systems.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.