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RNA velocity objects of FACS-sorted (CD31+/CD45-) endothelial cells of individual pathological entities
<p><strong>RNA velocity objects (zip files of .h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells of individual pathological entities<br></strong></p> <p><em><span>-> part of the manuscript: Single-cell atlas of the human brain vasculature across development, adulthood and disease</span></em><span><br><em><span>https://www.nature.com/articles/s41586-024-07493-y</span></em></span></p> <p> </p> <p>-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p><em>-i) AVM sorted endothelial cells_RNA velocity.zip: </em><br> -> this is a zip file of an RNA velocity object (.h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain arteriovenous malformations (AVM) (a brain vascular malformation).<br><br><em>- ii) LGG sorted endothelial cells_RNA velocity.zip: </em><br> -> this is a zip file of an RNA velocity object (.h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells isolated from lower-grade gliomas (LGG) (a brain tumor)<br><br><em>- iii) GBM sorted endothelial cells_RNA velocity.zip: </em><br> -> this is a zip file of an RNA velocity object (.h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells isolated from high-grade gliomas (glioblastoma (GBM)) (a brain tumor).<br><br><em>- iv) MET sorted endothelial cells_RNA velocity.zip: </em><br> -> this is a zip file of an RNA velocity object (.h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain metastasis (MET) (a brain tumor).<br><br><em>- v) MEN sorted endothelial cells_RNA velocity.zip: </em><br> -> this is a zip file of an RNA velocity object (.h5ad) of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain meningioma (MEN) (a brain tumor).</p>
seurat objects of FACS-sorted (CD31+/CD45-) endothelial cells - individual entities
<p><strong>Seurat objects of individual entities of FACS-sorted (CD31+/CD45-) endothelial cells<br></strong></p> <p><em><span>-> part of the manuscript: Single-cell atlas of the human brain vasculature across development, adulthood and disease</span></em><span><br><em><span>https://www.nature.com/articles/s41586-024-07493-y</span></em></span></p> <p><strong> </strong></p> <p>-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p> <p> </p> <p><em>-i) Fetal CNS sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal brain (Fetal CNS).<br><br><em>-ii) Fetal periphery sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal peripheral organs (Fetal periphery).<br><br><em>- iii) Adult control brain (temporal lobe) sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from adult/control brains (temporal lobes).<br><br><em>- iv) AVM sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain arteriovenous malformations (AVM) (a brain vascular malformation).<br><br><em>- v) LGG sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from lower-grade gliomas (LGG) (a brain tumor).<br><br><em>- vi) GBM sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from high-grade gliomas (glioblastoma (GBM)) (a brain tumor).<br><br><em>- vii) MET sorted endothelial cells_seurat object.rds:</em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain metastasis (MET) (a brain tumor).<br><br><em>- viii) MEN sorted endothelial cells_seurat object.rds: </em><br> -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain meningioma (MEN) (a brain tumor).</p>
Raw GC-TOF-MS data from individuals sampled in allopatric zones (see Methods) from Doniol-Valcroze et al.
<p>Raw .MZML data from GC-TOF-MS analysis of Cuticular compounds of the four species of the <em>Coenonympha </em><em>arcania-gardetta</em> hybrid species complex.</p> <p>Samples are labelled with letters as follow: Species_Sex__Extract-type_SampleID. Species: A= <em>C. arcania</em>; G= <em>C. gardetta</em>; D= <em>C. darwiniana</em>; C= <em>C. cephalidarwiniana</em>. Sex: M= male; F= female. Extract type: b= Full body extract; w= Wing extract.</p>
Schistomiasis morbidity evaluation in individuals aged 15 years and older, in Chókwè district, Mozambique
<p>Data regarding schistosomiasis epidemiology and morbidity in the adult population of Chókwè district, Mozambique</p>
Granulometric database of individual fragments of shredded Waste Electric and Electronic Equipments
<p>This dataset describes the granulometric properties of individual fragments of Waste from Electric and Electronic Equipments (WEEE). It was collected during the PhD thesis of Alexis Barthet (Mines Paris - PSL), under the supervision of Emilie Chautru (Mines Paris - PSL), Hervé CHauris (Mines Paris - PSL), Thomas Romary (Mines Paris PSL) and Vincent Semetey (Institut de Recherche de Chimie Paris), in 2021-2022.</p> <p>Two batches of WEEE were collected and sieved. Indivudal fragments were collected, and their picture, mass, density and type of fragments were measured. After segmentation of the pictures, their lengths, their widths, and their thickness were also collected. Both segmented and original pictures are available. The size of a pixel in mm for each image is also available for additional work on the pictures.</p> <p>A description of the fragments as well as the methods used to collect the data is avalaible in the article "Advanced granulometric characterization of shredded waste printed circuit boards for sampling" about to be published in the journal "Waste Management" by the authors mentionned in the first paragraph. </p>
code for: The cerebellum computes frequency dynamics for motions with numerical precision and cross-individual uniformity
<p>MATLAB codes for data analyses performed in "The cerebellum computes frequency dynamics for motions with numerical precision and cross-individual uniformity".</p>
Imunnesenescence of antibody repertoire in individuals from endemic areas for infectious diseases
<p>Heavy Chain Antibody Repertoire data in the AIRR format, clonotyped with YClon, of patients diagnosed with COVID-19 and a control group. The sample labels in the paper and the sample labels in this repository are correspondent according to the following table:</p> <table> <tbody> <tr> <td>Sample</td> <td>Deposite_code</td> </tr> <tr> <td>C_01</td> <td>A04</td> </tr> <tr> <td>C_02</td> <td>A20</td> </tr> <tr> <td>C_03</td> <td>A24</td> </tr> <tr> <td>C_04</td> <td>A65</td> </tr> <tr> <td>C_05</td> <td>A66</td> </tr> <tr> <td>C_06</td> <td>A67</td> </tr> <tr> <td>H_NEA_01</td> <td>ID141</td> </tr> <tr> <td>H_NEA_02</td> <td>ID143</td> </tr> <tr> <td>H_NEA_03</td> <td>ID144</td> </tr> <tr> <td>H_NEA_04</td> <td>ID187</td> </tr> <tr> <td>H_NEA_05</td> <td>ID195</td> </tr> <tr> <td>H_NEA_06</td> <td>ID226</td> </tr> <tr> <td>H_NEA_07</td> <td>ID248</td> </tr> <tr> <td>H_NEA_08</td> <td>ID268</td> </tr> <tr> <td>H_NEA_09</td> <td>ID310</td> </tr> <tr> <td>H_NEA_10</td> <td>ID375</td> </tr> <tr> <td>M_EA_01</td> <td>GV43</td> </tr> <tr> <td>M_EA_02</td> <td>GV68</td> </tr> <tr> <td>M_EA_03</td> <td>GV106</td> </tr> <tr> <td>M_EA_04</td> <td>GV144</td> </tr> <tr> <td>M_EA_05</td> <td>GV146</td> </tr> <tr> <td>M_EA_06</td> <td>GV47</td> </tr> <tr> <td>M_EA_07</td> <td>GV50</td> </tr> <tr> <td>M_EA_08</td> <td>GV51</td> </tr> <tr> <td>M_EA_09</td> <td>GV54</td> </tr> <tr> <td>M_EA_10</td> <td>GV92</td> </tr> <tr> <td>M_NEA_01</td> <td>ID094</td> </tr> <tr> <td>M_NEA_02</td> <td>ID117</td> </tr> <tr> <td>M_NEA_03</td> <td>ID124</td> </tr> <tr> <td>M_NEA_04</td> <td>ID131</td> </tr> <tr> <td>M_NEA_05</td> <td>ID132</td> </tr> <tr> <td>M_NEA_06</td> <td>ID155</td> </tr> <tr> <td>M_NEA_07</td> <td>ID240</td> </tr> <tr> <td>M_NEA_08</td> <td>ID244</td> </tr> </tbody> </table>
Distribution of encounters of individual asteroid pairs
<p>The figures present the results for each new asteroid pair. The first subfigure of each panel shows the time distribution of encounters between clones of asteroids. The legend describes the parameters of the primary component for each pair and the cut-off parameters of the considered encounters. The second subplot demonstrates the distribution of encounters in terms of Hill sphere radii and escape velocities, and gives the information of how close the registered encounters were. </p>
FIGURE 9. Two individual cormidia from Doc Ricketts Dive 552 in Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals
FIGURE 9. Two individual cormidia from Doc Ricketts Dive 552 specimen of Tottonophyes enigmatica sp. nov. Scale bars 1 mm.
FIGURE 2. Individuals from a in Molecular evidence for conspecificity of two desert Liolaemus lizards (Iguania: Liolaemidae)
FIGURE 2. Individuals from a) near Caspana (MUAP-114), near type locality for Liolaemus audituvelatus; b) Diego de Almagro, type locality of L. manueli; c) and d) Altos Quebrada Agua Colorada; e) and f) Barranquilla (near Caseron). f) is a gravid female. Note that b) male of L. audituvelatus from known distribution and d) male of L. manueli from type locality, are identical and were found 300 km away (in straight line); and, a) and e) are also similar and were found 600 km away (in straight line).
Dataset from 'Hesse, C., Koroknai, L., & Billino, J. (2018). Individual differences in processing resources modulate bimanual interference in pointing. Psychological Research. doi: 10.1007/s00426-018-1050-3
<p>--------------------------------------------------------------</p> <p>The folder contains 8 data files and 1 readme file describing the content of the data files.</p> <p>-------------------------------------------------------------</p> <p>For further questions, please contact:<br> c.hesse[at]abdn.ac.uk</p> <p> </p>
Text-fig. 13. SMNK Ma1 Gips 13, right mandible of Hippopotamodon erymanthius from Mahmutgazi, Turkey, with worn p/3–m/3. A) lingual view, B) stereo occlusal view, C) buccal view. This mandible may represent the same individual as the maxilla Ma1 MP 8 (scale 5 cm). in Hippopotamodon erymanthius (Suidae, Mammalia) from Mahmutgazi, Denizli-Çal basin, Turkey
Text-fig. 13. SMNK Ma1 Gips 13, right mandible of Hippopotamodon erymanthius from Mahmutgazi, Turkey, with worn p/3–m/3. A) lingual view, B) stereo occlusal view, C) buccal view. This mandible may represent the same individual as the maxilla Ma1 MP 8 (scale 5 cm).
Dataset: Language and semantic processing in blind and sighted individuals. A simulation study
<p>-------------------<br> GENERAL INFORMATION<br> -------------------</p> <p>1. Title of Dataset <br> <br> Dataset_SimulationsOutput_BlindvsSightedModels<br> <br> 2. Author Information</p> <p>This dataset is being made public to act as supplementary data for publication. Running title: </p> <p>R. Tomasello, M. Garagnani, T. Wennekers, and F. Pulvermüller, Recruitment of visual cortex for language processing in blind individuals is explained by Hebbian learning.</p> <p> Corresponding author:<br> Name: Rosario Tomasello <br> Institution: Brain Language Laboratory, Freie Universität Berlin<br> Address: Habelschwerdter Allee 45, 14195 Berlin<br> Email: Tomasello.r@fu-berlin.de</p> <p>--------------------------<br> RESEARCH PROJECT & METHODOLOGICAL INFORMATION<br> --------------------------</p> <p>The data were generated by a neurobiologically constrained cortex model of the fronto-temporal-occipital lobes applied to simulate word meaning acquisition of object- and action-related words in action and perception system under undeprived and visually deprived conditions. The purpose of this study was to investigate how and why the visual system is recruited for language processing in blind individuals, as documented by neurocognitive empirical experiments.</p> <p>The files listed above shows the cell assemblies (CA) distributions across the different cortical areas spontaneously emerged as a result of Hebbian learning. For more information about the general features of the model see our previous publications:</p> <p>R. Tomasello, M. Garagnani, T. Wennekers, and F. Pulvermüller, (2018) A Neurobiologically Constrained Cortex Model of Semantic Grounding With Spiking Neurons and Brain-Like Connectivity, Front. Comput. Neurosci., vol. 12, p. 88.</p> <p>M. Garagnani, G. Lucchese, R. Tomasello, T. Wennekers, and F. Pulvermüller, (2017) A Spiking Neurocomputational Model of High-Frequency Oscillatory Brain Responses to Words and Pseudowords, Front. Comput. Neurosci., vol. 10, no. January, pp. 1–19.</p> <p><br> ---------------------<br> DATA & FILE OVERVIEW<br> ---------------------</p> <p><br> 1. File List<br> <br> Filename: CA_Structure_Blind VS SightedModel.xlsx (size 150KB) <br> <br> The excel file includes the cell assembly (CA) distributions of the learnt action and object words of both sighted and blind models along with their CA structure comparisons and the related figures. <br> <br> Folders: Raw_Data_SightedModel (size 6KB) & Raw_Data_BlindModel (size 6KB)<br> <br> These folders include the raw data output of the CA structure of the 13 sighted and 13 blind simulated models after word meaning acquisition. </p>
DATS 6401- Individual Project - Mo Zhou
<p>These are images I used in my project.</p>
INDICATORS TO DISTINGUISH SYMPTOM ACCENTUATORS FROM SYMPTOM PRODUCERS IN INDIVIDUALS WITH A DIAGNOSED ADJUSTMENT DISORDER: A PILOT STUDY ON INCONSISTENCY SUBTYPES USING SIMS AND MMPI-2-RF
<p>In the context of legal damage evaluations, evaluees may exaggerate or simulate symptoms in an attempt to obtain greater economic compensation. To date, practitioners and researchers have focused on detecting malingering behavior as an exclusively unitary construct. However, we argue that there are two types of inconsistent behavior that speak to possible malingering—accentuating (i.e., exaggerating symptoms that are actually experienced) and simulating (i.e., fabricating symptoms entirely)—each with its own unique attributes; thus, it is necessary to distinguish between them. The aim of the present study was to identify objective indicators to differentiate symptom accentuators from symptom producers and consistent participants. </p>
Experiment Data - 952 Assessments of 8 Vision Videos Regarding Overall Video Quality and 15 Individual Quality Characteristics
<p>In 2018, we conducted a within-subjects experiment to investigate how individual quality characteristics of vision videos relate to the overall quality of vision videos from a developer's point of view. 139 undergraduate students who had the role of a developer and actively developed software in projects with real customers at the time of the experiment participated in the experiment. The subjects can be considered as developers due to their experience at the time of the experiment. The subjects were put in the situation that they join an ongoing project in their familiar role as a developer. In this context, we showed the 8 vision videos (one after the other) always with the intent to share the vision of the particular project with the subjects. The undergraduate students subjectively assessed the overall quality and 15 individual quality characteristics of the 8 vision videos by completing an assessment form for each video. After data cleaning, the final data set contains 952 complete assessments of 119 subjects for the 8 vision videos.</p> <p>Each entry of the data set consists of:</p> <ul> <li>Entry ID: The ID of the entry in the dataset.</li> <li>Subject ID: The ID of the subject.</li> <li>Video ID: The ID of the vision video assessed.</li> <li>Overall quality: The subject's assessment of the overall quality of the vision video.</li> <li>Image quality: The subject's assessment of the visual quality of the image of the vision video.</li> <li>Sound quality: The subject's assessment of the auditory quality of the sound of the vision video.</li> <li>Video length [s]: The duration of the vision video in seconds.</li> <li>Focus: The subject's assessment of the compact representation of the vision which is presented in the vision video.</li> <li>Plot: The subject's assessment of the structured presentation of the content of the vision video.</li> <li>Prior knowledge: The subject's assessment of the presupposed prior knowledge to understand the content of the vision video.</li> <li>Clarity: The subject's assessment of the intelligibility of the aspired goals of the vision which is presented in the vision video.</li> <li>Essence: The subject's assessment of the amount of important core elements, e.g., persons, locations, and entities, which are to be presented in the vision video.</li> <li>Clutter: The subject's assessment of the amount of disrupting and distracting elements, e.g., background actions or noises, that can be inadvertently recorded in the vision video.</li> <li>Completeness: The subject's assessment of the coverage of the three contents of a vision which is presented in the vision video, i.e., the considered problem, the proposed solution, and the improvement of the problem due to the solution.</li> <li>Pleasure: The subject's assessment of the enjoyment of watching the vision video.</li> <li>Intention: The subject's assessment of how well the vision video is suitable for the intended purpose of the given scenario.</li> <li>Sense of responsibility: The subject's assessment of the compliance of the vision video with legal regulations.</li> <li>Support: The subject's assessment of his or her level of acceptance of the vision which is presented in the vision video.</li> <li>Stability: The subject's assessment of the consistency of the vision which is presented in the vision video.</li> </ul> <p>This dataset includes the following files:</p> <ul> <li>"Dataset_Assessments.xlsx" contains the anonymized 952 assessments of the 119 subjects for the 8 vision videos</li> <li>"Assessment_form.docx" contains the assessment form which was used to assess each of the 8 vision videos</li> <li>"Assessment_form.pdf" contains the assessment form which was used to assess each of the 8 vision videos</li> </ul> <p>The 8 vision videos are not included in this dataset since we do not have the explicit consent of the actors to distribute the vision videos.</p> <p>This experiment was designed, conducted, and analyzed by Oliver Karras (<a href="https://twitter.com/KarrasOliver">@KarrasOliver</a>), Kurt Schneider, and Samuel A. Fricker (<a href="https://twitter.com/samuelfricker">@samuelfricker</a>).</p>
Fig. 1 Pattern representing a in Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common
Fig. 1 Pattern representing a distribution of microsatellite alleles in individual dicyemids. Dicyemids in each host individual did not share identical patterns of microsatellite alleles. Each row represents a single dicyemid individual. Microsatellite alleles are colour coded according to
Fig. 3 in Genetic analysis of dicyemid infrapopulations suggests sexual reproduction and host colonization by multiple individuals is common
Fig. 3 Percentage of variance present in the samples (based on the four-level AMOVA computed in Arlequin using Rst metrics). Groups set as two localities from Tyrrhenian (Italy, Naples) and Adriatic seas (Pula, Croatia). Hierarchical levels showing significant variation (p <0.05) are marked by an asterisk
Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals
<p>We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.</p>
Data of individuals who are in Preclinical RA
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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.