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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 Authority Synonyms Record Last Update Mentions Count
Read Codes Clinical Terms Version 3
 
Resource Report
Resource Website
1+ mentions
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) RCD controlled vocabulary, data or information resource, ontology Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre umls is listed by: BioPortal nlx_157570 SCR_006055 SciCrunch Registry Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) 2026-10-24 12:45:36 1
Genome Research Foundation
 
Resource Report
Resource Website
1+ mentions
Genome Research Foundation (RRID:SCR_006056) GRF, GF institution The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure has parent organization: Korean Ministry of Education Science and Technology
is parent organization of: MetaBase
Content is available under BioLicense: the freest license. grid.410888.d, nlx_151458, Wikidata: Q5533483 https://ror.org/03khjyh83 SCR_006056 SciCrunch Registry Genome Foundation 2026-10-24 12:45:37 1
OCDM - Ontology of Craniofacial Development and Malformation
 
Resource Report
Resource Website
1+ mentions
OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) OCDM controlled vocabulary, data or information resource, ontology To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language. craniofacial development, malformation, craniofacial malformation, anatomy has parent organization: FaceBase nlx_151377 SCR_005999 SciCrunch Registry Ontology of Craniofacial Development Malformation (OCDM), Ontology of Craniofacial Development and Malformation (OCDM), OCDM - Ontology of Craniofacial Development Malformation 2026-10-24 12:45:35 1
University of Michigan Department of Neuroscience Graduate Program
 
Resource Report
Resource Website
1+ mentions
University of Michigan Department of Neuroscience Graduate Program (RRID:SCR_006002) U-M Neuroscience Graduate Program data or information resource, department portal, graduate program resource, organization portal, portal The Graduate Program at the University of Michigan was constituted in 1971, making it the longest-standing neuroscience graduate program in the United States. We are a collegial and interactive group of 75 students and 115 faculty that perform research across the breadth of the neuroscience field. Neuroscience graduate students on this campus form a cohesive group, which promotes interactions among the faculty, making the Graduate Program the nexus of the neuroscience community. Graduates receive a Ph.D. in Neuroscience, which provides tremendous flexibility in choosing one's career path. There are more than 100 alumni of our Program, and these graduates work in academic research, industrial research and development, academic medicine and biotechnology. Our program captures the excitement and interaction intrinsic to the field of neuroscience. Students can seek admission to the Neuroscience Program by three different routes direct application to the Neuroscience Program, application via the Program in Biomedical Sciences and application via the Medical Scientist Training Program. has parent organization: University of Michigan; Ann Arbor; USA nif-0000-02211 SCR_006002 SciCrunch Registry University of Michigan Neuroscience Graduate Program 2026-10-24 12:45:35 1
Voronoia
 
Resource Report
Resource Website
10+ mentions
Voronoia (RRID:SCR_006005) data or information resource, database, software resource, software toolkit Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins. has parent organization: University Medicine Berlin; Berlin; Germany nif-0000-03641 http://141.42.202.21/voronoia/index.php SCR_006005 SciCrunch Registry Voronoia 2026-10-24 12:45:36 10
MetaQC
 
Resource Report
Resource Website
10+ mentions
MetaQC (RRID:SCR_006000) software resource Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. standalone software, mac os x, unix/linux, windows, r, FASEB list is listed by: OMICtools
has parent organization: CRAN
PMID:22116060 GNU General Public License, v2 OMICS_04032 https://github.com/donkang34/MetaQC SCR_006000 SciCrunch Registry MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis 2026-10-24 12:45:36 40
MIALAB - Medical Image Analysis Lab
 
Resource Report
Resource Website
10+ mentions
MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) MIALAB data or information resource, laboratory portal, organization portal, portal MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition. software, data, data visualization, medical image, image, neuroimaging, fmri, diffusion tensor imaging, electroencephalography, structural imaging, genetic data, brain, image processing, adaptive signal processing, estimation theory, neural network, statistical signal processing, pattern recognition, mri has parent organization: Mind Research Network
is parent organization of: Group ICA of fMRI Toolbox
is parent organization of: Group ICA Of EEG Toolbox
is parent organization of: MIALAB - Resting State Data
Mental disease nlx_151551 SCR_006089 SciCrunch Registry Medical Image Analysis Lab, Medical Image Analysis Laboratory, MIA Laboratory, Medical Image Analysis (MIA) Laboratory 2026-10-24 12:45:37 27
Scholarly Electronic Publishing Bibliography
 
Resource Report
Resource Website
Scholarly Electronic Publishing Bibliography (RRID:SCR_005949) SEPB bibliography, book, data or information resource, narrative resource Bibliography with over 3,800 selected English-language articles, books, and other printed and electronic sources that are useful in understanding scholarly electronic publishing efforts on the Internet. It covers a wide range of topics, such as digital copyright, digital libraries, digital preservation, digital repositories, e-books, e-journals, license agreements, metadata, and open access. It includes Scholarly Electronic Publishing Resources, a selective directory of related Web sites, and the Scholarly Electronic Publishing Weblog, a frequently updated list of new publications and other resources that may be of interest to bibliography readers. Most sources have been published from January 1, 1990 through October 30, 2011; however, a limited number of earlier key sources are also included. The bibliography includes links to freely available versions of included works. It does not include digital media works (such as MP3 files), editorials, e mail messages, letters to the editor, daily newspaper articles, presentation slides or transcripts, or weblog postings. An archive of prior versions of SEPB is available as a downloadable compressed file (.zip) that includes all versions of the bibliography. The Scholarly Electronic Publishing Bibliography 2010 is available as a paperback (466 pages, $18.95, ISBN-10: 1456453289 and ISBN-13: 9781456453282) and an open access PDF file. digital copyright, digital library, digital preservation, digital repository, e-book, e-journal, license agreement, metadata, open access, digital publication, digital publication, scholarly, publishing is listed by: FORCE11 Creative Commons Attribution-NonCommercial License, v3 United States nlx_151306 SCR_005949 SciCrunch Registry 2026-10-24 12:45:35 0
Automated Image Registration
 
Resource Report
Resource Website
10+ mentions
Automated Image Registration (RRID:SCR_005944) AIR alignment software, data processing software, image analysis software, registration software, software application, software library, software resource, software toolkit A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs. registration, alignment is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
GNU General Public License nif-0000-00260 http://www.nitrc.org/projects/air SCR_005944 SciCrunch Registry 2026-10-24 12:45:35 29
Quantum Dot Corporation
 
Resource Report
Resource Website
Quantum Dot Corporation (RRID:SCR_005941) commercial organization THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\
\\\\\\
An Antibody supplier
THIS RESOURCE IS NO LONGER IN SERVICE nlx_152443 SCR_005941 SciCrunch Registry 2026-10-24 12:45:35 0
DiseaseMeth
 
Resource Report
Resource Website
10+ mentions
DiseaseMeth (RRID:SCR_005942) data or information resource, data repository, database, service resource, storage service resource Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools is listed by: 3DVC
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Harbin Medical University; Heilongjiang; China
National Natural Science Foundation of China ;
Natural Science Foundation of Heilongjiang Province ;
Scientific Research Fund of Heilongjiang Provincial Education Department ;
State Key Laboratory of Urban Water Resource and Environment
PMID:22135302
PMID:27899673
Free,Freely available OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth http://202.97.205.78/diseasemeth/ SCR_005942 SciCrunch Registry , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 2026-10-24 12:45:34 44
DistiLD - Diseases and Traits in LD
 
Resource Report
Resource Website
1+ mentions
DistiLD - Diseases and Traits in LD (RRID:SCR_005943) DistiLD analysis service resource, data analysis service, data or information resource, database, production service resource, service resource The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block. disease, mutation, gene, linkage disequilibrium, trait, genome-wide association study, single nucleotide polymorphism, chromosomal region, chromosome, linkage disequilibrium block, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: International HapMap Project
has parent organization: University of Copenhagen; Copenhagen; Denmark
Novo Nordisk Foundation Center for Protein Research PMID:22058129 Files are published under the Creative Commons Attribution v3 License biotools:distild, nlx_151291 https://bio.tools/distild SCR_005943 SciCrunch Registry DistiLD - Diseases & Traits in LD, Diseases and Traits In Linkage Disequilibrium blocks, Diseases and Traits In Linkage Disequilibrium, DistiLD Database, DistiLD - Diseases Traits in LD 2026-10-24 12:45:35 5
ProQuest Dissertation Publishing
 
Resource Report
Resource Website
ProQuest Dissertation Publishing (RRID:SCR_006075) ProQuest Dissertation Publishing service resource ProQuest Dissertation Publishing has been publishing dissertations and theses since 1938. In that time, we have published over 2 million graduate works from graduate schools around the world. We have over 700 active university publishing partners, and publish more than 70,000 new graduate works each year. In addition to publishing, we provide access to graduate works for thousands of libraries around the world. Based on your interests, you should find the information you need below: * Authors - Information for authors on why and how to publish their graduate work with us. * Grad Schools & Libraries - Learn about the benefits of publishing, and why to submit online. * Researchers - We can help you find the dissertation or thesis you need. dissertation, publishing, thesis, graduate, library, research, author is related to: ProQuest Dissertations and Theses Global
has parent organization: ProQuest
nlx_151558 SCR_006075 SciCrunch Registry 2026-10-24 12:45:37 0
PartiGene ARTHROPODA Database
 
Resource Report
Resource Website
1+ mentions
PartiGene ARTHROPODA Database (RRID:SCR_006071) ARTHROPODA PartiGene Databases data or information resource, database, organism-related portal, portal, topical portal As part of our effort in PhyloGenomics, we have developed the PartiGene ARTHROPODA Database. In these databases, we have analyzed the EST datasets for sixty different arthropod species. To aid searching we have split the interface between four class-based views: Chelicerata, Hexapoda, Crustacea, Myriapoda. Amongst other analyses, we have included Alfried Vogler's lab's PartiGene analysis of ~30 different arthropod species ESTs. A separate access point for that dataset is also available. expressed sequence tag, cluster, arthropod has parent organization: nematodes.org nlx_151477 SCR_006071 SciCrunch Registry 2026-10-24 12:45:36 1
Newtomics
 
Resource Report
Resource Website
1+ mentions
Newtomics (RRID:SCR_006073) Newt-Omics analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169 gene expression, regeneration, annotation, expression data, peptide sequence, gene sequence, tissue regeneration, newt, pathway, mammal, blast, contigs, peptide, tissue, microarray, heart, lens, dorsal, ventral, transcript, functional annotation, molecular process, model organism, expressed sequence tag, sequence, mass spectrometry, protein, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Max Planck Institute for Heart and Lung Research; Bad Nauheim; Germany
Hessian Ministry for Science and Art PMID:22039101 To be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the MPI for heart and lung research. nlx_151479, biotools:newt-omics https://bio.tools/newt-omics SCR_006073 SciCrunch Registry newt db, Newt database 2026-10-24 12:45:37 1
NEMBASE
 
Resource Report
Resource Website
10+ mentions
NEMBASE (RRID:SCR_006070) NEMBASE analysis service resource, data analysis service, data or information resource, database, production service resource, service resource NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: nematodes.org
Wellcome Trust ;
Hospital for Sick Children ;
BBSRC ;
MRC ;
NERC
PMID:21550347
PMID:14681449
Public nlx_151476, biotools:nembase4 https://bio.tools/nembase4 SCR_006070 SciCrunch Registry NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses 2026-10-24 12:45:37 25
W3C Provenance Working Group
 
Resource Report
Resource Website
W3C Provenance Working Group (RRID:SCR_005938) Provenance Working Group data or information resource, knowledge environment, narrative resource, standard specification Working group to support the widespread publication and use of provenance information of Web documents, data, and resources. The Working Group will publish W3C Recommendations that define a language for exchanging provenance information among applications. The Working Group is based on an extensive review and roadmap developed by a prior incubator group. Specifications: * PROV Primer * PROV Ontology * PROV Data Model * PROV Notation * PROV Constraints * PROV Access and Query web, exchange format, provenance, publication, working group is listed by: FORCE11
is related to: W3C Provenance Incubator Group Wiki
has parent organization: University of Southampton; Southampton; United Kingdom
has parent organization: VU University; Amsterdam; Netherlands
nlx_151285 SCR_005938 SciCrunch Registry 2026-10-24 12:45:35 0
Workflow4Ever
 
Resource Report
Resource Website
1+ mentions
Workflow4Ever (RRID:SCR_005939) Wf4Ever knowledge environment Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment. preservation, workflow, provenance, archive, research object, workflow model, management, experimental method is listed by: FORCE11
is related to: myExperiment
is related to: RightField
European Union nlx_151286 SCR_005939 SciCrunch Registry 2026-10-24 12:45:34 1
University of North Texas; Texas; USA
 
Resource Report
Resource Website
University of North Texas; Texas; USA (RRID:SCR_005935) UNT university Public research university in Denton, Texas. is related to: Alzheimers Disease Genetics Consortium grid.266869.5, nlx_157964, Wikidata:Q860527, ISNI:0000 0001 1008 957X, Crossref funder ID:100008973 https://ror.org/00v97ad02 SCR_005935 SciCrunch Registry University of North Texas 2026-10-24 12:45:35 0
ReproCELL Incorporated
 
Resource Report
Resource Website
ReproCELL Incorporated (RRID:SCR_005973) commercial organization An Antibody supplier nlx_152450 SCR_005973 SciCrunch Registry 2026-10-24 12:45:35 0

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