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98 results for “Interaction process”
STREAMS Project: Emergent landscape patterns in stream ecosystem processes resulting from groundwater/surface water interactions
This Data Set is hosted by the Luquillo LTER Program (LUQ) and owned by a LUQ's investigator. Our primary objective is to understand the linkage between surface-subsurface water interactions and ecosystem processes in neotropical lowland streams over an extended time frame (>25 yrs). Proposed research will occur at La Selva Biological Reserve in Costa Rica, which is owned and operated by the Organization for Tropical Studies In tectonically active regions of Central America, it is common for solute-rich groundwater to emerge at gradient breaks within the complex volcanic topography of mountains and foothills which intergrade with the coastal plain. These groundwaters can significantly influence solute chemistry and related ecological and ecosystem-level processes in receiving surface waters. Many solute-rich groundwaters are associated with underlying volcanic activity which has altered the chemistry of receiving streams throughout Central America. Geothermally-modified groundwaters, surfacing at the gradient break between the Central Mountain range and the coastal plain at La Selva Biological Station, have high levels of P (up to 400 mg SRP L-1) and other solutes (Ca, Cl, Mg, SO4) but are not elevated in temperature. Spatial patterns in stream solute chemistry are determined by geomorphic features of the volcanic landscape that include: upland lavas drained by P-poor streams; a gradient break (~50 m.a.s.l.), at or near where P-rich springs emerge; and lowland alluvial areas drained by streams that are both P-rich and P-poor depending on whether they receive the input of solute-rich springs. Our project is the first to determine long-term effects of nutrient enrichment in a detrital-based stream within the wet tropics. We will continue to build upon our long-term(1988-present) data set on stream solute chemistry, which is the only one that we are aware of for lowland primary rainforest of Central America. The proposed project will build on 18 years of past resear
Processed data for the study on "Chromatin 3D interactions mediate genetic effects on gene expression"
<p>This repository contains the processed data that was generated as part of the following study:</p> <p>Delaneau et al. (2019) <strong>Chromatin 3D interactions mediate genetic effects on gene expression.</strong></p> <p><em>Abstract:</em> Studying the genetic basis of gene expression and chromatin organization is key to characterize the effect of genetic variability on the function and structure of the human genome. Here, we unravel how genetic variation perturbs gene regulation using a dataset combining activity of regulatory elements, gene expression and genetic variants across 317 individuals and two cell types. We show that variability in regulatory activity is structured at the intra- and inter-chromosomal levels within 12,583 Cis Regulatory Domains and 30 Trans Regulatory Hubs that highly reflect the local (i.e. Topologically Associating Domains) and global (i.e. open/close chromatin compartments) nuclear chromatin organization. These structures delimit cell type specific regulatory networks that control gene expression/co-expression and mediate the genetic effects of <em>cis</em>- and <em>trans</em>-acting regulatory variants on genes.</p> <p> </p> <p>This repository contains:</p> <ol> <li>Chromatin QTLs for H3K27ac, H3K4me1 and H3K4me3 discovered in 317 Lymphoblastoids Cell Lines (LCLs) and 78 Fibroblasts.</li> <li>Molecular QTLs affecting the activity and structure of Cis Regulatory Domains (CRDs) in LCLs.</li> <li>Basic information about the full set of genetic variants being analyzed in the study.</li> <li>The peak coordinates, their hierarchy based on inter-individual correlation and the CRD calls for both LCLs and Fibroblasts.</li> <li>The functional links discovered in LCLs between CRDs and genes.</li> <li>eQTLs for LCLs.</li> <li>A README file containing the description of the file format for each file.</li> </ol>
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm
Figure 11. Cognitive architecture of the process of social signals perception-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>A possible cognitive architecture and formalization of the process of learning via<br> multisensory integration is presented in figure 11. The formal description of the proposed cognitive<br> architecture, capable of interpreting social-communication signals, signs and symbols, is based on<br> multisensory integration at the level of perception, parallel processing at the level of interpretation<br> and decision making followed by verbalization, as well as performing an action (eye contact,<br> gesture, mimicking) at the level of behaviour.</p>
Figure 9. The impossible figure (right) is not noticeable as such at first glance-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>In the lexical domain a similar effect of holistic word processing is described in (Anstis,<br> 2005b). The viewers were presented with pairs of three-letter words in quick succession and asked<br> to report if the upper halves of the successively presented words were identical. Surprisingly, even<br> when the upper halves of the words were orthographically identical, the error rate was reliably<br> higher than expected and in comparison with matching identical successive words. As the author of<br> the study Stuart Anstis points out: “students were processing the words not as separable parts, but<br> holistically as perceptual units that could not be perceptually split apart. These results show that in<br> normal circumstances, the visual system cannot, or does not, divide words into upper and lower<br> halves” (Anstis, 2005b, p. 239).The author relates the results of his study to studies of visual<br> perception of faces as evidence that the mechanism of holistic processing in the visual and the<br> lexical domains is essentially the same.</p>
Figure 8. Machine faces, perceived as more figure-like(left) and less figure-like (right)-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>In an experimental study on visual perception, addressing directly Gestalt phenomena, a new<br> Gestalt cue for figure-ground assignment was introduced (Vechera et al., 2002). The foreground<br> versus the background organization is a strong determinant for decisions on objects seen among<br> image elements. A well-known set of perceptual cues that are often called Gestalt cues are the size<br> or area, the symmetry and the convexity vs. concavity judgments. It is generally assumed that<br> figures are ‘small, symmetrical and convex’. The authors asked the question whether these cues are<br> all that are necessary for a region of the image to be judged as a figure. The main result of this study<br> is that regions in the lower portion of a stimulus array appear more figure-like than regions in the<br> upper portion of the display.</p>
Figure 6. Noticeable subjective response to the distorted face to the right-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>Quite surprisingly, if the distortion is viewed in the normal upward position, it evokes strong<br> emotional response to the distorted face to the right in figure 6.</p>
Figure 5. The distortion is barely noticeable if the faces are viewed in the reversed position-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>According to the feature-based processing theories of human faces the main elements,<br> noticed and remembered in a face, are the eyes, the nose and the mouth (Thompson, 1980; Anstis,<br> 2005a). If, however, we distort some of the elements of a face, these should influence perception,regardless of the position of the image – upright or reversed – from the observer viewpoint. Figure 5<br> presents the reversed image of the face on the left and the reversed distorted face on the right. The<br> distortion was achieved by rotating the eyes of the image in the vertical direction.<br> Figure</p>
Figure 4. Main elements of a face, according to the feature-based processing theories-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>In 1980 Peter Thompson proposed a new experimental paradigm for investigation of<br> perception, called “face thatcherization” (also named “Thomson illusion”) (Thompson, 1980).<br> Imagine that the following face, depicted in figure 4, is a photo of the then UK Prime Minister<br> Margaret Thatcher.</p>
Figure 3. Robotic faces, similar to smiley emoticons-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>The smiley Gestalt is the result from a dynamic (evolved in time) cognitive process, it is<br> immediately given in cognition, memorable, emotionally rich and socially relevant and reflects the<br> special kind of Gestalt complexity as defined by Edwin Rausch (1988). Conventional representations<br> of holistic entities like smileys or novel robotic faces come to life because they capture essential<br> Gestalt qualities of the perceived image. For example, in figure 3 the robotic faces resemble the<br> smileys in terms of the evoked internal/emotional reactions.</p>
Figure 2. Taxonomy of the educational technologies for children with ASC-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>learner (Perlin, 1997).<br> MOSOCO is an emergent technology implemented in a smartphone called “Mobile Social<br> Compass” (Escobedo et al., 2012). Six basic social skills are being encouraged by prompting the<br> user to initiate social contact. The menu displays symbols for the basic social skills – eye contact,<br> space and proximity, start an interaction, asking questions, sharing interests and finish an<br> interaction. The MOSOCO application has turned out to be an extremely useful tool as an online<br> prompt in starting, maintaining and finishing social interaction for both typical and autistic students,<br> as well as to anyone that feels need for improving their social competence.</p>
Figure 1. Necker cube depth illusion (Adapted from [http://en.wikipedia.org/wiki/Necker_cube])-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>Often the term Gestalt is used interchangeably with the term “emergent whole” (Johansson,<br> 1998). The emergence of a cognitive Gestalt structure adds dynamical and psychophysical forces,<br> which are different from the static notion of the “emergent whole”. An eminent example for the<br> dynamic nature of the emergent process is the Necker cube, which cannot be perceived as static, but<br> rotates in front of our eyes to the complete exhaustion of the eye gazing process (figure 1).</p>
Figure 7. Kanizsa square makes us see a non-existing figure – white square (Adapted from [http://en.wikipedia.org/wiki/Optical_illusion]-Gestalt Processing in Human-Robot Interaction: A Novel Account for Autism Research
<p>A special case of Gestalt processing is the perceiving of illusions. Illusions make us see<br> things or processes that are not there – for example the Kanizsa square like the one depicted in<br> figure 7.</p>
Processed Hi-C contact matrices for "Three invariant Hi-C interaction patterns: applications to genome assembly"
<p>Processed Hi-C interaction matrices, saved in numpy npz format.</p> <p>Matrices were processed using Dekker lab cMapping pipeline.</p> <p>Raw sequence data was taken from:</p> <p>Hap1: Haarhuis et al 10.1016/j.cell.2017.04.013</p> <p>IMR90, H1ESC, MESC, MCORTEX: Dixon et al 10.1038/nature11082</p> <p>Worm: Crane et al 10.1038/nature14450</p> <p>Caulobacter: Le et al 10.1126/science.1242059</p> <p> </p>
Processed data from "Chromatin information content landscapes inform transcription factor and DNA interactions"
<p><strong>Chromatin information content landscapes inform transcription factor and DNA interactions</strong></p> <p>Authors: Ricardo D’Oliveira Albanus, Yasuhiro Kyono, John Hensley, Arushi Varshney, Peter Orchard, Jacob O. Kitzman, Stephen C. J. Parker</p> <p><a href="https://doi.org/10.1101/777532">https://doi.org/10.1101/777532</a></p> <p> </p> <p>This record contains the processed data used in our manuscript. For instructions on how to use or regenerate this data, please refer to <a href="https://github.com/ParkerLab/chromatin_information">https://github.com/ParkerLab/chromatin_information</a>.</p>
The turnover of plant-frugivore interactions along plant range expansion: consequences for natural colonisation processes
<p><span>Plant-animal mutualisms such as seed dispersal are key interactions for sustaining plant range shifts. Whether the organisation of interactions with seed dispersers is reconfigured along the expansion landscape template, and its effects accelerating or slowing colonisation, remain elusive. Here we analyse plant-frugivore interactions in a scenario of rapid population expansion of a Mediterranean juniper. We combined complex network analyses with intensive field surveys, sampling interactions between individual plants and frugivores by DNA-Barcoding and phototrapping over two seasons. We assess the role of intrinsic and extrinsic intraspecific variability in shaping interactions and we estimate the contribution of individual plants to seed rain. The whole interaction network was highly structured, with a distinct set of modules including individual plants and frugivore species arranged concordantly along the expansion gradient. The modular configuration found was partially shaped by individual neighbourhood context (density and fecundity) and phenotypic traits (cone size). Interaction reconfiguration resulted in a higher and uneven contribution to seed dispersal rain by individuals of the expansion boundaries, providing signals of the colonisation local-history. Our study provides novel insights into the key role of mutualistic interactions in colonisation scenarios by promoting fast plant expansion processes.</span></p>
The turnover of plant-frugivore interactions along plant range expansion: consequences for natural colonisation processes
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Data from: How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology—An Experimental and Genomic Approach
<p><strong>Abstract: </strong>In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, our results showed that genetically different PUUV strains and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans and in turn at least partly shape NE epidemiology in France.</p>
Dataset for paper "Process Modeling of Aerosol-cloud Interaction in Summertime Precipitating Shallow Cumulus over the Western North Atlantic"
<p>This dataset contains LES model input and post-processed model output used in paper "Process Modeling of Aerosol-cloud Interaction in Summertime Precipitating Shallow Cumulus over the Western North Atlantic".</p>
Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"
<p>Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores. <br> <br> For the details please see the original publication or the bioarxiv preprint: https://doi.org/10.1101/2021.04.05.438521<br> <br> The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment. <br> <br> For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)</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.