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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Automated recognition of brain region mentions in neuroscience literature.
 
Resource Report
Resource Website
1+ mentions
Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) WhiteText data or information resource, data set Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology. brain region, annotation, journal of comparative neurology, neuroanatomy, brain is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: PubMed
is related to: MEDLINE
has parent organization: University of British Columbia; British Columbia; Canada
PMID:19750194 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24027 http://www.nitrc.org/projects/whitetext/ SCR_002731 WhiteText - annotated neuroscience text 2026-09-03 05:06:03 3
Colorado Assessment Tests - Tower of London
 
Resource Report
Resource Website
Colorado Assessment Tests - Tower of London (RRID:SCR_003507) CAT Tower of London assessment test provider, material resource CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle. frontal lobe, assessment, brain, human, left anterior frontal lobe, left frontal lobe, left mesial frontal lobe, problem solving has parent organization: University of Colorado; Colorado Springs; USA nif-0000-00208 http://www.catstests.com/Product03.htm SCR_003507 Tower of London 2026-09-03 05:04:09 0
Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders
 
Resource Report
Resource Website
1+ mentions
Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders (RRID:SCR_003282) Pleiades Promoter Project biomaterial supply resource, material resource Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy. Human, DNA, promoter, gene, expression, brain, disorder, therapy is listed by: One Mind Biospecimen Bank Listing
is related to: CanEuCre
is related to: JAX Cre Repository
is related to: Recombinase (cre) Activity
has parent organization: University of British Columbia; British Columbia; Canada
Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, Cancer Child and Family Research Institute ;
Genome British Columbia ;
Genome Canada ;
UBC Institute of Mental Health
Free, Freely available nif-0000-01868 https://plone.bcgsc.ca/project/pleiades-promoter-project http://www.pleiades.org/ SCR_003282 2026-09-03 05:03:35 4
Brown University Rhode Island Biobank Core Facility
 
Resource Report
Resource Website
Brown University Rhode Island Biobank Core Facility (RRID:SCR_004289) RIBB biomaterial supply resource, material resource Cryogenic facility for human tissue and fluid samples under management of Brown University Division of Biology and Medicine and supports biomedical research on Brown campus and across affiliated hospitals of Warren Alpert Medical School. Cryogenic, facility, human, tissue, fluid, sample, brain, cerebral, spinal, fluid, blood, neuromuscular, urine, saliva, tumor, sample, skeletal muscle, ABRF is listed by: One Mind Biospecimen Bank Listing
is listed by: ABRF CoreMarketplace
is related to: USEDit
has parent organization: Brown University; Rhode Island; USA
Alzheimer's disease Restricted nlx_30512, ABRF_167 SCR_004289 Rhode Island Biobank, RI BioBank, Brown University Rhode Island Biobank Cryogenic Core Facility 2026-09-03 05:04:13 0
Banyan Biomarkers
 
Resource Report
Resource Website
1+ mentions
Banyan Biomarkers (RRID:SCR_004515) Banyan Biomarkers assessment test provider, material resource Banyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes. traumatic brain injury, blood test, human, brain, stroke, liver injury, biomarker, immunoassay, neurodegenerative disease, neurological disorder, mental disease, neuroinflammation, microglial activation, apoptosis, necrosis, hepatoxicity, in vitro, diagnostic test, enzyme linked immunosorbent assay, one mind tbi nlx_143797 SCR_004515 2026-09-03 05:04:24 1
zfishbook
 
Resource Report
Resource Website
1+ mentions
zfishbook (RRID:SCR_006896) zfishbook biomaterial supply resource, material resource Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools is listed by: One Mind Biospecimen Bank Listing
is listed by: Debian
is listed by: bio.tools
is related to: Addgene
is related to: Zebrafish International Resource Center
has parent organization: Mayo Clinic Minnesota; Minnesota; USA
Mayo Clinic Cancer Center ;
Mayo Foundation ;
NHGRI HG006431;
NIDA DA14546;
NIGMS GM63904
PMID:22067444 Free, Freely available biotools:zfishbook, nlx_151613 https://bio.tools/zfishbook SCR_006896 book, z fish book, zfishbook, fish, z 2026-09-03 05:03:49 4
PyMVPA
 
Resource Report
Resource Website
100+ mentions
PyMVPA (RRID:SCR_006099) PyMVPA software application, software resource, software toolkit A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. python, machine learning, fmri, eeg, neuroimaging, image analysis, scripting, multivariate pattern analysis, brain, meg, extracellular recording, algorithm, reusable library, analyze, c, console (text based), eeg, meg, electrocorticography, frequency domain, independent component analysis, linear, modeling, magnetic resonance, multivariate analysis, nifti, nonlinear, os independent, pet, spect, principal component analysis, python, regression, spatial transformation, statistical operation, temporal transformation, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: neurodebian
is related to: CoSMoMVPA
has parent organization: Dartmouth College; New Hampshire; USA
has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany
German Academic Exchange Service PPP-USA D/05/504/7;
NIMH MH080526;
NSF SBE 0751008;
James McDonnell Foundation 220020127
PMID:19184561
PMID:19212459
PMID:20582270
MIT License nlx_151596 http://www.nitrc.org/projects/pymvpa SCR_006099 Python MVPA, Multivariate Pattern Analysis in Python, PyMVPA - Multivariate Pattern Analysis in Python 2026-09-03 05:03:47 144
Hierarchical Region Splitting
 
Resource Report
Resource Website
1+ mentions
Hierarchical Region Splitting (RRID:SCR_016398) HRS algorithm resource, software resource Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes. mri, neuroimaging, modality, t2, diffusion, 3d, brain, lesion, nabm, core, penumbra, computation, hypoxia, ischemic PMID:22929436 Freely available SCR_016398 Hierarchical Region Splitting (HRS) 2026-09-03 05:04:36 1
elmr
 
Resource Report
Resource Website
elmr (RRID:SCR_017249) software resource, software toolkit Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package. support, working, light, electron, microscopy, fly, brain, data is related to: NeuroAnatomy Toolbox Free, Available for download, Freely available https://jefferis.github.io/elmr/ SCR_017249 2026-09-03 05:04:41 0
Neurolucida Explorer
 
Resource Report
Resource Website
100+ mentions
Neurolucida Explorer (RRID:SCR_017348) data analytics software, software application, software resource Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps. Morphometric, analysis, neuron, reconstruction, section, brain, map, mbfbioscience, MBF Bioscience SCR_017348 2026-09-03 05:04:58 116
BVA import/export EEGLAB plugin
 
Resource Report
Resource Website
1+ mentions
BVA import/export EEGLAB plugin (RRID:SCR_016333) bva-io software application, software resource, software toolkit Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB is related to: SourceForge
is related to: EEGLAB
is related to: MATLAB
Free, Available for download, Freely available SCR_016333 Brain Vision Analyser 2026-09-03 05:04:35 4
DCBC toolbox
 
Resource Report
Resource Website
DCBC toolbox (RRID:SCR_022176) software resource, software toolkit Software Python toolbox for brain parcellation evaluation. brain parcellation evaluation, brain, parcellation evaluation, brain parcellation Free, Available for download, Freely available SCR_022176 DCBC 2026-09-03 05:05:15 0
Resting State Hemodynamic Response Function Retrieval and Deconvolution
 
Resource Report
Resource Website
1+ mentions
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) rsHRF software resource, software toolkit Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain European Union Horizon 2020 Framework Programme ;
Fund for Scientific Research-Flanders ;
National Natural Science Foundation of China
PMID:34560269 Free, Available for download, Freely available https://github.com/compneuro-da/rsHRF SCR_023663 2026-09-03 05:05:16 4
Neural Stem Cell Institute NeuraCell Core Facility
 
Resource Report
Resource Website
1+ mentions
Neural Stem Cell Institute NeuraCell Core Facility (RRID:SCR_017821) access service resource, core facility, service resource Core facility provides neural stem cells (NSC) and everything you need to grow them, custom lentiviral shRNA and over-expression vectors, consult based characterization service where we can assess how your products or reagents affect stem cell performance and behavior. Services include:Cell Supply,Adult SVZ Neural Stem Cells,Any Age Embryonic stem cells from any region of the brain,Human Retinal Pigmented Epithelial cells,RPE iPSCs,iPSCs,Neural Progenitor Cells (NPCs),Custom Orders,Media/ Dissociation Reagents,High-performance Media formulated according to optimal cell growth conditions,Complete Defined Media for Neural Stem Cell Culture,Complete Defined Media for Human Retinal Pigmented Epithelial Culture,Cell characterization. Performs assays to verify how stem cell populations behave in response to certain environments, plastics, reagents, etc., using trade secret assays via FACS and cell culture techniques. This can be used for neural stem cells as well as embryonic stem cells.Cell banking solutions shall ensure that their integrity is maintained, and that sufficient supply is readily available. We will also expand cells, harvest cells, generation the freezing medium and thaw cells to test performance. Provides Generation of custom lentiviral shRNA constructs,Generation of custom lentiviral over-expression constructs,Supply of NSC lines already expressing these shRNA or over-expression constructs. Neural, stem, cell, provide, custom, lentiviral, shRNA, vector, embryonic, brain, human, retinal, pigmented, epithelial, progenitor, media, culture, formula, behave, response, environment, plastic, reagent, service, core, ABRF is listed by: ABRF CoreMarketplace Open ABRF_588 SCR_017821 NeuraCell 2026-09-03 05:08:01 3
Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility
 
Resource Report
Resource Website
50+ mentions
Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility (RRID:SCR_017949) WBMF access service resource, core facility, service resource Core suited to advance study of traumatic brain injury, as well as other neurological and psychiatric disorders.Utilizes microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. Provides access to microscopes including TissueCyte 1000 multi-photon microscopes,Hamamatsu NanoZoomer 2.0-HT,Zeiss Axioscan.Z1. Offers access to fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Provide computer available for use running MicroBrightField Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets. Traumatic, brain, injury, neurological, psychiatric, disorder, microscopy, evaluate, neuropathy, stereological, analysis, neuron, tracing, 3D, rendering, dataset, service, core, ABRF is listed by: ABRF CoreMarketplace Open ABRF_975 SCR_017949 Whole Brain Microscopy Facility 2026-09-03 05:08:08 80
Beth Israel Deaconess Medical Center Translational MRI Research Core Facility
 
Resource Report
Resource Website
Beth Israel Deaconess Medical Center Translational MRI Research Core Facility (RRID:SCR_017950) access service resource, core facility, service resource Core provides MRI capabilities for imaging human subjects and potentially large animals as part of research studies. Facility operates GE Discovery MR750 3T whole-body scanner and can provide access to 1.5T system. Scanner is FDA cleared for clinical use. It has proprietary software including pulse programming environments and reconstruction programs and customizable software and protocols for applications including functional and structural brain imaging, abdominal perfusion and diffusion, muscle functional imaging and spectroscopy are available to users.Support for fMRI acquisition and visual and auditory stimulus presentation, diffusion tensor imaging, spectroscopy, and high quality anatomic imaging is available. The system has specialized receiver coils for sensitive imaging of particular anatomy. Additional customized coils can be manufactured in our RF lab. The system also has full broadband capability for multinuclear MRI and MRS, including (F-19, C-13, P-31, and Na-23).Our facility can also provide Image Post-processing and computerized image transfer, assistance to ensure MRI equipment safety, and can facilitate Clinical Readings. MRI, imaging, human, animal, whole, body, scanner, clinical, functional, structural, brain, abdominal, perfusion, diffusion, muscle, MRS, service, core, ABRF is listed by: ABRF CoreMarketplace
has parent organization: Harvard Medical School; Massachusetts; USA
ABRF_982 SCR_017950 Translational MRI Research Core 2026-09-03 05:08:26 0
CellTax vignette
 
Resource Report
Resource Website
1+ mentions
CellTax vignette (RRID:SCR_017000) data or information resource, data set Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region is related to: Allen Brain Atlas API
is related to: Allen Mouse Brain Reference Atlas
is related to: Allen Cell Types Database
has parent organization: Allen Institute for Brain Science
has parent organization: Allen Brain Atlas
Allen Institute for Brain Science ;
NEI R01 EY023173;
NIMH U01 MH105982
PMID:26727548 Free, Public SCR_017000 Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science 2026-09-03 05:07:55 3
University of Washington I-LABS MEG Brain Imaging Center Core Facility
 
Resource Report
Resource Website
1+ mentions
University of Washington I-LABS MEG Brain Imaging Center Core Facility (RRID:SCR_024836) access service resource, core facility, service resource Magnetoencephalography facility focusing on children. Equipped with MEGIN TRIUX Neo system with helium recycler, MAGSTIM EEG data acquisition system, Tucker-Davis Technologies RZ6 for stimulus generation, Epson Home Cinema 3200 for video projection, custom video recording system with 4 cameras, Eyelink eyetracker, and Polhemus 3D digitizer. ABRF, Magnetoencephalography facility, brain, children, is listed by: ABRF CoreMarketplace
has parent organization: University of Washington; Seattle; USA
ABRF_2606 https://coremarketplace.org/?FacilityID=2606&citation=1 SCR_024836 , Institute for Learning and Brain Sciences (I-LABS) MEG Brain Imaging Center, I-LABS MEG Brain Imaging Center, MagnetoEncephaloGraphy Brain Imaging, MEG Brain Imaging 2026-09-03 05:09:05 1
FMRIB's Diffusion Toolbox
 
Resource Report
Resource Website
10+ mentions
FMRIB's Diffusion Toolbox (RRID:SCR_024931) FDT data processing software, image analysis software, software application, software resource Software toolbox for analysis of diffusion weighted images. Functional Magnetic Resonance Imaging, MRI, brain, diffusion weighted images, diffusion weighted images analysis is a plug in for: FSL Free, Freely available SCR_024931 Functional Magnetic Resonance Imaging of the Brain Diffusion Toolbox 2026-09-03 05:09:08 15
Cardio-Neuro-Mind Data Platform
 
Resource Report
Resource Website
Cardio-Neuro-Mind Data Platform (RRID:SCR_027008) CNMDP data or information resource, portal, topical portal Platform to store, analyze, and share large amounts of various types of data to facilitate research, and ultimately, unravel the complex connections between the brain and the heart. brain and heart connection data, brain, heart, data has parent organization: University of Ottawa; Ontario; Canada Free, Freely available SCR_027008 Cardio-Neuro-Mind Data Platform (CNMDP) 2026-09-03 05:10:44 0

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