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2,142 results for “by contact”
CoMix social contact data (Croatia)
<p>CoMix social contact data for Croatia.</p> <p>We gratefully acknowledge the efforts of all teams involved in the implementation of the CoMix study in their country. More specifically: the team of Goranka Petrović at the Croatian Institute of Public Health (CIPH).</p>
Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data
<p>Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus <em>Erinaceus</em>, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the <em>Erinaceus</em> hedgehogs species complex, offering a unique comparison of two secondary contact zones between <em>Erinaceus</em> <em>europaeus</em> and <em>E</em>. <em>roumanicus</em>. Results confirmed diversification of the genus during the Pleistocene period and detected a new refugial lineage of <em>E</em>. <em>roumanicus</em> outside the Mediterranean region, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from <em>E</em>. <em>europaeus</em> to <em>E</em>. <em>roumanicus</em> suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different ages and thus of the different stages of evolution of reproductive isolating mechanisms in each hybrid zone.</p>
Is there hybridisation between diploid and tetraploid Euphrasia in a secondary contact zone?
<p>• Premise of the study: Hybridisation between species with contrasting ploidy is usually considered rare in nature due to strong ploidy related postzygotic reproductive isolating barriers. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridisation, suggesting this phenomenon may be more common than once thought. Here, we investigate potential cross-ploidy hybridisation in British eyebrights (Euphrasia, Orobanchaceae), a group where thirteen putative cross-ploidy hybrid combinations have been reported based on morphology. • Methods: We analysed a contact zone between diploid E. rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer of nuclear ribosomal DNA (ITS1) and used Genotyping by Sequencing (GBS) to look for evidence of cross-ploidy hybridisation and introgression. • Key results: All variant sites in the ITS1 region were fixed between diploids and tetraploids, indicating a strong barrier to hybridisation. Clustering analyses of 356 SNPs generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference with dadI suggested potential gene flow – with this limited to around one or fewer migrants per generation. • Conclusions: Our results suggest recent cross-ploidy hybridisation is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridisation over ecological time-scales, such hybrids may form in stable populations over evolutionary time-scales and may allow for cross-ploidy introgression to take place.</p>
Data from: Gardner-like crossover from variable to persistent force contacts in granular crystals
<p>We report experimental evidence of a Gardner-like crossover from variable to persistent force contacts in a two-dimensional, bidisperse granular crystal by analyzing the variability of both particle positions and force networks formed under uniaxial compression. Starting from densities just above the freezing transition, and for variable amounts of additional compression, we compare configurations to both their own initial state, and to an ensemble of equivalent, reinitialized states. This protocol shows that force contacts are largely undetermined when the density is below a Gardner-like crossover, after which they gradually transition to being persistent, being fully so only above the jamming point. We associate the disorder that underlies this effect to the size of the microscopic asperities of the photoelastic disks used, by analogy to other mechanisms that have been previously predicted theoretically.</p>
Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones
<p>The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognised pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or <em>de</em> <em>novo</em> mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six <em>Triturus</em> newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of <em>Triturus</em> species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple <em>Triturus</em> hybrid zones, indicating that MHC introgression between divergent hybridising species may be widespread and adaptive.</p>
CoMix 2.0 social contact data
<p>CoMix social contact data collected in:<br> - Austria (at)<br> - Belgium (be)<br> - Denmark (dk)<br> - Croatia (hr)<br> - Estonia (ee)<br> - Greece (gr)<br> - Italy (it)<br> - Poland (pl)<br> - Portugal (pt)<br> Format follows the http://www.socialcontactdata.org/ guidelines.</p> <p>Questionnaire available on <a href="https://www.ecdc.europa.eu/en/publications-data/social-contact-patterns-eueea-during-covid-19-pandemic">ECDC website.</a><br> We gratefully acknowledge the efforts of all teams involved in the implementation of the CoMix study in their country. More specifically: in <strong>Austria</strong>: the team of Andrea Schmidt at the Austrian National Public Health Institute, in <strong>Croatia</strong>: the team of Goranka Petrović at the Croatian Institute of Public Health (CIPH), in <strong>Denmark</strong>: the team of Michael Bang Petersen at Aarhus University, in <strong>Estonia</strong>: the team of Sigrid Vorobjov at the National Institute for Health Development, in <strong>Greece</strong>: the team of Elpida Pavi at the University of West Attica (UniWA),in <strong>Poland</strong>: the team of Magdalena Rosinska at the National Institute of Public Health - National Institute of Hygiene, in <strong>Portugal</strong>: the team of Baltazar Nunes at the National Health Institute Doutor Ricardo Jorge (INSA), in <strong>Italy</strong>: the team of Daniela Paolotti at the ISI Foundation.<br> <br> For problems with the dataset, please contact:<br> <br> socialcontactdata@gmail.com<br> <br> Changelog for V2:<br> - Added "country" column in "participant_extra" files to allow easier sub-setting by country.<br> <br> Changelog for V3:<br> - Merged files from different countries in one file.</p>
Relating hydro-mechanical and elastodynamic properties of dynamically-stressed tensile-fractured rock in relation to fracture aperture and contact area
<p>We exploit nonlinear elastodynamic properties of fractured rock to probe the micro-scale mechanics of fractures and understand the relation between fluid transport and fracture aperture and area, stiffness proxy, under dynamic stressing. Experiments are conducted on rough, tensile-fractured Westerly granite specimen subject to triaxial stresses. Fracture permeability is measured from steady-state fluid flow with deionized water. Pore pressure oscillations are applied at amplitudes ranging from 0.2 to 1~MPa at 1~Hz frequency. During dynamic stressing we transmit acoustic signals through the fracture using an array of piezoelectric transducers (PZTs) to monitor the evolution of fracture interface properties. We examine the influence of fracture aperture and contact area by conducting measurements at effective normal stresses of 10, 12.5, 15, 17.5, and 20~MPa. Additionally, the evolution of contact area with stress is characterized using pressure sensitive film. These experiments are conducted separately with the same fracture and they map contact area at stresses from 9 to 21~MPa. The resulting `true' area of contact measurements made for the entire fracture surface and within the calculated PZT sensor footprints, numerical modeling of Fresnel zone. We compare the elastodynamic response of the the fracture using the stress-induced changes ultrasonic wave velocities for a range of transmitter-receiver pairs to image spatial variations in contact properties, which is informed by fracture contact area measurements. These measurements of the nonlinear elasticity are related to the fluid-flow, permeability, in response to dynamic stressing and similar comparisons are made for the slow-dynamics, recovery, of the fracture interface following the stress perturbations.</p>
Universal chiral Luttinger liquid behavior in a graphene fractional quantum Hall point contact
<p>Raw source data for manuscript</p> <p>Data analysis code for processing raw data</p>
Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts"
<p>Data for "Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts" by Julia R Rogers and Phillip L Geissler (<a href="https://doi.org/10.1371/journal.pcbi.1010992">Rogers, J. R.; Geissler, P. L. <em>PLoS Comput. Biol.</em> <strong>2023</strong>, <em>19</em>, e1010992</a>; bioRxiv DOI: https://doi.org/10.1101/2022.09.10.507427). All input coordinates, topologies, and parameter files in addition to equilibrium simulation trajectories and analysis results are provided.</p>
GramAdapt Social Contact Dataset
<p>The GramAdapt Social Contact Dataset is a curated dataset of 34 language pairs from across the globe, with quantitative and qualitative data on social interaction between pairs of language communities in contact. The language pairs were sampled globally, with the intention of avoiding areal and cultural biases. The data were collected by distributing a questionnaire to experts who have experience with either one or both of the language communities. The responses are subjective expert assessments. Authors 1-3 manually checked each response for judgement of responses. This results in a dataset containing 12554 data points.</p>
Agta hunter-gatherer oral microbiomes are shaped by contact network structure
<p>Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African Bayaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses, and even unrelated friends, can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.<strong> </strong></p>
Data from: Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the Variable Seedeater (Sporophila corvina)
<p>After establishing secondary contact, recently diverged populations may remain reproductively isolated or may hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the Variable Seedeater (<em>Sporophila corvina</em>) to examine how coloration and genetic divergence shape patterns of hybridization. We found that differences in plumage coloration are likely maintained by divergent selection across contact zones; however, the degree of plumage differentiation does not match overall patterns of hybridization. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage), populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting frequent reproduction and high survivorship for hybrid individuals. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic structure between populations. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.</p>
Height covariance correlation function in Contact Process
<p>Data of the correlation function, namely, the height covariance c1(r,t) for 1, 2 and 3 dimensions. It has been measured for the interface representation of a contact process system at its critical point. See <a href="https://arxiv.org/abs/2304.10883">arXiv:2304.10883</a> for more details.</p> <p>Each file contain two headers starting with #. The columns show, in order, the time, the coordinate r, the value of c1(r,t), the error estimate by the jackknife procedure and the numbers of files used. All the columns are separated by space.</p> <p>Data for one-dimensional system in: c1JK-1D-L8192-t4000000-f2000.dat<br> Data for two-dimensional system in: c1JK-2D-L512-t200000-f498.dat<br> Data for three-dimensional system in: c1JK-3D-L128-t40000-f20.dat</p> <p>The datasets have been produced and employed in the context of a scientific work currently published in <a href="https://arxiv.org/abs/2304.10883">arXiv:2304.10883</a>.</p>
PDF of rescaled front fluctuations in Contact Process
<p>Data of the PDF of chi (rescaled front fluctuations), for 1, 2 and 3 dimensions. It has been measured for the interface representation of a contact process system at its critical point. See <a href="https://arxiv.org/abs/2304.10883">arXiv:2304.10883</a> for more details.</p> <p>Each file contain four headers starting with #. The columns show, in order, the chi, the probability and the error estimate by the jackknife procedure. All the columns are separated by space.</p> <p>Data for one-dimensional system in: chiPDF-1D-L8192-f2000.dat<br> Data for two-dimensional system in: chiPDF-2D-L512-f498.dat<br> Data for three-dimensional system in: chiPDF-3D-L128-f20.dat</p> <p>The datasets have been produced and employed in the context of a scientific work currently published in <a href="https://arxiv.org/abs/2304.10883">arXiv:2304.10883</a>. </p>
Supplemental Data File for Resetting Archaeological Interpretations of Pre-Contact Indigenous Agriculture: Maize Isotopic Evidence from Three Ancestral Mohawk Iroquoian Villages
<p>Supplemental data tables for the paper "Resetting Archaeological Interpretations of Pre-Contact Indigenous Agriculture: Maize Isotopic Evidence from Three Ancestral Mohawk Iroquoian Villages" revised manuscript submitted for peer review.</p>
Household contact survey (Belgium)
<p>Data from household contact survey.</p>
Foot sole contact forces vs. ground contact forces to obtain foot joint moments in in-shoe gait. A preliminary study: Experiment data
<p>Experiment data containing the kinematics (joint angles) and the kinetics (joint moments) of the ankle, midtarsal (MT) and metatarsophalangeal (MP) joints during gait for <strong>10</strong> subjects.</p> <ul> <li><strong>I</strong> stands for instrumented <strong>I</strong>nsoles</li> <li><strong>P </strong>stands for pressure <strong>P</strong>latform</li> <li><strong>F</strong> stands for <strong>F</strong>lexible shoes</li> <li><strong>R</strong> stands for <strong>R</strong>igid shoes</li> </ul> <p>Last number in the file name corresponds to trial number (<strong>5</strong> trials each subject)</p> <p>Thus, e.g., Subject0<strong>2</strong>_I<strong>R4</strong>.xls refers to the trial <strong>4 </strong>of subject <strong>2 </strong>wearing <strong>R</strong>igid shoes with instrumented <strong>I</strong>nsoles.</p> <p> </p>
Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson's disease
<p>Mutations in the E3 ubiquitin ligase parkin are the most common cause of early-onset Parkinson's disease (PD). Although parkin modulates mitochondrial and endolysosomal homeostasis during cellular stress, whether parkin regulates mitochondrial and lysosomal crosstalk under physiologic conditions remains unresolved. Using transcriptomics, metabolomics, and super-resolution microscopy, we identify amino acid metabolism as a disrupted pathway in iPSC-derived dopaminergic neurons from parkin PD patients. Compared to isogenic controls, parkin mutant neurons exhibit decreased mitochondria-lysosome contacts via destabilization of active Rab7. Subcellular metabolomics in parkin mutant neurons reveals amino acid accumulation in lysosomes and their deficiency in mitochondria. Knockdown of the Rab7 GTPase-activating protein TBC1D15 restores mitochondria-lysosome tethering and ameliorates cellular and subcellular amino acid profiles in parkin mutant neurons. Our data thus uncover a function of parkin in promoting mitochondrial and lysosomal amino acid homeostasis through stabilization of mitochondria-lysosome contacts and suggest that modulation of inter-organelle contacts may serve as a potential target for ameliorating amino acid dyshomeostasis in disease.</p>
Non-contact measurement of a free flying bumblebee's (Bombus terrestris) electrical potential as it approaches and leaves a fixed electrode
<p>With increasing evidence of electroreception in terrestrial arthropods, understanding receptor level processes is vital to appreciating the capabilities and limits of this sense. Here, we examine the spatio-temporal sensitivity of mechanoreceptive filiform hairs in detecting electrical fields. We first present empirical data, highlighting the time-varying characteristics of biological electrical signals. We then explore how electrically sensitive hairs may respond to such stimuli.</p> <p>The main findings are: 1) oscillatory signals (elicited by wingbeats) influence the spatial sensitivity of hairs, unveiling an inextricable spatio-temporal link; 2) wingbeat direction modulates spatial sensitivity; 3) electrical wingbeats can be approximated by sinusoidally modulated DC signals; and 4) for a moving point charge, maximum sensitivity occurs at a faster timescale than a hair's frequency-based tuning. </p> <p>Our results show that electro-mechanical sensory hairs may capture different spatio-temporal information, depending on an object's movement and wingbeat and in comparison, to aero-acoustic stimuli. Crucially, we suggest that electrostatic and aero-acoustic signals may provide distinguishable channels of information for arthropods.</p> <p>Given the pervasiveness of electric fields in nature, our results suggest further study to understand electrostatics in the ecology of arthropods and to reveal unknown ecological relationships and novel interactions between species.</p>
Multi-contact loco-manipulation trajectories for the ANYmal robot with a 6-DoF Arm
<p>Loco-manipulation planning skills are pivotal for expanding the utility of robots in everyday environments. These skills can be assessed based on a system's ability to coordinate complex holistic movements and multiple contact interactions when solving different tasks. However, existing approaches have been merely able to shape such behaviors with hand-crafted state machines, densely engineered rewards, or pre-recorded expert demonstrations. Here, we propose a minimally-guided framework that automatically discovers whole-body trajectories jointly with contact schedules for solving general loco-manipulation tasks in pre-modeled environments. The key insight is that multi-modal problems of this nature can be modeled within the context of integrated Task and Motion Planning (TAMP), resulting in a tractable bilevel optimization formulation. An effective bilevel search strategy is achieved owing to the fusion of domain-specific rules with the well-established strengths of different planning techniques: trajectory optimization and informed graph search, coupled with sampling-based planning. We showcase emergent behaviors for a quadrupedal mobile manipulator exploiting both prehensile and non-prehensile interactions to perform real-world tasks such as opening/closing heavy dishwashers and traversing spring-loaded doors. These behaviors are also deployed on the real system using a two-layer whole-body tracking controller.</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.