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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
aGEM
 
Resource Report
Resource Website
10+ mentions
aGEM (RRID:SCR_013349) aGEM database, data or information resource Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics is related to: EMAGE Gene Expression Database
is related to: Gene Expression Database
is related to: Gene Expression Nervous System Atlas
is related to: BioGPS: The Gene Portal Hub
is related to: Allen Mouse Brain Reference Atlas
is related to: Eurexpress
is related to: HUDSEN
is related to: The Human Protein Atlas
is related to: OMIM
is related to: KEGG
has parent organization: Autonomous University of Madrid; Madrid; Spain
National Institute for Bioinformatics ;
AMIT Programme CDTI CEN-20101014;
RESOLVE UE CE:FP7-202047;
Ministerio de Ciencia e Innovacion BIO2010-16566;
Biostruct-X FP7-Infrastructures-2011-1;
Centrosoma 3D CSD2006-00023
PMID:22106336 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152022 SCR_013349 anatomic Gene Expression Mapping 2026-08-08 12:04:32 12
Japanese Single Nucleotide Polymorphisms
 
Resource Report
Resource Website
10+ mentions
Japanese Single Nucleotide Polymorphisms (RRID:SCR_013076) database, data or information resource JSNP is a database of Japanese Single Nucleotide Polymorphisms. It includes BLAST capability, keyword search, mapping information, and other tools that allow users to gather information on SNP's. SNPs are the most common form of DNA sequence variation. They are useful polymorphic markers to investigate genes susceptible to diseases or those related to drug responsiveness. Furthermore, a small subset of SNPs directly influences to the quality and/or quantity of the gene product, and increase a risk to certain diseases and to severe side effect by drugs. Through a discovery of a large number of SNPs, we would like to contribute to identification of disease-related genes and also to establish a diagnostic method to avoid drug side-effect. FASEB list has parent organization: University of Tokyo; Tokyo; Japan nif-0000-03063 SCR_013076 JSNP 2026-08-08 12:04:30 42
MIT-BIH polysomnographic
 
Resource Report
Resource Website
1+ mentions
MIT-BIH polysomnographic (RRID:SCR_013078) database, data or information resource MIT-BIH Polysomnographic Database is a collection of recordings of multiple physiologic signals during sleep. Subjects were monitored in Boston''s Beth Israel Hospital Sleep Laboratory for evaluation of chronic obstructive sleep apnea syndrome, and to test the effects of constant positive airway pressure (CPAP), a standard therapeutic intervention that usually prevents or substantially reduces airway obstruction in these subjects. The database contains over 80 hours'' worth of four-, six-, and seven-channel polysomnographic recordings, each with an ECG signal annotated beat-by-beat, and EEG and respiration signals annotated with respect to sleep stages and apnea has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; nlx_45862 SCR_013078 MIT-BIH polysomnographic 2026-08-08 12:04:25 1
Death Domain database
 
Resource Report
Resource Website
1+ mentions
Death Domain database (RRID:SCR_013231) DD database database, data or information resource A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily protein interaction, death domain superfamily, death domain, protein-protein interaction, apoptosis, inflammation, immune cell signaling pathway, cellular signaling pathway, interaction, bio.tools is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
has parent organization: Yeungnam University; North Gyeongsang; South Korea
has parent organization: Seoul National University College of Medicine; Seoul; South Korea
has parent organization: Myongji University; Gyeonggi-do; South Korea
Korean Ministry of Education Science and Technology 2011-0003406;
Korean Ministry of Education Science and Technology 2011-0025697;
Korean Ministry of Education Science and Technology 2008-05943;
Korean Ministry of Education Science and Technology 2011-0022437
PMID:22135292 nlx_149482, biotools:deathdomain https://bio.tools/deathdomain SCR_013231 DeathDomain.org/, DeathDomain Database, Death Domain database: A manually curated database of protein-protein interactions for Death Domain Superfamily 2026-08-08 12:04:26 2
FlyTrap- GFP Protein Trap Database
 
Resource Report
Resource Website
10+ mentions
FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) database, data or information resource The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. gfp-tagged protein, protein, protein trapping screen has parent organization: Yale University; Connecticut; USA nif-0000-02849 SCR_013354 FlyTrap 2026-08-08 12:04:27 26
CollecTF
 
Resource Report
Resource Website
10+ mentions
CollecTF (RRID:SCR_014405) database, data or information resource A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements. database, transcription factor binding site, bacteria is related to: xFITOM NSF MCB-1158056 PMID:24234444 The community can contribute to this resource SCR_014405 2026-08-08 12:04:30 33
GlycoEpitope
 
Resource Report
Resource Website
1+ mentions
GlycoEpitope (RRID:SCR_014404) database, data or information resource A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields. database, carbohydrate, antigen, antibody has parent organization: Ritsumeikan University; Kyoto; Japan DOI:10.4172/jpb.10000e24 Public, Free http://www.ebi.ac.uk/miriam/main/collections/MIR:00000478 SCR_014404 GlycoEpitope: Index, GlycoEpitope Index 2026-08-08 12:04:35 5
UniCarb-DB
 
Resource Report
Resource Website
1+ mentions
UniCarb-DB (RRID:SCR_014407) database, data or information resource An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS. database, carbohydrate, glycomic ms, spectral library, structural ms, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of Gothenburg; Gothenburg; Sweden
has parent organization: UniCarbKB
Nectar ;
Australian National Data Service ;
Swedish Foundation for International Cooperation in Research and Higher Education ;
Swiss Institute of Bioinformatics ExPASy
DOI:10.1093/bioinformatics/btr137 Available to the research community biotools:unicarb-db https://bio.tools/unicarb-db SCR_014407 UniCarb-DB structural- MS spectral library database 2026-08-08 12:04:37 8
Drosophila melanogaster Exon Database
 
Resource Report
Resource Website
1+ mentions
Drosophila melanogaster Exon Database (RRID:SCR_013441) DEDB database, data or information resource Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast is listed by: OMICtools
is related to: FlyBase
has parent organization: National University of Singapore; Singapore; Singapore
Agency for Science Technology and Research PMID:15581431 nif-0000-21118, OMICS_01894 SCR_013441 DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database 2026-08-08 12:04:28 2
NIDDK Research Resources
 
Resource Report
Resource Website
NIDDK Research Resources (RRID:SCR_014372) database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Registry listing NIDDK resources, such as reagents, data, and protocols. They are derived from publicly available information provided by NIDDK-funded investigators, projects, and publications. research, registry, diabetes, kidney disease, reagent, data, protocol lists: NIDDK Information Network (dkNET)
lists: Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION)
lists: Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT)
lists: Lifestyle Interventions for Expectant Moms (LIFE-Moms)
lists: Hyperglycemia and Pregnancy Outcomes Follow-Up Study Consortium (HAPO-FUS)
lists: Nephrotic Syndrome Study Network (NEPTUNE)
lists: CKD Biomarkers Consortium
lists: Porphyria Consortium
lists: Vitamin D to Prevent Type 2 Diabetes (D2d)
lists: Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE)
lists: Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN)
lists: Clinical Islet Transplantation Consortium (CITC)
lists: Restoring Insulin Secretion Consortium (RISE)
lists: Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI)
lists: Integrated Islet Distribution Program (IIDP)
lists: Rare Kidney Stone Consortium (RKSC)
lists: Evaluating Predictors and Interventions in Sphincter of Oddi Dysfunction
lists: Efficacy and Mechanisms of Glutamine Dipeptide in the Surgical Intensive Care Unit
lists: Intestinal Stem Cell Consortium
lists: RiVuR
lists: Gastroparesis Clinical Research Consortium
lists: Urologic Diseases in America
lists: United States Renal Data System
lists: HALT PKD
lists: Chronic Renal Insufficiency Cohort Study
lists: HEALTHY study
lists: Viral Resistance to Antiviral Therapy of Chronic Hepatitis C
lists: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C
lists: HALT-C Trial
lists: TRIGR
lists: Treatment Options for type 2 Diabetes in Adolescents and Youth
lists: Study of Nutrition in Acute Pancreatitis
lists: SEARCH for Diabetes in Youth
lists: Organ Procurement and Transplantation Network
lists: Nuclear Receptor Signaling Atlas
lists: NIH Common Fund
lists: Mutant Mouse Resource and Research Center
lists: GenitoUrinary Development Molecular Anatomy Project
lists: National Mouse Metabolic Phenotyping Centers
lists: IPD-MHC- Major Histocompatibility Complex
lists: High-dose Ursodiol Therapy of Primary Sclerosing Cholangitis
lists: Hepatitis B Research Network
lists: Functional Dyspepsia Treatment Trial
lists: Cooperative Study Group for Autoimmune Disease Prevention
lists: Clinical Outcomes Research Initiative
lists: BISC
lists: The Immunology Database and Analysis Portal (ImmPort)
lists: Beta Cell Biology Consortium
lists: Autoimmunity Centers of Excellence
lists: HemBase
lists: Longitudinal Assessment of Bariatric Surgery
lists: Minnesota Liver Tissue Cell Distribution System
lists: Knockout Mouse Project
lists: Immune Tolerance Network (ITN)
lists: Multi-Disciplinary Approach to the Study of Chronic Pelvic Pain
is listed by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
Diabetes, Kidney disease THIS RESOURCE IS NO LONGER IN SERVICE SCR_014372 National Institute of Diabetes and Digestive and Kidney Diseases Research Resources 2026-08-08 12:04:35 0
Psychotropics
 
Resource Report
Resource Website
1+ mentions
Psychotropics (RRID:SCR_013600) database, data or information resource The Lundbeck Institute is pleased to present Psychotropics Online, a comprehensive guide to CNS compounds and products. A database of psychotropic and neurological drugs. Generic name, Trade name, Description, Code numbers, Monographies, Tranquilizers - Anxiolytics, Anxiolytics / Antipsychotics, Neuroleptics and Antipsychotics, Monoamine Oxidase Inhibitors, Antidepressants, Antidementia drugs, Sympathomimetics, Antiparkinsonians, Anticonvulsants, Hallucinogenic Agents, Additional Group, Biochemical profiles, Side-effects, Antipsychotics, Tranquilizers - anxiolytics, Tricyclic Antidepressants (TCAs), Selective Serotonin Reuptake Inhibitors (SSRIs), Selective Serotonin and Noradrenaline Reuptake Inhibitors (SNRIs), Selective Noradrenaline Reuptake Inhibitors (NARIs), MAO inhibitors (MAOIs), Sympathomimetics, Anticonvulsants, Lithium, Barbiturates, Street names, Terminal plasma half-lives, Orphan drugs nif-0000-00433 SCR_013600 Psychotropics 2026-08-08 12:04:29 1
Secreted Protein Database
 
Resource Report
Resource Website
10+ mentions
Secreted Protein Database (RRID:SCR_013448) SPD database, data or information resource A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. The 18,152 entries are classified into fourteen functional categories, including "apolipoprotein", "cytokine", "protease", "toxin", etc. To make the dataset more comprehensive, nine related datasets were also collected, such as SPDI, Riken mouse secretome, SwissProt vertebrate secreted proteins, SubLoc etc. has parent organization: Peking University; Beijing; China nif-0000-03449 SCR_013448 Secreted Protein Database 2026-08-08 12:04:33 11
Paper Critic
 
Resource Report
Resource Website
Paper Critic (RRID:SCR_014019) database, data or information resource A database that archives publications and allows users to review and critique them. Users can write comments for and rate submitted publications for references, originality, argumentation, and reliability. Papercritic also collects tweets and blog posts about published papers to add as reviews and comments. Researchers who submit their published work to PaperCritic can keep track of multiple types of feedback. All reviews must be submitted with full identity disclosure. database, authoring, evaluation, peer review is listed by: Connected Researchers
is related to: Mendeley
is related to: Connected Researchers
The community can contribute to this resource SCR_014019 2026-08-08 12:04:36 0
BSORF - Bacillus Subtilis Genome Database
 
Resource Report
Resource Website
1+ mentions
BSORF - Bacillus Subtilis Genome Database (RRID:SCR_013451) database, data or information resource This website provides a resource for the Bacillus subtilis genome. It provides a list of mutants, DNA array data, and search features against both the whole genome and coding sequences. It also contains Kegarrays and access to the KEGG Expression Database. bacillus subtilis, bacillus subtilis genome, bacillus subtilis mutant has parent organization: Kyoto University; Kyoto; Japan nif-0000-02624 SCR_013451 BSORF 2026-08-08 12:04:28 2
ApiDB ToxoDB
 
Resource Report
Resource Website
100+ mentions
ApiDB ToxoDB (RRID:SCR_013453) ApiDB ToxoDB database, data or information resource A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info end-sequencing, bac clone, data mining tool, microarray, proteomic sequencing, toxoplasma gondii, bac clone, 8x random shotgun, genomic sequencing project, snp, qtl, sequencing, genomic, non-vertebrate, unicellular, eukaryote, genome, pathogen, toxoplasmosis, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Eukaryotic Pathogen Database Resources
NIAID contract HHSN266200400037C PMID:18003657
PMID:12519989
r3d100012266, nif-0000-03572, biotools:toxodb https://bio.tools/toxodb http://ToxoDB.org SCR_013453 Toxoplasma Genomics Resource, ToxoDB 2026-08-08 12:04:33 153
Animal Diversity Web
 
Resource Report
Resource Website
1+ mentions
Animal Diversity Web (RRID:SCR_013658) database, data or information resource Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan :Animal Diversity Web Has: Thousands of species accounts about individual animal species. These may include text, pictures of living animals, photographs and movies of specimens, and/or recordings of sounds. Students write the text of these accounts and we cannot guarantee their accuracy. Descriptions of levels of organization above the species level, especially phyla, classes, and in some cases, orders and families. Hundreds of hyperlinked pages and images illustrate the traits and general biology of these groups. Professional biologists prepare this part. :Animal Diversity Web Is An Online Encyclopedia: ADW is a large searchable encyclopedia of the natural history of animals. Every day, thousands of classroom students and informal visitors use it to answer animal questions. Other sites specialize in local, endangered, or particular kinds of animals. We aim to be as comprehensive as possible. :A Science Learning Tool: ADW facilitates inquiry-driven learning, that is, teaching about science by leading students to use the methods of science. Our large database is structured, providing consistent information for all species to foster comparisons. An advanced search tool allows a user to call up species accounts fitting any combination of descriptors. Students can explore for patterns and relationships, learn how to frame and answer scientific questions and, with the help of a good teacher, experience the excitement and satisfaction of doing science. Our long-term goal is to create a database rich enough that students can discover for themselves basic concepts in ecology and conservation biology. :A Virtual Museum: ADW provides a way to make the contents of research museums available globally for teaching and research. So far, our efforts have been directed mainly at mammals. Photographs of scientific specimens are available for representative species from most mammal families. We''ve also included several hundred Quick Time Virtual Reality Movies of skulls. These allow the user to rotate the specimen, providing an excellent impression of its 3-dimensional structure. We''ve written in depth about and illustrated many of the characteristics of interest to students of mammals. An important goal for the future is to expand to cover other groups of animals and include other media such as animal behavior video. :Wiki features, database, teaching tool : has parent organization: University of Michigan; Ann Arbor; USA nif-0000-00419 SCR_013658 Animal Diversity Web 2026-08-08 12:04:36 3
SHERPA RoMEO
 
Resource Report
Resource Website
SHERPA RoMEO (RRID:SCR_013815) database, data or information resource A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit. database, publisher policy, open access is listed by: Connected Researchers
is related to: Connected Researchers
has parent organization: University of Nottingham; Nottingham; United Kingdom
JISC ;
Wellcome Trust
Free, Public SCR_013815 RoMEO 2026-08-08 12:04:35 0
Mouse Phylogeny Viewer
 
Resource Report
Resource Website
10+ mentions
Mouse Phylogeny Viewer (RRID:SCR_014071) database, data or information resource A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others. mouse, genetic, software, phylogeny, browser has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA NHGRI P50 HG 006582;
NIAID U54 AI 081680;
NSF ISS 0534580
PMID:22536897 SCR_014071 2026-08-08 12:04:35 11
Nanomaterial Registry
 
Resource Report
Resource Website
100+ mentions
Nanomaterial Registry (RRID:SCR_013700) MIAN database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop. registry, information resource, nanomaterial, data management is listed by: NIH Data Sharing Repositories NIH DOI:10.1109/BIBMW.2012.6470258 THIS RESOURCE IS NO LONGER IN SERVICE SCR_013793, r3d100011129 https://doi.org/10.17616/R38S53 SCR_013700 2026-08-08 12:04:34 151
SciTran
 
Resource Report
Resource Website
1+ mentions
SciTran (RRID:SCR_013666) database, data or information resource Scientific Transparency (SciTran) is a software project that has grown out of the Project on Scientific Transparency at Stanford University. At the heart of SciTran is a scientific data management system – SDM – designed to enable and foster reproducible research. SciTran SDM delivers efficient and robust archiving, organization, and sharing of scientific data. We have developed the system around neuroimaging data, but our goal is to build a system that is flexible enough to accomodate all types of scientific data – from paper-and-pencil tests to genomics data. SDM will also allow for the sharing of data and computations between remote sites. SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. Feel free to try it out or to contribute. Commercial support for SciTran SDM is available through our partners at Flywheel. Check out their demo, if you''d like to give SDM a quick try. open science has parent organization: Stanford University; Stanford; California SCR_013666 2026-08-08 12:04:29 3

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