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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
Collaborative Islet Transplant Registry
 
Resource Report
Resource Website
1+ mentions
Collaborative Islet Transplant Registry (RRID:SCR_001466) CITR service resource, data or information resource, report, database, narrative resource, resource, data repository, storage service resource Collect, analyze, and communicate on comprehensive and current data on all islet/beta cell transplants in human recipients performed in North America, as well as some European and Australian centers to expedite progress and promote safety in islet/beta cell transplantation. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. Annual Reports are available. Islet/beta cell transplantation is a complex procedure with many factors contributing to the outcome. Compiling and analyzing data from all transplant centers in the US, Canada, as well as some European and Australian centers will accelerate the identification of both critical risk factors and key determinants of success and thereby guide transplant centers in developing and refining islet/beta cell transplant protocols. The inclusion of the term collaborative in the name of the Registry emphasizes the importance of collaboration in fulfilling the CITR mission and goals. Close collaboration with the transplant centers will ensure that relevant questions are addressed, that data submitted are accurate and complete, and that the needs of the transplant community are served. Information on how to participate as a CITR Transplant Center and to receive a transplant center application is available through the website. Progress in islet transplantation depends entirely on complete, high-quality medical data, including the information patients consented to report to the Collaborative Islet Transplant Registry. To make it as easy as possible to provide updated information about patient's health, an on-line questionnaire is available or patients can mail it to their transplant center. This information is very important in the continuing search for a cure for Type 1 diabetes. transplant center, transplant, islet, beta cell, clinical, islet transplantation, beta cell transplantation, outcome, metadata standard, adverse event report, diabetes, data element, bibliography, questionnaire, protocol, risk factor, case report form, allograft, pancreatectomy, autograft, islet processing is listed by: NIDDK Information Network (dkNET) Type 1 diabetes, Diabetes NIDDK N01-DK6-2868;
NIDDK N01-DK1-2472
PMID:15387102 Free, Freely Available nlx_152693 SCR_001466 2026-08-12 10:48:24 9
Teen-Longitudinal Assessment of Bariatric Surgery
 
Resource Report
Resource Website
Teen-Longitudinal Assessment of Bariatric Surgery (RRID:SCR_001492) data or information resource, portal, consortium, organization portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Consortium made up of five clinical centers and a data coordinating center. The goal of Teen-LABS is to conduct clinical, epidemiological, and behavioral research in adolescent bariatric surgery, through an observational prospective study protocol. Teen-LABS is an ancillary study to LABS, an observational study of adult bariatric surgery. Research staff, certified in standardized uniform data collection according to the protocol, collect data at pre-operative research visits, at surgery, 30 days and six months post-operative, and annual post-operative research visits at the five participating centers. adolescent human, bariatrics, pre-operative, at surgery, post-operative, clinical, epidemiology, behavior, surgical outcome, metadata standard, observational study, clinical, experimental protocol, evidence-based recommendation, patient evaluation, follow-up care is listed by: NIDDK Information Network (dkNET) Bariatric surgery, Obesity NIDDK R01DK080020 THIS RESOURCE IS NO LONGER IN SERVICE SCR_014388, nlx_152747 SCR_001492 Teen-LABS, Adolescent Bariatrics: Assessing Health Benefits and Risks, Teen-Longitudinal Assessment of Bariatric Surgery, Adolescent Bariatrics: Assessing Health Benefits and Risks (Teen-LABS) 2026-08-12 10:48:24 0
CGEN
 
Resource Report
Resource Website
10+ mentions
CGEN (RRID:SCR_001251) CGEN data processing software, data analysis software, software resource, software application Software R package for analysis of case-control studies in genetic epidemiology. genetic, epidemiology, r, case-control, clustering, multiple comparison, snp is listed by: OMICtools
has parent organization: Bioconductor
PMID:21387464 Free, Available for download, Freely available OMICS_02089 SCR_001251 CGEN - An R package for analysis of case-control studies in genetic epidemiology 2026-08-12 10:48:22 18
Morpholino Database
 
Resource Report
Resource Website
1+ mentions
Morpholino Database (RRID:SCR_001378) MODB service resource, data or information resource, database, data repository, storage service resource Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password. morpholino, target mrna, embryonic zebrafish, sequence, target, blast, phenotype, anatomy, development, behavior, morphology, pigmentation, toxicity, pax2 expression, craniofacial structure, eye, kidney, pituitary, skin, name, target name, target sequence, gene target, genetic, mortality, toxicity, defect, function, gene annotation, genome, data analysis service uses: Zebrafish Information Network (ZFIN)
uses: PATO
has parent organization: Mayo Clinic Minnesota; Minnesota; USA
NIGMS GM63904;
NIA CA65493
PMID:18179718 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152566 SCR_001378 MODB (MOprholino DataBase) 2026-08-12 10:48:23 1
Brede Wiki
 
Resource Report
Resource Website
Brede Wiki (RRID:SCR_001411) data or information resource, narrative resource, wiki THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format. neuroinformatics, neuroscience, functional neuroimaging, molecular neuroimaging, fmri, mri, talairach, brain region, data sharing, mediawiki, sql is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is related to: Brede Database
is related to: Brede Toolbox
is related to: Brede Database
has parent organization: Technical University of Denmark; Lyngby; Denmark
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-08130 http://www.nitrc.org/projects/bredewiki SCR_001411 Brede Wiki - a neuroinformatics wiki 2026-08-12 10:48:23 0
Open metadata mark up language
 
Resource Report
Resource Website
10+ mentions
Open metadata mark up language (RRID:SCR_001376) odML data or information resource, narrative resource, standard specification, interchange format, markup language Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability. mark-up language, electrophysiology, neurophysiology, terminology, metadata, data sharing, interoperability, annotate, ontology is used by: NIX
is used by: EEGbase
is used by: odMLtables
has parent organization: German Neuroinformatics Node (G-Node)
BMBF 01GQ0802;
BMBF 01GQ0801
PMID:21941477 Free, Available for download, Freely available nlx_152533 SCR_001376 open metadata Markup Language 2026-08-12 10:48:23 27
Jmosaics
 
Resource Report
Resource Website
Jmosaics (RRID:SCR_001094) sequence analysis software, software application, data processing software, software resource, data analysis software R software that detects enriched regions of ChIP-seq data sets jointly. chip seq, data, genomics, sequencing, r, sequence analysis software is listed by: OMICtools
is hosted by: Bioconductor
Free, Available for download, Freely available OMICS_00445 SCR_001094 2026-08-12 10:48:20 0
Mutation Surveyor
 
Resource Report
Resource Website
500+ mentions
Mutation Surveyor (RRID:SCR_001247) sequence analysis software, software application, data processing software, software resource, data analysis software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects. dna, sequencing, dna-seq, sanger sequencing, sequence analysis software is listed by: OMICtools PMID:21780000
PMID:20938837
Restricted OMICS_01816 Mutation Surveyor software version 5.0 http://www.softgenetics.com/mutationSurveyor.html SCR_001247 2026-08-12 10:48:22 668
Sequencher
 
Resource Report
Resource Website
5000+ mentions
Sequencher (RRID:SCR_001528) Sequencher sequence analysis software sequence analysis software, software application, data processing software, software resource, data analysis software Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. dna, sequencing, sequence analysis software, NGS, sanger, data visualization is listed by: OMICtools
is listed by: SoftCite
Available for download OMICS_01817 http://genecodes.com/sequencher-features SCR_001528 Sequencher sequence analysis software 2026-08-12 10:48:25 5032
Kyoto Encyclopedia of Genes and Genomes Expression Database
 
Resource Report
Resource Website
1000+ mentions
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) KEGG Expression Database service resource, data or information resource, database, data repository, storage service resource Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list is listed by: LabWorm
is affiliated with: KEGG
has parent organization: Kyoto University; Kyoto; Japan
PMID:9847135
PMID:10592173
Free, Available for download, Freely available r3d100011570, nif-0000-21234 https://doi.org/10.17616/R3792T SCR_001120 Kyoto Encyclopedia of Genes and Genomes Expression Database 2026-08-12 10:48:20 1279
Integrated DNA Technologies OligoAnalyzer
 
Resource Report
Resource Website
500+ mentions
Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) OligoAnalyzer web application, sequence analysis software, software application, data processing software, software resource, data analysis software Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration. oligos, oligonucleotides, sequence, web, analyzer Free, Freely Available nif-0000-07754 SCR_001363 IDT OligoAnalyzer, OligoAnalyzer, IDT Oligo Analyzer, OligoAnalyzer 3.1 2026-08-12 10:48:23 620
UNAFold
 
Resource Report
Resource Website
100+ mentions
UNAFold (RRID:SCR_001360) data processing software, data analysis software, software resource, software application Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows. software, nucleic acid, folding, hybridization, prediction, rna, dna, stochastic sampling, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: University at Albany; New York; USA
Free, Available for download, Freely available biotools:unafold, nif-0000-07753 http://mfold.rna.albany.edu/ SCR_001360 The UNAFold Web Server, UNAFold Web Server 2026-08-12 10:48:22 373
THOR Center for Neuroinformatics
 
Resource Report
Resource Website
1+ mentions
THOR Center for Neuroinformatics (RRID:SCR_001400) THOR Center portal, data or information resource, software application, topical portal, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization. neuroinformatics, neural network, functional neuroimaging, multimedia, signal processing, biomedical, neuroscience, biomedical, brain has parent organization: Technical University of Denmark; Lyngby; Denmark
is parent organization of: MRIWarp
is parent organization of: Brede Toolbox
is parent organization of: Lyngby
Danish Research Council THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-08128 SCR_001400 Technology by Highly Oriented Research Center for Neuroinformatics 2026-08-12 10:48:23 1
Globin Gene Server
 
Resource Report
Resource Website
10+ mentions
Globin Gene Server (RRID:SCR_001480) Globin Gene Server service resource, data or information resource, production service resource, database, narrative resource, source code, training material, resource, analysis service resource, software resource, data analysis service Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna is listed by: NIDDK Information Network (dkNET)
has parent organization: Pennsylvania State University
NLM R01LM05773;
NLM R01LM05110;
NIDDK DK27635
PMID:11857738
PMID:11480780
PMID:9799599
PMID:9576329
PMID:8088828
Free, Freely available nlx_152723 SCR_001480 2026-08-12 10:48:24 30
Nonalcoholic Steatohepatitis Clinical Research Network
 
Resource Report
Resource Website
10+ mentions
Nonalcoholic Steatohepatitis Clinical Research Network (RRID:SCR_001519) NASH CRN research forum portal, portal, data or information resource, clinical trial, disease-related portal, topical portal, resource Clinical research network to focus on the etiology, contributing factors, natural history, complications, and therapy of nonalcoholic steatohepatitis. They research the nature and underlying cause of Nonalcoholic Steatohepatitis (NASH) and conduct clinical studies on prevention and treatment. Approximately 1,500 pediatric and adult participants throughout the United States and Canada with nonalcoholic fatty liver disease (NAFLD) have enrolled into a database. The NASH CRN has recently reopened the database to enroll additional pediatric and adult participants with NAFLD. Serum, liver tissue, and genomic DNA samples are being collected and stored in the NIDDKrepository for ongoing as well as future studies. A three-arm randomized, placebo-controlled clinical trial of pioglitazone versus vitamin E completed enrollment in 2009. In addition to this adult trial, a similar trial in pediatric NASH patients randomized 180 children to receive treatment with vitamin E, metformin, or placebo. prevention, treatment, pediatric, child, adult human, serum, liver tissue, dna, placebo, pioglitazone, vitamin e, metformin, etiology, contributing factor, natural history, complication, therapy, young human, database, clinical trial, bibliography, patient registry is listed by: One Mind Biospecimen Bank Listing
is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Central Repository
has parent organization: Johns Hopkins University; Maryland; USA
Nonalcoholic steatohepatitis, Nonalcoholic fatty liver disease NIDDK 1ZIADK075013 Free, Freely available nlx_152845 https://www.nashcrn.com SCR_001519 Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN), Clinical Research Network in Nonalcoholic Steatohepatitis 2026-08-12 10:48:25 21
Pediatric Acute Liver Failure Study
 
Resource Report
Resource Website
Pediatric Acute Liver Failure Study (RRID:SCR_001478) PALF research forum portal, portal, data or information resource, disease-related portal, topical portal, resource Study group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA. management strategy, infant, child, adolescent, clinical, liver, patient care, rare disease, blood, tissue, longitudinal, urine, bile, serum, liver tissue, cell line, fibroblast culture, dna, etiology, diagnosis, treatment, outcome is listed by: NIDDK Information Network (dkNET)
is related to: Acute Liver Failure Study Group
has parent organization: University of Pittsburgh; Pennsylvania; USA
Acute liver failure NIDDK U01DK072146 Free, Freely available nlx_152715 http://www.palfstudy.org/ SCR_001478 Pediatric Acute Liver Failure (PALF) Study, Pediatric Acute Liver Failure (PALF) Study Group 2026-08-12 10:48:24 0
Brain Gene Expression Map
 
Resource Report
Resource Website
10+ mentions
Brain Gene Expression Map (RRID:SCR_001517) BGEM data or information resource, atlas, database, expression atlas This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world. embryonic, expression pattern, gene expression, gene, adult, brain, brain development, in situ hybridization, mouse, nervous tissue, postnatal, molecular neuroanatomy resource, image NINDS 5R37NS036558;
NINDS N01-NS-0-2331
PMID:16602821 nif-0000-09579 SCR_001517 BGEM - Brain Gene Expression Map, Mousebrain Gene Expression Map 2026-08-12 10:48:25 10
Happy
 
Resource Report
Resource Website
10+ mentions
Happy (RRID:SCR_001395) HAPPY source code, software application, data processing software, software resource, data analysis software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping is listed by: Genetic Analysis Software
is listed by: Debian
has parent organization: Wellcome Trust Centre for Human Genetics
Wellcome Trust PMID:11050180
DOI:10.1073/pnas.230304397
THIS RESOURCE IS NO LONGER IN SERVICE nlx_152594 http://www.well.ox.ac.uk/~rmott/happy.html https://sources.debian.org/src/r-other-mott-happy.hbrem/ SCR_001395 reconstructing HAPlotYpes 2026-08-12 10:48:23 46
GenoSet
 
Resource Report
Resource Website
GenoSet (RRID:SCR_001275) GenoSet data processing software, data analysis software, software resource, software application Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. copy number variation, data representation, infrastructure, microarray, snp is listed by: OMICtools
has parent organization: Bioconductor
Artistic License, v2 OMICS_02063 SCR_001275 genoset - Provides classes similar to ExpressionSet for copy number analysis 2026-08-12 10:48:22 0
Retinal Topography Maps Database
 
Resource Report
Resource Website
1+ mentions
Retinal Topography Maps Database (RRID:SCR_001399) Retinal Topography Maps Database service resource, data or information resource, database, data repository, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded. retinal map, retina, vision, retinal neuron, topography, eye has parent organization: University of Western Australia; Perth; Australia PMID:26230981 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152606 SCR_001399 Retinal topography maps, retinalmaps.org 2026-08-12 10:48:23 1

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