Monthly Archives: December 2015

December 7, 2015

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Not many new microbiome papers, but a nice oversight of the microbiological quality of Rio de Janeiro’s Guanabara Bay, where the 2016 Olympics will be held.

Also, there was an interesting discussion online yesterday on IBM’s new campaign aimed to get more women interested to join them – which backfired and was pulled. IBM was trying to recruit more women with a video called “Hack a Hairdryer”, showing how you can use a hairdryer to iron your clothes or blow confetti. It was unclear how emphasizing feminine applications was supposed to attract smart women wanting to work at a computer company.

HackAHairDryer

Hack a hairdryer: Campaign aimed at women suddenly backfires – BBC

IBM Asks Women In Tech To Hack Hair Dryers, Women Tweet Back To Tell IBM It’s Not The 1950s – Sarah Buhr – Tech Crunch

Remember Massacred Women Engineers with a Hairdryer Hackathon – Mika McKinnon- Gizmodo

Jobs (posting again)

Two job openings in our lab / UCSF School of Dentistry (San Francisco) for our hyposalivation project: Full time study coordinator and Part time dental assistant (20 hours per week)

Animal microbiome

DGGE: Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks – M.T. Silva Neta – Genet. Mol. Res

Plants, roots, and soil microbiome

Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow – Yaoming Li – FEMS Microbiology Ecology

Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant-Parasitic Nematodes: A Review of the Mechanisms Involved – Nele Schouteden – Frontiers in Microbiology

Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks – Marie Uksa – Frontiers in Microbiology

Water microbiome

Environmental and Sanitary Conditions of Guanabara Bay, Rio de Janeiro – Giovana O. Fistarol – Frontiers in Microbiology

Microbes in the news

Metformin Users Have Different Gut Bugs: The popular type 2 diabetes drug may cause profound changes in patients’ microbiomes – Kerry Grens – The Scientist

Biologists Are Engineering Kill Switches for GM Microbes – Sarah Zhang – Wired

Bacteria containing mcr-1 gene resistant to all known antibiotics found in Denmark – News Australia

‘Bik’s Picks’ blogger describes features of a good microbiome study – Kristina Campbell in Gut microbiota

Microbiology and art

Paper Life – The artist Rogan Brown cuts thousands of microorganisms in paper – Ufunk

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December 5, 2015

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Two job openings in our lab / UCSF, parasitism in TM6, and colonization of a new island.

Jobs and Events

Two job openings in our lab / UCSF School of Dentistry (San Francisco) for our hyposalivation project: Full time study coordinator and Part time dental assistant (20 hours per week)

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11–12 April 2016, London, United Kingdom

General microbiome

The Hologenome Concept: Helpful or Hollow? – Nancy A. Moran , Daniel B. Sloan – PLOS Biology

Opinion: Cross-Kingdom Similarities in Microbiome Ecology and Biocontrol of Pathogens – Gabriele Berg – Frontiers in Microbiology

Review: Molecular Players Involved in the Interaction Between Beneficial Bacteria and the Immune System – Arancha Hevia – Frontiers in Microbiology

Commentary: Towards biome-specific analysis of meta-omics data – Youssef Darzi – ISME Journal

Human gut microbiome

Insights into the Role of Erysipelotrichaceae in the Human Host – Nadeem O. Kaakoush – Frontier sin Cellular and Infection Microbiology

Review: Interaction of Intestinal Microorganisms with the Human Host in the Framework of Autoimmune Diseases – Borja Sánchez – Frontiers in Immunology

Review: Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection – Ludovica F. Buttó – Frontiers in Immunology

Review: The role of gut microbiota and diet in experimental autoimmune encephalitis and multiple sclerosis – Tatsusada Okuno – Clinical and Experimental Neuroimmunology

Animal and bioreactor models

Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species – Maria Elisa Perez-Muñoz – PLOS ONE

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid – Sylvia H Duncan – Environmental Microbiology

Animal microbiome

Composition of the Spruce Budworm (Choristoneura fumiferana) Midgut Microbiota as Affected by Rearing Conditions – Mathieu Landry – PLOS ONE

Plant, root, and soil microbiome

Carbon-fixation rates and associated microbial communities residing in arid and ephemerally wet Antarctic Dry Valley soils – Thomas Niederberger – Frontiers in Microbiology

Forest wildfire and grassland prescribed fire effects on soil biogeochemical processes and microbial communities: Two case studies in the semi-arid Southwest – Lisa M. Fultz – Applied Soil Ecology

Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests – Tera E. Lewandowski – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Comparative genomics of candidate phylum TM6 suggests that parasitism is
widespread and ancestral in this lineage – Yun Kit Yeoh – Molecular Biology and Evolution

Carbon constrains fungal endophyte assemblages along the timberline – Teng Yang – Environmental Microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Water and extremophile microbiome

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake – Jason Nicholas Woodhouse – ISME Journal

Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions – Tianliang He – Marine Biotechnology

Air microbiome

PhD thesis: Microbial biodiversity of the atmosphere – Ann Maureen Klein – University of Oregon

Built environment microbiome

The biogeography of the Plastisphere: implications for policy – Linda A Amaral-Zettler – Frontiers in Ecology and the Environment

Colonization of new land by arbuscular mycorrhizal fungi – Knud Brian Nielsen – Fungal Ecology

Bioinformatics and metagenomics

COMMET: comparing and combining multiple metagenomic datasets – Nicolas Maillet – ArXiv

MetaScope – Fast and accurate identification of microbes in metagenomic sequencing data – Benjamin Buchfink – ArXiv

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Unit based on Homopolymer Compaction – Seunghyun Park – ACM Transactions on Computational Biology and Bioinformatics

Functional metagenomic selection of RubisCO from uncultivated bacteria – Vanessa A. Varaljay – Environmental Microbiology

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments – Yonghui Zeng – Environmental Microbiology Reports

Book Chapter: Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes – Ana Popovic – Prokaryotic Systems Biology

Microbes in the news

Superbug known as ‘phantom menace’ on the rise in U.S – Lena H. Sun – Washington Post

Petri dish Art: Holiday deer – Microbe World

The Blob, but smaller: Tasmania’s slime moulds – Ann Jones – ABC Australia
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December 4, 2015

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A short digest today. Microbiome of Cheyenne and Arapaho Oklahomans, and COPD. Have a great weekend!

Jobs

Full-time postdoctoral-level Chief Scientist – Azitra (Skin microbiome therapeutics startup)

Human respiratory microbiome

Not clear if just 16S rRNA gene-implied or real metagenomics: Functional Metagenomics of the Bronchial Microbiome in COPD – Laura Millares – PLOS ONE

Human gut microbiome

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma – Krithivasan Sankaranarayanan – Current Biology

Animal models of microbiome research

Prevention of Diet-Induced Obesity Effects on Body Weight and Gut Microbiota in Mice Treated Chronically with Δ9-Tetrahydrocannabinol – Nina L. Cluny – PLOS ONE

Microbes in the news

Who is in the operating room during c-section deliveries? – Anne M Estes – MicroBEnet

Toolkit for microbiota research – Science Codex

A radically simple idea might open the door to a new world of antibiotics – Carl Zimmer – STAT news

First look at gut microbes in an American Indian community – EurekAlert

Whether by Stealth or Aggression, Viruses Get to Make a Meal of it – Aswin Sai Narain Seshasayee – The Wire

Fluorescent-glowing bacteria help scientists see inside the body’s ‘dark places’ – Curt Woodward – Beta Boston

Shining light on microbial growth and death inside our guts – Wyss Institute

Artist Creates Beautiful Art Using Subway Bacteria – Gillian Mohney – ABC News

December 3, 2015

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Microbiomes of gallstones, soil along a bike trip, nematodes in cattle, kiddie pools, and 100 years of phage research.

Pregnancy and birth

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota – Gabriele Andrea Lugli – Environmental Microbiology

Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446 – Umberto Simeoni – Environmental Microbiology

Human skin microbiome

Alas no pictures: Microbial colonization of normal skin: direct visualization of 194 skin biopsies – Anika C. Jahns – Anaerobe

Human gut microbiome

Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery – S Mondot – Gut

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria – Hongzhang Shen – Scientific Reports

Improvement in Human Immune Function with Changes in Intestinal Microbiota by Salacia reticulata Extract Ingestion: A Randomized Placebo-Controlled Trial – Yuriko Oda – PLOS ONE

Establishing a Fecal Microbiota Transplant Service for the treatment of Clostridium difficile Infection – Samuel P. Costello – Clinical Infectious Diseases

Review: From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease –
Peter T. McKenney – Cell

Research Highlight: Can Your Microbiome Tell You What to Eat? – Jairam K.P. Vanamala – Cell Metabolism

Review: Nutrition in cancer patients with cachexia: a role for the gut microbiota? – Laure B. Bindels – Clinical Nutrition Experimental

Review: What’s bugging the gut in OCD? A review of the gut microbiome in obsessive-compulsive disorder – Jasmine Turna – Depression and Anxiety

Book Chapter: Bile Acids, the Microbiome and Metabolic Disease-Implications for Surgery – Cyrus Jahansouz – Metabolic Syndrome and Diabetes

Animal and bioreactor models

Gut Microbiota Orchestrates Energy Homeostasis during Cold – Claire Chevalier – Cell

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling – Maayan Levy – Cell

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota – Kaarel Adamberg – PLOS ONE

Animal microbiome

Cattle: Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities – Russell W. Avramenko – PLOS ONE

Seals: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event – Stephanie M. Rosales – PLOS ONE

Shrimp: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment – D. Sylvain Dabadé – International Journal of Food Microbiology

Plant, root, and soil microbiome

Science and art: Soil microbial communities along the route of a venturous cycling trip – Magdalena Nagler – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices – Fabio Battini – Microbiological Research

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem – Aaron S. David – Plant Microbe Interactions

The impact of charcoal and soil mixtures on decomposition and soil microbial communities in boreal forest – Nathalie Pluchon – Applied Soil Ecology

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants – Martha E. Trujillo – Frontiers in Microbiology

The microbiome and functions of black soils are altered by dibutyl phthalate contamination – Zhigang Wang – Applied Soil Ecology

Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil – D.R. Lammel – Brazilian Journal of Biology

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

Extremophile microbiome

Bacterial biogeography influenced by shelf–basin exchange in the Arctic surface sediment at the Chukchi Borderland – Dukki Han – Environmental Microbiology

Built environment microbiology

First microbiota assessments of children’s paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis – Toko Sawabe – Journal of Infection and Public Health

Summary of Sloan symposium: healthy buildings 2015-Europe – Hal Levin – Microbiome

Waste microbiology

Characterization of a microbial consortium that converts mariculture fish waste to biomethane – Brigit Quinn – Aquaculture

More microbiology

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus – Carey Lambert – Nature Communications

Phages and viruses

In retrospect: A century of phage lessons – Forest Rohwer & Anca M. Segall – Nature

Science, publishing, and career

Scientific Misconduct: Red Flags: Warning signs that scandal might be brewing in your lab – John R. Thomas Jr – The Scientist

Explaining Retractions: Editors and publishers should use a standardized form to detail why they are pulling papers from the scientific literature – Hervé Maisonneuve and Evelyne Decullier – The Scientist

Self Correction: What to do when you realize your publication is fatally flawed – Kerry Grens – The Scientist

Microbes in the news

Why It’s Time to Map the Microbiome (Kavli Roundtable) – Alan Brown, The Kavli Foundation – LiveScience

Scientists Argue Appendix Might Not Be ‘Irrelevant’ to Our Health, Propose This as the Organ’s Current Function – Liz Klimas – The Blaze

Immune cells make appendix ‘silent hero’ of digestive health – Walter and Eliza Hall Institute – EurekAlert

Bugs Against Disease: Could bacteria help fight colorectal cancer? A collaborative group of Tufts researchers hope to find out – Jacqueline Mitchell – Tufts Now

New research: Intestinal bacteria are affected by antidiabetic drugs – EurekAlert
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December 2, 2015

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General microbiome

Microbiology: Microbiome studies need local leaders – Victor S. Pylro – Nature

Human skin microbiome

Conclusions not strongly supported by data: Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial – Cristina Lopes – PLOS ONE

Human respiratory microbiome

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome – Robert A Quinn – The ISME Journal

Perspective: In the name of ventilator-associated pneumonia prevention: lung microbiota blown away by colistin! – Saad Nseir – European Respiratory Journal

Human gut microbiome

Better link than yesterday: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Kristoffer Forslund – Nature

Animal microbiome

Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions – Xiaoling Wan – Current Microbiology

Plant, root, and soil microbiome

Commentary: Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature

Better link than yesterday: Functional overlap of the Arabidopsis leaf and root microbiota – Yang Bai – Nature

Bioinformatics and metagenomics

A New Approach for Scalable Analysis of Microbial Communities – Ehsaneddin Asgari – ArXiv

Microbial ecology

Networks of energetic and metabolic interactions define dynamics in microbial communities – Mallory Embree

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria – João Barroso-Batista – Nature Communications

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils – Christina Kaiser – Nature Communications

Proteomics

Enhancing Metaproteomics – The value of models and defined environmental microbial systems – Florian-Alexander Herbst – Proteomics

Infection microbiology

Nature Supplement: Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings – Azra C. Ghani – Nature

Microbes in the news

Bacteriophage therapy: an alternative to antibiotics? An interview with Professor Martha Clokie – April Cashin-Garbutt – News Medical

Friends for Life: How Good Bugs Keep You Healthy (Op-Ed) – Jeremy Taylor – LiveScience

Science, publishing, and career

How to build a better PhD: There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved – Julie Gould – Nature

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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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