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2022
Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species
Journal of Hazardous Materials
2022
Response of soil protozoa to acid mine drainage in a contaminated terrace
Journal of Hazardous Materials
2021
Challenges in benchmarking metagenomic profilers
Nature Methods
2021
Endophytic Bacterial Communities in Apple Leaves Are Minimally Impacted by Streptomycin Use for Fire Blight Management
Phytobiomes Journal
2021
Dental calculus as a proxy for animal microbiomes
Quaternary International
2021
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
Nature Communications
2021
Nanopore sequencing and its application to the study of microbial communities
Computational and Structural Biotechnology Journal
2021
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil
Microbial Genomics
2021
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
Bioinformatics
2021
The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles
Genes
2021
Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants
Journal of Hazardous Materials
2021
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health
Nature Communications
2021
Metagenomics: a path to understanding the gut microbiome
Mammalian Genome
2021
Active DNRA and denitrification in oxic hypereutrophic waters
Water Research
2021
Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits
International Journal of Molecular Sciences
2021
Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS
Genes
2021
Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling
Microbiome
2021
Isolation and characterization of fast‐growing green snow bacteria from coastal East Antarctica
MicrobiologyOpen
2021
Identifying biases and their potential solutions in human microbiome studies
Microbiome
2021
Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data
Frontiers in Genetics
2021
Characterization of the Blood and Cerebrospinal Fluid Microbiome in Children with Bacterial Meningitis and Its Potential Correlation with Inflammation
mSystems
2021
Mapping the Terrain for Pathogen Persistence and Proliferation in Non-potable Reuse Distribution Systems: Interactive Effects of Biofiltration, Disinfection, and Water Age
Environmental Science & Technology
2021
Gulf of Mexico blue hole harbors high levels of novel microbial lineages
The ISME Journal
2021
Skin Microbiota and Clinical Associations in Netherton Syndrome
JID Innovations
2021
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank
Microbiome
2021
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut
mSystems
2021
Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Nature Protocols
2021
Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria
Pathogens
2021
Treatments of porcine fecal samples affect high-throughput virome sequencing results
Journal of Virological Methods
2021
Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum
Foods
2021
Microbiomes of commercially-available pine nuts and sesame seeds
PLOS ONE
2021
Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers
Journal of Experimental Medicine
2021
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Nature Communications
2021
Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management
Frontiers in Microbiology
2021
Colonization Dynamics of Multidrug-Resistant Klebsiella pneumoniae Are Dictated by Microbiota-Cluster Group Behavior over Individual Antibiotic Susceptibility: A Metataxonomic Analysis
Antibiotics
2021
Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility
Frontiers in Microbiology
2021
Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer
Communications Biology
2021
Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria
Microbiome
2021
Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces
Proceedings of the National Academy of Sciences
2021
A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing
Animal Microbiome
2021
Microbiome degrading linear alkylbenzene sulfonate in activated sludge
Journal of Hazardous Materials
2021
The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México
Journal of Fungi
2021
Characterization of the public transit air microbiome and resistome reveals geographical specificity
Microbiome
2021
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
Frontiers in Microbiology
2021
Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes
International Journal of Molecular Sciences
2021
Population structure and transmission of Mycobacterium bovis in Ethiopia
Microbial Genomics
2021
Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans
mSystems
2021
Disease-induced changes in plant microbiome assembly and functional adaptation
Microbiome
2021
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets
PeerJ
2021
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Bioinformatics
2021
A Statistical Perspective on the Challenges in Molecular Microbial Biology
Journal of Agricultural, Biological and Environmental Statistics
2021
Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
Proceedings of the National Academy of Sciences
2021
Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China
Current Microbiology
2021
Nickel complexation as an innovative approach for nickel-cobalt selective recovery using sulfate-reducing bacteria
Journal of Hazardous Materials
2021
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner
Nature Microbiology
2021
Metagenomic Geolocation Prediction Using an Adaptive Ensemble Classifier
Frontiers in Genetics
2021
A Fructo-Oligosaccharide Prebiotic Is Well Tolerated in Adults Undergoing Allogeneic Hematopoietic Stem Cell Transplantation: A Phase I Dose-Escalation Trial
Transplantation and Cellular Therapy
2021
Imported human norovirus in travelers, Shanghai port, China 2018: An epidemiological and whole genome sequencing study
Travel Medicine and Infectious Disease
2021
Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi)
PeerJ
2021
Metagenome-Wide Analysis of Rural and Urban Surface Waters and Sediments in Bangladesh Identifies Human Waste as a Driver of Antibiotic Resistance
mSystems
2021
TaxonKit: A practical and efficient NCBI taxonomy toolkit
Journal of Genetics and Genomics
2021
The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans
Current Biology
2021
Application of computational approaches to analyze metagenomic data
Journal of Microbiology
2021
Distribution patterns of antibiotic resistance genes and their bacterial hosts in pig farm wastewater treatment systems and soil fertilized with pig manure
Science of The Total Environment
2021
Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design
PLOS ONE
2021
Metataxonomic Profiling of Native and Starter Microbiota During Ripening of Gouda Cheese Made With Listeria monocytogenes-Contaminated Unpasteurized Milk
Frontiers in Microbiology
2021
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
eLife
2021
A unified catalog of 204,938 reference genomes from the human gut microbiome
Nature Biotechnology
2021
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
PeerJ
2021
Reduced metagenome sequencing for strain-resolution taxonomic profiles
Microbiome
2021
Elevated rates of horizontal gene transfer in the industrialized human microbiome
Cell
2021
Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Frontiers in Endocrinology
2021
HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data
Microbiome
2021
Metagenomics reveals contrasting energy utilization efficiencies of captive and wild camels ( Camelus ferus )
Integrative Zoology
2021
Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors
Scientific Reports
2021
Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence
Yeast
2021
Correlation of Salmonella enterica and Listeria monocytogenes in Irrigation Water to Environmental Factors, Fecal Indicators, and Bacterial Communities
Frontiers in Microbiology
2021
Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
npj Science of Food
2021
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
Bioinformatics
2021
High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics
Frontiers in Microbiology
2021
Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state
Cell Reports
2021
Identification of Reductive Dehalogenases That Mediate Complete Debromination of Penta- and Tetrabrominated Diphenyl Ethers in Dehalococcoides spp.
Applied and Environmental Microbiology
2021
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method
Folia Microbiologica
2021
Metagenomic Survey Reveals More Diverse and Abundant Antibiotic Resistance Genes in Municipal Wastewater Than Hospital Wastewater
Frontiers in Microbiology
2021
The gut microbiome in konzo
Nature Communications
2021
DNA traces the origin of honey by identifying plants, bacteria and fungi
Scientific Reports
2021
Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil
mBio
2021
Characterization of Bacterial Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic, Metatranscriptomic, and Culturing Techniques
Frontiers in Microbiology
2021
Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts
Frontiers in Microbiology
2021
High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient
Molecular Ecology
2021
Beware of pharyngeal Fusobacterium nucleatum in COVID-19
BMC Microbiology
2021
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts
Microbial Genomics
2021
Enhanced metal recovery by efficient agglomeration of precipitates in an up-flow fixed-bed bioreactor
Chemical Engineering Journal
2021
Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents
Pathogens
2021
Metabarcoding analysis of gut microbiota of healthy individuals reveals impact of probiotic and maltodextrin consumption
Beneficial Microbes
2021
Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
PLOS ONE
2020
Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce
Journal of Microbiological Methods
2020
Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
Scientific Reports
2020
Skin Microbiome in Cutaneous T-Cell Lymphoma by 16S and Whole-Genome Shotgun Sequencing
Journal of Investigative Dermatology
2020
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
Genome Medicine
2020
Dairy Products and Dairy-Processing Environments as a Reservoir of Antibiotic Resistance and Quorum-Quenching Determinants as Revealed through Functional Metagenomics
mSystems
2020
The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania
Environmental Microbiome
2020
Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome
mSphere
2020
Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples
Journal of Microbiological Methods
2020
Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts
iScience
2020
Prevalence of methanogens in the uncultured Sikkim hot spring solfataric mud archaeal microbiome
Environmental Sustainability
2020
LEMMI: a continuous benchmarking platform for metagenomics classifiers
Genome Research
2020
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
Microbiome
2020
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity
mSystems
2020
Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Frontiers in Microbiology
2020
Improving Oral Health and Modulating the Oral Microbiome to Reduce Bloodstream Infections from Oral Organisms in Pediatric and Young Adult Hematopoietic Stem Cell Transplantation Recipients: A Randomized Controlled Trial
Biology of Blood and Marrow Transplantation
2020
Difference in the rhizosphere microbiome of Melia azedarach during removal of benzo(a)pyrene from cadmium co-contaminated soil
Chemosphere
2020
Distinct microbiome composition and metabolome exists across subgroups of elite Irish athletes
Journal of Science and Medicine in Sport
2020
Meeting report of the third annual Tri-Service Microbiome Consortium symposium
Environmental Microbiome
2020
Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data
Biology Direct
2020
Colony-Level Effects of Amygdalin on Honeybees and Their Microbes
Insects
2020
Proximal colon–derived O-glycosylated mucus encapsulates and modulates the microbiota
Science
2020
Impact of narrow-spectrum penicillin V on the oral and faecal resistome in a young child treated for otitis media
Journal of Global Antimicrobial Resistance
2020
Big Data in metagenomics: Apache Spark vs MPI
PLOS ONE
2020
Syntrophy via Interspecies H 2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut
mBio
2020
A big data approach to metagenomics for all-food-sequencing
BMC Bioinformatics
2020
Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae
Experimental and Applied Acarology
2020
Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication
PeerJ
2020
Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae
Microorganisms
2020
The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
Molecular Ecology Resources
2020
Gut bacterial deamination of residual levodopa medication for Parkinson’s disease
BMC Biology
2020
Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study
Frontiers in Microbiology
2020
Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey
Environmental Microbiology Reports
2020
Metavirome and its functional diversity analysis through microbiome study of the Sikkim Himalayan hot spring solfataric mud sediments
Current Research in Microbial Sciences
2020
SHOGUN: a modular, accurate and scalable framework for microbiome quantification
Bioinformatics
2020
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
Nature Communications
2020
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
F1000Research
2020
Mutations in Mycobacterium tuberculosis Isolates with Discordant Results for Drug-Susceptibility Testing in Peru
International Journal of Microbiology
2020
Detection of Antimicrobial Resistance Genes in the Milk Production Environment: Impact of Host DNA and Sequencing Depth
Frontiers in Microbiology
2020
A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
PLOS ONE
2020
Microbiota composition data of imago and larval stage of the anhydrobiotic midge
Data in Brief
2020
IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
GigaScience
2020
Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation
Frontiers in Microbiology
2020
Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer
Frontiers in Cellular and Infection Microbiology
2020
The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome
Scientific Reports
2020
Developing standards for the microbiome field
Microbiome
2020
Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome
Annual Review of Biomedical Data Science
2020
Improved gastrointestinal health for irritable bowel syndrome with metagenome-guided interventions
Precision Clinical Medicine
2020
Sensitivity of shotgun metagenomics to host DNA: abundance estimates depend on bioinformatic tools and contamination is the main issue
Access Microbiology
2020
A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce
Food Microbiology
2020
Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
mSystems
2020
Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Pathogens
2020
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
BMC Biology
2020
Metalign: efficient alignment-based metagenomic profiling via containment min hash
Genome Biology
2020
Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage
PLOS ONE
2020
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
mSystems
2020
Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry
Science of The Total Environment
2020
RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis
PLOS ONE
2020
Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils
Journal of Hazardous Materials
2020
A Pilot Study of the Effect of Deployment on the Gut Microbiome and Traveler’s Diarrhea Susceptibility
Frontiers in Cellular and Infection Microbiology
2020
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics
Microorganisms
2020
The Nubeam reference-free approach to analyze metagenomic sequencing reads
Genome Research
2020
Oral microbiome-systemic link studies: perspectives on current limitations and future artificial intelligence-based approaches
Critical Reviews in Microbiology
2020
Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study
mSphere
2020
Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake
Limnology and Oceanography
2020
The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
mBio
2019
Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway
mBio
2019
Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition
Pathogens and Disease
2019
Benchmarking Metagenomics Tools for Taxonomic Classification
Cell
2019
Microbial abundance, activity and population genomic profiling with mOTUs2
Nature Communications
2019
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Genome Biology
2019
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications
2019
Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases
Microbiome
2019
Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics
mSystems
2019
The Rice Leaf Microbiome Has a Conserved Community Structure Controlled by Complex Host-Microbe Interactions
SSRN Electronic Journal
2019
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction
Methods
2019
Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation
EBioMedicine
2019
Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
BMC Bioinformatics
2019
Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome
Cell Metabolism
2019
Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study
Environment International
2019
Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Frontiers in Microbiology
2019
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
F1000Research
2019
Mycobacterium avium Complex Diversity within Lung Disease, as Revealed by Whole-Genome Sequencing
American Journal of Respiratory and Critical Care Medicine
2019
MSC: a metagenomic sequence classification algorithm
Bioinformatics
2019
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Nature
2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
Genome Biology
2019
The fecal resistome of dairy cattle is associated with diet during nursing
Nature Communications
2019
Improved metagenomic analysis with Kraken 2
Genome Biology
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2019
Ultrafast search of all deposited bacterial and viral genomic data
Nature Biotechnology
2019
The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity?
Systematic and Applied Microbiology
2018
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time
Genome Research
2018
Bone formation transcripts dominate the differential gene expression profile in an equine osteoporotic condition associated with pulmonary silicosis
PLOS ONE
2018
American Gut: an Open Platform for Citizen Science Microbiome Research
mSystems
2018
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Genome Biology
2018
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Microbiome
2017
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics
2017
Abundance estimation and differential testing on strain level in metagenomics data
Bioinformatics
2017
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Frontiers in Marine Science
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