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207 results for “spatial response”
Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity
<p>We acquired 10x Visium spatial transcriptomics (ST) data from 9 patients with invasive adenocarcinomas [1–5] to explore the role of the tumour microenvironment (TME) on intratumor heterogeneity (ITH) and drug response in breast cancer. By leveraging a new version of Beyondcell [6] (<a href="https://github.com/cnio-bu/beyondcell" target="_blank" rel="noopener">cnio-bu/beyondcell</a>), a tool for identifying tumour cell subpopulations with distinct drug response patterns, we predicted sensitivity to over 1,200 drugs while accounting for the spatial context and interaction between the tumour and TME compartments. Moreover, we also used Beyondcell to compute spot-wise functional enrichment scores and identify niche-specific biological functions.</p> <p>Here, you can find:</p> <p>In signatures folder:</p> <ul> <li><strong>SSc breast:</strong> Collection of gene signatures used to predict sensitivity to > 1,200 drugs derived from breast cancer cell lines.</li> <li><strong>Functional signatures:</strong> Collection of gene signatures used to compute enrichment in different biological pathways.</li> </ul> <p>In visium folder:</p> <ul> <li><strong>Visium objects:</strong> Processed ST Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [7]. These objects, together with the signatures, were used to compute the Beyondcell objects.</li> </ul> <p>In single-cell folder:</p> <ul> <li><strong>Single-cell objects:</strong> Raw and filtered merged single-cell RNA-seq (scRNA-seq) Seurat objects with unnormalised counts used as a reference for spot deconvolution.</li> </ul> <p>In beyondcell folder:</p> <ul> <li><strong>Beyondcell </strong><strong>sensitivity </strong><strong>objects</strong> with prediction scores for all drug response signatures in SSc breast.</li> <li><strong>Beyondcell functional objects </strong>with enrichment scores for all functional signatures.</li> </ul>
HOMULA-RIR: A Room Impulse Response Dataset for Teleconferencing and Spatial Audio Applications Acquired Through Higher-Order Microphones and Uniform Linear Microphone Arrays
<p>In this paper, we present HOMULA-RIR, a dataset of room impulse responses (RIRs) acquired using both higher-order microphones (HOMs) and a uniform linear array (ULA), in order to model a remote attendance teleconferencing scenario. Specifically, measurements were performed in a seminar room, where a 64-microphone ULA was used as a multichannel audio acquisition system in the proximity of the speakers, while HOMs were used to model 25 attendees actually present in the seminar room. The HOMs cover a wide area of the room, making the dataset suitable also for applications of virtual acoustics. Through the measurement of the reverberation time and clarity index, and sample applications such as source localization and separation we demonstrate the effectiveness of the HOMULA-RIR dataset.</p>
Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens
<ul> <li>Changing precipitation regimes are a challenge for forest health under future climate scenarios. If belowground symbionts can acclimate to changing moisture regimes it may buffer forest trees from these changes.</li> <li>In this study we exposed the ectomycorrhizal fungus <i>Suillus pungens</i> to acute and chronic drought stress and used RNASeq of both ectomycorrhizal roots and extraradical mycelium to gauge the magnitude of stress, identify key genes involved in drought response, and gauge potential ecosystem consequences of drought.</li> <li>We found that there were major transcriptional differences for <i>S. pungens</i> in ectomycorrhizal roots (28% of genes) and extraradical mycelium (41% of genes) under acute drought stress, but only 0.1-2% of genes were differentially expressed in chronic drought treatments. Up to 56% of differentially expressed genes under acute drought were unique to either roots or mycelium. While a number of implicated genes, such as those encoding for trehalose, have well-known roles in osmotic stress, others, such as fungal hydrophobins and atromentin, have received less study and may also impact other ecosystem functions.</li> <li>These results suggest that functional compartmentalization is key to ectomycorrhizal fungal adaptation to stressful climatic conditions and there is high potential for fungal acclimation to ameliorate future climate stress. </li> </ul>
Response of East Asian Precipitation to Precessional Orbital Forcing during Glacials –Sensitivity to Model Spatial Resolution
<p>Output data (precipitation, wind vector, etc) from three resolution experiments (F19,F09,F05) . LGM means Last glacial maximum. cntl means control run(21ka), HighSolin means the orbital year modified to 174ka. Please see more in the publication. </p>
Number space is made by response space: Evidence from left spatial neglect
<p>Whether the semantic representation of numbers is endowed with an intrinsic spatial component, so that smaller numbers are inherently represented to the left of larger ones on a Mental Number Line (MNL), is a central matter of debate in numerical cognition. To gain an insight into this issue, we investigated the performance of right brain damaged patients with left spatial neglect (N+) in a bimanual Magnitude Comparison SNARC task and in a uni-manual Magnitude Comparison Go/No-Go task (i.e. “is the number smaller or larger than 5?“). While the first task requires the use of contrasting left/right spatial codes for response selection, the second task does not require the use of these codes. In line with previous evidence, in the SNARC task N+ patients displayed a significant asymmetry in Reaction Times (RTs), with slower RTs to number “4”, that was immediately precedent to the numerical reference “5”, with respect to the number “6”, that immediately followed the same reference. This RTs asymmetry was correlated with lesion of white matter tracts, i.e. Fronto-Occipital-Fasciculus, that allows prefrontal Ba 8 and 46 to regulate the distribution of attention on sensory and memory traces in posterior occipital, temporal and parietal areas. In contrast, no similar RTs asymmetry was found in the Go/No-Go task. These findings suggest that while in the SNARC task numbers get mentally organised from left-to-right as a function of their increasing magnitude, so that N+ patients display a delay in the processing of number-magnitudes that are immediately smaller than a given numerical reference, in the Go/No-Go task no left-to-right organization is activated. These results support the idea that it is the use of contrasting left/right spatial codes, whether motor or conceptual, that triggers the generation of a spatially left-to-right organised MNL and that the representation of number magnitude is not endowed with an inherent spatial component. </p>
Predicting changes in molluscan spatial distributions in mangrove forests in response to sea-level rise
<p class="MsoNormal"><span>Molluscs are an important component of the mangrove ecosystem, and the vertical distributions of molluscan species in this ecosystem are primarily dictated by tidal inundation. Thus, sea-level rise (SLR) may have profound effects on mangrove mollusc communities. Here, we used dynamic empirical models, based on measurements of surface elevation change, sediment accretion, and molluscan zonation patterns, to predict changes in molluscan spatial distributions in response to different sea-level rise rates in the mangrove forests of Zhenzhu Bay (Guangxi, China). The change in surface elevation was 4.76–9.61 mm yr</span><sup><span>−</span></sup><sup><span>1</span></sup><span> during the study period (2016–2020), and the magnitude of surface-elevation change decreased exponentially as original surface elevation increased. Based on our model results, we predicted that mangrove molluscs might successfully adapt to a low rate of SLR (2.00–4.57 mm yr</span><sup><span>−</span></sup><sup><span>1</span></sup><span>) by 2100, with molluscs moving seaward and those in the lower intertidal zones expanding into newly available zones. However, as SLR rate increased (4.57–8.14 mm yr</span><sup><span>−</span></sup><sup><span>1</span></sup><span>), our models predicted that surface elevations would decrease beginning in the high intertidal zones and gradually spread to the low intertidal zones. Finally, at high rates of SLR (8.14–16.00 mm yr</span><sup><span>−</span></sup><sup><span>1</span></sup><span>), surface elevations were predicted to decrease across the elevation gradient, with molluscs moving landward and species in higher intertidal zones blocked by landward barriers. Tidal inundation and the consequent increases in interspecific competition and predation pressure were predicted to threaten the survival of many molluscan groups in higher intertidal zones, especially arboreal and infaunal molluscs at the landward edge of the mangroves, resulting in a substantial reduction in the abundance of original species on the landward edge. Thus, future efforts to conserve mangrove floral and faunal diversity should prioritize species restricted to landward mangrove areas and protect potential species habitats.</span></p>
Dataset for "Spatial distribution and physicochemical properties of respirable volcanic ash from the 16-17 August 2006 Tungurahua eruption (Ecuador), and alveolar epithelium response in-vitro" published in GeoHealth
<p>Data Repository for:</p> <p><strong>"Spatial distribution and physicochemical properties of respirable volcanic ash from the 16-17 August 2006 Tungurahua eruption (Ecuador), and alveolar epithelium response <em>in-vitro" </em></strong>published in GeoHealth.<br> </p> <p>Julia Eychenne<sup>1,2*</sup>, Lucia Gurioli<sup>1</sup>, David Damby<sup>3</sup>, Corinne Belville², Federica Schiavi<sup>1</sup>, Geoffroy Marceau<sup>2,4</sup>, Claire Szczepaniak<sup>5</sup>, Christelle Blavignac<sup>5</sup>, Mickael Laumonier<sup>1</sup>, Emmanuel Gardés<sup>1</sup>, Jean-Luc Le Pennec<sup>6,7</sup>, Jean-Marie Nedelec<sup>8</sup>, Loïc Blanchon², Vincent Sapin<sup>2,4 </sup></p> <p><sup>1</sup> Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, F-63000 Clermont-Ferrand, France</p> <p><sup>2</sup> Université Clermont Auvergne, CNRS, INSERM, Institut de Génétique Reproduction et Développement, F-63000 Clermont-Ferrand, France</p> <p><sup>3</sup> U.S. Geological Survey, California Volcano Observatory, Moffett Field, CA, USA</p> <p><sup>4</sup> Biochemistry and Molecular Genetic Department, University Hospital, F-63000 Clermont-Ferrand, France</p> <p><sup>5</sup> Université Clermont Auvergne, UCA PARTNER, Centre Imagerie Cellulaire Santé, F-63000 Clermont-Ferrand, France</p> <p><sup>6</sup> Geo-Ocean, CNRS, Ifremer, UMR6538, F-29280 Plouzané, France</p> <p><sup>7</sup> IRD Office for Indonesia & Timor Leste, Jalan Kemang Raya n°4, Jakarta 12730, Indonesia</p> <p><sup>8</sup> Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCFn, F-63000 Clermont-Ferrand, France</p> <p><strong>This repository includes the grainsize distributions of the individual tephra fall samples, the grainsize distribution of the respirable ash sample isolated from F2, the Raman point counting data and individual spectra, the SEM images and EDX maps of the respirable ash sample, the SEM and TEM images of the <em>in-vitro</em> experiments, and the data from the LDH assays, multiplex immunoassays and RT-qPCR.</strong></p>
Data and figure production code for 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry'
<p>Time mean data, and python code, used to create figures in 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry', Biogeosciences, Hogikyan and Resplandy 2024</p>
360° Binaural Room Impulse Response (BRIR) Database for 6DOF spatial perception research
<p>by Applied Psychoacoustics Lab, University of Huddersfield</p> <p> </p> <p>Authors: Bogdan Bacila and Hyunkook Lee</p> <p>bogdan.bacila@hud.ac.uk, h.lee@hud.ac.uk</p> <p> </p> <p><strong>Description</strong></p> <p>An open-access database for 360° binaural room impulse responses (BRIR) captured in a reverberant concert hall. Head-rotated BRIRs were acquired with 3.6° angular resolution for each of 13 different receiver positions, using a custom-made head-rotation system that was automated and integrated with the Huddersfield Acoustical Analysis Research Toolbox. The BRIRs are provided in the SOFA format. The library also contains impulse responses captured using a first-order Ambisonic microphone and an omnidirectional microphone. It is expected that the database would be useful for studying the perception of spatial attributes in a six degrees-of-freedom context.</p> <p> </p> <p><strong>Folder Structure</strong></p> <p>The impulse responses are organised into two main folders:</p> <p>* Binaural: Contains the SOFA files and MATLAB files for each position, with a 3.6° angular resolution, recorded with the Neumann KU100 binaural head.</p> <p>* FOA: Contains the First Order Ambisonics audio files in A format and B format for each individual position, recorded with an Sennheiser Ambeo microphone in an end-fire configuration. </p> <p> </p> <p><strong>Naming Convention</strong></p> <p>The files are named after their relative position on the stage and the distance from the stage:</p> <p>* C = Centre</p> <p>* L = Left</p> <p>* LW = Left Wide</p> <p> </p> <p><strong>License</strong></p> <p>This project is licensed under the CC-BY-4.0 License - see the License.txt file for details</p> <p> </p> <p><strong>Publication</strong></p> <p>This database was presented at the Audio Engineering Society 146th International Convention.</p> <p>Download link: http://www.aes.org/e-lib/browse.cfm?elib=20371</p> <p> </p> <p><strong>Referencing</strong></p> <p>If you use the database for your research, please reference it as follows.</p> <p>Bacila, B. I., & Lee, H. (2019). 360° Binaural Room Impulse Response (BRIR) Database for 6DOF Spatial Perception Research. Presented at the Audio Engineering Society Convention 146, Dublin, e-Brief 513</p>
Spatial heterogeneity and driving mechanism of the response of lake area to drought for lakes in China
<p>This is the lake area data from the article "Spatial heterogeneity and driving mechanism of the response of lake area to drought for lakes in China".</p>
Spatial Dissection of the Distinct Cellular Responses to Normal Aging and Alzheimer's Disease in Human Prefrontal Cortex at Single-Nucleus Resolution
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Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle
<p>Spatial Transcriptomics Data of murine skeletal muscle undergoing reversible nerve injury. Accompanying the manuscript, D'Ercole et al. <strong>"Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle".</strong></p> <p> </p> <p><strong>Release v1: </strong>This release Includes all the code used to generate the figures and the processed and integrated original dataset in rds format.</p> <p> </p>
A dataset of measured spatial room impulse responses for the transition between coupled rooms
<p>For a detailed description of the measurement and analysis methods, please see:</p> <p>McKenzie, T., Schlecht, S. J., and Pulkki, V. (2021). Acoustic Analysis and Dataset of Transitions between Coupled Rooms. <em>IEEE International Conference on Acoustics, Speech and Signal Processing.</em></p> <p> </p> <p>This dataset contains measured spatial room impulse responses for the transition between coupled rooms. Four coupled room pairs are included:</p> <ul> <li>Meeting Room to Hallway</li> <li>Office to Anechoic Chamber</li> <li>Office to Kitchen</li> <li>Office to Stairwell</li> </ul> <p>All were recorded at the Aalto University campus using a Genelec 8331A coaxial loudspeaker and an mh acoustics Eigenmike (32 capsule spherical microphone array for fourth order spherical harmonic capture). Each transition features 101 measurements in 5cm intervals from 2.5m inside the first room to 2.5m inside the second room. Transitions are repeated four times corresponding to four different source positions: two inside each room, one which has no continuous line-of-sight with the microphone when in the opposing room, and one which retains a direct continuous line-of-sight with the microphone for all measurement positions. </p> <p>The spatial room impulse responses are downloadable in either Spatially Oriented Format for Acoustics (SOFA) and Wav formats. Supplementary data includes amplitude plots, direct-to-reverberant graphs, estimated direction-of-arrival plots and scaled illustrations of room geometries and source positions. </p> <p>Changelog: </p> <p>V 1.0 - Initial version<br> V 1.1 - Added plots only download option<br> V 1.2 - Improved time alignment of impulse responses and changed normalisation to a single value relative to the maximum of the entire dataset<br> V 1.3 - SOFA files updated to latest Matlab API (1.1.3), 'SingleRoomDRIR' convention, with SourcePosition data corrected. The SOFA files for each transition are also now downloadable separately, in case the entire dataset is not required. <br> V 1.4 - SRIRs have been denoised using the technique described in https://www.aes.org/e-lib/browse.cfm?elib=21800 and available at https://github.com/chris-hld/Directional-Multi-Slope-Room-Impulse-Response-Denoising. This is particularly noticeable for measurements with a low SNR, such as where there is a large distance between source and receiver and occluded direct path. Note that the wav files have not been included in this release - see previous releases if wav files (not denoised) are required. SOFA files are renamed and available to download separately.</p>
Data from: Reproduction under light pollution: maladaptive response to spatial variation in artificial light in a glow-worm
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Data from: Spatial heterogeneity in soil nutrient supply modulates nutrient and biomass responses to multiple global change drivers in model grassland communities
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Data from: Spatial pattern and scale influence invader demographic response to simulated precipitation change in an annual grassland community
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Data from: Functional responses in animal movement explain spatial heterogeneity in animal-habitat relationships
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Data from: Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease
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Data from: Foraging responses of sheep to plant spatial micro-patterns can cause diverse associational effects of focal plant at individual and population levels
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Data from: Revisiting the functional response in habitat selection for large herbivores: a matter of spatial variation in resource distribution?
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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.