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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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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
AxoGen
 
Resource Report
Resource Website
AxoGen (RRID:SCR_000326) material resource, tissue bank, biomaterial supply resource A medical technology company whose research and products revolve around peripheral nerve repair. commercial, peripheral nerve repair, nerve repair, nerve repair technology, nerve injury, nerve, regenerative medicine, porcine submucosa extracellular matrix Commercial nlx_47454 SCR_000326 2026-08-06 09:25:09 0
Smart Dictionary Lookup
 
Resource Report
Resource Website
Smart Dictionary Lookup (RRID:SCR_000568) Smart Dictionary Lookup service resource, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm. gene, protein uses: UniProt
uses: BioThesaurus
is listed by: OMICtools
has parent organization: University of Manchester; Manchester; United Kingdom
PMID:17698493 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01198 SCR_000568 2026-08-06 09:25:12 0
CryoCord Stem Cell Bank
 
Resource Report
Resource Website
1+ mentions
CryoCord Stem Cell Bank (RRID:SCR_000329) material resource, tissue bank, biomaterial supply resource A stem cell bank in Malaysia which provides and carries out long-term human stem cells and tissue cryopreservation and research. The general public can use their biobanking services for personal use. stem cell, cryopreservation, tissue bank, indonesia, asia, stem cell bank, human stem cell Commercial, Available to the general public nlx_57364 SCR_000329 CryoCord Premier Stem Cell Bank, CryoCord Sdn Bhd 2026-08-06 09:25:09 1
Disease Genes Conserved Sequence Tags Database
 
Resource Report
Resource Website
Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) database, data or information resource A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions. database, conserved sequence element, genomic sequence, human gene, pathogenesis, genetic disorder, blastz, cst Telethon Foundation ;
the Associazione Italiana per la Ricerca sul Cancro (AIRC) ;
the Federazione Italiana per la Ricerca sul Cancro (FIRC) ;
the Italian Ministry for Research (MURST) ;
the National Council for Research (CNR) ;
Regione Campania ;
BioGeM
PMID:15608249 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21121 SCR_000760 DG CST Database 2026-08-06 09:25:16 0
Healthy People
 
Resource Report
Resource Website
10+ mentions
Healthy People (RRID:SCR_001446) Healthy People database, data or information resource Database portal for science-based, 10-year national objectives resulting from a multiyear process that reflects input from a diverse group of individuals and organizations for improving the health of all Americans. 2020 Topics & Objectives are available in an A-Z format. DATA2020, the Healthy People 2020 interactive data tool, allows users to explore the data and technical information related to the Healthy People 2020 objectives. For 3 decades, Healthy People has established benchmarks and monitored progress over time in order to: * Encourage collaborations across communities and sectors. * Empower individuals toward making informed health decisions. * Measure the impact of prevention activities. Healthy People 2020 strives to: * Identify nationwide health improvement priorities. * Increase public awareness and understanding of the determinants of health, disease, and disability and the opportunities for progress. * Provide measurable objectives and goals that are applicable at the national, State, and local levels. * Engage multiple sectors to take actions to strengthen policies and improve practices that are driven by the best available evidence and knowledge. * Identify critical research, evaluation, and data collection needs. health, prevention, improvement, disease, disability, public awareness, injury, quality of life, healthy development, healthy behavior, healthy, public health, data set is listed by: NIDDK Information Network (dkNET)
has parent organization: U.S. Department of Health and Human Services
Free, Freely Available nlx_152705 SCR_001446 HealthyPeople.gov, Healthy People 2020 2026-08-06 09:25:23 32
Current Research Information System
 
Resource Report
Resource Website
1+ mentions
Current Research Information System (RRID:SCR_001441) CRIS database, data or information resource A database of documentation and reporting for ongoing agricultural, food science, human nutrition, and forestry research, education and extension activities for the United States Department of Agriculture; with a focus on the National Institute of Food and Agriculture (NIFA) grant programs. Projects are conducted or sponsored by USDA research agencies, state agricultural experiment stations, land-grant universities, other cooperating state institutions, and participants in NIFA-administered grant programs, including Small Business Innovation Research and Agriculture and Food Research Initiative. agricultural, food science, human nutrition, nutrition, forestry research, education, data set is listed by: NIDDK Information Network (dkNET)
has parent organization: USDA National Institute of Food and Agriculture
Free, Freely Available nlx_152704 http://cris.csrees.usda.gov/ SCR_001441 Current Research Information System (CRIS), U.S. Department of Agriculture Current Research Information System 2026-08-06 09:25:23 4
SSCprofiler
 
Resource Report
Resource Website
1+ mentions
SSCprofiler (RRID:SCR_001282) SSCprofiler data analysis service, production service resource, analysis service resource, service resource Tool which can be used to identify novel miRNA gene candidates in the human genome. microrna, gene, genome, sequence, structure, conservation is listed by: OMICtools
has parent organization: Institute of Molecular Biology and Biotechnology; Heraklion; Greece
PMID:19324892 Free, Freely available OMICS_02055 SCR_001282 Sequence Structure and Conservation profiler 2026-08-06 09:25:22 3
Human Nutrition Research Information Management
 
Resource Report
Resource Website
Human Nutrition Research Information Management (RRID:SCR_001471) HNRIM database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of human nutrition research and research training activities supported by the federal government. Information regarding trends in nutrition research, specific institutions and investigators involved in this research, or areas of agency emphases can be obtained from database searches or from published summary reports. Data for the system is prepared and submitted by participating agencies, and is updated annually. The database contains several thousand projects for each of fiscal years 1985present. Participating agencies include the Department of Health and Human Services, the U.S. Department of Agriculture, the Department of Veteran Affairs, the Agency for International Development, the Department of Defense, Department of Commerce, National Science Foundation, and the National Aeronautics and Space Administration. nutrition is listed by: NIDDK Information Network (dkNET)
is related to: CARDS Database
has parent organization: NIH Division of Nutrition Research Coordination
NIH THIS RESOURCE IS NO LONGER IN SERVICE nlx_152702 SCR_001471 HNRIM System Database, Federal Human Nutrition Research and Information Management (HNRIM) System Database, Federal Human Nutrition Research and Information Management System Database 2026-08-06 09:25:24 0
Childhood Liver Disease Research and Education Network
 
Resource Report
Resource Website
1+ mentions
Childhood Liver Disease Research and Education Network (RRID:SCR_001497) ChiLDREN material resource, tissue bank, biomaterial supply resource Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study. child, clinical, epidemiology, therapy, pediatric, young human, rare disease, diagnostics, treatment, infant, liver, longitudinal, gall bladder, bile duct, small intestine, colon, lymph node, blood, urine, tissue, serum, plasma, dna, bile, liver tissue, gall bladder tissue, bile duct tissue, small intestine tissue, colon tissue, lymph node tissue is listed by: One Mind Biospecimen Bank Listing
is listed by: NIDDK Information Network (dkNET)
has parent organization: University of Michigan; Ann Arbor; USA
Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defect, Mitochondrial Hepatopathy, Progressive Familial Intrahepatic Cholestasis, Liver disease, Metabolism defect, Cholestasis NIDDK 2U01DK062456 nlx_152755 SCR_001497 Childhood Liver Disease Research and Education Network (ChiLDREN) 2026-08-06 09:25:24 3
MitoMiner
 
Resource Report
Resource Website
50+ mentions
MitoMiner (RRID:SCR_001368) database, data or information resource A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list uses: HomoloGene
uses: UniProt
uses: KEGG
uses: OMIM
uses: The Human Protein Atlas
uses: Gene Ontology
MRC PMID:22121219
PMID:19208617
Public, Acknowledgement requested, Code: nlx_152504 SCR_001368 MitoMiner - A database of the mitochondrial proteome 2026-08-06 09:25:23 76
BraVa
 
Resource Report
Resource Website
1+ mentions
BraVa (RRID:SCR_001407) BraVa database, data or information resource A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs). digital reconstruction, morphometric analysis, cerebrum, arterial vasculature, magnetic resonance angiography, adult human, morphology, artery, arborization, circle of willis, cerebral artery, male, female, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Bravissima
has parent organization: George Mason University: Krasnow Institute for Advanced Study
Healthy NINDS NS39600;
NIBIB EB001955;
NINDS NS061770;
NIMH P20 MH52176
PMID:23727319 Free, Freely Available nlx_152630 http://www.nitrc.org/projects/breva SCR_001407 2026-08-06 09:25:23 8
BodyMap-Xs
 
Resource Report
Resource Website
1+ mentions
BodyMap-Xs (RRID:SCR_001147) BodyMap-Xs database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008 expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralog has parent organization: DNA DataBank of Japan (DDBJ) Neoplasm, Normal Japanese Ministry of Education Culture Sports Science and Technology MEXT ;
New Energy and Industrial Technology Development Organization
PMID:16381946
PMID:11125076
PMID:10592203
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02617 http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/ SCR_001147 BodyMap-Xs: anatomical and taxonomical breakdown of animal EST, BodyMap, BodyMap- human and mouse gene expression database, BodyMap: human and mouse gene expression database, BodyMap-cross species, BodyMap-Xs(cross species) 2026-08-06 09:25:21 1
Surface-Based Atlases
 
Resource Report
Resource Website
1+ mentions
Surface-Based Atlases (RRID:SCR_002099) Caret:Atlases database, data or information resource, atlas THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex. atlas, human, macaque, mouse, cerebral cortex, cerebellar cortex, database, primate, magnetic resonance imaging, neuroanatomy is listed by: Biositemaps
has parent organization: Washington University in St. Louis; Missouri; USA
PMID:22052704 THIS RESOURCE IS NO LONGER IS SERVICE. nif-0000-00346 SCR_002099 Surface-Based Atlas 2026-08-06 09:25:32 2
cisRED: cis-regulatory element
 
Resource Report
Resource Website
10+ mentions
cisRED: cis-regulatory element (RRID:SCR_002098) cisRED database, data or information resource Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species. atomic motif, conserved sequence motif, motif pattern, regulatory element, motif, atomic, promoter, chip-seq, transcription factor binding site, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: BC Cancer Agency
Genome Canada ;
BC Cancer Foundation ;
Michael Smith Foundation for Health Research
PMID:16381958 Free, Freely available nif-0000-02665, biotools:cisred, OMICS_01857, r3d100010619 https://bio.tools/cisred, https://doi.org/10.17616/R3XK69 SCR_002098 cisRED - Databases of genome-wide regulatory module and element predictions 2026-08-06 09:25:35 14
Spliceosome Database
 
Resource Report
Resource Website
10+ mentions
Spliceosome Database (RRID:SCR_002097) Spliceosome Database database, data or information resource A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. splicing, mass spectrometry, protein, rna, complex, spliceosome, small nuclear rna, structure, dynamics, ortholog, gene is listed by: OMICtools
has parent organization: University of California at Santa Cruz; California; USA
PMID:23118483 Free, Freely available OMICS_01891 SCR_002097 Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing, Spliceosome Component Database 2026-08-06 09:25:34 11
MPromDb
 
Resource Report
Resource Website
1+ mentions
MPromDb (RRID:SCR_002136) MPromDb database, data or information resource A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations. gene, promoter, chip-seq, chip-chip, visualization, gene promoter, annotation, rna pol-ii chip-seq, protein-coding gene is listed by: OMICtools
is related to: Gene Expression Omnibus
has parent organization: Wistar Institute
PMID:21097880
PMID:16381984
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01876 SCR_002136 Mammalian Promoter Database 2026-08-06 09:25:36 8
New Energy and Industrial Technology Development Organization
 
Resource Report
Resource Website
New Energy and Industrial Technology Development Organization (RRID:SCR_002153) NEDO database, data or information resource A database of sequence data of cDNA clones from the Kazusa DNA Research Institute human spleen cDNA library, which was determined by the NEDO human cDNA sequencing project. The cDNAs supplied by Kazusa DNA Research Institute were generated by conventional methods and strictly size-selected from a cDNA library of adult human spleen. Consequently, not all of the cDNAs may be full-length, though all possess relatively long cDNA inserts, whose average size is about 4.5 kb. cDNAs having unknown end sequences and high protein-coding probability at their 5-prime ends were selected and sequenced. The physical maps were constructed on the basis of the sequence data of the cDNA clones. RepeatMasker, which is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes, was applied to detect repeat sequences in cDNA sequences. The predicted protein sequences were examined for motifs present in the PROSITE database. Because weakly defined sequence motifs appear too many times in the HUGE database and are, thus, unlikely to be informative, several motifs were excluded from the analysis, including amidation site, N-glycosylation site, and cAMP- and cGMP-dependent protein kinase phosphorylation site. database, 5 prime end, sequence data, adult human spleen, physical map Free, Freely available nif-0000-20945 SCR_002153 New Energy and Industrial Technology Development Database, NEDO Database 2026-08-06 09:25:36 0
TcoF
 
Resource Report
Resource Website
10+ mentions
TcoF (RRID:SCR_002158) TcoF database, data or information resource Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). protein, regulation, transcription, transcription factor, transcription co-factor, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia
PMID:20965969 THIS RESOURCE IS NO LONGER IN SERVICE biotools:tcof-db, OMICS_01865 https://bio.tools/tcof-db SCR_002158 Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins, TcoF-DB, TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins 2026-08-06 09:25:33 10
Genome Network Platform
 
Resource Report
Resource Website
10+ mentions
Genome Network Platform (RRID:SCR_001737) GNP database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed. gene, genome, chip, human, interaction, micro array, protein, protein-protein interaction, qrt-pcr, rat, rna, sequence, short rna, tiling array, transcription, transcription control, transcription factor, transcription starting position, yeast two hybrid, data set, cage, data analysis service is listed by: 3DVC
has parent organization: National Institute of Genetics; Shizuoka; Japan
PMID:24927841 Free, Freely Available nif-0000-10237 http://genomenetwork.nig.ac.jp/index_e.html SCR_001737 2026-08-06 09:25:27 20
EMBASE
 
Resource Report
Resource Website
10000+ mentions
EMBASE (RRID:SCR_001650) Embase database, data or information resource Comprehensive international bibliographic biomedical database that enables users to track and retrieve precise information on drugs and diseases from pre-clinical studies to searches on critical toxicological information. It contains bibliographic records with citations, abstracts and indexing derived from biomedical articles in peer reviewed journals, and is especially strong in its coverage of drug and pharmaceutical research. Embase can help with everything from clinical trials research to pharmacovigilance and is updated online daily and weekly. Its broad biomedical scope covers the following areas: * Drug therapy and research, including pharmaceutics, pharmacology and toxicology * Clinical and experimental (human) medicine * Basic biological science relevant to human medicine * Biotechnology and biomedical engineering, including medical devices * Health policy and management, including pharmacoeconomics * Public, occupational and environmental health, including pollution control * Veterinary science, dentistry, and nursing The Embase Application Programming Interface supports export, RSS feeds, and integration services, making it possible to share data with a wide range of systems. biomedical, drug, disease, regulatory requirement, drug research, pharmacology, pharmaceutics, toxicology, clinical, experimental medicine, health policy, management, public health, occupational health, environmental health, drug dependence, drug abuse, psychiatry, forensic medicine, biomedical engineering, biomedical instrumentation, nursing, dentistry, veterinary medicine, psychology, alternative medicine, clinical trial, pharmacovigilance, pharmacology, drug safety, adverse drug reaction, chemical, bibliography, FASEB list is related to: Cochrane Central Register of Controlled Trials Restricted nlx_153929 SCR_001650 EMBASE: Excerpta Medica, Excerpta Medica Database, Embase: Biomedical Database, EMBASE (Excerpta Medica Database) 2026-08-06 09:25:26 62975

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