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203 results for “visual function”
Effects of Phase Regression on High-Resolution Functional MRI of the Primary Visual Cortex
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Dataset Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T
<p>Scientific Reports - Nature - DOI : 10.1038/s41598-018-37825-8</p> <p>##################################<br> "Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T"<br> ##################################</p> <p>E. Najdenovska*, C. Tuleasca*, J. Jorge, P. Maeder, J.P. Marques, T. Roine, D. Gallichan, J.-P. Thiran, M. Levivier, and M. Bach Cuadra</p> <p>*Equally contributed authors</p> <p><br> Copyright (c) - All rights reserved. University of Lausanne. 2018.</p> <p><br> To reproduce the analyses presented in the referred study, in this repository you could find the MR images acquired from nine young healthy subjects (YS1-YS5), four elderly healthy subject (ES1-ES4) and two drug-resistant tremor patients treated treated with Vim radiosurgery by Gamma Knife (P1 and P2).</p> <p>The provided dataset includes the following NifTI files:</p> <p>- MPRRAGE @3T<br> - DWI @3T (together with the corresponding bvals and bvecs)<br> - MP2RAGE @7T<br> - SWI @7T<br> - binary masks of the manual delineation of both left and right Vim respectively that were done on the SWI (as NifTI files as well).</p> <p>Additionally, for the young cohort (YS1-YS5) we include as well the images used for building the quadrilateral of Guiot:<br> - T2-w @3T<br> - T2 CISS @3T</p> <p>For the patients (P1 and P2), a follow-up MPRAGE (acquired at 3T) with Gadolinium enhancement is also provided.</p> <p>——————————————<br> Notes:<br> 1. For YS3 MP2RAGE at 7T is missing, instead MPRAGE at 3T was used</p> <p>2. The code performing the thalamic nuclei clustering could be found in Zenodo (DOI: 10.5281/zenodo.123768)</p>
Dataset for Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity
<p>Per-trial dataset accompanying the publication Stauch, Peter, Schuler, and Fries (2020): Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity.<br> Additionaly, preprocessing code is provided as Codebase.zip.</p>
Data to: "Despite impaired binocular function, binocular disparity integration across the visual field is spared in normal aging and glaucoma"
<p>This record contains experimental and analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p> <p>Maiello G., & Kwon, M. (in press) Despite impaired binocular function, binocular disparity integration across the visual field is spared in normal aging and glaucoma. IOVS</p> <p>A preprint version of the manuscript is available at: https://doi.org/10.1101/2022.11.28.518250</p>
Basic visual functions of children and adolescents with Autism, Attention Deficit Hyperactivity Disorder, and Dyslexia
<p>Data for the manuscript Basic visual functions of children and adolescents with Autism, Attention Deficit Hyperactivity Disorder, and Dyslexia</p> <div> </div>
Dataset of Reaction Times for the Study of Differential Functional Changes in Visual Performance During Acute Exposure to Microgravity Analogue and their Potential Links with Spaceflight-Associated Neuro-Ocular Syndrome
<p><strong>Title</strong>: "Dataset of Reaction Times for the Study of Differential Functional Changes in Visual Performance During Acute Exposure to Microgravity Analogue and their Potential Links with Spaceflight-Associated Neuro-Ocular Syndrome"<br>Zenodo DOI: 10.5281/zenodo.11840654</p> <p><strong>Contains</strong>: simple-reaction-times-VBRHDT-data.csv<br>Dateset of SRT (simple reaction time) values to visual stimuli in different positions in visual field, binocularly observed, in a microgravity analogue study, in four body positions (vertical, horizontal, -6 deg tild, -15 deg tilt). <br>Total records contained: 3584.</p> <p><strong>Institutional Review Board Statement</strong>: The study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethics Committee “Carol Davila” University of Medicine and Pharmacy Bucharest, Romania, 14877/26.05.2023. Data was collected in SpaceMed Laboratory , CIeH (Center for Innovation and eHealth) of UMF Carol Davila Bucharest, Romania.</p> <p><strong>Citation and</strong> <strong>Detailed description:</strong> see "<em>Differential functional changes in visual performance during acute exposure to microgravity analogue and their potential links with Spaceflight-Associated Neuro-Ocular Syndrome</em>", 2024, by Iftime A, Tofolean IT, Pintilie V, Călinescu O, Busnatu S, Papacocea IR, Diagnostics ,2024; 14(17):1918. doi: 10.3390/diagnostics14171918 <br>https://pubmed.ncbi.nlm.nih.gov/39272703/</p> <p><strong>Structure</strong>: Dataset is in CSV (Comma-Separated Values) format, UTF-8 encoded, text field delimited with quotation marks, in tidy format; one row is one record from the SRT task, variables values are in columns). The first row is the variable name. The variable are:</p> <p>1) "live_row"<br>- type: integer numbers, sequential;<br>- values: the index (order) of each SRT measurement performed in a body position, by a participant (ID). The value is C-based (first measurement is "0", second measurement is "1", etc).</p> <p>2) "response_time"<br>- type: real numbers, continuous values;<br>- values: response time recorded from the participant; values in miliseconds.</p> <p>3) "target_position_x_deg"<br>- type: real numbers, categorical (4 values: +/- 18.478, +/- 0.75);<br>- values: horizontal visual angle, in visual degrees in the visual field, of the position of the stimulus. Screen coordinates are computed from "0" position, foveal fixation, positive values to the right, negative values to the left.</p> <p>4) "target_position_y_deg"<br>- type: real numbers, categorical (2 values: -0.75, -7.654);<br>- values: vertical visual angle, in visual degrees in the visual field, of the position of the stimulus. Screen coordinates are computed from "0" position, foveal fixation, positive values downward, negative values upward.<br>-Note: For the equivalent polar coordinates (as in planimetry testing) see Figure 2 of the mentioned paper. </p> <p>5) "Contrast_Weber_calibrated"<br>- type: real numbers, categorical (2 values: 50.58, 99.3);<br>- values: Measured Weber contrast of the visual stimulus shown, values in percents.</p> <p>6) "hand"<br>- type: categorical, 1 value ("right");<br>- values: hand used by the participant during SRT task.</p> <p>7) "body_position"<br>- type: categorical (4 values: "vertical (90 deg)", "horizontal (0 deg)", "inclined (-6 deg)", "inclined (-15 deg)" );<br>- values: Body position during the SRT task.</p> <p>8) "ID(anon)"<br>- type: integer number, categorical, 8 values;<br>- values: anonymized ID of the participants in the study (8 persons).</p>
Visualization of the numerical pose optimization with the JAMDA scoring function using the BFGS and the LSL-BFGS algorithm
<p>These videos demonstrate the behavior of two different optimization algorithms (BFGS and LSL-BFGS) during pose optimization using the JAMDA protein-ligand scoring function.</p> <p>Flachsenberg et al. (2020) (<a href="http://doi.org/10.1021/acs.jcim.0c01095" target="_blank" rel="noopener">10.1021/acs.jcim.0c01095</a>) describes the JAMDA protein-ligand scoring function and the LSL-BFGS algorithm.<br>The data for these videos stems from Experiment 5 in Flachsenberg et al. (2020). In this experiment, the crystal structure of a ligand was numerically optimized in the binding site with respect to the JAMDA scoring function to create the JAMDA-minimized crystal structure. The JAMDA-minimized crystal structure was randomly deflected to generate various starting poses for the numerical optimization.</p> <p>These videos demonstrate the behavior of two optimization algorithms (BFGS and LSL-BFGS) when optimizing one of the generated starting poses. The chosen example for the videos is a structure of ribonuclease A with a 5'-deoxy-5'-N-piperidinouridine inhibitor (PDB code 3d6q, <a href="https://doi.org/10.2210/pdb3D6Q/pdb" target="_blank" rel="noopener">10.2210/pdb3D6Q/pdb</a>, <a href="https://doi.org/10.1021/jm800724t" target="_blank" rel="noopener">10.1021/jm800724t</a>). Each of the videos shows all the intermediate steps the optimization algorithm takes until convergence.</p> <p>The main observation (that is discussed in detail in Flachsenberg et al. (2020)) is that the BFGS algorithm tends to take inappropriately large steps when clashes are present in the structure, resulting in unwanted binding mode changes. This is <em>not</em> the case for the LSL-BFGS algorithm.</p> <h3>Legend</h3> <p>For each iteration, the JAMDA score value, the RMSD to the JAMDA-minimized crystal structure (yellow), and the RMSD to the optimization's starting point (blue) are given. Furthermore, the gradient's norm (representing the main convergence criterion) is shown. In addition to the optimized ligand, also the JAMDA-minimized crystal structure (yellow) and the optimization's starting structure (blue) are shown.</p> <p><br>Each optimization algorithm is shown in two videos: In one video, the optimized ligand is colored by elements. Here, atoms with clashes (positive JAMDA scores) are marked with orange balls. In the other video, the atoms and bonds of the optimized ligand are colored by their individual JAMDA score.</p> <h3>Used Software</h3> <p>The snapshots of the optimization algorithms were rendered using PyMOL 3.0 (<a href="https://pymol.org/" target="_blank" rel="noopener">https://pymol.org/</a>) and further processed using the Pillow 10.4 Python library (<a href="https://doi.org/10.5281/zenodo.12606429" target="_blank" rel="noopener">10.5281/zenodo.12606429</a>). Videos were created from the individual snapshots using FFmpeg 7.0 (<a href="https://www.ffmpeg.org/" target="_blank" rel="noopener">https://www.ffmpeg.org/</a>).</p>
The visualization of the dynamics of the empirical liquidity cost function (for the Brent futures contracts)
<p>The dynamics of the <strong>empirical liquidity cost function</strong> for a futures contract for Brent oil is presented. The top panel shows the empirical liquidity cost function. The bottom panel shows the dynamics of the average price of a futures contract. The time interval between each value is 5 seconds. Visualization is performed in accelerated mode.</p>
Visualization and quantification of carbon 'rusty sink' by rice root iron plaque: mechanisms, functions, and global implications
<p><span>Paddies contain 78% higher organic carbon (C) stocks than adjacent upland soils, and iron (Fe) plaque formation on rice roots is one of the mechanisms that traps C. The process sequence, extent and global relevance of this C stabilization mechanism under oxic/anoxic conditions remains unclear. We quantified and localized the contribution of Fe plaque to C stabilization in a microoxic area (</span><span>rice </span><span>rhizosphere) and</span> <span>evaluated the role of this C trap toward global C sequestration in paddy soils. Visualization and localization of pH by imaging with planar optodes, enzyme activities by zymography,</span> <span>and root exudation by 14C imaging, as well as upscale modeling enabled linkage of three groups of rhizosphere processes that are responsible for C stabilization from the micro- (root) to the macro- (ecosystem) level. The 14C activity in soil (reflecting stabilization of rhizodeposits) with Fe2+ addition was 1.4−1.5 times higher than that in the control and phosphate addition soils. Perfect co-localization of the hotspots of β-glucosidase activity (by zymography) with exudation showed that labile C and high enzyme activities were localized within Fe plaques. </span><span>Fe</span><span>2+</span> <span>addition </span><span>to </span><span>soil and its</span><span> microbial oxidation to Fe3+ by radial oxygen release from rice roots increased </span><span>Fe</span><span> plaque (Fe3+) formation by 1.7−2.5 times. The C trapped</span><span> by </span><span>Fe plaque was 1.1 times higher after Fe2+ addition. Therefore, Fe plaque formed from amorphous and complex Fe on root surface act as a "rusty sink" for C. Upscaling by model revealed the global significance of C preservation within Fe3+ complexes in paddy soils. Considering the area of coverage of paddy soils globally, radial oxygen loss from roots and bacterial Fe oxidation may trap up to 130 Mg C in Fe plaques per rice season. This represents an important annual surplus of new and stable C to the existing C pool</span> <span>under long-term rice cropping.</span></p>
Functional near-infrared spectroscopy visually evoked measurements and Autism Questionnaire score in adults and children
<p><strong>Functional near-infrared spectroscopy (fNIRS) visually-evoked data collected from healthy adults and children. We recruited a total of 40 adult participants (20 women, age: 31.05 ± 3.94 (SD) years) and 19 children (5 girls, age: 7.20 ± 3.01 (SD) years). Adult participants filled in the Autistic-traits Quotient (AQ) questionnaire, a 50-items self-administered report validated for the Italian version. The items consist of descriptive statements assessing personal preferences and typical behavior. Since child self-report might be affected by reading and comprehension difficulties, the children's version of Autism Spectrum Quotient (Italian version of AQ-child) was completed by parents. To measure changes in total Hb (THb) concentration and relative oxygenation levels (OHb and DHb) in the occipital cortex during the task, we used a continuous-wave NIRS system with 8 red light-sources operating at 760 nm and 850 nm, and 7 detectors, forming an array of 22 multi-distant channels. </strong></p> <p> </p> <p><strong>The dataset includes 2 '.zip' files containing artifact-free visually-evoked transients HDF data, exported from Homer 3 (https://github.com/BUNPC/Homer3) in '.txt' format. Subfolders correspond to different stimulation conditions, for details refer to this paper [preprint coming soon].</strong></p> <p><strong>Each txt file is named with the corresponding subject code and contains two events [tagged as 1 (baseline) and 2 (stimulus)]. </strong></p> <p><strong>The file 'annotations.csv' contains the following fields:</strong></p> <p><strong>Code [Subjects id name, that corresponds to the filename in the recording folders]</strong></p> <p><strong>Sex [M or F]</strong></p> <p><strong>Valid [1 or 0, 0 means excluded subject]</strong></p> <p><strong>Age [int]</strong></p> <p><strong>CH_exclude [list of excluded channels]</strong></p> <p><strong>CH_Red [ list of channels that did not passed the calibration step]</strong></p> <p><strong>Category [adult or child] </strong></p> <p><strong>Cartoon_fixed [cartoon name]</strong></p> <p><strong>Cartoon_chosen [cartoon name]</strong></p> <p><strong>AQ [global AQ score] </strong></p> <p><strong>AQ_S [ AQ subscale social ] </strong></p> <p><strong>AQ_C [ AQ subscale communication ] </strong></p> <p><strong>AQ_A [ AQ subscale attention] </strong></p> <p><strong>AQ_D [ AQ subscale detail] </strong></p> <p><strong>AQ_I [ AQ subscale imagination] </strong><br> </p> <p> </p> <p> </p> <p> </p>
Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe
<p>Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from that of other highly visual species, such as vertebrates, and therefore the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, since there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. Examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods.</p>
The Association of Dry Eye Disease with Functional Visual Acuity and Quality of Life
<p>Background: Dry eye disease (DED) is a common chronic condition with increasing prevalence. Standard discriminative visual acuity is not reflective of real-world visual function as patients can achieve normal acuities by blinking. Methods: Participants recruited from a tertiary referral eye center were divided into 2 groups – severe DED (with significant, central staining) and comparison group with mild DED (absence of such staining). FVA in both groups were assessed using DryeyeKT mobile application and Impact of Vision Impairment (IVI) questionnaire to assess quality of life (QOL). Results: Among 78 participants (74.4% women), 30 (38.5%) had severe DED and 48 (61.5%) milder DED. In women, severe DED produced significantly worse FVA of 0.53 ± 0.20 vs. 0.73 ± 0.30 in comparison group (p = 0.0064). FVA decreased with increasing age, significant inverse correlation (r = -0.55). A poorer FVA =<0.6 was seen in older patients (68.2 years ± 7.68) vs. FVA > 0.6 in younger patients (58.9 years ± 10.7), p <0.05. When<strong> </strong>adjusting for age, FVA was still 0.107 lower in the severe DED group, p < 0.05. There was significant difficulty in performing specific daily activities in the severe DED group, after adjusting for age, gender and FVA. Conclusions: FVA is reduced in severe DED and older people. Severe DED significantly impacts certain QOL. However, no significant relationship was found between FVA and QOL. FVA is not the only reason for the compromise of health-related QOL in severe dry eye.</p>
An Open Label Trial to Investigate Macugen for the Preservation of Visual Function in Subjects With Neovascular AMD
ClinicalTrials.gov study NCT00327470. IPD Sharing: Not stated. Countries: 15. Publications: 1.
Visual Function During Gait in Parkinson's Disease: Impact of Cognition and Response to Visual Cues
ClinicalTrials.gov study NCT02610634. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Investigation of the Effectiveness of Visual Feedback Training on Upper Extremity Functions in Cerebral Palsy
ClinicalTrials.gov study NCT03726385. IPD Sharing: UNDECIDED. Countries: 1. Publications: 26.
The Zeaxanthin and Visual Function Study
ClinicalTrials.gov study NCT00564902. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Investigating Brain Function in People With and Without Visual Snow Syndrome Using Adaptation to Visual Stimuli
ClinicalTrials.gov study NCT06961864. IPD Sharing: YES. Countries: 1. Publications: 3.
Fromsight to sequence: Underwater visual census vs eDNA metabarcoding for the monitoring of taxonomic and functional fish diversity
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Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe
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Visualization and quantification of carbon 'rusty sink' by rice root iron plaque: mechanisms, functions, and global implications
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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.