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  1. Article ; Online: Genomic potential for arsenic efflux and methylation varies among global Prochlorococcus populations.

    Saunders, Jaclyn K / Rocap, Gabrielle

    The ISME journal

    2016  Volume 10, Issue 1, Page(s) 197–209

    Abstract: The globally significant picocyanobacterium Prochlorococcus is the main primary producer in oligotrophic subtropical gyres. When phosphate concentrations are very low in the marine environment, the mol:mol availability of phosphate relative to the ... ...

    Abstract The globally significant picocyanobacterium Prochlorococcus is the main primary producer in oligotrophic subtropical gyres. When phosphate concentrations are very low in the marine environment, the mol:mol availability of phosphate relative to the chemically similar arsenate molecule is reduced, potentially resulting in increased cellular arsenic exposure. To mediate accidental arsenate uptake, some Prochlorococcus isolates contain genes encoding a full or partial efflux detoxification pathway, consisting of an arsenate reductase (arsC), an arsenite-specific efflux pump (acr3) and an arsenic-related repressive regulator (arsR). This efflux pathway was the only previously known arsenic detox pathway in Prochlorococcus. We have identified an additional putative arsenic mediation strategy in Prochlorococcus driven by the enzyme arsenite S-adenosylmethionine methyltransferase (ArsM) which can convert inorganic arsenic into more innocuous organic forms and appears to be a more widespread mode of detoxification. We used a phylogenetically informed approach to identify Prochlorococcus linked arsenic genes from both pathways in the Global Ocean Sampling survey. The putative arsenic methylation pathway is nearly ubiquitously present in global Prochlorococcus populations. In contrast, the complete efflux pathway is only maintained in populations which experience extremely low PO4:AsO4, such as regions in the tropical and subtropical Atlantic. Thus, environmental exposure to arsenic appears to select for maintenance of the efflux detoxification pathway in Prochlorococcus. The differential distribution of these two pathways has implications for global arsenic cycling, as their associated end products, arsenite or organoarsenicals, have differing biochemical activities and residence times.
    MeSH term(s) Arsenate Reductases/genetics ; Arsenate Reductases/metabolism ; Arsenates/metabolism ; Arsenic/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Genomics ; Methylation ; Phylogeny ; Prochlorococcus/classification ; Prochlorococcus/genetics ; Prochlorococcus/isolation & purification ; Prochlorococcus/metabolism
    Chemical Substances Arsenates ; Bacterial Proteins ; Arsenate Reductases (EC 1.20.-) ; Arsenic (N712M78A8G) ; arsenic acid (N7CIZ75ZPN)
    Language English
    Publishing date 2016-01
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2406536-5
    ISSN 1751-7370 ; 1751-7362
    ISSN (online) 1751-7370
    ISSN 1751-7362
    DOI 10.1038/ismej.2015.85
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones.

    Saunders, Jaclyn K / Fuchsman, Clara A / McKay, Cedar / Rocap, Gabrielle

    Proceedings of the National Academy of Sciences of the United States of America

    2019  Volume 116, Issue 20, Page(s) 9925–9930

    Abstract: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating ... ...

    Abstract Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene
    MeSH term(s) Anaerobiosis ; Aquatic Organisms/genetics ; Aquatic Organisms/metabolism ; Arsenic/metabolism ; Metagenome ; Oxidation-Reduction ; Pacific Ocean ; Water Microbiology
    Chemical Substances Arsenic (N712M78A8G)
    Language English
    Publishing date 2019-04-29
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1818349116
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cohort-based learning for microbiome research community standards.

    Kelliher, Julia M / Rudolph, Marisa / Vangay, Pajau / Abbas, Arwa / Borton, Mikayla A / Davenport, Emily R / Davenport, Karen W / Erazo, Natalia G / Herman, Chloe / Karstens, Lisa / Kocurek, Brandon / Lutz, Holly L / Myers, Kevin S / Ockert, Ingrid / Rodriguez, Francisca E / Santistevan, Camille / Saunders, Jaclyn K / Smith, Montana L / Vogtmann, Emily /
    Windsor, Amanda / Wood-Charlson, Elisha M / Woodley, Lou / Eloe-Fadrosh, Emiley A

    Nature microbiology

    2023  Volume 8, Issue 5, Page(s) 751–753

    MeSH term(s) Humans ; Microbiota ; Reference Standards
    Language English
    Publishing date 2023-04-18
    Publishing country England
    Document type Letter
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01361-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.

    Saunders, Jaclyn K / McIlvin, Matthew R / Dupont, Chris L / Kaul, Drishti / Moran, Dawn M / Horner, Tristan / Laperriere, Sarah M / Webb, Eric A / Bosak, Tanja / Santoro, Alyson E / Saito, Mak A

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 37, Page(s) e2200014119

    Abstract: Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central ... ...

    Abstract Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO
    MeSH term(s) Archaea/classification ; Archaea/enzymology ; Archaeal Proteins/analysis ; Bacteria/classification ; Bacteria/enzymology ; Bacterial Proteins/analysis ; Biodiversity ; Microbiota ; Nitrification ; Nitrite Reductases/metabolism ; Pacific Ocean ; Proteomics/methods ; Seawater/microbiology
    Chemical Substances Archaeal Proteins ; Bacterial Proteins ; Nitrite Reductases (EC 1.7.-)
    Language English
    Publishing date 2022-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2200014119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone.

    Fuchsman, Clara A / Devol, Allan H / Saunders, Jaclyn K / McKay, Cedar / Rocap, Gabrielle

    Frontiers in microbiology

    2017  Volume 8, Page(s) 2384

    Abstract: Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to ... ...

    Abstract Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N
    Language English
    Publishing date 2017-12-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2017.02384
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses.

    Saunders, Jaclyn K / Gaylord, David A / Held, Noelle A / Symmonds, Nicholas / Dupont, Christopher L / Shepherd, Adam / Kinkade, Danie B / Saito, Mak A

    Journal of proteome research

    2020  Volume 19, Issue 11, Page(s) 4718–4729

    Abstract: We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements ... ...

    Abstract We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing <1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.
    MeSH term(s) Aquatic Organisms/genetics ; Bacterial Proteins/classification ; Bacterial Proteins/genetics ; Betacoronavirus/genetics ; COVID-19 ; Cluster Analysis ; Coronavirus/genetics ; Coronavirus Infections/virology ; Humans ; Metagenomics/methods ; Molecular Sequence Annotation ; Pandemics ; Peptides/classification ; Peptides/genetics ; Pneumonia, Viral/virology ; Proteome/classification ; Proteome/genetics ; SARS-CoV-2 ; Sequence Analysis, Protein ; Software ; Transcriptome/genetics ; Viral Proteins/classification ; Viral Proteins/genetics
    Chemical Substances Bacterial Proteins ; Peptides ; Proteome ; Viral Proteins
    Keywords covid19
    Language English
    Publishing date 2020-09-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.0c00385
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Development of an Ocean Protein Portal for Interactive Discovery and Education.

    Saito, Mak A / Saunders, Jaclyn K / Chagnon, Michael / Gaylord, David A / Shepherd, Adam / Held, Noelle A / Dupont, Christopher / Symmonds, Nicholas / York, Amber / Charron, Matthew / Kinkade, Danie B

    Journal of proteome research

    2020  Volume 20, Issue 1, Page(s) 326–336

    Abstract: Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial ... ...

    Abstract Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: "Where is my protein of interest?", "Who makes it?", and "How much is there?" and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.
    MeSH term(s) Information Dissemination ; Oceans and Seas ; Proteomics
    Language English
    Publishing date 2020-12-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.0c00382
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean.

    Cohen, Natalie R / McIlvin, Matthew R / Moran, Dawn M / Held, Noelle A / Saunders, Jaclyn K / Hawco, Nicholas J / Brosnahan, Michael / DiTullio, Giacomo R / Lamborg, Carl / McCrow, John P / Dupont, Chris L / Allen, Andrew E / Saito, Mak A

    Nature microbiology

    2021  Volume 6, Issue 2, Page(s) 173–186

    Abstract: Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and ... ...

    Abstract Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
    MeSH term(s) Carbon Cycle ; Dinoflagellida/classification ; Dinoflagellida/metabolism ; Pacific Ocean ; Phylogeny ; Protozoan Proteins/metabolism ; Seawater/parasitology
    Chemical Substances Protozoan Proteins
    Language English
    Publishing date 2021-01-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-020-00814-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

    Saunders, Jaclyn K / Gaylord, David A / Held, Noelle A / Symmonds, Nicholas / Dupont, Christopher L / Shepherd, Adam / Kinkade, Danie B / Saito, Mak A

    J Proteome Res

    Abstract: We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements ... ...

    Abstract We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing <1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #748160
    Database COVID19

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  10. Book ; Online: Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison

    Saito, Mak A. / Saunders, Jaclyn K. / McIlvin, Matthew R. / Bertrand, Erin M. / Breier, John A. / Brisbin, Margaret Mars / Colston, Sophie M. / Compton, Jaimee R. / Griffin, Tim J. / Hervey, W. Judson / Hettich, Robert L. / Jagtap, Pratik D. / Janech, Michael / Johnson, Rod / Keil, Rick / Kleikamp, Hugo / Leary, Dagmar / Martens, Lennart / McCain, J. Scott P. /
    Moore, Eli / Mehta, Subina / Moran, Dawn M. / Neibauer, Jaqui / Neely, Benjamin A. / Jakuba, Michael V. / Johnson, Jim / Duffy, Megan / Herndl, Gerhard J. / Giannone, Richard / Mueller, Ryan / Nunn, Brook L. / Pabst, Martin / Peters, Samantha / Rajczewski, Andrew / Rowland, Elden / Searle, Brian / Bossche, Tim / Vora, Gary J. / Waldbauer, Jacob R. / Zheng, Haiyan / Zhao, Zihao

    eISSN:

    Effects of LC-MS Acquisition and Data Analysis Procedures

    2024  

    Abstract: Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory ... ...

    Abstract Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-Series Study in the North Atlantic Ocean collected by in situ pumps and the AUV Clio were distributed with a paired metagenome, and one-dimensional liquid chromatographic data dependent acquisition mass spectrometry analyses was stipulated. Analysis of mass spectra from seven laboratories through a common informatic pipeline identified a shared set of 1056 proteins from 1395 shared peptides constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values ranging from 0.43 to 0.83, and a Sørensen similarity analysis of the top 1,000 proteins revealed 70–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. An informatic intercomparison study, involving 10 laboratories using 8 software packages successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research including integration into global scale ocean surveys and ocean biogeochemical models.
    Subject code 551
    Language English
    Publishing date 2024-01-16
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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