2021
2323737
2RQKSFR5
2021
items
1
0
author
asc
1
1
135571
https://isbscience.org/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3A%22zotpress-7c15ebad3f0aaf2dba21dc3dfe4d72e3%22%2C%22meta%22%3A%7B%22request_last%22%3A100%2C%22request_next%22%3A50%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%227J9LFUG3%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Aguad%5Cu00e9-Gorgori%5Cu00f3%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EAguad%26%23xE9%3B-Gorgori%26%23xF3%3B%2C%20Guim%2C%20Stuart%20Kauffman%2C%20and%20Ricard%20Sol%26%23xE9%3B.%202021.%20%26%23x201C%3BTransition%20Therapy%3A%20Tackling%20the%20Ecology%20of%20Tumor%20Phenotypic%20Plasticity.%26%23x201D%3B%20%3Ci%3EBulletin%20of%20Mathematical%20Biology%3C%5C%2Fi%3E%2084%20%281%29%3A%2024.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs11538-021-00970-9%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs11538-021-00970-9%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D7J9LFUG3%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DB8GB2426%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Transition%20Therapy%3A%20Tackling%20the%20Ecology%20of%20Tumor%20Phenotypic%20Plasticity%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guim%22%2C%22lastName%22%3A%22Aguad%5Cu00e9-Gorgori%5Cu00f3%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stuart%22%2C%22lastName%22%3A%22Kauffman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ricard%22%2C%22lastName%22%3A%22Sol%5Cu00e9%22%7D%5D%2C%22abstractNote%22%3A%22Phenotypic%20switching%20in%20cancer%20cells%20has%20been%20found%20to%20be%20present%20across%20tumor%20types.%20Recent%20studies%20on%20Glioblastoma%20report%20a%20remarkably%20common%20architecture%20of%20four%20well-defined%20phenotypes%20coexisting%20within%20high%20levels%20of%20intra-tumor%20genetic%20heterogeneity.%20Similar%20dynamics%20have%20been%20shown%20to%20occur%20in%20breast%20cancer%20and%20melanoma%20and%20are%20likely%20to%20be%20found%20across%20cancer%20types.%20Given%20the%20adaptive%20potential%20of%20phenotypic%20switching%20%28PHS%29%20strategies%2C%20understanding%20how%20it%20drives%20tumor%20evolution%20and%20therapy%20resistance%20is%20a%20major%20priority.%20Here%20we%20present%20a%20mathematical%20framework%20uncovering%20the%20ecological%20dynamics%20behind%20PHS.%20The%20model%20is%20able%20to%20reproduce%20experimental%20results%2C%20and%20mathematical%20conditions%20for%20cancer%20progression%20reveal%20PHS-specific%20features%20of%20tumors%20with%20direct%20consequences%20on%20therapy%20resistance.%20In%20particular%2C%20our%20model%20reveals%20a%20threshold%20for%20the%20resistant-to-sensitive%20phenotype%20transition%20rate%2C%20below%20which%20any%20cytotoxic%20or%20switch-inhibition%20therapy%20is%20likely%20to%20fail.%20The%20model%20is%20able%20to%20capture%20therapeutic%20success%20thresholds%20for%20cancers%20where%20nonlinear%20growth%20dynamics%20or%20larger%20PHS%20architectures%20are%20in%20place%2C%20such%20as%20glioblastoma%20or%20melanoma.%20By%20doing%20so%2C%20the%20model%20presents%20a%20novel%20set%20of%20conditions%20for%20the%20success%20of%20combination%20therapies%20able%20to%20target%20replication%20and%20phenotypic%20transitions%20at%20once.%20Following%20our%20results%2C%20we%20discuss%20transition%20therapy%20as%20a%20novel%20scheme%20to%20target%20not%20only%20combined%20cytotoxicity%20but%20also%20the%20rates%20of%20phenotypic%20switching.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1007%5C%2Fs11538-021-00970-9%22%2C%22ISSN%22%3A%221522-9602%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222022-01-31T17%3A52%3A21Z%22%7D%7D%2C%7B%22key%22%3A%22BZL2W3PU%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Akbari%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EAkbari%2C%20Amir%2C%20James%20T.%20Yurkovich%2C%20Daniel%20C.%20Zielinski%2C%20and%20Bernhard%20O.%20Palsson.%202021.%20%26%23x201C%3BThe%20Quantitative%20Metabolome%20Is%20Shaped%20by%20Abiotic%20Constraints.%26%23x201D%3B%20%3Ci%3ENature%20Communications%3C%5C%2Fi%3E%2012%20%281%29%3A%203178.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-021-23214-9%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-021-23214-9%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DBZL2W3PU%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DN2PT5HZ6%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22The%20quantitative%20metabolome%20is%20shaped%20by%20abiotic%20constraints%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amir%22%2C%22lastName%22%3A%22Akbari%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20T.%22%2C%22lastName%22%3A%22Yurkovich%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%20C.%22%2C%22lastName%22%3A%22Zielinski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bernhard%20O.%22%2C%22lastName%22%3A%22Palsson%22%7D%5D%2C%22abstractNote%22%3A%22Living%20systems%20formed%20and%20evolved%20under%20constraints%20that%20govern%20their%20interactions%20with%20the%20inorganic%20world.%20These%20interactions%20are%20definable%20using%20basic%20physico-chemical%20principles.%20Here%2C%20we%20formulate%20a%20comprehensive%20set%20of%20ten%20governing%20abiotic%20constraints%20that%20define%20possible%20quantitative%20metabolomes.%20We%20apply%20these%20constraints%20to%20a%20metabolic%20network%20of%20Escherichia%20coli%20that%20represents%2090%25%20of%20its%20metabolome.%20We%20show%20that%20the%20quantitative%20metabolomes%20allowed%20by%20the%20abiotic%20constraints%20are%20consistent%20with%20metabolomic%20and%20isotope-labeling%20data.%20We%20find%20that%3A%20%28i%29%20abiotic%20constraints%20drive%20the%20evolution%20of%20high-affinity%20phosphate%20transporters%3B%20%28ii%29%20Charge-%2C%20hydrogen-%20and%20magnesium-related%20constraints%20underlie%20transcriptional%20regulatory%20responses%20to%20osmotic%20stress%3B%20and%20%28iii%29%20hydrogen-ion%20and%20charge%20imbalance%20underlie%20transcriptional%20regulatory%20responses%20to%20acid%20stress.%20Thus%2C%20quantifying%20the%20constraints%20that%20the%20inorganic%20world%20imposes%20on%20living%20systems%20provides%20insights%20into%20their%20key%20characteristics%2C%20helps%20understand%20the%20outcomes%20of%20evolutionary%20adaptation%2C%20and%20should%20be%20considered%20as%20a%20fundamental%20part%20of%20theoretical%20biology%20and%20for%20understanding%20the%20constraints%20on%20evolution.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41467-021-23214-9%22%2C%22ISSN%22%3A%222041-1723%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A16%3A30Z%22%7D%7D%2C%7B%22key%22%3A%22YJEJLJ8L%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Arrieta-Ortiz%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EArrieta-Ortiz%2C%20Mario%20L.%2C%20Selva%20Rupa%20Christinal%20Immanuel%2C%20Serdar%20Turkarslan%2C%20Wei-Ju%20Wu%2C%20Brintha%20P.%20Girinathan%2C%20Jay%20N.%20Worley%2C%20Nicholas%20DiBenedetto%2C%20et%20al.%202021.%20%26%23x201C%3BPredictive%20Regulatory%20and%20Metabolic%20Network%20Models%20for%20Systems%20Analysis%20of%20Clostridioides%20Difficile.%26%23x201D%3B%20%3Ci%3ECell%20Host%20%26amp%3B%20Microbe%3C%5C%2Fi%3E%2C%20S1931-3128%2821%2900424-8.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.chom.2021.09.008%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.chom.2021.09.008%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DYJEJLJ8L%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Predictive%20regulatory%20and%20metabolic%20network%20models%20for%20systems%20analysis%20of%20Clostridioides%20difficile%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mario%20L.%22%2C%22lastName%22%3A%22Arrieta-Ortiz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Selva%20Rupa%20Christinal%22%2C%22lastName%22%3A%22Immanuel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Serdar%22%2C%22lastName%22%3A%22Turkarslan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wei-Ju%22%2C%22lastName%22%3A%22Wu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brintha%20P.%22%2C%22lastName%22%3A%22Girinathan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jay%20N.%22%2C%22lastName%22%3A%22Worley%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicholas%22%2C%22lastName%22%3A%22DiBenedetto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olga%22%2C%22lastName%22%3A%22Soutourina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Johann%22%2C%22lastName%22%3A%22Peltier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Dupuy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lynn%22%2C%22lastName%22%3A%22Bry%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nitin%20S.%22%2C%22lastName%22%3A%22Baliga%22%7D%5D%2C%22abstractNote%22%3A%22We%20present%20predictive%20models%20for%20comprehensive%20systems%20analysis%20of%20Clostridioides%20difficile%2C%20the%20etiology%20of%20pseudomembranous%20colitis.%20By%20leveraging%20151%20published%20transcriptomes%2C%20we%20generated%20an%20EGRIN%20model%20that%20organizes%2090%25%20of%20C.%5Cu00a0difficile%20genes%20into%20a%20transcriptional%20regulatory%20network%20of%20297%20co-regulated%20modules%2C%20implicating%20genes%20in%20sporulation%2C%20carbohydrate%20transport%2C%20and%20metabolism.%20By%20advancing%20a%20metabolic%20model%20through%20addition%20and%20curation%20of%20metabolic%20reactions%20including%20nutrient%20uptake%2C%20we%20discovered%2014%20amino%20acids%2C%20diverse%20carbohydrates%2C%20and%2010%20metabolic%20genes%20as%20essential%20for%20C.%5Cu00a0difficile%20growth%20in%20the%20intestinal%20environment.%20Finally%2C%20we%20developed%20a%20PRIME%20model%20to%20uncover%20how%20EGRIN-inferred%20combinatorial%20gene%20regulation%20by%20transcription%20factors%2C%20such%20as%20CcpA%20and%20CodY%2C%20modulates%20essential%20metabolic%20processes%20to%20enable%20C.%5Cu00a0difficile%20growth%20relative%20to%20commensal%20colonization.%20The%20C.%5Cu00a0difficile%20interactive%20web%20portal%20provides%20access%20to%20these%20model%20resources%20to%20support%20collaborative%20systems-level%20studies%20of%20context-specific%20virulence%20mechanisms%20in%20C.%5Cu00a0difficile.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.chom.2021.09.008%22%2C%22ISSN%22%3A%221934-6069%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A34%3A24Z%22%7D%7D%2C%7B%22key%22%3A%22UDQGD7YP%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Azer%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EAzer%2C%20Karim%2C%20Chanchala%20D.%20Kaddi%2C%20Jeffrey%20S.%20Barrett%2C%20Jane%20P.%20F.%20Bai%2C%20Sean%20T.%20McQuade%2C%20Nathaniel%20J.%20Merrill%2C%20Benedetto%20Piccoli%2C%20et%20al.%202021.%20%26%23x201C%3BHistory%20and%20Future%20Perspectives%20on%20the%20Discipline%20of%20Quantitative%20Systems%20Pharmacology%20Modeling%20and%20Its%20Applications.%26%23x201D%3B%20%3Ci%3EFrontiers%20in%20Physiology%3C%5C%2Fi%3E%2012%3A637999.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffphys.2021.637999%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffphys.2021.637999%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DUDQGD7YP%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DRK6HN7VC%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22History%20and%20Future%20Perspectives%20on%20the%20Discipline%20of%20Quantitative%20Systems%20Pharmacology%20Modeling%20and%20Its%20Applications%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karim%22%2C%22lastName%22%3A%22Azer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chanchala%20D.%22%2C%22lastName%22%3A%22Kaddi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffrey%20S.%22%2C%22lastName%22%3A%22Barrett%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jane%20P.%20F.%22%2C%22lastName%22%3A%22Bai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20T.%22%2C%22lastName%22%3A%22McQuade%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nathaniel%20J.%22%2C%22lastName%22%3A%22Merrill%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benedetto%22%2C%22lastName%22%3A%22Piccoli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Susana%22%2C%22lastName%22%3A%22Neves-Zaph%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luca%22%2C%22lastName%22%3A%22Marchetti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rosario%22%2C%22lastName%22%3A%22Lombardo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Silvia%22%2C%22lastName%22%3A%22Parolo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Selva%20Rupa%20Christinal%22%2C%22lastName%22%3A%22Immanuel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nitin%20S.%22%2C%22lastName%22%3A%22Baliga%22%7D%5D%2C%22abstractNote%22%3A%22Mathematical%20biology%20and%20pharmacology%20models%20have%20a%20long%20and%20rich%20history%20in%20the%20fields%20of%20medicine%20and%20physiology%2C%20impacting%20our%20understanding%20of%20disease%20mechanisms%20and%20the%20development%20of%20novel%20therapeutics.%20With%20an%20increased%20focus%20on%20the%20pharmacology%20application%20of%20system%20models%20and%20the%20advances%20in%20data%20science%20spanning%20mechanistic%20and%20empirical%20approaches%2C%20there%20is%20a%20significant%20opportunity%20and%20promise%20to%20leverage%20these%20advancements%20to%20enhance%20the%20development%20and%20application%20of%20the%20systems%20pharmacology%20field.%20In%20this%20paper%2C%20we%20will%20review%20milestones%20in%20the%20evolution%20of%20mathematical%20biology%20and%20pharmacology%20models%2C%20highlight%20some%20of%20the%20gaps%20and%20challenges%20in%20developing%20and%20applying%20systems%20pharmacology%20models%2C%20and%20provide%20a%20vision%20for%20an%20integrated%20strategy%20that%20leverages%20advances%20in%20adjacent%20fields%20to%20overcome%20these%20challenges.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3389%5C%2Ffphys.2021.637999%22%2C%22ISSN%22%3A%221664-042X%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A09%3A17Z%22%7D%7D%2C%7B%22key%22%3A%229PW8QSXE%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Baloni%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBaloni%2C%20Priyanka%2C%20Wikum%20Dinalankara%2C%20John%20C.%20Earls%2C%20Theo%20A.%20Knijnenburg%2C%20Donald%20Geman%2C%20Luigi%20Marchionni%2C%20and%20Nathan%20D.%20Price.%202021.%20%26%23x201C%3BIdentifying%20Personalized%20Metabolic%20Signatures%20in%20Breast%20Cancer.%26%23x201D%3B%20%3Ci%3EMetabolites%3C%5C%2Fi%3E%2011%20%281%29%3A%2020.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fmetabo11010020%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fmetabo11010020%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D9PW8QSXE%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DR8ENE9M7%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Identifying%20Personalized%20Metabolic%20Signatures%20in%20Breast%20Cancer%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Priyanka%22%2C%22lastName%22%3A%22Baloni%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wikum%22%2C%22lastName%22%3A%22Dinalankara%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%20C.%22%2C%22lastName%22%3A%22Earls%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Theo%20A.%22%2C%22lastName%22%3A%22Knijnenburg%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Donald%22%2C%22lastName%22%3A%22Geman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luigi%22%2C%22lastName%22%3A%22Marchionni%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nathan%20D.%22%2C%22lastName%22%3A%22Price%22%7D%5D%2C%22abstractNote%22%3A%22Cancer%20cells%20are%20adept%20at%20reprogramming%20energy%20metabolism%2C%20and%20the%20precise%20manifestation%20of%20this%20metabolic%20reprogramming%20exhibits%20heterogeneity%20across%20individuals%20%28and%20from%20cell%20to%20cell%29.%20In%20this%20study%2C%20we%20analyzed%20the%20metabolic%20differences%20between%20interpersonal%20heterogeneous%20cancer%20phenotypes.%20We%20used%20divergence%20analysis%20on%20gene%20expression%20data%20of%201156%20breast%20normal%20and%20tumor%20samples%20from%20The%20Cancer%20Genome%20Atlas%20%28TCGA%29%20and%20integrated%20this%20information%20with%20a%20genome-scale%20reconstruction%20of%20human%20metabolism%20to%20generate%20personalized%2C%20context-specific%20metabolic%20networks.%20Using%20this%20approach%2C%20we%20classified%20the%20samples%20into%20four%20distinct%20groups%20based%20on%20their%20metabolic%20profiles.%20Enrichment%20analysis%20of%20the%20subsystems%20indicated%20that%20amino%20acid%20metabolism%2C%20fatty%20acid%20oxidation%2C%20citric%20acid%20cycle%2C%20androgen%20and%20estrogen%20metabolism%2C%20and%20reactive%20oxygen%20species%20%28ROS%29%20detoxification%20distinguished%20these%20four%20groups.%20Additionally%2C%20we%20developed%20a%20workflow%20to%20identify%20potential%20drugs%20that%20can%20selectively%20target%20genes%20associated%20with%20the%20reactions%20of%20interest.%20MG-132%20%28a%20proteasome%20inhibitor%29%20and%20OSU-03012%20%28a%20celecoxib%20derivative%29%20were%20the%20top-ranking%20drugs%20identified%20from%20our%20analysis%20and%20known%20to%20have%20anti-tumor%20activity.%20Our%20approach%20has%20the%20potential%20to%20provide%20mechanistic%20insights%20into%20cancer-specific%20metabolic%20dependencies%2C%20ultimately%20enabling%20the%20identification%20of%20potential%20drug%20targets%20for%20each%20patient%20independently%2C%20contributing%20to%20a%20rational%20personalized%20medicine%20approach.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.3390%5C%2Fmetabo11010020%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.mdpi.com%5C%2F2218-1989%5C%2F11%5C%2F1%5C%2F20%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-01-04T18%3A58%3A58Z%22%7D%7D%2C%7B%22key%22%3A%22FBLXGXUD%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Baloni%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBaloni%2C%20Priyanka%2C%20Cory%20C.%20Funk%2C%20Ben%20Readhead%2C%20and%20Nathan%20D.%20Price.%202021.%20%26%23x201C%3BSystems%20Modeling%20of%20Metabolic%20Dysregulation%20in%20Neurodegenerative%20Diseases.%26%23x201D%3B%20%3Ci%3ECurrent%20Opinion%20in%20Pharmacology%3C%5C%2Fi%3E%2060%3A59%26%23x2013%3B65.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.coph.2021.06.012%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.coph.2021.06.012%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DFBLXGXUD%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Systems%20modeling%20of%20metabolic%20dysregulation%20in%20neurodegenerative%20diseases%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Priyanka%22%2C%22lastName%22%3A%22Baloni%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Cory%20C.%22%2C%22lastName%22%3A%22Funk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ben%22%2C%22lastName%22%3A%22Readhead%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nathan%20D.%22%2C%22lastName%22%3A%22Price%22%7D%5D%2C%22abstractNote%22%3A%22Neurodegenerative%20diseases%20%28NDDs%29%20encompass%20a%20wide%20range%20of%20conditions%20that%20arise%20owing%20to%20progressive%20degeneration%20and%20the%20ultimate%20loss%20of%20nerve%20cells%20in%20the%20brain%20and%20peripheral%20nervous%20system.%20NDDs%20such%20as%20Alzheimer%27s%2C%20Parkinson%27s%2C%20and%20Huntington%27s%20diseases%20negatively%20impact%20both%20length%20and%20quality%20of%20life%2C%20due%20to%20lack%20of%20effective%20disease-modifying%20treatments.%20Herein%2C%20we%20review%20the%20use%20of%20genome-scale%20metabolic%20models%2C%20network-based%20approaches%2C%20and%20integration%20with%20multiomics%20data%20to%20identify%20key%20biological%20processes%20that%20characterize%20NDDs.%20We%20describe%20powerful%20systems%20biology%20approaches%20for%20modeling%20NDD%20pathophysiology%20by%20leveraging%20in%20silico%20models%20that%20are%20informed%20by%20patient-derived%20multiomics%20data.%20These%20approaches%20can%20enable%20mechanistic%20insights%20into%20NDD-specific%20metabolic%20dysregulations%20that%20can%20be%20leveraged%20to%20identify%20potential%20metabolic%20markers%20of%20disease%20and%20predisease%20states.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.coph.2021.06.012%22%2C%22ISSN%22%3A%221471-4973%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A31%3A09Z%22%7D%7D%2C%7B%22key%22%3A%22663GSPVT%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Bandeira%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBandeira%2C%20Nuno%2C%20Eric%20W.%20Deutsch%2C%20Oliver%20Kohlbacher%2C%20Lennart%20Martens%2C%20and%20Juan%20Antonio%20Vizca%26%23xED%3Bno.%202021.%20%26%23x201C%3BData%20Management%20of%20Sensitive%20Human%20Proteomics%20Data%3A%20Current%20Practices%2C%20Recommendations%2C%20and%20Perspectives%20for%20the%20Future.%26%23x201D%3B%20%3Ci%3EMolecular%20%26amp%3B%20Cellular%20Proteomics%3A%20MCP%3C%5C%2Fi%3E%2020%3A100071.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.mcpro.2021.100071%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.mcpro.2021.100071%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D663GSPVT%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DVX3EPR2S%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Data%20Management%20of%20Sensitive%20Human%20Proteomics%20Data%3A%20Current%20Practices%2C%20Recommendations%2C%20and%20Perspectives%20for%20the%20Future%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nuno%22%2C%22lastName%22%3A%22Bandeira%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%20W.%22%2C%22lastName%22%3A%22Deutsch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Oliver%22%2C%22lastName%22%3A%22Kohlbacher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lennart%22%2C%22lastName%22%3A%22Martens%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Juan%20Antonio%22%2C%22lastName%22%3A%22Vizca%5Cu00edno%22%7D%5D%2C%22abstractNote%22%3A%22Today%20it%20is%20the%20norm%20that%20all%20relevant%20proteomics%20data%20that%20support%20the%20conclusions%20in%20scientific%20publications%20are%20made%20available%20in%20public%20proteomics%20data%20repositories.%20However%2C%20given%20the%20increase%20in%20the%20number%20of%20clinical%20proteomics%20studies%2C%20an%20important%20emerging%20topic%20is%20the%20management%20and%20dissemination%20of%20clinical%2C%20and%20thus%20potentially%20sensitive%2C%20human%20proteomics%20data.%20Both%20in%20the%20United%20States%20and%20in%20the%20European%20Union%2C%20there%20are%20legal%20frameworks%20protecting%20the%20privacy%20of%20individuals.%20Implementing%20privacy%20standards%20for%20publicly%20released%20research%20data%20in%20genomics%20and%20transcriptomics%20has%20led%20to%20processes%20to%20control%20who%20may%20access%20the%20data%2C%20so-called%20%5C%22controlled%20access%5C%22%20data.%20In%20parallel%20with%20the%20technological%20developments%20in%20the%20field%2C%20it%20is%20clear%20that%20the%20privacy%20risks%20of%20sharing%20proteomics%20data%20need%20to%20be%20properly%20assessed%20and%20managed.%20In%20our%20view%2C%20the%20proteomics%20community%20must%20be%20proactive%20in%20addressing%20these%20issues.%20Yet%20a%20careful%20balance%20must%20be%20kept.%20On%20the%20one%20hand%2C%20neglecting%20to%20address%20the%20potential%20of%20identifiability%20in%20human%20proteomics%20data%20could%20lead%20to%20reputational%20damage%20of%20the%20field%2C%20while%20on%20the%20other%20hand%2C%20erecting%20barriers%20to%20open%20access%20to%20clinical%20proteomics%20data%20will%20inevitably%20reduce%20reuse%20of%20proteomics%20data%20and%20could%20substantially%20delay%20critical%20discoveries%20in%20biomedical%20research.%20In%20order%20to%20balance%20these%20apparently%20conflicting%20requirements%20for%20data%20privacy%20and%20efficient%20use%20and%20reuse%20of%20research%20efforts%20through%20the%20sharing%20of%20clinical%20proteomics%20data%2C%20development%20efforts%20will%20be%20needed%20at%20different%20levels%20including%20bioinformatics%20infrastructure%2C%20policymaking%2C%20and%20mechanisms%20of%20oversight.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.mcpro.2021.100071%22%2C%22ISSN%22%3A%221535-9484%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A18%3A15Z%22%7D%7D%2C%7B%22key%22%3A%22YVPZ9CEG%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Banerjee%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBanerjee%2C%20Ushashi%2C%20Priyanka%20Baloni%2C%20Amit%20Singh%2C%20and%20Nagasuma%20Chandra.%202021.%20%26%23x201C%3BImmune%20Subtyping%20in%20Latent%20Tuberculosis.%26%23x201D%3B%20%3Ci%3EFrontiers%20in%20Immunology%3C%5C%2Fi%3E%2012.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffimmu.2021.595746%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffimmu.2021.595746%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DYVPZ9CEG%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DLR33Y83H%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Immune%20Subtyping%20in%20Latent%20Tuberculosis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ushashi%22%2C%22lastName%22%3A%22Banerjee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Priyanka%22%2C%22lastName%22%3A%22Baloni%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amit%22%2C%22lastName%22%3A%22Singh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nagasuma%22%2C%22lastName%22%3A%22Chandra%22%7D%5D%2C%22abstractNote%22%3A%22Latent%20tuberculosis%20infection%20%28LTBI%29%20poses%20a%20major%20roadblock%20in%20the%20global%20effort%20to%20eradicate%20tuberculosis%20%28TB%29.%20A%20deep%20understanding%20of%20the%20host%20responses%20involved%20in%20establishment%20and%20maintenance%20of%20TB%20latency%20is%20required%20to%20propel%20the%20development%20of%20sensitive%20methods%20to%20detect%20and%20treat%20LTBI.%20Given%20that%20LTBI%20individuals%20are%20typically%20asymptomatic%2C%20it%20is%20challenging%20to%20differentiate%20latently%20infected%20from%20uninfected%20individuals.%20A%20major%20contributor%20to%20this%20problem%20is%20that%20no%20clear%20pattern%20of%20host%20response%20is%20linked%20with%20LTBI%2C%20as%20molecular%20correlates%20of%20latent%20infection%20have%20been%20hard%20to%20identify.%20In%20this%20study%2C%20we%20have%20analysed%20the%20global%20perturbations%20in%20host%20response%20in%20LTBI%20individuals%20as%20compared%20to%20uninfected%20individuals%20and%20particularly%20the%20heterogeneity%20in%20such%20response%2C%20across%20LTBI%20cohorts.%20For%20this%2C%20we%20constructed%20individualized%20genome-wide%20host%20response%20networks%20informed%20by%20blood%20transcriptomes%20for%20136%20LTBI%20cases%20and%20have%20used%20a%20sensitive%20network%20mining%20algorithm%20to%20identify%20top-ranked%20host%20response%20subnetworks%20in%20each%20case.%20Our%20analysis%20indicates%20that%20despite%20the%20high%20heterogeneity%20in%20the%20gene%20expression%20profiles%20among%20LTBI%20samples%2C%20clear%20patterns%20of%20perturbation%20are%20found%20in%20the%20immune%20response%20pathways%2C%20leading%20to%20grouping%20LTBI%20samples%20into%204%20different%20immune-subtypes.%20Our%20results%20suggest%20that%20different%20subnetworks%20of%20molecular%20perturbations%20are%20associated%20with%20latent%20tuberculosis.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22English%22%2C%22DOI%22%3A%2210.3389%5C%2Ffimmu.2021.595746%22%2C%22ISSN%22%3A%221664-3224%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.frontiersin.org%5C%2Farticles%5C%2F10.3389%5C%2Ffimmu.2021.595746%5C%2Ffull%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A01%3A11Z%22%7D%7D%2C%7B%22key%22%3A%22TH5DV4RT%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Bastard%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBastard%2C%20Paul%2C%20Adrian%20Gervais%2C%20Tom%20Le%20Voyer%2C%20J%26%23xE9%3Br%26%23xE9%3Bmie%20Rosain%2C%20Quentin%20Philippot%2C%20J%26%23xE9%3Br%26%23xE9%3Bmy%20Manry%2C%20Eleftherios%20Michailidis%2C%20et%20al.%202021.%20%26%23x201C%3BAutoantibodies%20Neutralizing%20Type%20I%20IFNs%20Are%20Present%20in%20~4%25%20of%20Uninfected%20Individuals%20over%2070%20Years%20Old%20and%20Account%20for%20~20%25%20of%20COVID-19%20Deaths.%26%23x201D%3B%20%3Ci%3EScience%20Immunology%3C%5C%2Fi%3E%206%20%2862%29%3A%20eabl4340.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1126%5C%2Fsciimmunol.abl4340%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1126%5C%2Fsciimmunol.abl4340%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DTH5DV4RT%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3D4I2TLDU6%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Autoantibodies%20neutralizing%20type%20I%20IFNs%20are%20present%20in%20~4%25%20of%20uninfected%20individuals%20over%2070%20years%20old%20and%20account%20for%20~20%25%20of%20COVID-19%20deaths%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Paul%22%2C%22lastName%22%3A%22Bastard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adrian%22%2C%22lastName%22%3A%22Gervais%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tom%22%2C%22lastName%22%3A%22Le%20Voyer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J%5Cu00e9r%5Cu00e9mie%22%2C%22lastName%22%3A%22Rosain%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Quentin%22%2C%22lastName%22%3A%22Philippot%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J%5Cu00e9r%5Cu00e9my%22%2C%22lastName%22%3A%22Manry%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eleftherios%22%2C%22lastName%22%3A%22Michailidis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hans-Heinrich%22%2C%22lastName%22%3A%22Hoffmann%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shohei%22%2C%22lastName%22%3A%22Eto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marina%22%2C%22lastName%22%3A%22Garcia-Prat%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lucy%22%2C%22lastName%22%3A%22Bizien%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alba%22%2C%22lastName%22%3A%22Parra-Mart%5Cu00ednez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rui%22%2C%22lastName%22%3A%22Yang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Liis%22%2C%22lastName%22%3A%22Haljasm%5Cu00e4gi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22M%5Cu00e9lanie%22%2C%22lastName%22%3A%22Migaud%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karita%22%2C%22lastName%22%3A%22S%5Cu00e4rekannu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julia%22%2C%22lastName%22%3A%22Maslovskaja%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22de%20Prost%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yacine%22%2C%22lastName%22%3A%22Tandjaoui-Lambiotte%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles-Edouard%22%2C%22lastName%22%3A%22Luyt%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Blanca%22%2C%22lastName%22%3A%22Amador-Borrero%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexandre%22%2C%22lastName%22%3A%22Gaudet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julien%22%2C%22lastName%22%3A%22Poissy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pascal%22%2C%22lastName%22%3A%22Morel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pascale%22%2C%22lastName%22%3A%22Richard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabrice%22%2C%22lastName%22%3A%22Cognasse%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jesus%22%2C%22lastName%22%3A%22Troya%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Trouillet-Assant%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexandre%22%2C%22lastName%22%3A%22Belot%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kahina%22%2C%22lastName%22%3A%22Saker%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre%22%2C%22lastName%22%3A%22Gar%5Cu00e7on%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jacques%20G.%22%2C%22lastName%22%3A%22Rivi%5Cu00e8re%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jean-Christophe%22%2C%22lastName%22%3A%22Lagier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22St%5Cu00e9phanie%22%2C%22lastName%22%3A%22Gentile%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lindsey%20B.%22%2C%22lastName%22%3A%22Rosen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elana%22%2C%22lastName%22%3A%22Shaw%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tomohiro%22%2C%22lastName%22%3A%22Morio%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Junko%22%2C%22lastName%22%3A%22Tanaka%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Dalmau%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre-Louis%22%2C%22lastName%22%3A%22Tharaux%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Damien%22%2C%22lastName%22%3A%22Sene%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alain%22%2C%22lastName%22%3A%22Stepanian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Megarbane%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vasiliki%22%2C%22lastName%22%3A%22Triantafyllia%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Arnaud%22%2C%22lastName%22%3A%22Fekkar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20R.%22%2C%22lastName%22%3A%22Heath%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jos%5Cu00e9%20Luis%22%2C%22lastName%22%3A%22Franco%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Juan-Manuel%22%2C%22lastName%22%3A%22Anaya%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jordi%22%2C%22lastName%22%3A%22Sol%5Cu00e9-Viol%5Cu00e1n%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luisa%22%2C%22lastName%22%3A%22Imberti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrea%22%2C%22lastName%22%3A%22Biondi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Paolo%22%2C%22lastName%22%3A%22Bonfanti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Riccardo%22%2C%22lastName%22%3A%22Castagnoli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ottavia%20M.%22%2C%22lastName%22%3A%22Delmonte%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yu%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20L.%22%2C%22lastName%22%3A%22Snow%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Steven%20M.%22%2C%22lastName%22%3A%22Holland%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Catherine%22%2C%22lastName%22%3A%22Biggs%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marcela%22%2C%22lastName%22%3A%22Moncada-V%5Cu00e9lez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9s%20Augusto%22%2C%22lastName%22%3A%22Arias%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lazaro%22%2C%22lastName%22%3A%22Lorenzo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Soraya%22%2C%22lastName%22%3A%22Boucherit%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Boubacar%22%2C%22lastName%22%3A%22Coulibaly%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dany%22%2C%22lastName%22%3A%22Anglicheau%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anna%20M.%22%2C%22lastName%22%3A%22Planas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Filomeen%22%2C%22lastName%22%3A%22Haerynck%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sotirija%22%2C%22lastName%22%3A%22Duvlis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%20L.%22%2C%22lastName%22%3A%22Nussbaum%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tayfun%22%2C%22lastName%22%3A%22Ozcelik%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sevgi%22%2C%22lastName%22%3A%22Keles%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ahmed%20A.%22%2C%22lastName%22%3A%22Bousfiha%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jalila%22%2C%22lastName%22%3A%22El%20Bakkouri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carolina%22%2C%22lastName%22%3A%22Ramirez-Santana%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22St%5Cu00e9phane%22%2C%22lastName%22%3A%22Paul%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Qiang%22%2C%22lastName%22%3A%22Pan-Hammarstr%5Cu00f6m%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lennart%22%2C%22lastName%22%3A%22Hammarstr%5Cu00f6m%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Annabelle%22%2C%22lastName%22%3A%22Dupont%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alina%22%2C%22lastName%22%3A%22Kurolap%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christine%20N.%22%2C%22lastName%22%3A%22Metz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alessandro%22%2C%22lastName%22%3A%22Aiuti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Giorgio%22%2C%22lastName%22%3A%22Casari%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vito%22%2C%22lastName%22%3A%22Lampasona%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabio%22%2C%22lastName%22%3A%22Ciceri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lucila%20A.%22%2C%22lastName%22%3A%22Barreiros%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elena%22%2C%22lastName%22%3A%22Dominguez-Garrido%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mateus%22%2C%22lastName%22%3A%22Vidigal%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mayana%22%2C%22lastName%22%3A%22Zatz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Diederik%22%2C%22lastName%22%3A%22van%20de%20Beek%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sabina%22%2C%22lastName%22%3A%22Sahanic%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ivan%22%2C%22lastName%22%3A%22Tancevski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yurii%22%2C%22lastName%22%3A%22Stepanovskyy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Oksana%22%2C%22lastName%22%3A%22Boyarchuk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yoko%22%2C%22lastName%22%3A%22Nukui%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Miyuki%22%2C%22lastName%22%3A%22Tsumura%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Loreto%22%2C%22lastName%22%3A%22Vidaur%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stuart%20G.%22%2C%22lastName%22%3A%22Tangye%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sonia%22%2C%22lastName%22%3A%22Burrel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Darragh%22%2C%22lastName%22%3A%22Duffy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lluis%22%2C%22lastName%22%3A%22Quintana-Murci%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adam%22%2C%22lastName%22%3A%22Klocperk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nelli%20Y.%22%2C%22lastName%22%3A%22Kann%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anna%22%2C%22lastName%22%3A%22Shcherbina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yu-Lung%22%2C%22lastName%22%3A%22Lau%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%22%2C%22lastName%22%3A%22Leung%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthieu%22%2C%22lastName%22%3A%22Coulongeat%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julien%22%2C%22lastName%22%3A%22Marlet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rutger%22%2C%22lastName%22%3A%22Koning%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luis%20Felipe%22%2C%22lastName%22%3A%22Reyes%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ang%5Cu00e9lique%22%2C%22lastName%22%3A%22Chauvineau-Grenier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabienne%22%2C%22lastName%22%3A%22Venet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guillaume%22%2C%22lastName%22%3A%22Monneret%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michel%20C.%22%2C%22lastName%22%3A%22Nussenzweig%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Romain%22%2C%22lastName%22%3A%22Arrestier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Idris%22%2C%22lastName%22%3A%22Boudhabhay%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hagit%22%2C%22lastName%22%3A%22Baris-Feldman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Hagin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Joost%22%2C%22lastName%22%3A%22Wauters%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Isabelle%22%2C%22lastName%22%3A%22Meyts%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adam%20H.%22%2C%22lastName%22%3A%22Dyer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20P.%22%2C%22lastName%22%3A%22Kennelly%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nollaig%20M.%22%2C%22lastName%22%3A%22Bourke%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rabih%22%2C%22lastName%22%3A%22Halwani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Narjes%20Saheb%22%2C%22lastName%22%3A%22Sharif-Askari%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karim%22%2C%22lastName%22%3A%22Dorgham%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J%5Cu00e9rome%22%2C%22lastName%22%3A%22Sallette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Souad%20Mehlal%22%2C%22lastName%22%3A%22Sedkaoui%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Suzan%22%2C%22lastName%22%3A%22AlKhater%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ra%5Cu00fal%22%2C%22lastName%22%3A%22Rigo-Bonnin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Francisco%22%2C%22lastName%22%3A%22Morandeira%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lucie%22%2C%22lastName%22%3A%22Roussel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Donald%20C.%22%2C%22lastName%22%3A%22Vinh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sisse%20Rye%22%2C%22lastName%22%3A%22Ostrowski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Antonio%22%2C%22lastName%22%3A%22Condino-Neto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carolina%22%2C%22lastName%22%3A%22Prando%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anastasiia%22%2C%22lastName%22%3A%22Bonradenko%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e1s%20N.%22%2C%22lastName%22%3A%22Spaan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laurent%22%2C%22lastName%22%3A%22Gilardin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jacques%22%2C%22lastName%22%3A%22Fellay%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stanislas%22%2C%22lastName%22%3A%22Lyonnet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kaya%22%2C%22lastName%22%3A%22Bilguvar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Richard%20P.%22%2C%22lastName%22%3A%22Lifton%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shrikant%22%2C%22lastName%22%3A%22Mane%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22HGID%20Lab%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22COVID%20Clinicians%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22COVID-STORM%20Clinicians%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22NIAID%20Immune%20Response%20to%20COVID%20Group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22NH-COVAIR%20Study%20Group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Danish%20CHGE%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Danish%20Blood%20Donor%20Study%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22St.%20James%27s%20Hospital%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22SARS%20CoV2%20Interest%20group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22French%20COVID%20Cohort%20Study%20Group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Imagine%20COVID-Group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Milieu%20Int%5Cu00e9rieur%20Consortium%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22CoV-Contact%20Cohort%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Amsterdam%20UMC%20Covid-19%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Biobank%20Investigators%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22COVID%20Human%20Genetic%20Effort%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22CONSTANCES%20cohort%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%223C-Dijon%20Study%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Cerba%20Health-Care%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22name%22%3A%22Etablissement%20du%20Sang%20study%20group%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mark%20S.%22%2C%22lastName%22%3A%22Anderson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bertrand%22%2C%22lastName%22%3A%22Boisson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vivien%22%2C%22lastName%22%3A%22B%5Cu00e9ziat%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shen-Ying%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Evangelos%22%2C%22lastName%22%3A%22Vandreakos%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olivier%22%2C%22lastName%22%3A%22Hermine%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Aurora%22%2C%22lastName%22%3A%22Pujol%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22P%5Cu00e4rt%22%2C%22lastName%22%3A%22Peterson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Trine%20H.%22%2C%22lastName%22%3A%22Mogensen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lee%22%2C%22lastName%22%3A%22Rowen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%22%2C%22lastName%22%3A%22Mond%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22St%5Cu00e9phanie%22%2C%22lastName%22%3A%22Debette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22de%20Lamballerie%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Duval%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22France%22%2C%22lastName%22%3A%22Mentr%5Cu00e9%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marie%22%2C%22lastName%22%3A%22Zins%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pere%22%2C%22lastName%22%3A%22Soler-Palacin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Roger%22%2C%22lastName%22%3A%22Colobran%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guy%22%2C%22lastName%22%3A%22Gorochov%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Solanich%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Susen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Javier%22%2C%22lastName%22%3A%22Martinez-Picado%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Didier%22%2C%22lastName%22%3A%22Raoult%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Vasse%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Peter%20K.%22%2C%22lastName%22%3A%22Gregersen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lorenzo%22%2C%22lastName%22%3A%22Piemonti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlos%22%2C%22lastName%22%3A%22Rodr%5Cu00edguez-Gallego%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luigi%20D.%22%2C%22lastName%22%3A%22Notarangelo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Helen%20C.%22%2C%22lastName%22%3A%22Su%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kai%22%2C%22lastName%22%3A%22Kisand%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Satoshi%22%2C%22lastName%22%3A%22Okada%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anne%22%2C%22lastName%22%3A%22Puel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Emmanuelle%22%2C%22lastName%22%3A%22Jouanguy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles%20M.%22%2C%22lastName%22%3A%22Rice%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre%22%2C%22lastName%22%3A%22Tiberghien%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Qian%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Aur%5Cu00e9lie%22%2C%22lastName%22%3A%22Cobat%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laurent%22%2C%22lastName%22%3A%22Abel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jean-Laurent%22%2C%22lastName%22%3A%22Casanova%22%7D%5D%2C%22abstractNote%22%3A%22Circulating%20autoantibodies%20%28auto-Abs%29%20neutralizing%20high%20concentrations%20%2810%20ng%5C%2FmL%2C%20in%20plasma%20diluted%201%20to%2010%29%20of%20IFN-%5Cu03b1%20and%5C%2For%20-%5Cu03c9%20are%20found%20in%20about%2010%25%20of%20patients%20with%20critical%20COVID-19%20pneumonia%2C%20but%20not%20in%20subjects%20with%20asymptomatic%20infections.%20We%20detect%20auto-Abs%20neutralizing%20100-fold%20lower%2C%20more%20physiological%2C%20concentrations%20of%20IFN-%5Cu03b1%20and%5C%2For%20-%5Cu03c9%20%28100%20pg%5C%2FmL%2C%20in%201%5C%2F10%20dilutions%20of%20plasma%29%20in%2013.6%25%20of%203%2C595%20patients%20with%20critical%20COVID-19%2C%20including%2021%25%20of%20374%20patients%20%3E%2080%20years%2C%20and%206.5%25%20of%20522%20patients%20with%20severe%20COVID-19.%20These%20antibodies%20are%20also%20detected%20in%2018%25%20of%20the%201%2C124%20deceased%20patients%20%28aged%2020%20days-99%20years%3B%20mean%3A%2070%20years%29.%20Moreover%2C%20another%201.3%25%20of%20patients%20with%20critical%20COVID-19%20and%200.9%25%20of%20the%20deceased%20patients%20have%20auto-Abs%20neutralizing%20high%20concentrations%20of%20IFN-%5Cu03b2.%20We%20also%20show%2C%20in%20a%20sample%20of%2034%2C159%20uninfected%20subjects%20from%20the%20general%20population%2C%20that%20auto-Abs%20neutralizing%20high%20concentrations%20of%20IFN-%5Cu03b1%20and%5C%2For%20-%5Cu03c9%20are%20present%20in%200.18%25%20of%20individuals%20between%2018%20and%2069%20years%2C%201.1%25%20between%2070%20and%2079%20years%2C%20and%203.4%25%20%3E80%20years.%20Moreover%2C%20the%20proportion%20of%20subjects%20carrying%20auto-Abs%20neutralizing%20lower%20concentrations%20is%20greater%20in%20a%20subsample%20of%2010%2C778%20uninfected%20individuals%3A%201%25%20of%20individuals%20%3C70%20years%2C%202.3%25%20between%2070%20and%2080%20years%2C%20and%206.3%25%20%3E80%20years.%20By%20contrast%2C%20auto-Abs%20neutralizing%20IFN-%5Cu03b2%20do%20not%20become%20more%20frequent%20with%20age.%20Auto-Abs%20neutralizing%20type%20I%20IFNs%20predate%20SARS-CoV-2%20infection%20and%20sharply%20increase%20in%20prevalence%20after%20the%20age%20of%2070%20years.%20They%20account%20for%20about%2020%25%20of%20both%20critical%20COVID-19%20cases%20in%20the%20over-80s%2C%20and%20total%20fatal%20COVID-19%20cases.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1126%5C%2Fsciimmunol.abl4340%22%2C%22ISSN%22%3A%222470-9468%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A33%3A18Z%22%7D%7D%2C%7B%22key%22%3A%22IBM9K8NR%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Bobe%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBobe%2C%20Jason%20R.%2C%20Brandon%20L.%20Jutras%2C%20Elizabeth%20J.%20Horn%2C%20Monica%20E.%20Embers%2C%20Allison%20Bailey%2C%20Robert%20L.%20Moritz%2C%20Ying%20Zhang%2C%20et%20al.%202021.%20%26%23x201C%3BRecent%20Progress%20in%20Lyme%20Disease%20and%20Remaining%20Challenges.%26%23x201D%3B%20%3Ci%3EFrontiers%20in%20Medicine%3C%5C%2Fi%3E%208%3A666554.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffmed.2021.666554%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffmed.2021.666554%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DIBM9K8NR%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DHIWAEW6C%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Recent%20Progress%20in%20Lyme%20Disease%20and%20Remaining%20Challenges%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jason%20R.%22%2C%22lastName%22%3A%22Bobe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brandon%20L.%22%2C%22lastName%22%3A%22Jutras%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elizabeth%20J.%22%2C%22lastName%22%3A%22Horn%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Monica%20E.%22%2C%22lastName%22%3A%22Embers%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Allison%22%2C%22lastName%22%3A%22Bailey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%20L.%22%2C%22lastName%22%3A%22Moritz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ying%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mark%20J.%22%2C%22lastName%22%3A%22Soloski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Richard%20S.%22%2C%22lastName%22%3A%22Ostfeld%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Richard%20T.%22%2C%22lastName%22%3A%22Marconi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%22%2C%22lastName%22%3A%22Aucott%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Avi%22%2C%22lastName%22%3A%22Ma%27ayan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Felicia%22%2C%22lastName%22%3A%22Keesing%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kim%22%2C%22lastName%22%3A%22Lewis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Choukri%22%2C%22lastName%22%3A%22Ben%20Mamoun%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alison%20W.%22%2C%22lastName%22%3A%22Rebman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mecaila%20E.%22%2C%22lastName%22%3A%22McClune%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Edward%20B.%22%2C%22lastName%22%3A%22Breitschwerdt%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Panga%20Jaipal%22%2C%22lastName%22%3A%22Reddy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ricardo%22%2C%22lastName%22%3A%22Maggi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Frank%22%2C%22lastName%22%3A%22Yang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bennett%22%2C%22lastName%22%3A%22Nemser%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Aydogan%22%2C%22lastName%22%3A%22Ozcan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Omai%22%2C%22lastName%22%3A%22Garner%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dino%22%2C%22lastName%22%3A%22Di%20Carlo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zachary%22%2C%22lastName%22%3A%22Ballard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hyou-Arm%22%2C%22lastName%22%3A%22Joung%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Albert%22%2C%22lastName%22%3A%22Garcia-Romeu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Roland%20R.%22%2C%22lastName%22%3A%22Griffiths%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicole%22%2C%22lastName%22%3A%22Baumgarth%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brian%20A.%22%2C%22lastName%22%3A%22Fallon%22%7D%5D%2C%22abstractNote%22%3A%22Lyme%20disease%20%28also%20known%20as%20Lyme%20borreliosis%29%20is%20the%20most%20common%20vector-borne%20disease%20in%20the%20United%20States%20with%20an%20estimated%20476%2C000%20cases%20per%20year.%20While%20historically%2C%20the%20long-term%20impact%20of%20Lyme%20disease%20on%20patients%20has%20been%20controversial%2C%20mounting%20evidence%20supports%20the%20idea%20that%20a%20substantial%20number%20of%20patients%20experience%20persistent%20symptoms%20following%20treatment.%20The%20research%20community%20has%20largely%20lacked%20the%20necessary%20funding%20to%20properly%20advance%20the%20scientific%20and%20clinical%20understanding%20of%20the%20disease%2C%20or%20to%20develop%20and%20evaluate%20innovative%20approaches%20for%20prevention%2C%20diagnosis%2C%20and%20treatment.%20Given%20the%20many%20outstanding%20questions%20raised%20into%20the%20diagnosis%2C%20clinical%20presentation%20and%20treatment%20of%20Lyme%20disease%2C%20and%20the%20underlying%20molecular%20mechanisms%20that%20trigger%20persistent%20disease%2C%20there%20is%20an%20urgent%20need%20for%20more%20support.%20This%20review%20article%20summarizes%20progress%20over%20the%20past%205%20years%20in%20our%20understanding%20of%20Lyme%20and%20tick-borne%20diseases%20in%20the%20United%20States%20and%20highlights%20remaining%20challenges.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3389%5C%2Ffmed.2021.666554%22%2C%22ISSN%22%3A%222296-858X%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T19%3A18%3A08Z%22%7D%7D%2C%7B%22key%22%3A%22NHEPRX4Q%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Brand%20and%20Ranish%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EBrand%2C%20Marjorie%2C%20and%20Jeffrey%20A.%20Ranish.%202021.%20%26%23x201C%3BProteomic%5C%2FTranscriptomic%20Analysis%20of%20Erythropoiesis.%26%23x201D%3B%20%3Ci%3ECurrent%20Opinion%20in%20Hematology%3C%5C%2Fi%3E%2028%20%283%29%3A%20150%26%23x2013%3B57.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1097%5C%2FMOH.0000000000000647%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1097%5C%2FMOH.0000000000000647%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DNHEPRX4Q%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Proteomic%5C%2Ftranscriptomic%20analysis%20of%20erythropoiesis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marjorie%22%2C%22lastName%22%3A%22Brand%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffrey%20A.%22%2C%22lastName%22%3A%22Ranish%22%7D%5D%2C%22abstractNote%22%3A%22PURPOSE%20OF%20REVIEW%3A%20Erythropoiesis%20is%20a%20hierarchical%20process%20by%20which%20hematopoietic%20stem%20cells%20give%20rise%20to%20red%20blood%20cells%20through%20gradual%20cell%20fate%20restriction%20and%20maturation.%20Deciphering%20this%20process%20requires%20the%20establishment%20of%20dynamic%20gene%20regulatory%20networks%20%28GRNs%29%20that%20predict%20the%20response%20of%20hematopoietic%20cells%20to%20signals%20from%20the%20environment.%20Although%20GRNs%20have%20historically%20been%20derived%20from%20transcriptomic%20data%2C%20recent%20proteomic%20studies%20have%20revealed%20a%20major%20role%20for%20posttranscriptional%20mechanisms%20in%20regulating%20gene%20expression%20during%20erythropoiesis.%20These%20new%20findings%20highlight%20the%20need%20to%20integrate%20proteomic%20data%20into%20GRNs%20for%20a%20refined%20understanding%20of%20erythropoiesis.%5CnRECENT%20FINDINGS%3A%20Here%2C%20we%20review%20recent%20proteomic%20studies%20that%20have%20furthered%20our%20understanding%20of%20erythropoiesis%20with%20a%20focus%20on%20quantitative%20mass%20spectrometry%20approaches%20to%20measure%20the%20abundance%20of%20transcription%20factors%20and%20cofactors%20during%20differentiation.%20Furthermore%2C%20we%20highlight%20challenges%20that%20remain%20in%20integrating%20transcriptomic%2C%20proteomic%2C%20and%20other%20omics%20data%20into%20a%20predictive%20model%20of%20erythropoiesis%2C%20and%20discuss%20the%20future%20prospect%20of%20single-cell%20proteomics.%5CnSUMMARY%3A%20Recent%20proteomic%20studies%20have%20considerably%20expanded%20our%20knowledge%20of%20erythropoiesis%20beyond%20the%20traditional%20transcriptomic-centric%20perspective.%20These%20findings%20have%20both%20opened%20up%20new%20avenues%20of%20research%20to%20increase%20our%20understanding%20of%20erythroid%20differentiation%2C%20while%20at%20the%20same%20time%20presenting%20new%20challenges%20in%20integrating%20multiple%20layers%20of%20information%20into%20a%20comprehensive%20gene%20regulatory%20model.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1097%5C%2FMOH.0000000000000647%22%2C%22ISSN%22%3A%221531-7048%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A17%3A10Z%22%7D%7D%2C%7B%22key%22%3A%22JPXUSGH8%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Cheng%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ECheng%2C%20Hanjun%2C%20Zhonghan%20Li%2C%20Zhili%20Guo%2C%20Shiqun%20Shao%2C%20Li%20Mo%2C%20Wei%20Wei%2C%20and%20Min%20Xue.%202021.%20%26%23x201C%3BSingle-Cell%20Profiling%20of%20D-2-Hydroxyglutarate%20Using%20Surface-Immobilized%20Resazurin%20Analogs.%26%23x201D%3B%20%3Ci%3EBiosensors%20%26amp%3B%20Bioelectronics%3C%5C%2Fi%3E%20190%3A113368.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.bios.2021.113368%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.bios.2021.113368%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DJPXUSGH8%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Single-cell%20profiling%20of%20D-2-hydroxyglutarate%20using%20surface-immobilized%20resazurin%20analogs%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hanjun%22%2C%22lastName%22%3A%22Cheng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhonghan%22%2C%22lastName%22%3A%22Li%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhili%22%2C%22lastName%22%3A%22Guo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shiqun%22%2C%22lastName%22%3A%22Shao%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Li%22%2C%22lastName%22%3A%22Mo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wei%22%2C%22lastName%22%3A%22Wei%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Min%22%2C%22lastName%22%3A%22Xue%22%7D%5D%2C%22abstractNote%22%3A%22D-2-hydroxyglutarate%20%28D2HG%29%20is%20over-produced%20as%20an%20oncometabolite%20due%20to%20mutations%20in%20isocitrate%20dehydrogenases%20%28IDHs%29.%20Accumulation%20of%20D2HG%20can%20cause%20the%20dysfunction%20of%20many%20enzymes%20and%20genome-wide%20epigenetic%20alterations%2C%20which%20can%20promote%20oncogenesis.%20Quantification%20of%20D2HG%20at%20single-cell%20resolution%20can%20help%20understand%20the%20phenotypic%20signatures%20of%20IDH-mutant%20cancers%20and%20identify%20effective%20therapeutics.%20In%20this%20study%2C%20we%20developed%20an%20analytical%20method%20to%20detect%20D2HG%20levels%20in%20single%20cancer%20cells%20by%20adapting%20cascade%20enzymatic%20reactions%20on%20a%20resazurin-based%20fluorescence%20reporter.%20The%20resazurin%20probe%20was%20immobilized%20to%20the%20sensing%20surface%20via%20biotin-streptavidin%20interaction.%20This%20surface%20chemistry%20was%20rationally%20optimized%20to%20translate%20the%20D2HG%20levels%20to%20sensitive%20fluorescence%20readouts%20efficiently.%20This%20D2HG%20assay%20demonstrated%20good%20selectivity%20and%20high%20sensitivity%20toward%20D2HG%2C%20and%20it%20was%20compatible%20with%20the%20previously%20developed%20single-cell%20barcode%20chip%20%28SCBC%29%20technology.%20Using%20the%20SCBC%20platform%2C%20we%20performed%20simultaneous%20single-cell%20profiling%20of%20D2HG%2C%20glucose%20uptake%2C%20and%20critical%20oncogenic%20signaling%20proteins%20in%20single%20IDH-mutant%20glioma%20cells.%20The%20results%20unveiled%20the%20complex%20interplays%20between%20metabolic%20and%20oncogenic%20signaling%20and%20led%20to%20the%20identification%20of%20effective%20combination%20targeted%20therapy%20against%20these%20IDH-mutant%20glioma%20cells.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.bios.2021.113368%22%2C%22ISSN%22%3A%221873-4235%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A29%3A52Z%22%7D%7D%2C%7B%22key%22%3A%227HA5WAH8%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Cobb%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ECobb%2C%20David%20W.%2C%20Heather%20M.%20Kudyba%2C%20Alejandra%20Villegas%2C%20Michael%20R.%20Hoopmann%2C%20Rodrigo%20P.%20Baptista%2C%20Baylee%20Bruton%2C%20Michelle%20Krakowiak%2C%20Robert%20L.%20Moritz%2C%20and%20Vasant%20Muralidharan.%202021.%20%26%23x201C%3BA%20Redox-Active%20Crosslinker%20Reveals%20an%20Essential%20and%20Inhibitable%20Oxidative%20Folding%20Network%20in%20the%20Endoplasmic%20Reticulum%20of%20Malaria%20Parasites.%26%23x201D%3B%20%3Ci%3EPLoS%20Pathogens%3C%5C%2Fi%3E%2017%20%282%29%3A%20e1009293.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.ppat.1009293%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.ppat.1009293%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D7HA5WAH8%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DXDZZ9H7K%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20redox-active%20crosslinker%20reveals%20an%20essential%20and%20inhibitable%20oxidative%20folding%20network%20in%20the%20endoplasmic%20reticulum%20of%20malaria%20parasites%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%20W.%22%2C%22lastName%22%3A%22Cobb%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Heather%20M.%22%2C%22lastName%22%3A%22Kudyba%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alejandra%22%2C%22lastName%22%3A%22Villegas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michael%20R.%22%2C%22lastName%22%3A%22Hoopmann%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rodrigo%20P.%22%2C%22lastName%22%3A%22Baptista%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Baylee%22%2C%22lastName%22%3A%22Bruton%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michelle%22%2C%22lastName%22%3A%22Krakowiak%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%20L.%22%2C%22lastName%22%3A%22Moritz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vasant%22%2C%22lastName%22%3A%22Muralidharan%22%7D%5D%2C%22abstractNote%22%3A%22Malaria%20remains%20a%20major%20global%20health%20problem%2C%20creating%20a%20constant%20need%20for%20research%20to%20identify%20druggable%20weaknesses%20in%20P.%20falciparum%20biology.%20As%20important%20components%20of%20cellular%20redox%20biology%2C%20members%20of%20the%20Thioredoxin%20%28Trx%29%20superfamily%20of%20proteins%20have%20received%20interest%20as%20potential%20drug%20targets%20in%20Apicomplexans.%20However%2C%20the%20function%20and%20essentiality%20of%20endoplasmic%20reticulum%20%28ER%29-localized%20Trx-domain%20proteins%20within%20P.%20falciparum%20has%20not%20been%20investigated.%20We%20generated%20conditional%20mutants%20of%20the%20protein%20PfJ2-an%20ER%20chaperone%20and%20member%20of%20the%20Trx%20superfamily-and%20show%20that%20it%20is%20essential%20for%20asexual%20parasite%20survival.%20Using%20a%20crosslinker%20specific%20for%20redox-active%20cysteines%2C%20we%20identified%20PfJ2%20substrates%20as%20PfPDI8%20and%20PfPDI11%2C%20both%20members%20of%20the%20Trx%20superfamily%20as%20well%2C%20which%20suggests%20a%20redox-regulatory%20role%20for%20PfJ2.%20Knockdown%20of%20these%20PDIs%20in%20PfJ2%20conditional%20mutants%20show%20that%20PfPDI11%20may%20not%20be%20essential.%20However%2C%20PfPDI8%20is%20required%20for%20asexual%20growth%20and%20our%20data%20suggest%20it%20may%20work%20in%20a%20complex%20with%20PfJ2%20and%20other%20ER%20chaperones.%20Finally%2C%20we%20show%20that%20the%20redox%20interactions%20between%20these%20Trx-domain%20proteins%20in%20the%20parasite%20ER%20and%20their%20substrates%20are%20sensitive%20to%20small%20molecule%20inhibition.%20Together%20these%20data%20build%20a%20model%20for%20how%20Trx-domain%20proteins%20in%20the%20P.%20falciparum%20ER%20work%20together%20to%20assist%20protein%20folding%20and%20demonstrate%20the%20suitability%20of%20ER-localized%20Trx-domain%20proteins%20for%20antimalarial%20drug%20development.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1371%5C%2Fjournal.ppat.1009293%22%2C%22ISSN%22%3A%221553-7374%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A20%3A52Z%22%7D%7D%2C%7B%22key%22%3A%22TMLGMAGA%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Corpas%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ECorpas%2C%20Manuel%2C%20Stephan%20Beck%2C%20Gustavo%20Glusman%2C%20and%20Mahsa%20Shabani.%202021.%20%26%23x201C%3BEditorial%3A%20Personal%20Genomes%3A%20Accessing%2C%20Sharing%2C%20and%20Interpretation.%26%23x201D%3B%20%3Ci%3EFrontiers%20in%20Genetics%3C%5C%2Fi%3E%2012%3A687584.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffgene.2021.687584%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffgene.2021.687584%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DTMLGMAGA%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DGRC7Y9QN%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Editorial%3A%20Personal%20Genomes%3A%20Accessing%2C%20Sharing%2C%20and%20Interpretation%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Manuel%22%2C%22lastName%22%3A%22Corpas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stephan%22%2C%22lastName%22%3A%22Beck%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gustavo%22%2C%22lastName%22%3A%22Glusman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mahsa%22%2C%22lastName%22%3A%22Shabani%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3389%5C%2Ffgene.2021.687584%22%2C%22ISSN%22%3A%221664-8021%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A08%3A02Z%22%7D%7D%2C%7B%22key%22%3A%22SHHU4TWS%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Crouser%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ECrouser%2C%20Elliott%20D.%2C%20Mark%20W.%20Julian%2C%20Sabahattin%20Bicer%2C%20Vikas%20Ghai%2C%20Taek-Kyun%20Kim%2C%20Lisa%20A.%20Maier%2C%20May%20Gillespie%2C%20Nabeel%20Y.%20Hamzeh%2C%20and%20Kai%20Wang.%202021.%20%26%23x201C%3BCirculating%20Exosomal%20MicroRNA%20Expression%20Patterns%20Distinguish%20Cardiac%20Sarcoidosis%20from%20Myocardial%20Ischemia.%26%23x201D%3B%20%3Ci%3EPloS%20One%3C%5C%2Fi%3E%2016%20%281%29%3A%20e0246083.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pone.0246083%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pone.0246083%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DSHHU4TWS%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DAAA9T2HI%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Circulating%20exosomal%20microRNA%20expression%20patterns%20distinguish%20cardiac%20sarcoidosis%20from%20myocardial%20ischemia%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elliott%20D.%22%2C%22lastName%22%3A%22Crouser%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mark%20W.%22%2C%22lastName%22%3A%22Julian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sabahattin%22%2C%22lastName%22%3A%22Bicer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vikas%22%2C%22lastName%22%3A%22Ghai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Taek-Kyun%22%2C%22lastName%22%3A%22Kim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lisa%20A.%22%2C%22lastName%22%3A%22Maier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22May%22%2C%22lastName%22%3A%22Gillespie%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nabeel%20Y.%22%2C%22lastName%22%3A%22Hamzeh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kai%22%2C%22lastName%22%3A%22Wang%22%7D%5D%2C%22abstractNote%22%3A%22OBJECTIVE%3A%20Cardiac%20sarcoidosis%20is%20difficult%20to%20diagnose%2C%20often%20requiring%20expensive%20and%20inconvenient%20advanced%20imaging%20techniques.%20Circulating%20exosomes%20contain%20genetic%20material%2C%20such%20as%20microRNA%20%28miRNA%29%2C%20that%20are%20derived%20from%20diseased%20tissues%20and%20may%20serve%20as%20potential%20disease-specific%20biomarkers.%20We%20thus%20sought%20to%20determine%20whether%20circulating%20exosome-derived%20miRNA%20expression%20patterns%20would%20distinguish%20cardiac%20sarcoidosis%20%28CS%29%20from%20acute%20myocardial%20infarction%20%28AMI%29.%5CnMETHODS%3A%20Plasma%20and%20serum%20samples%20conforming%20to%20CS%2C%20AMI%20or%20disease-free%20controls%20were%20procured%20from%20the%20Biologic%20Specimen%20and%20Data%20Repository%20Information%20Coordinating%20Center%20repository%20and%20National%20Jewish%20Health.%20Next%20generation%20sequencing%20%28NGS%29%20was%20performed%20on%20exosome-derived%20total%20RNA%20%28n%20%3D%2010%20for%20each%20group%29%2C%20and%20miRNA%20expression%20levels%20were%20compared%20after%20normalization%20using%20housekeeping%20miRNA.%20Quality%20assurance%20measures%20excluded%20poor%20quality%20RNA%20samples.%20Differentially%20expressed%20%28DE%29%20miRNA%20patterns%2C%20based%20upon%20%3E2-fold%20change%20%28p%20%3C%200.01%29%2C%20were%20established%20in%20CS%20compared%20to%20controls%2C%20and%20in%20CS%20compared%20to%20AMI.%20Relative%20expression%20of%20several%20DE-miRNA%20were%20validated%20by%20qRT-PCR.%5CnRESULTS%3A%20Despite%20the%20advanced%20age%20of%20the%20stored%20samples%20%28~5-30%20years%29%2C%20the%20quality%20of%20the%20exosome-derived%20miRNA%20was%20intact%20in%20~88%25%20of%20samples.%20Comparing%20plasma%20exosomal%20miRNA%20in%20CS%20versus%20controls%2C%20NGS%20yielded%2018%20DE%20transcripts%20%2812%20up-regulated%2C%206%20down-regulated%29%2C%20including%20miRNA%20previously%20implicated%20in%20mechanisms%20of%20myocardial%20injury%20%28miR-92%2C%20miR-21%29%20and%20immune%20responses%20%28miR-618%2C%20miR-27a%29.%20NGS%20further%20yielded%2052%20DE%20miRNA%20in%20serum%20exosomes%20from%20CS%20versus%20AMI%3A%205%20up-regulated%20in%20CS%3B%2047%20up-regulated%20in%20AMI%2C%20including%20transcripts%20previously%20detected%20in%20AMI%20patients%20%28miR-1-1%2C%20miR-133a%2C%20miR-208b%2C%20miR-423%2C%20miR-499%29.%20Five%20miRNAs%20with%20increased%20DE%20in%20CS%20included%20two%20isoforms%20of%20miR-624%20and%20miR-144%2C%20previously%20reported%20as%20markers%20of%20cardiomyopathy.%5CnCONCLUSIONS%3A%20MiRNA%20patterns%20of%20exosomes%20derived%20from%20CS%20and%20AMI%20patients%20are%20distinct%2C%20suggesting%20that%20circulating%20exosomal%20miRNA%20patterns%20could%20serve%20as%20disease%20biomarkers.%20Further%20studies%20are%20required%20to%20establish%20their%20specificity%20relative%20to%20other%20cardiac%20disorders.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1371%5C%2Fjournal.pone.0246083%22%2C%22ISSN%22%3A%221932-6203%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A14%3A26Z%22%7D%7D%2C%7B%22key%22%3A%22U7K7LIKS%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22D%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A3%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ED%2C%20Park%2C%20Anisuzzaman%20Asm%2C%20Magis%20At%2C%20Chen%20G%2C%20Xie%20M%2C%20Zhang%20G%2C%20Behera%20M%2C%20et%20al.%202021.%20%26%23x201C%3BDiscovery%20of%20Small%20Molecule%20Bak%20Activator%20for%20Lung%20Cancer%20Therapy.%26%23x201D%3B%20%3Ci%3ETheranostics%3C%5C%2Fi%3E%2011%20%2817%29.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.7150%5C%2Fthno.60349%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.7150%5C%2Fthno.60349%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DU7K7LIKS%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DH93L9XCZ%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Discovery%20of%20Small%20Molecule%20Bak%20Activator%20for%20Lung%20Cancer%20Therapy%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Park%22%2C%22lastName%22%3A%22D%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anisuzzaman%22%2C%22lastName%22%3A%22Asm%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Magis%22%2C%22lastName%22%3A%22At%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chen%22%2C%22lastName%22%3A%22G%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xie%22%2C%22lastName%22%3A%22M%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhang%22%2C%22lastName%22%3A%22G%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Behera%22%2C%22lastName%22%3A%22M%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sica%22%2C%22lastName%22%3A%22Gl%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ramalingam%22%2C%22lastName%22%3A%22Ss%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Owonikoko%22%2C%22lastName%22%3A%22Tk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Deng%22%2C%22lastName%22%3A%22X%22%7D%5D%2C%22abstractNote%22%3A%22%3Cspan%3E%3Cb%3ERationale%3A%3C%5C%2Fb%3E%20Bak%20is%20a%20major%20proapoptotic%20Bcl2%20family%20member%20and%20a%20required%20molecule%20for%20apoptotic%20cell%20death.%20High%20levels%20of%20endogenous%20Bak%20were%20observed%20in%20both%20small%20cell%20lung%20cancer%20%28SCLC%29%20and%20non-small%20cell%20lung%20cancer%20%28NSCLC%29%20cell%20lines.%20Increased%20Bak%20expression%20was%20correlated%20with%20poor%20pr%3C%5C%2Fspan%3E%20%5Cu2026%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.7150%5C%2Fthno.60349%22%2C%22ISSN%22%3A%221838-7640%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fpubmed.ncbi.nlm.nih.gov%5C%2F34373755%5C%2F%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A32%3A50Z%22%7D%7D%2C%7B%22key%22%3A%2246TRUMNE%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22D%27Agnillo%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3ED%26%23x2019%3BAgnillo%2C%20Felice%2C%20K.A.%20Walters%2C%20Yongli%20Xiao%2C%20Zong-Mei%20Sheng%2C%20Kelsey%20Scherler%2C%20Jaekeun%20Park%2C%20Sebastian%20Gygli%2C%20et%20al.%202021.%20%26%23x201C%3BLung%20Epithelial%20and%20Endothelial%20Damage%2C%20Loss%20of%20Tissue%20Repair%2C%20Inhibition%20of%20Fibrinolysis%2C%20and%20Cellular%20Senescence%20in%20Fatal%20COVID-19.%26%23x201D%3B%20%3Ci%3EScience%20Translational%20Medicine%3C%5C%2Fi%3E%2013%20%28620%29%3A%20eabj7790.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1126%5C%2Fscitranslmed.abj7790%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1126%5C%2Fscitranslmed.abj7790%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D46TRUMNE%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DEPJJHWV5%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Lung%20epithelial%20and%20endothelial%20damage%2C%20loss%20of%20tissue%20repair%2C%20inhibition%20of%20fibrinolysis%2C%20and%20cellular%20senescence%20in%20fatal%20COVID-19%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Felice%22%2C%22lastName%22%3A%22D%27Agnillo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22K.A.%22%2C%22lastName%22%3A%22Walters%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yongli%22%2C%22lastName%22%3A%22Xiao%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zong-Mei%22%2C%22lastName%22%3A%22Sheng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kelsey%22%2C%22lastName%22%3A%22Scherler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jaekeun%22%2C%22lastName%22%3A%22Park%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sebastian%22%2C%22lastName%22%3A%22Gygli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luz%20Angela%22%2C%22lastName%22%3A%22Rosas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kaitlyn%22%2C%22lastName%22%3A%22Sadtler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Heather%22%2C%22lastName%22%3A%22Kalish%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles%20A.%22%2C%22lastName%22%3A%22Blatti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ruoqing%22%2C%22lastName%22%3A%22Zhu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lisa%22%2C%22lastName%22%3A%22Gatzke%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Colleen%22%2C%22lastName%22%3A%22Bushell%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20J.%22%2C%22lastName%22%3A%22Memoli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Steven%20J.%22%2C%22lastName%22%3A%22O%27Day%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Trevan%20D.%22%2C%22lastName%22%3A%22Fischer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Terese%20C.%22%2C%22lastName%22%3A%22Hammond%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Raymond%20C.%22%2C%22lastName%22%3A%22Lee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20Christian%22%2C%22lastName%22%3A%22Cash%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20E.%22%2C%22lastName%22%3A%22Powers%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Grant%20E.%22%2C%22lastName%22%3A%22O%27Keefe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kelly%20J.%22%2C%22lastName%22%3A%22Butnor%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amy%20V.%22%2C%22lastName%22%3A%22Rapkiewicz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22William%20D.%22%2C%22lastName%22%3A%22Travis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Scott%20P.%22%2C%22lastName%22%3A%22Layne%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%20C.%22%2C%22lastName%22%3A%22Kash%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffery%20K.%22%2C%22lastName%22%3A%22Taubenberger%22%7D%5D%2C%22abstractNote%22%3A%22%5BFigure%3A%20see%20text%5D.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1126%5C%2Fscitranslmed.abj7790%22%2C%22ISSN%22%3A%221946-6242%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A41%3A10Z%22%7D%7D%2C%7B%22key%22%3A%22LJPISBNC%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Dai%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDai%2C%20Chengzhen%20L.%2C%20Sergey%20A.%20Kornilov%2C%20Ryan%20T.%20Roper%2C%20Hannah%20Cohen-Cline%2C%20Kathleen%20Jade%2C%20Brett%20Smith%2C%20James%20R.%20Heath%2C%20et%20al.%202021.%20%26%23x201C%3BCharacteristics%20and%20Factors%20Associated%20with%20COVID-19%20Infection%2C%20Hospitalization%2C%20and%20Mortality%20Across%20Race%20and%20Ethnicity.%26%23x201D%3B%20%3Ci%3EClinical%20Infectious%20Diseases%3A%20An%20Official%20Publication%20of%20the%20Infectious%20Diseases%20Society%20of%20America%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Fcid%5C%2Fciab154%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Fcid%5C%2Fciab154%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DLJPISBNC%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DP97VUN5R%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Characteristics%20and%20Factors%20Associated%20with%20COVID-19%20Infection%2C%20Hospitalization%2C%20and%20Mortality%20Across%20Race%20and%20Ethnicity%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chengzhen%20L.%22%2C%22lastName%22%3A%22Dai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sergey%20A.%22%2C%22lastName%22%3A%22Kornilov%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ryan%20T.%22%2C%22lastName%22%3A%22Roper%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hannah%22%2C%22lastName%22%3A%22Cohen-Cline%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kathleen%22%2C%22lastName%22%3A%22Jade%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brett%22%2C%22lastName%22%3A%22Smith%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20R.%22%2C%22lastName%22%3A%22Heath%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22George%22%2C%22lastName%22%3A%22Diaz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jason%20D.%22%2C%22lastName%22%3A%22Goldman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20T.%22%2C%22lastName%22%3A%22Magis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%20J.%22%2C%22lastName%22%3A%22Hadlock%22%7D%5D%2C%22abstractNote%22%3A%22BACKGROUND%3A%20Data%20on%20the%20characteristics%20of%20COVID-19%20patients%20disaggregated%20by%20race%5C%2Fethnicity%20remain%20limited.%20We%20evaluated%20the%20sociodemographic%20and%20clinical%20characteristics%20of%20patients%20across%20racial%5C%2Fethnic%20groups%20and%20assessed%20their%20associations%20with%20COVID-19%20outcomes.%5CnMETHODS%3A%20This%20retrospective%20cohort%20study%20examined%20629%2C953%20patients%20tested%20for%20SARS-CoV-2%20in%20a%20large%20health%20system%20spanning%20California%2C%20Oregon%2C%20and%20Washington%20between%20March%201%20and%20December%2031%2C%202020.%20Sociodemographic%20and%20clinical%20characteristics%20were%20obtained%20from%20electronic%20health%20records.%20Odds%20of%20SARS-CoV-2%20infection%2C%20COVID-19%20hospitalization%2C%20and%20in-hospital%20death%20were%20assessed%20with%20multivariate%20logistic%20regression.%5CnRESULTS%3A%20570%2C298%20patients%20with%20known%20race%5C%2Fethnicity%20were%20tested%20for%20SARS-CoV-2%2C%20of%20whom%2027.8%25%20were%20non-White%20minorities.%2054%2C645%20individuals%20tested%20positive%2C%20with%20minorities%20representing%2050.1%25.%20Hispanics%20represented%2034.3%25%20of%20infections%20but%20only%2013.4%25%20of%20tests.%20While%20generally%20younger%20than%20White%20patients%2C%20Hispanics%20had%20higher%20rates%20of%20diabetes%20but%20fewer%20other%20comorbidities.%208%2C536%20patients%20were%20hospitalized%20and%201%2C246%20died%2C%20of%20whom%2056.1%25%20and%2054.4%25%20were%20non-White%2C%20respectively.%20Racial%5C%2Fethnic%20distributions%20of%20outcomes%20across%20the%20health%20system%20tracked%20with%20state-level%20statistics.%20Increased%20odds%20of%20testing%20positive%20and%20hospitalization%20were%20associated%20with%20all%20minority%20races%5C%2Fethnicities.%20Hispanic%20patients%20also%20exhibited%20increased%20morbidity%2C%20and%20Hispanic%20race%5C%2Fethnicity%20was%20associated%20with%20in-hospital%20mortality%20%28OR%3A%201.39%20%5B95%25%20CI%3A%201.14-1.70%5D%29.%5CnCONCLUSION%3A%20Major%20healthcare%20disparities%20were%20evident%2C%20especially%20among%20Hispanics%20who%20tested%20positive%20at%20a%20higher%20rate%2C%20required%20excess%20hospitalization%20and%20mechanical%20ventilation%2C%20and%20had%20higher%20odds%20of%20in-hospital%20mortality%20despite%20younger%20age.%20Targeted%2C%20culturally-responsive%20interventions%20and%20equitable%20vaccine%20development%20and%20distribution%20are%20needed%20to%20address%20the%20increased%20risk%20of%20poorer%20COVID-19%20outcomes%20among%20minority%20populations.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1093%5C%2Fcid%5C%2Fciab154%22%2C%22ISSN%22%3A%221537-6591%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A21%3A11Z%22%7D%7D%2C%7B%22key%22%3A%22SXIB9RHA%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Dai%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDai%2C%20Chengxin%2C%20Anja%20F%26%23xFC%3Bllgrabe%2C%20Julianus%20Pfeuffer%2C%20Elizaveta%20M.%20Solovyeva%2C%20Jingwen%20Deng%2C%20Pablo%20Moreno%2C%20Selvakumar%20Kamatchinathan%2C%20et%20al.%202021.%20%26%23x201C%3BA%20Proteomics%20Sample%20Metadata%20Representation%20for%20Multiomics%20Integration%20and%20Big%20Data%20Analysis.%26%23x201D%3B%20%3Ci%3ENature%20Communications%3C%5C%2Fi%3E%2012%20%281%29%3A%205854.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-021-26111-3%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41467-021-26111-3%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DSXIB9RHA%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20proteomics%20sample%20metadata%20representation%20for%20multiomics%20integration%20and%20big%20data%20analysis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chengxin%22%2C%22lastName%22%3A%22Dai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anja%22%2C%22lastName%22%3A%22F%5Cu00fcllgrabe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julianus%22%2C%22lastName%22%3A%22Pfeuffer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elizaveta%20M.%22%2C%22lastName%22%3A%22Solovyeva%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jingwen%22%2C%22lastName%22%3A%22Deng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pablo%22%2C%22lastName%22%3A%22Moreno%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Selvakumar%22%2C%22lastName%22%3A%22Kamatchinathan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Deepti%20Jaiswal%22%2C%22lastName%22%3A%22Kundu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nancy%22%2C%22lastName%22%3A%22George%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Silvie%22%2C%22lastName%22%3A%22Fexova%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bj%5Cu00f6rn%22%2C%22lastName%22%3A%22Gr%5Cu00fcning%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Melanie%20Christine%22%2C%22lastName%22%3A%22F%5Cu00f6ll%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Johannes%22%2C%22lastName%22%3A%22Griss%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Vaudel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Enrique%22%2C%22lastName%22%3A%22Audain%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marie%22%2C%22lastName%22%3A%22Locard-Paulet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michael%22%2C%22lastName%22%3A%22Turewicz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Martin%22%2C%22lastName%22%3A%22Eisenacher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Julian%22%2C%22lastName%22%3A%22Uszkoreit%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tim%22%2C%22lastName%22%3A%22Van%20Den%20Bossche%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Veit%22%2C%22lastName%22%3A%22Schw%5Cu00e4mmle%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Henry%22%2C%22lastName%22%3A%22Webel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stefan%22%2C%22lastName%22%3A%22Schulze%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Bouyssi%5Cu00e9%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Savita%22%2C%22lastName%22%3A%22Jayaram%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vinay%20Kumar%22%2C%22lastName%22%3A%22Duggineni%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Patroklos%22%2C%22lastName%22%3A%22Samaras%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mathias%22%2C%22lastName%22%3A%22Wilhelm%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Meena%22%2C%22lastName%22%3A%22Choi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mingxun%22%2C%22lastName%22%3A%22Wang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Oliver%22%2C%22lastName%22%3A%22Kohlbacher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alvis%22%2C%22lastName%22%3A%22Brazma%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irene%22%2C%22lastName%22%3A%22Papatheodorou%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nuno%22%2C%22lastName%22%3A%22Bandeira%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%20W.%22%2C%22lastName%22%3A%22Deutsch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Juan%20Antonio%22%2C%22lastName%22%3A%22Vizca%5Cu00edno%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mingze%22%2C%22lastName%22%3A%22Bai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Timo%22%2C%22lastName%22%3A%22Sachsenberg%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lev%20I.%22%2C%22lastName%22%3A%22Levitsky%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yasset%22%2C%22lastName%22%3A%22Perez-Riverol%22%7D%5D%2C%22abstractNote%22%3A%22The%20amount%20of%20public%20proteomics%20data%20is%20rapidly%20increasing%20but%20there%20is%20no%20standardized%20format%20to%20describe%20the%20sample%20metadata%20and%20their%20relationship%20with%20the%20dataset%20files%20in%20a%20way%20that%20fully%20supports%20their%20understanding%20or%20reanalysis.%20Here%20we%20propose%20to%20develop%20the%20transcriptomics%20data%20format%20MAGE-TAB%20into%20a%20standard%20representation%20for%20proteomics%20sample%20metadata.%20We%20implement%20MAGE-TAB-Proteomics%20in%20a%20crowdsourcing%20project%20to%20manually%20curate%20over%20200%20public%20datasets.%20We%20also%20describe%20tools%20and%20libraries%20to%20validate%20and%20submit%20sample%20metadata-related%20information%20to%20the%20PRIDE%20repository.%20We%20expect%20that%20these%20developments%20will%20improve%20the%20reproducibility%20and%20facilitate%20the%20reanalysis%20and%20integration%20of%20public%20proteomics%20datasets.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41467-021-26111-3%22%2C%22ISSN%22%3A%222041-1723%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A34%3A11Z%22%7D%7D%2C%7B%22key%22%3A%22BDAFK26T%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Day%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDay%2C%20JA%2C%20CM%20Ludwig%2C%20and%20NS%20Baliga.%202021.%20%26%23x201C%3BCultivating%20Environmental%20Sustainable%20Food%20through%20a%20Community%20Ambassador%20Program.%26%23x201D%3B%20%3Ci%3EClearing%3A%20Journal%20of%20Community-Based%20Environmental%20Literacy%20Education%3C%5C%2Fi%3E%20Winter%20Edition%3A12%26%23x2013%3B16.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DBDAFK26T%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Cultivating%20Environmental%20Sustainable%20Food%20through%20a%20Community%20Ambassador%20Program%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22JA%22%2C%22lastName%22%3A%22Day%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22CM%22%2C%22lastName%22%3A%22Ludwig%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22NS%22%2C%22lastName%22%3A%22Baliga%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%22%22%2C%22ISSN%22%3A%22%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A06%3A27Z%22%7D%7D%2C%7B%22key%22%3A%227LZHR3A8%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Day%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDay%2C%20Jessica%20A.%2C%20Christian%20Diener%2C%20Anne%20E.%20Otwell%2C%20Kourtney%20E.%20Tams%2C%20Brad%20Bebout%2C%20Angela%20M.%20Detweiler%2C%20Michael%20D.%20Lee%2C%20et%20al.%202021.%20%26%23x201C%3BLettuce%20%28Lactuca%20Sativa%29%20Productivity%20Influenced%20by%20Microbial%20Inocula%20under%20Nitrogen-Limited%20Conditions%20in%20Aquaponics.%26%23x201D%3B%20%3Ci%3EPloS%20One%3C%5C%2Fi%3E%2016%20%282%29%3A%20e0247534.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pone.0247534%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pone.0247534%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D7LZHR3A8%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DCCRA3YM2%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Lettuce%20%28Lactuca%20sativa%29%20productivity%20influenced%20by%20microbial%20inocula%20under%20nitrogen-limited%20conditions%20in%20aquaponics%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jessica%20A.%22%2C%22lastName%22%3A%22Day%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christian%22%2C%22lastName%22%3A%22Diener%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anne%20E.%22%2C%22lastName%22%3A%22Otwell%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kourtney%20E.%22%2C%22lastName%22%3A%22Tams%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brad%22%2C%22lastName%22%3A%22Bebout%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Angela%20M.%22%2C%22lastName%22%3A%22Detweiler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michael%20D.%22%2C%22lastName%22%3A%22Lee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Madeline%20T.%22%2C%22lastName%22%3A%22Scott%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wilson%22%2C%22lastName%22%3A%22Ta%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Monica%22%2C%22lastName%22%3A%22Ha%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shienna%20A.%22%2C%22lastName%22%3A%22Carreon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kenny%22%2C%22lastName%22%3A%22Tong%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Abdirizak%20A.%22%2C%22lastName%22%3A%22Ali%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20M.%22%2C%22lastName%22%3A%22Gibbons%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nitin%20S.%22%2C%22lastName%22%3A%22Baliga%22%7D%5D%2C%22abstractNote%22%3A%22The%20demand%20for%20food%20will%20outpace%20productivity%20of%20conventional%20agriculture%20due%20to%20projected%20growth%20of%20the%20human%20population%2C%20concomitant%20with%20shrinkage%20of%20arable%20land%2C%20increasing%20scarcity%20of%20freshwater%2C%20and%20a%20rapidly%20changing%20climate.%20While%20aquaponics%20has%20potential%20to%20sustainably%20supplement%20food%20production%20with%20minimal%20environmental%20impact%2C%20there%20is%20a%20need%20to%20better%20characterize%20the%20complex%20interplay%20between%20the%20various%20components%20%28fish%2C%20plant%2C%20microbiome%29%20of%20these%20systems%20to%20optimize%20scale%20up%20and%20productivity.%20Here%2C%20we%20investigated%20how%20the%20commonly-implemented%20practice%20of%20continued%20microbial%20community%20transfer%20from%20pre-existing%20systems%20might%20promote%20or%20impede%20productivity%20of%20aquaponics.%20Specifically%2C%20we%20monitored%20plant%20growth%20phenotypes%2C%20water%20chemistry%2C%20and%20microbiome%20composition%20of%20rhizospheres%2C%20biofilters%2C%20and%20fish%20feces%20over%2061-days%20of%20lettuce%20%28Lactuca%20sativa%20var.%20crispa%29%20growth%20in%20nitrogen-limited%20aquaponic%20systems%20inoculated%20with%20bacteria%20that%20were%20either%20commercially%20sourced%20or%20originating%20from%20a%20pre-existing%20aquaponic%20system.%20Lettuce%20above-%20and%20below-ground%20growth%20were%20significantly%20reduced%20across%20replicates%20treated%20with%20a%20pre-existing%20aquaponic%20system%20inoculum%20when%20compared%20to%20replicates%20treated%20with%20a%20commercial%20inoculum.%20Reduced%20productivity%20was%20associated%20with%20enrichment%20in%20specific%20bacterial%20genera%20in%20plant%20roots%2C%20including%20Pseudomonas%2C%20following%20inoculum%20transfer%20from%20pre-existing%20systems.%20Increased%20productivity%20was%20associated%20with%20enrichment%20of%20nitrogen-fixing%20Rahnella%20in%20roots%20of%20plants%20treated%20with%20the%20commercial%20inoculum.%20Thus%2C%20we%20show%20that%20inoculation%20from%20a%20pre-existing%20system%2C%20rather%20than%20from%20a%20commercial%20inoculum%2C%20is%20associated%20with%20lower%20yields.%20Further%20work%20will%20be%20necessary%20to%20test%20the%20putative%20mechanisms%20involved.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1371%5C%2Fjournal.pone.0247534%22%2C%22ISSN%22%3A%221932-6203%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A11%3A31Z%22%7D%7D%2C%7B%22key%22%3A%22ZRVY3W4C%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Deutsch%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDeutsch%2C%20Eric%20W.%2C%20Yasset%20Perez-Riverol%2C%20Jeremy%20Carver%2C%20Shin%20Kawano%2C%20Luis%20Mendoza%2C%20Tim%20Van%20Den%20Bossche%2C%20Ralf%20Gabriels%2C%20et%20al.%202021.%20%26%23x201C%3BUniversal%20Spectrum%20Identifier%20for%20Mass%20Spectra.%26%23x201D%3B%20%3Ci%3ENature%20Methods%3C%5C%2Fi%3E%2018%20%287%29%3A%20768%26%23x2013%3B70.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41592-021-01184-6%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41592-021-01184-6%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DZRVY3W4C%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DZ7KUQVHL%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Universal%20Spectrum%20Identifier%20for%20mass%20spectra%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%20W.%22%2C%22lastName%22%3A%22Deutsch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yasset%22%2C%22lastName%22%3A%22Perez-Riverol%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeremy%22%2C%22lastName%22%3A%22Carver%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shin%22%2C%22lastName%22%3A%22Kawano%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luis%22%2C%22lastName%22%3A%22Mendoza%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tim%22%2C%22lastName%22%3A%22Van%20Den%20Bossche%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ralf%22%2C%22lastName%22%3A%22Gabriels%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre-Alain%22%2C%22lastName%22%3A%22Binz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benjamin%22%2C%22lastName%22%3A%22Pullman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhi%22%2C%22lastName%22%3A%22Sun%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jim%22%2C%22lastName%22%3A%22Shofstahl%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wout%22%2C%22lastName%22%3A%22Bittremieux%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tytus%20D.%22%2C%22lastName%22%3A%22Mak%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Joshua%22%2C%22lastName%22%3A%22Klein%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yunping%22%2C%22lastName%22%3A%22Zhu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Henry%22%2C%22lastName%22%3A%22Lam%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Juan%20Antonio%22%2C%22lastName%22%3A%22Vizca%5Cu00edno%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nuno%22%2C%22lastName%22%3A%22Bandeira%22%7D%5D%2C%22abstractNote%22%3A%22Mass%20spectra%20provide%20the%20ultimate%20evidence%20to%20support%20the%20findings%20of%20mass%20spectrometry%20proteomics%20studies%20in%20publications%2C%20and%20it%20is%20therefore%20crucial%20to%20be%20able%20to%20trace%20the%20conclusions%20back%20to%20the%20spectra.%20The%20Universal%20Spectrum%20Identifier%20%28USI%29%20provides%20a%20standardized%20mechanism%20for%20encoding%20a%20virtual%20path%20to%20any%20mass%20spectrum%20contained%20in%20datasets%20deposited%20to%20public%20proteomics%20repositories.%20USI%20enables%20greater%20transparency%20of%20spectral%20evidence%2C%20with%20more%20than%201%20billion%20USI%20identifications%20from%20over%203%20billion%20spectra%20already%20available%20through%20ProteomeXchange%20repositories.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41592-021-01184-6%22%2C%22ISSN%22%3A%221548-7105%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A30%3A45Z%22%7D%7D%2C%7B%22key%22%3A%22C5AD7NS3%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Deutsch%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDeutsch%2C%20Eric%20W.%2C%20Gilbert%20S.%20Omenn%2C%20Zhi%20Sun%2C%20Michal%20Maes%2C%20Maria%20Pernemalm%2C%20Krishnan%20K.%20Palaniappan%2C%20Natasha%20Letunica%2C%20et%20al.%202021.%20%26%23x201C%3BAdvances%20and%20Utility%20of%20the%20Human%20Plasma%20Proteome.%26%23x201D%3B%20%3Ci%3EJournal%20of%20Proteome%20Research%3C%5C%2Fi%3E%2020%20%2812%29%3A%205241%26%23x2013%3B63.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Facs.jproteome.1c00657%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Facs.jproteome.1c00657%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DC5AD7NS3%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Advances%20and%20Utility%20of%20the%20Human%20Plasma%20Proteome%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%20W.%22%2C%22lastName%22%3A%22Deutsch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gilbert%20S.%22%2C%22lastName%22%3A%22Omenn%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhi%22%2C%22lastName%22%3A%22Sun%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Michal%22%2C%22lastName%22%3A%22Maes%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Maria%22%2C%22lastName%22%3A%22Pernemalm%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Krishnan%20K.%22%2C%22lastName%22%3A%22Palaniappan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Natasha%22%2C%22lastName%22%3A%22Letunica%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yves%22%2C%22lastName%22%3A%22Vandenbrouck%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Virginie%22%2C%22lastName%22%3A%22Brun%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sheng-Ce%22%2C%22lastName%22%3A%22Tao%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xiaobo%22%2C%22lastName%22%3A%22Yu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Philipp%20E.%22%2C%22lastName%22%3A%22Geyer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vera%22%2C%22lastName%22%3A%22Ignjatovic%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%20L.%22%2C%22lastName%22%3A%22Moritz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jochen%20M.%22%2C%22lastName%22%3A%22Schwenk%22%7D%5D%2C%22abstractNote%22%3A%22The%20study%20of%20proteins%20circulating%20in%20blood%20offers%20tremendous%20opportunities%20to%20diagnose%2C%20stratify%2C%20or%20possibly%20prevent%20diseases.%20With%20recent%20technological%20advances%20and%20the%20urgent%20need%20to%20understand%20the%20effects%20of%20COVID-19%2C%20the%20proteomic%20analysis%20of%20blood-derived%20serum%20and%20plasma%20has%20become%20even%20more%20important%20for%20studying%20human%20biology%20and%20pathophysiology.%20Here%20we%20provide%20views%20and%20perspectives%20about%20technological%20developments%20and%20possible%20clinical%20applications%20that%20use%20mass-spectrometry%28MS%29-%20or%20affinity-based%20methods.%20We%20discuss%20examples%20where%20plasma%20proteomics%20contributed%20valuable%20insights%20into%20SARS-CoV-2%20infections%2C%20aging%2C%20and%20hemostasis%20and%20the%20opportunities%20offered%20by%20combining%20proteomics%20with%20genetic%20data.%20As%20a%20contribution%20to%20the%20Human%20Proteome%20Organization%20%28HUPO%29%20Human%20Plasma%20Proteome%20Project%20%28HPPP%29%2C%20we%20present%20the%20Human%20Plasma%20PeptideAtlas%20build%202021-07%20that%20comprises%204395%20canonical%20and%201482%20additional%20nonredundant%20human%20proteins%20detected%20in%20240%20MS-based%20experiments.%20In%20addition%2C%20we%20report%20the%20new%20Human%20Extracellular%20Vesicle%20PeptideAtlas%202021-06%2C%20which%20comprises%20five%20studies%20and%202757%20canonical%20proteins%20detected%20in%20extracellular%20vesicles%20circulating%20in%20blood%2C%20of%20which%2074%25%20%282047%29%20are%20in%20common%20with%20the%20plasma%20PeptideAtlas.%20Our%20overview%20summarizes%20the%20recent%20advances%2C%20impactful%20applications%2C%20and%20ongoing%20challenges%20for%20translating%20plasma%20proteomics%20into%20utility%20for%20precision%20medicine.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1021%5C%2Facs.jproteome.1c00657%22%2C%22ISSN%22%3A%221535-3907%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A37%3A41Z%22%7D%7D%2C%7B%22key%22%3A%229UY932RL%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Diaz%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDiaz%2C%20George%20A%2C%20Alyssa%20B%20Christensen%2C%20Tobias%20Pusch%2C%20Delaney%20Goulet%2C%20Shu-Ching%20Chang%2C%20Gary%20L%20Grunkemeier%2C%20Paul%20A%20McKelvey%2C%20et%20al.%202021.%20%26%23x201C%3BRemdesivir%20and%20Mortality%20in%20Patients%20With%20Coronavirus%20Disease%202019.%26%23x201D%3B%20%3Ci%3EClinical%20Infectious%20Diseases%3C%5C%2Fi%3E%2C%20ciab698.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Fcid%5C%2Fciab698%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Fcid%5C%2Fciab698%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D9UY932RL%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3D5JTS52UM%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Remdesivir%20and%20Mortality%20in%20Patients%20With%20Coronavirus%20Disease%202019%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22George%20A%22%2C%22lastName%22%3A%22Diaz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alyssa%20B%22%2C%22lastName%22%3A%22Christensen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tobias%22%2C%22lastName%22%3A%22Pusch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Delaney%22%2C%22lastName%22%3A%22Goulet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shu-Ching%22%2C%22lastName%22%3A%22Chang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gary%20L%22%2C%22lastName%22%3A%22Grunkemeier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Paul%20A%22%2C%22lastName%22%3A%22McKelvey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ari%22%2C%22lastName%22%3A%22Robicsek%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tom%22%2C%22lastName%22%3A%22French%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guilford%20T%22%2C%22lastName%22%3A%22Parsons%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Glenn%22%2C%22lastName%22%3A%22Doherty%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles%22%2C%22lastName%22%3A%22Laurenson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ryan%22%2C%22lastName%22%3A%22Roper%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Hadlock%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Cameron%20J%22%2C%22lastName%22%3A%22Cover%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brent%22%2C%22lastName%22%3A%22Footer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Philip%22%2C%22lastName%22%3A%22Robinson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mary%22%2C%22lastName%22%3A%22Micikas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%20E%22%2C%22lastName%22%3A%22Marfori%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charlotte%22%2C%22lastName%22%3A%22Cronenweth%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yogavedya%22%2C%22lastName%22%3A%22Mukkamala%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jamie%22%2C%22lastName%22%3A%22Mackiewicz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ekra%22%2C%22lastName%22%3A%22Rai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Martha%20Dickinson%22%2C%22lastName%22%3A%22Matson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jodie%22%2C%22lastName%22%3A%22Davila%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Justin%22%2C%22lastName%22%3A%22Rueda%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Reda%22%2C%22lastName%22%3A%22Tipton%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Heather%22%2C%22lastName%22%3A%22Algren%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brittney%20C%22%2C%22lastName%22%3A%22Ward%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stephen%22%2C%22lastName%22%3A%22Malkoski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tyler%22%2C%22lastName%22%3A%22Gluckman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gregory%20B%22%2C%22lastName%22%3A%22Tallman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Henry%22%2C%22lastName%22%3A%22Arguinchona%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Terese%20C%22%2C%22lastName%22%3A%22Hammond%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Steven%22%2C%22lastName%22%3A%22Standaert%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Joshua%22%2C%22lastName%22%3A%22Christensen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jose%20F%22%2C%22lastName%22%3A%22Echaiz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%22%2C%22lastName%22%3A%22Choi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%22%2C%22lastName%22%3A%22McClung%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Albert%22%2C%22lastName%22%3A%22Pacifico%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Martin%22%2C%22lastName%22%3A%22Fee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Farjad%22%2C%22lastName%22%3A%22Sarafian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22William%20R%22%2C%22lastName%22%3A%22Berrington%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jason%20D%22%2C%22lastName%22%3A%22Goldman%22%7D%5D%2C%22abstractNote%22%3A%22The%20impact%20of%20remdesivir%20%28RDV%29%20on%20mortality%20rates%20in%20coronavirus%20disease%202019%20%28COVID-19%29%20is%20controversial%2C%20and%20the%20mortality%20effect%20in%20subgroups%20of%20baseline%20disease%20severity%20has%20been%20incompletely%20explored.%20The%20purpose%20of%20this%20study%20was%20to%20assess%20the%20association%20of%20RDV%20with%20mortality%20rates%20in%20patients%20with%20COVID-19.In%20this%20retrospective%20cohort%20study%20we%20compared%20persons%20receiving%20RDV%20with%20those%20receiving%20best%20supportive%20care%20%28BSC%29.%20Patients%20hospitalized%20between%2028%20February%20and%2028%20May%202020%20with%20laboratory-confirmed%20severe%20acute%20respiratory%20syndrome%20coronavirus%202%20infection%20were%20included%20with%20the%20development%20of%20COVID-19%20pneumonia%20on%20chest%20radiography%20and%20hypoxia%20requiring%20supplemental%20oxygen%20or%20oxygen%20saturation%20%5Cu226494%25%20with%20room%20air.%20The%20primary%20outcome%20was%20overall%20survival%2C%20assessed%20with%20time-dependent%20Cox%20proportional%20hazards%20regression%20and%20multivariable%20adjustment%2C%20including%20calendar%20time%2C%20baseline%20patient%20characteristics%2C%20corticosteroid%20use%2C%20and%20random%20effects%20for%20hospital.A%20total%20of%201138%20patients%20were%20enrolled%2C%20including%20286%20who%20received%20RDV%20and%20852%20treated%20with%20BSC%2C%20400%20of%20whom%20received%20hydroxychloroquine.%20Corticosteroids%20were%20used%20in%2020.4%25%20of%20the%20cohort%20%2812.6%25%20in%20RDV%20and%2023%25%20in%20BSC%29.%20Comparing%20persons%20receiving%20RDV%20with%20those%20receiving%20BSC%2C%20the%20hazard%20ratio%20%2895%25%20confidence%20interval%29%20for%20death%20was%200.46%20%28.31%5Cu2013.69%29%20in%20the%20univariate%20model%20%28P%20%26lt%3B%20.001%29%20and%200.60%20%28.40%5Cu2013.90%29%20in%20the%20risk-adjusted%20model%20%28P%20%3D%20.01%29.%20In%20the%20subgroup%20of%20persons%20with%20baseline%20use%20of%20low-flow%20oxygen%2C%20the%20hazard%20ratio%20%2895%25%20confidence%20interval%29%20for%20death%20in%20RDV%20compared%20with%20BSC%20was%200.63%20%28.39%5Cu20131.00%3B%20P%20%3D%20.049%29.Treatment%20with%20RDV%20was%20associated%20with%20lower%20mortality%20rates%20than%20BSC.%20These%20findings%20remain%20the%20same%20in%20the%20subgroup%20with%20baseline%20use%20of%20low-flow%20oxygen.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1093%5C%2Fcid%5C%2Fciab698%22%2C%22ISSN%22%3A%221058-4838%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Fcid%5C%2Fciab698%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A45%3A51Z%22%7D%7D%2C%7B%22key%22%3A%22F5A2KFTG%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Diener%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDiener%2C%20Christian%2C%20Anna%20C.%20H.%20Hoge%2C%20Sean%20M.%20Kearney%2C%20Ulrike%20Kusebauch%2C%20Sushmita%20Patwardhan%2C%20Robert%20L.%20Moritz%2C%20Susan%20E.%20Erdman%2C%20and%20Sean%20M.%20Gibbons.%202021.%20%26%23x201C%3BNon-Responder%20Phenotype%20Reveals%20Apparent%20Microbiome-Wide%20Antibiotic%20Tolerance%20in%20the%20Murine%20Gut.%26%23x201D%3B%20%3Ci%3ECommunications%20Biology%3C%5C%2Fi%3E%204%20%281%29%3A%20316.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs42003-021-01841-8%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs42003-021-01841-8%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DF5A2KFTG%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DU9X3FS3A%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Non-responder%20phenotype%20reveals%20apparent%20microbiome-wide%20antibiotic%20tolerance%20in%20the%20murine%20gut%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christian%22%2C%22lastName%22%3A%22Diener%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anna%20C.%20H.%22%2C%22lastName%22%3A%22Hoge%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20M.%22%2C%22lastName%22%3A%22Kearney%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ulrike%22%2C%22lastName%22%3A%22Kusebauch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sushmita%22%2C%22lastName%22%3A%22Patwardhan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Robert%20L.%22%2C%22lastName%22%3A%22Moritz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Susan%20E.%22%2C%22lastName%22%3A%22Erdman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20M.%22%2C%22lastName%22%3A%22Gibbons%22%7D%5D%2C%22abstractNote%22%3A%22Broad%20spectrum%20antibiotics%20cause%20both%20transient%20and%20lasting%20damage%20to%20the%20ecology%20of%20the%20gut%20microbiome.%20Antibiotic-induced%20loss%20of%20gut%20bacterial%20diversity%20has%20been%20linked%20to%20susceptibility%20to%20enteric%20infections.%20Prior%20work%20on%20subtherapeutic%20antibiotic%20treatment%20in%20humans%20and%20non-human%20animals%20has%20suggested%20that%20entire%20gut%20communities%20may%20exhibit%20tolerance%20phenotypes.%20In%20this%20study%2C%20we%20validate%20the%20existence%20of%20these%20community%20tolerance%20phenotypes%20in%20the%20murine%20gut%20and%20explore%20how%20antibiotic%20treatment%20duration%20or%20a%20diet%20enriched%20in%20antimicrobial%20phytochemicals%20might%20influence%20the%20frequency%20of%20this%20phenotype.%20Almost%20a%20third%20of%20mice%20exhibited%20whole-community%20tolerance%20to%20a%20high%20dose%20of%20the%20%5Cu03b2-lactam%20antibiotic%20cefoperazone%2C%20independent%20of%20antibiotic%20treatment%20duration%20or%20dietary%20phytochemical%20amendment.%20We%20observed%20few%20compositional%20differences%20between%20non-responder%20microbiota%20during%20antibiotic%20treatment%20and%20the%20untreated%20control%20microbiota.%20However%2C%20gene%20expression%20was%20vastly%20different%20between%20non-responder%20microbiota%20and%20controls%20during%20treatment%2C%20with%20non-responder%20communities%20showing%20an%20upregulation%20of%20antimicrobial%20tolerance%20genes%2C%20like%20efflux%20transporters%2C%20and%20a%20down-regulation%20of%20central%20metabolism.%20Future%20work%20should%20focus%20on%20what%20specific%20host-%20or%20microbiome-associated%20factors%20are%20responsible%20for%20tipping%20communities%20between%20responder%20and%20non-responder%20phenotypes%20so%20that%20we%20might%20learn%20to%20harness%20this%20phenomenon%20to%20protect%20our%20microbiota%20from%20routine%20antibiotic%20treatment.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs42003-021-01841-8%22%2C%22ISSN%22%3A%222399-3642%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A18%3A11Z%22%7D%7D%2C%7B%22key%22%3A%22Q437VE3P%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Doan%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDoan%2C%20Phuong%2C%20Phung%20Nguyen%2C%20Akshaya%20Murugesan%2C%20Kumar%20Subramanian%2C%20Saravanan%20Konda%20Mani%2C%20Vignesh%20Kalimuthu%2C%20Bobin%20George%20Abraham%2C%20et%20al.%202021.%20%26%23x201C%3BTargeting%20Orphan%20G%20Protein-Coupled%20Receptor%2017%20with%20T0%20Ligand%20Impairs%20Glioblastoma%20Growth.%26%23x201D%3B%20%3Ci%3ECancers%3C%5C%2Fi%3E%2013%20%2815%29%3A%203773.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcancers13153773%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcancers13153773%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DQ437VE3P%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DFBYQDII5%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Targeting%20Orphan%20G%20Protein-Coupled%20Receptor%2017%20with%20T0%20Ligand%20Impairs%20Glioblastoma%20Growth%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Phuong%22%2C%22lastName%22%3A%22Doan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Phung%22%2C%22lastName%22%3A%22Nguyen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Akshaya%22%2C%22lastName%22%3A%22Murugesan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kumar%22%2C%22lastName%22%3A%22Subramanian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Saravanan%22%2C%22lastName%22%3A%22Konda%20Mani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vignesh%22%2C%22lastName%22%3A%22Kalimuthu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bobin%20George%22%2C%22lastName%22%3A%22Abraham%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brett%20W.%22%2C%22lastName%22%3A%22Stringer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kadalmani%22%2C%22lastName%22%3A%22Balamuthu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olli%22%2C%22lastName%22%3A%22Yli-Harja%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Meenakshisundaram%22%2C%22lastName%22%3A%22Kandhavelu%22%7D%5D%2C%22abstractNote%22%3A%22Glioblastoma%2C%20an%20invasive%20high-grade%20brain%20cancer%2C%20exhibits%20numerous%20treatment%20challenges.%20Amongst%20the%20current%20therapies%2C%20targeting%20functional%20receptors%20and%20active%20signaling%20pathways%20were%20found%20to%20be%20a%20potential%20approach%20for%20treating%20GBM.%20We%20exploited%20the%20role%20of%20endogenous%20expression%20of%20GPR17%2C%20a%20G%20protein-coupled%20receptor%20%28GPCR%29%2C%20with%20agonist%20GA-T0%20in%20the%20survival%20and%20treatment%20of%20GBM.%20RNA%20sequencing%20was%20performed%20to%20understand%20the%20association%20of%20GPR17%20expression%20with%20LGG%20and%20GBM.%20RT-PCR%20and%20immunoblotting%20were%20performed%20to%20confirm%20the%20endogenous%20expression%20of%20GPR17%20mRNA%20and%20its%20encoded%20protein.%20Biological%20functions%20of%20GPR17%20in%20the%20GBM%20cells%20was%20assessed%20by%20in%20vitro%20analysis.%20HPLC%20and%20histopathology%20in%20wild%20mice%20and%20an%20acute-toxicity%20analysis%20in%20a%20patient-derived%20xenograft%20model%20were%20performed%20to%20understand%20the%20clinical%20implication%20of%20GA-T0%20targeting%20GPR17.%20We%20observed%20the%20upregulation%20of%20GPR17%20in%20association%20with%20improved%20survival%20of%20LGG%20and%20GBM%2C%20confirming%20it%20as%20a%20predictive%20biomarker.%20GA-T0-stimulated%20GPR17%20leads%20to%20the%20inhibition%20of%20cyclic%20AMP%20and%20calcium%20flux.%20GPR17%20signaling%20activation%20enhances%20cytotoxicity%20against%20GBM%20cells%20and%2C%20in%20patient%20tissue-derived%20mesenchymal%20subtype%20GBM%20cells%2C%20induces%20apoptosis%20and%20prevents%20proliferation%20by%20stoppage%20of%20the%20cell%20cycle%20at%20the%20G1%20phase.%20Modulation%20of%20the%20key%20genes%20involved%20in%20DNA%20damage%2C%20cell%20cycle%20arrest%2C%20and%20in%20several%20signaling%20pathways%2C%20including%20MAPK%5C%2FERK%2C%20PI3K-Akt%2C%20STAT%2C%20and%20NF-%5Cu03baB%2C%20prevents%20tumor%20regression.%20In%20vivo%20activation%20of%20GPR17%20by%20GA-T0%20reduces%20the%20tumor%20volume%2C%20uncovering%20the%20potential%20of%20GA-T0-GPR17%20as%20a%20targeted%20therapy%20for%20GBM%20treatment.%20Conclusion%3A%20Our%20analysis%20suggests%20that%20GA-T0%20targeting%20the%20GPR17%20receptor%20presents%20a%20novel%20therapy%20for%20treating%20glioblastoma.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3390%5C%2Fcancers13153773%22%2C%22ISSN%22%3A%222072-6694%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A32%3A42Z%22%7D%7D%2C%7B%22key%22%3A%22YC75NR9P%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Doan%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDoan%2C%20Phuong%2C%20Phung%20Nguyen%2C%20Akshaya%20Murugesan%2C%20Nuno%20R.%20Candeias%2C%20Olli%20Yli-Harja%2C%20and%20Meenakshisundaram%20Kandhavelu.%202021.%20%26%23x201C%3BAlkylaminophenol%20and%20GPR17%20Agonist%20for%20Glioblastoma%20Therapy%3A%20A%20Combinational%20Approach%20for%20Enhanced%20Cell%20Death%20Activity.%26%23x201D%3B%20%3Ci%3ECells%3C%5C%2Fi%3E%2010%20%288%29%3A%201975.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcells10081975%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcells10081975%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DYC75NR9P%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3D7WFP28QL%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Alkylaminophenol%20and%20GPR17%20Agonist%20for%20Glioblastoma%20Therapy%3A%20A%20Combinational%20Approach%20for%20Enhanced%20Cell%20Death%20Activity%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Phuong%22%2C%22lastName%22%3A%22Doan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Phung%22%2C%22lastName%22%3A%22Nguyen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Akshaya%22%2C%22lastName%22%3A%22Murugesan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nuno%20R.%22%2C%22lastName%22%3A%22Candeias%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olli%22%2C%22lastName%22%3A%22Yli-Harja%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Meenakshisundaram%22%2C%22lastName%22%3A%22Kandhavelu%22%7D%5D%2C%22abstractNote%22%3A%22Drug%20resistance%20and%20tumor%20heterogeneity%20limits%20the%20therapeutic%20efficacy%20in%20treating%20glioblastoma%2C%20an%20aggressive%20infiltrative%20type%20of%20brain%20tumor.%20GBM%20cells%20develops%20resistance%20against%20chemotherapeutic%20agent%2C%20temozolomide%20%28TMZ%29%2C%20which%20leads%20to%20the%20failure%20in%20treatment%20strategies.%20This%20enduring%20challenge%20of%20GBM%20drug%20resistance%20could%20be%20rational%20by%20combinatorial%20targeted%20therapy.%20Here%2C%20we%20evaluated%20the%20combinatorial%20effect%20of%20phenolic%20compound%20%282-%283%2C4-dihydroquinolin-1%282H%29-yl%29%28p-tolyl%29methyl%29phenol%20%28THTMP%29%2C%20GPR17%20agonist%202-%28%7B5-%5B3-%28Morpholine-4-sulfonyl%29phenyl%5D-4-%5B4-%28trifluoromethoxy%29phenyl%5D-4H-1%2C2%2C4-triazol-3-yl%7Dsulfanyl%29-N-%5B4-%28propan-2-yl%29phenyl%5Dacetamide%20%28T0510.3657%20or%20T0%29%20with%20the%20frontline%20drug%2C%20TMZ%2C%20on%20the%20inhibition%20of%20GBM%20cells.%20Mesenchymal%20cell%20lines%20derived%20from%20patients%27%20tumors%2C%20MMK1%20and%20JK2%20were%20treated%20with%20the%20combination%20of%20THTMP%20%2B%20T0%2C%20THTMP%20%2B%20TMZ%20and%20T0%20%2B%20TMZ.%20Cellular%20migration%2C%20invasion%20and%20clonogenicity%20assays%20were%20performed%20to%20check%20the%20migratory%20behavior%20and%20the%20ability%20to%20form%20colony%20of%20GBM%20cells.%20Mitochondrial%20membrane%20permeability%20%28MMP%29%20assay%20and%20intracellular%20calcium%2C%20%5BCa2%2B%5Di%2C%20assay%20was%20done%20to%20comprehend%20the%20mechanism%20of%20apoptosis.%20Role%20of%20apoptosis-related%20signaling%20molecules%20was%20analyzed%20in%20the%20induction%20of%20programmed%20cell%20death.%20In%20vivo%20validation%20in%20the%20xenograft%20models%20further%20validates%20the%20preclinical%20efficacy%20of%20the%20combinatorial%20drug.%20GBM%20cells%20exert%20better%20synergistic%20effect%20when%20exposed%20to%20the%20cytotoxic%20concentration%20of%20THTMP%20%2B%20T0%2C%20than%20other%20combinations.%20It%20also%20inhibited%20tumor%20cell%20proliferation%2C%20migration%2C%20invasion%2C%20colony-forming%20ability%20and%20cell%20cycle%20progression%20in%20S%20phase%2C%20better%20than%20the%20other%20combinations.%20Moreover%2C%20the%20combination%20of%20THTMP%20%2B%20T0%20profoundly%20increased%20the%20%5BCa2%2B%5Di%2C%20reactive%20oxygen%20species%20in%20a%20time-dependent%20manner%2C%20thus%20affecting%20MMP%20and%20leading%20to%20apoptosis.%20The%20activation%20of%20intrinsic%20apoptotic%20pathway%20was%20regulated%20by%20the%20expression%20of%20Bcl-2%2C%20cleaved%20caspases-3%2C%20cytochrome%20c%2C%20HSP27%2C%20cIAP-1%2C%20cIAP-2%2C%20p53%2C%20and%20XIAP.%20The%20combinatorial%20drug%20showed%20promising%20anti-tumor%20efficacy%20in%20GBM%20xenograft%20model%20by%20reducing%20the%20tumor%20volume%2C%20suggesting%20it%20as%20an%20alternative%20drug%20to%20TMZ.%20Our%20findings%20indicate%20the%20coordinated%20administration%20of%20THTMP%20%2B%20T0%20as%20an%20efficient%20therapy%20for%20inhibiting%20GBM%20cell%20proliferation.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3390%5C%2Fcells10081975%22%2C%22ISSN%22%3A%222073-4409%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A33%3A26Z%22%7D%7D%2C%7B%22key%22%3A%22MU56ZW9W%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Dokic%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDokic%2C%20Anja%2C%20Eliza%20Peterson%2C%20Mario%20L.%20Arrieta-Ortiz%2C%20Min%20Pan%2C%20Alessandro%20Di%20Maio%2C%20Nitin%20Baliga%2C%20and%20Apoorva%20Bhatt.%202021.%20%26%23x201C%3BMycobacterium%20Abscessus%20Biofilms%20Produce%20an%20Extracellular%20Matrix%20and%20Have%20a%20Distinct%20Mycolic%20Acid%20Profile.%26%23x201D%3B%20%3Ci%3ECell%20Surface%20%28Amsterdam%2C%20Netherlands%29%3C%5C%2Fi%3E%207%3A100051.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.tcsw.2021.100051%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.tcsw.2021.100051%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DMU56ZW9W%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DIJMP9QHY%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Mycobacterium%20abscessus%20biofilms%20produce%20an%20extracellular%20matrix%20and%20have%20a%20distinct%20mycolic%20acid%20profile%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anja%22%2C%22lastName%22%3A%22Dokic%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eliza%22%2C%22lastName%22%3A%22Peterson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mario%20L.%22%2C%22lastName%22%3A%22Arrieta-Ortiz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Min%22%2C%22lastName%22%3A%22Pan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alessandro%22%2C%22lastName%22%3A%22Di%20Maio%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nitin%22%2C%22lastName%22%3A%22Baliga%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Apoorva%22%2C%22lastName%22%3A%22Bhatt%22%7D%5D%2C%22abstractNote%22%3A%22A%20non-tuberculous%20mycobacterium%2C%20Mycobacterium%20abscessus%20is%20an%20emerging%20opportunistic%20pathogen%20associated%20with%20difficult%20to%20treat%20pulmonary%20infections%2C%20particularly%20in%20patients%20suffering%20from%20cystic%20fibrosis.%20It%20is%20capable%20of%20forming%20biofilms%20in%20vitro%20that%20result%20in%20an%20increase%20of%20already%20high%20levels%20of%20antibiotic%20resistance%20in%20this%20bacterium.%20Evidence%20that%20M.%20abscessus%20forms%20biofilm-like%20microcolonies%20in%20patient%20lungs%20and%20on%20medical%20devices%20further%20implicated%20the%20need%20to%20investigate%20this%20biofilm%20in%20detail.%20Therefore%2C%20in%20this%20study%20we%20characterized%20the%20M.%20abscessus%20pellicular%20biofilm%2C%20formed%20on%20a%20liquid-air%20interface%2C%20by%20studying%20its%20molecular%20composition%2C%20and%20its%20transcriptional%20profile%20in%20comparison%20to%20planktonic%20cells.%20Using%20scanning%20electron%20micrographs%20and%20fluorescence%20microscopy%2C%20we%20showed%20that%20M.%20abscessus%20biofilms%20produce%20an%20extracellular%20matrix%20composed%20of%20lipids%2C%20proteins%2C%20carbohydrates%20and%20extracellular%20DNA.%20Transcriptomic%20analysis%20of%20biofilms%20revealed%20an%20upregulation%20of%20pathways%20involved%20in%20the%20glyoxylate%20shunt%2C%20redox%20metabolism%20and%20mycolic%20acid%20biosynthesis.%20Genes%20involved%20in%20elongation%20and%20desaturation%20of%20mycolic%20acids%20were%20highly%20upregulated%20in%20biofilms%20and%2C%20mirroring%20those%20findings%2C%20biochemical%20analysis%20of%20mycolates%20revealed%20molecular%20changes%20and%20an%20increase%20in%20mycolic%20acid%20chain%20length.%20Together%20these%20results%20give%20us%20an%20insight%20into%20the%20complex%20structure%20of%20M.%20abscessus%20biofilms%2C%20the%20understanding%20of%20which%20may%20be%20adapted%20for%20clinical%20use%20in%20treatment%20of%20biofilm%20infections%2C%20including%20strategies%20for%20dispersing%20the%20extracellular%20matrix%2C%20allowing%20antibiotics%20to%20gain%20access%20to%20bacteria%20within%20the%20biofilm.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.tcsw.2021.100051%22%2C%22ISSN%22%3A%222468-2330%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A16%3A10Z%22%7D%7D%2C%7B%22key%22%3A%22CU5Y4QMT%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Doty%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EDoty%2C%20Raymond%20T.%2C%20Xiaowei%20Yan%2C%20Changting%20Meng%2C%20Christopher%20Lausted%2C%20Qiang%20Tian%2C%20and%20Janis%20L.%20Abkowitz.%202021.%20%26%23x201C%3BSingle-Cell%20Analysis%20of%20Erythropoiesis%20in%20Rpl11%20Haploinsufficient%20Mice%20Reveals%20Insight%20into%20the%20Pathogenesis%20of%20Diamond%20Blackfan%20Anemia.%26%23x201D%3B%20%3Ci%3EExperimental%20Hematology%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.exphem.2021.02.010%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.exphem.2021.02.010%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DCU5Y4QMT%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Single-cell%20analysis%20of%20erythropoiesis%20in%20Rpl11%20haploinsufficient%20mice%20reveals%20insight%20into%20the%20pathogenesis%20of%20Diamond%20Blackfan%20anemia%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Raymond%20T.%22%2C%22lastName%22%3A%22Doty%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xiaowei%22%2C%22lastName%22%3A%22Yan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Changting%22%2C%22lastName%22%3A%22Meng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christopher%22%2C%22lastName%22%3A%22Lausted%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Qiang%22%2C%22lastName%22%3A%22Tian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Janis%20L.%22%2C%22lastName%22%3A%22Abkowitz%22%7D%5D%2C%22abstractNote%22%3A%22Rpl11%20haploinsufficient%20mice%20develop%20a%20macrocytic%20anemia%20similar%20to%20patients%20with%20DBA.%20Here%2C%20we%20fully%20characterize%20this%20model%20from%20clinical%20and%20pathophysiological%20perspectives.%20Early%20erythroid%20precursors%20have%20increased%20heme%20content%20and%20high%20cytoplasmic%20ROS%2C%20impairing%20erythroid%20differentiation%20at%20the%20CFU-E%5C%2Fproerythroblast%20stage%20and%20subsequently.%20Using%20single-cell%20analyses%20that%20link%20a%20cell%27s%20surface%20protein%20expression%20to%20its%20total%20transcriptome%20and%20unbiased%20analyses%2C%20we%20show%20GATA1%2C%20GATA1%20target%20gene%20and%20mitotic%20spindle%20pathway%20gene%20transcription%20were%20the%20pathways%20most%20decreased.%20Expression%20of%20ribosome%20protein%20and%20globin%20genes%20were%20amplified.%20These%20changes%2C%20as%20well%20as%20the%20other%20transcriptional%20changes%20that%20were%20identified%2C%20closely%20resemble%20findings%20in%20mice%20that%20lack%20the%20heme%20export%20protein%20FLVCR%2C%20and%20thus%20suggest%20that%20heme%20excess%20and%20toxicity%20are%20the%20primary%20drivers%20of%20the%20macrocytic%20anemia.%20Consistent%20with%20this%2C%20treating%20Rpl11%20haploinsufficient%20mice%20with%20corticosteroids%20increased%20the%20numbers%20of%20earliest%20erythroblasts%20but%20failed%20to%20overcome%20heme%20toxicities%20and%20improve%20the%20anemia.%20Rpl11%20haploinsufficient%20mice%20uniquely%20upregulated%20mitochondrial%20genes%2C%20p53%20and%20CDKN1A%20pathway%20genes%2C%20and%20DNA%20damage%20checkpoint%20genes%2C%20which%20should%20contribute%20further%20to%20erythroid%20marrow%20failure.%20Together%20our%20data%20establish%20Rpl11%20haploinsufficient%20mice%20as%20an%20excellent%20model%20of%20DBA%20that%20can%20be%20used%20to%20study%20DBA%20pathogenesis%20and%20test%20novel%20therapies.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.exphem.2021.02.010%22%2C%22ISSN%22%3A%221873-2399%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A21%3A27Z%22%7D%7D%2C%7B%22key%22%3A%223DBQQ8JS%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Emmert-Streib%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EEmmert-Streib%2C%20Frank%2C%20Kalifa%20Manjang%2C%20Matthias%20Dehmer%2C%20Olli%20Yli-Harja%2C%20and%20Anssi%20Auvinen.%202021.%20%26%23x201C%3BAre%20There%20Limits%20in%20Explainability%20of%20Prognostic%20Biomarkers%3F%20Scrutinizing%20Biological%20Utility%20of%20Established%20Signatures.%26%23x201D%3B%20%3Ci%3ECancers%3C%5C%2Fi%3E%2013%20%2820%29%3A%205087.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcancers13205087%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fcancers13205087%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D3DBQQ8JS%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DM9Y7B5JA%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Are%20There%20Limits%20in%20Explainability%20of%20Prognostic%20Biomarkers%3F%20Scrutinizing%20Biological%20Utility%20of%20Established%20Signatures%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Frank%22%2C%22lastName%22%3A%22Emmert-Streib%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kalifa%22%2C%22lastName%22%3A%22Manjang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthias%22%2C%22lastName%22%3A%22Dehmer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olli%22%2C%22lastName%22%3A%22Yli-Harja%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anssi%22%2C%22lastName%22%3A%22Auvinen%22%7D%5D%2C%22abstractNote%22%3A%22Prognostic%20biomarkers%20can%20have%20an%20important%20role%20in%20the%20clinical%20practice%20because%20they%20allow%20stratification%20of%20patients%20in%20terms%20of%20predicting%20the%20outcome%20of%20a%20disorder.%20Obstacles%20for%20developing%20such%20markers%20include%20lack%20of%20robustness%20when%20using%20different%20data%20sets%20and%20limited%20concordance%20among%20similar%20signatures.%20In%20this%20paper%2C%20we%20highlight%20a%20new%20problem%20that%20relates%20to%20the%20biological%20meaning%20of%20already%20established%20prognostic%20gene%20expression%20signatures.%20Specifically%2C%20it%20is%20commonly%20assumed%20that%20prognostic%20markers%20provide%20sensible%20biological%20information%20and%20molecular%20explanations%20about%20the%20underlying%20disorder.%20However%2C%20recent%20studies%20on%20prognostic%20biomarkers%20investigating%2080%20established%20signatures%20of%20breast%20and%20prostate%20cancer%20demonstrated%20that%20this%20is%20not%20the%20case.%20We%20will%20show%20that%20this%20surprising%20result%20is%20related%20to%20the%20distinction%20between%20causal%20models%20and%20predictive%20models%20and%20the%20obfuscating%20usage%20of%20these%20models%20in%20the%20biomedical%20literature.%20Furthermore%2C%20we%20suggest%20a%20falsification%20procedure%20for%20studies%20aiming%20to%20establish%20a%20prognostic%20signature%20to%20safeguard%20against%20false%20expectations%20with%20respect%20to%20biological%20utility.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3390%5C%2Fcancers13205087%22%2C%22ISSN%22%3A%222072-6694%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A37%3A12Z%22%7D%7D%2C%7B%22key%22%3A%22NCDJM85A%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Fecho%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EFecho%2C%20Karamarie%2C%20James%20Balhoff%2C%20Chris%20Bizon%2C%20William%20E.%20Byrd%2C%20Sui%20Hang%2C%20David%20Koslicki%2C%20Stefano%20E.%20Rensi%2C%20et%20al.%202021.%20%26%23x201C%3BApplication%20of%20MCAT%20Questions%20as%20a%20Testing%20Tool%20and%20Evaluation%20Metric%20for%20Knowledge%20Graph-Based%20Reasoning%20Systems.%26%23x201D%3B%20%3Ci%3EClinical%20and%20Translational%20Science%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1111%5C%2Fcts.13021%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1111%5C%2Fcts.13021%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DNCDJM85A%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3D3L3EM4A8%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Application%20of%20MCAT%20questions%20as%20a%20testing%20tool%20and%20evaluation%20metric%20for%20knowledge%20graph-based%20reasoning%20systems%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karamarie%22%2C%22lastName%22%3A%22Fecho%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%22%2C%22lastName%22%3A%22Balhoff%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chris%22%2C%22lastName%22%3A%22Bizon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22William%20E.%22%2C%22lastName%22%3A%22Byrd%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sui%22%2C%22lastName%22%3A%22Hang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Koslicki%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stefano%20E.%22%2C%22lastName%22%3A%22Rensi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Patrick%20L.%22%2C%22lastName%22%3A%22Schmitt%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mathias%20J.%22%2C%22lastName%22%3A%22Wawer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mark%22%2C%22lastName%22%3A%22Williams%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stanley%20C.%22%2C%22lastName%22%3A%22Ahalt%22%7D%5D%2C%22abstractNote%22%3A%22%5C%22Knowledge%20graphs%5C%22%20%28KGs%29%20have%20become%20a%20common%20approach%20for%20representing%20biomedical%20knowledge.%20In%20a%20KG%2C%20multiple%20biomedical%20data%20sets%20can%20be%20linked%20together%20as%20a%20graph%20representation%2C%20with%20nodes%20representing%20entities%2C%20such%20as%20%5C%22chemical%20substance%5C%22%20or%20%5C%22genes%2C%5C%22%20and%20edges%20representing%20predicates%2C%20such%20as%20%5C%22causes%5C%22%20or%20%5C%22treats.%5C%22%20Reasoning%20and%20inference%20algorithms%20can%20then%20be%20applied%20to%20the%20KG%20and%20used%20to%20generate%20new%20knowledge.%20We%20developed%20three%20KG-based%20question-answering%20systems%20as%20part%20of%20the%20Biomedical%20Data%20Translator%20program.%20These%20systems%20are%20typically%20tested%20and%20evaluated%20using%20traditional%20software%20engineering%20tools%20and%20approaches.%20In%20this%20study%2C%20we%20explored%20a%20team-based%20approach%20to%20test%20and%20evaluate%20the%20prototype%20%5C%22Translator%20Reasoners%5C%22%20through%20the%20application%20of%20Medical%20College%20Admission%20Test%20%28MCAT%29%20questions.%20Specifically%2C%20we%20describe%20three%20%5C%22hackathons%2C%5C%22%20in%20which%20the%20developers%20of%20each%20of%20the%20three%20systems%20worked%20together%20with%20a%20moderator%20to%20determine%20whether%20the%20applications%20could%20be%20used%20to%20solve%20MCAT%20questions.%20The%20results%20demonstrate%20progressive%20improvement%20in%20system%20performance%2C%20with%200%25%20%280%5C%2F5%29%20correct%20answers%20during%20the%20first%20hackathon%2C%2075%25%20%283%5C%2F4%29%20correct%20during%20the%20second%20hackathon%2C%20and%20100%25%20%285%5C%2F5%29%20correct%20during%20the%20final%20hackathon.%20We%20discuss%20the%20technical%20and%20sociologic%20lessons%20learned%20and%20conclude%20that%20MCAT%20questions%20can%20be%20applied%20successfully%20in%20the%20context%20of%20moderated%20hackathons%20to%20test%20and%20evaluate%20prototype%20KG-based%20question-answering%20systems%2C%20identify%20gaps%20in%20current%20capabilities%2C%20and%20improve%20performance.%20Finally%2C%20we%20highlight%20several%20published%20clinical%20and%20translational%20science%20applications%20of%20the%20Translator%20Reasoners.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1111%5C%2Fcts.13021%22%2C%22ISSN%22%3A%221752-8062%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A18%3A01Z%22%7D%7D%2C%7B%22key%22%3A%22V4JQF5WK%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Fedorov%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EFedorov%2C%20Andrey%2C%20William%20J.%20R.%20Longabaugh%2C%20David%20Pot%2C%20David%20A.%20Clunie%2C%20Steve%20Pieper%2C%20Hugo%20J.%20W.%20L.%20Aerts%2C%20Andr%26%23xE9%3B%20Homeyer%2C%20et%20al.%202021.%20%26%23x201C%3BNCI%20Imaging%20Data%20Commons.%26%23x201D%3B%20%3Ci%3ECancer%20Research%3C%5C%2Fi%3E%2081%20%2816%29%3A%204188%26%23x2013%3B93.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1158%5C%2F0008-5472.CAN-21-0950%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1158%5C%2F0008-5472.CAN-21-0950%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DV4JQF5WK%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DIX3CJBMS%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22NCI%20Imaging%20Data%20Commons%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrey%22%2C%22lastName%22%3A%22Fedorov%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22William%20J.%20R.%22%2C%22lastName%22%3A%22Longabaugh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Pot%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%20A.%22%2C%22lastName%22%3A%22Clunie%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Steve%22%2C%22lastName%22%3A%22Pieper%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hugo%20J.%20W.%20L.%22%2C%22lastName%22%3A%22Aerts%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Homeyer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rob%22%2C%22lastName%22%3A%22Lewis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Afshin%22%2C%22lastName%22%3A%22Akbarzadeh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dennis%22%2C%22lastName%22%3A%22Bontempi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22William%22%2C%22lastName%22%3A%22Clifford%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Markus%20D.%22%2C%22lastName%22%3A%22Herrmann%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Henning%22%2C%22lastName%22%3A%22H%5Cu00f6fener%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Igor%22%2C%22lastName%22%3A%22Octaviano%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chad%22%2C%22lastName%22%3A%22Osborne%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Suzanne%22%2C%22lastName%22%3A%22Paquette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%22%2C%22lastName%22%3A%22Petts%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Davide%22%2C%22lastName%22%3A%22Punzo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Madelyn%22%2C%22lastName%22%3A%22Reyes%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniela%20P.%22%2C%22lastName%22%3A%22Schacherer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mi%22%2C%22lastName%22%3A%22Tian%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22George%22%2C%22lastName%22%3A%22White%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Erik%22%2C%22lastName%22%3A%22Ziegler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ilya%22%2C%22lastName%22%3A%22Shmulevich%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Todd%22%2C%22lastName%22%3A%22Pihl%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ulrike%22%2C%22lastName%22%3A%22Wagner%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Keyvan%22%2C%22lastName%22%3A%22Farahani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ron%22%2C%22lastName%22%3A%22Kikinis%22%7D%5D%2C%22abstractNote%22%3A%22The%20National%20Cancer%20Institute%20%28NCI%29%20Cancer%20Research%20Data%20Commons%20%28CRDC%29%20aims%20to%20establish%20a%20national%20cloud-based%20data%20science%20infrastructure.%20Imaging%20Data%20Commons%20%28IDC%29%20is%20a%20new%20component%20of%20CRDC%20supported%20by%20the%20Cancer%20Moonshot.%20The%20goal%20of%20IDC%20is%20to%20enable%20a%20broad%20spectrum%20of%20cancer%20researchers%2C%20with%20and%20without%20imaging%20expertise%2C%20to%20easily%20access%20and%20explore%20the%20value%20of%20deidentified%20imaging%20data%20and%20to%20support%20integrated%20analyses%20with%20nonimaging%20data.%20We%20achieve%20this%20goal%20by%20colocating%20versatile%20imaging%20collections%20with%20cloud-based%20computing%20resources%20and%20data%20exploration%2C%20visualization%2C%20and%20analysis%20tools.%20The%20IDC%20pilot%20was%20released%20in%20October%202020%20and%20is%20being%20continuously%20populated%20with%20radiology%20and%20histopathology%20collections.%20IDC%20provides%20access%20to%20curated%20imaging%20collections%2C%20accompanied%20by%20documentation%2C%20a%20user%20forum%2C%20and%20a%20growing%20number%20of%20analysis%20use%20cases%20that%20aim%20to%20demonstrate%20the%20value%20of%20a%20data%20commons%20framework%20applied%20to%20cancer%20imaging%20research.%20SIGNIFICANCE%3A%20This%20study%20introduces%20NCI%20Imaging%20Data%20Commons%2C%20a%20new%20repository%20of%20the%20NCI%20Cancer%20Research%20Data%20Commons%2C%20which%20will%20support%20cancer%20imaging%20research%20on%20the%20cloud.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1158%5C%2F0008-5472.CAN-21-0950%22%2C%22ISSN%22%3A%221538-7445%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A30%3A48Z%22%7D%7D%2C%7B%22key%22%3A%22SL6A8L8K%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Ghiselli%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGhiselli%2C%20Fabrizio%2C%20Andr%26%23xE9%3B%20Gomes-Dos-Santos%2C%20Coen%20M.%20Adema%2C%20Manuel%20Lopes-Lima%2C%20Joel%20Sharbrough%2C%20and%20Jeffrey%20L.%20Boore.%202021.%20%26%23x201C%3BMolluscan%20Mitochondrial%20Genomes%20Break%20the%20Rules.%26%23x201D%3B%20%3Ci%3EPhilosophical%20Transactions%20of%20the%20Royal%20Society%20of%20London.%20Series%20B%2C%20Biological%20Sciences%3C%5C%2Fi%3E%20376%20%281825%29%3A%2020200159.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1098%5C%2Frstb.2020.0159%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1098%5C%2Frstb.2020.0159%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DSL6A8L8K%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Molluscan%20mitochondrial%20genomes%20break%20the%20rules%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fabrizio%22%2C%22lastName%22%3A%22Ghiselli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Gomes-Dos-Santos%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Coen%20M.%22%2C%22lastName%22%3A%22Adema%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Manuel%22%2C%22lastName%22%3A%22Lopes-Lima%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Joel%22%2C%22lastName%22%3A%22Sharbrough%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffrey%20L.%22%2C%22lastName%22%3A%22Boore%22%7D%5D%2C%22abstractNote%22%3A%22The%20first%20animal%20mitochondrial%20genomes%20to%20be%20sequenced%20were%20of%20several%20vertebrates%20and%20model%20organisms%2C%20and%20the%20consistency%20of%20genomic%20features%20found%20has%20led%20to%20a%20%27textbook%20description%27.%20However%2C%20a%20more%20broad%20phylogenetic%20sampling%20of%20complete%20animal%20mitochondrial%20genomes%20has%20found%20many%20cases%20where%20these%20features%20do%20not%20exist%2C%20and%20the%20phylum%20Mollusca%20is%20especially%20replete%20with%20these%20exceptions.%20The%20characterization%20of%20full%20mollusc%20mitogenomes%20required%20considerable%20effort%20involving%20challenging%20molecular%20biology%2C%20but%20has%20created%20an%20enormous%20catalogue%20of%20surprising%20deviations%20from%20that%20textbook%20description%2C%20including%20wide%20variation%20in%20size%2C%20radical%20genome%20rearrangements%2C%20gene%20duplications%20and%20losses%2C%20the%20introduction%20of%20novel%20genes%2C%20and%20a%20complex%20system%20of%20inheritance%20dubbed%20%27doubly%20uniparental%20inheritance%27.%20Here%2C%20we%20review%20the%20extraordinary%20variation%20in%20architecture%2C%20molecular%20functioning%20and%20intergenerational%20transmission%20of%20molluscan%20mitochondrial%20genomes.%20Such%20features%20represent%20a%20great%20potential%20for%20the%20discovery%20of%20biological%20history%2C%20processes%20and%20functions%20that%20are%20novel%20for%20animal%20mitochondrial%20genomes.%20This%20provides%20a%20model%20system%20for%20studying%20the%20evolution%20and%20the%20manifold%20roles%20that%20mitochondria%20play%20in%20organismal%20physiology%2C%20and%20many%20ways%20that%20the%20study%20of%20mitochondrial%20genomes%20are%20useful%20for%20phylogeny%20and%20population%20biology.%20This%20article%20is%20part%20of%20the%20Theo%20Murphy%20meeting%20issue%20%27Molluscan%20genomics%3A%20broad%20insights%20and%20future%20directions%20for%20a%20neglected%20phylum%27.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1098%5C%2Frstb.2020.0159%22%2C%22ISSN%22%3A%221471-2970%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A16%3A34Z%22%7D%7D%2C%7B%22key%22%3A%22MZ678FTB%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Gibbs%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGibbs%2C%20David%20L.%2C%20Boris%20Aguilar%2C%20V%26%23xE9%3Bsteinn%20Thorsson%2C%20Alexander%20V.%20Ratushny%2C%20and%20Ilya%20Shmulevich.%202021.%20%26%23x201C%3BPatient-Specific%20Cell%20Communication%20Networks%20Associate%20With%20Disease%20Progression%20in%20Cancer.%26%23x201D%3B%20%3Ci%3EFrontiers%20in%20Genetics%3C%5C%2Fi%3E%2012%3A667382.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffgene.2021.667382%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3389%5C%2Ffgene.2021.667382%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DMZ678FTB%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DKT5GKWSI%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Patient-Specific%20Cell%20Communication%20Networks%20Associate%20With%20Disease%20Progression%20in%20Cancer%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%20L.%22%2C%22lastName%22%3A%22Gibbs%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Boris%22%2C%22lastName%22%3A%22Aguilar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22V%5Cu00e9steinn%22%2C%22lastName%22%3A%22Thorsson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexander%20V.%22%2C%22lastName%22%3A%22Ratushny%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ilya%22%2C%22lastName%22%3A%22Shmulevich%22%7D%5D%2C%22abstractNote%22%3A%22The%20maintenance%20and%20function%20of%20tissues%20in%20health%20and%20disease%20depends%20on%20cell-cell%20communication.%20This%20work%20shows%20how%20high-level%20features%2C%20representing%20cell-cell%20communication%2C%20can%20be%20defined%20and%20used%20to%20associate%20certain%20signaling%20%5C%22axes%5C%22%20with%20clinical%20outcomes.%20We%20generated%20a%20scaffold%20of%20cell-cell%20interactions%20and%20defined%20a%20probabilistic%20method%20for%20creating%20per-patient%20weighted%20graphs%20based%20on%20gene%20expression%20and%20cell%20deconvolution%20results.%20With%20this%20method%2C%20we%20generated%20over%209%2C000%20graphs%20for%20The%20Cancer%20Genome%20Atlas%20%28TCGA%29%20patient%20samples%2C%20each%20representing%20likely%20channels%20of%20intercellular%20communication%20in%20the%20tumor%20microenvironment%20%28TME%29.%20It%20was%20shown%20that%20cell-cell%20edges%20were%20strongly%20associated%20with%20disease%20severity%20and%20progression%2C%20in%20terms%20of%20survival%20time%20and%20tumor%20stage.%20Within%20individual%20tumor%20types%2C%20there%20are%20predominant%20cell%20types%2C%20and%20the%20collection%20of%20associated%20edges%20were%20found%20to%20be%20predictive%20of%20clinical%20phenotypes.%20Additionally%2C%20genes%20associated%20with%20differentially%20weighted%20edges%20were%20enriched%20in%20Gene%20Ontology%20terms%20associated%20with%20tissue%20structure%20and%20immune%20response.%20Code%2C%20data%2C%20and%20notebooks%20are%20provided%20to%20enable%20the%20application%20of%20this%20method%20to%20any%20expression%20dataset%20%28https%3A%5C%2F%5C%2Fgithub.com%5C%2FIlyaLab%5C%2FPan-Cancer-Cell-Cell-Comm-Net%29.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3389%5C%2Ffgene.2021.667382%22%2C%22ISSN%22%3A%221664-8021%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T19%3A16%3A54Z%22%7D%7D%2C%7B%22key%22%3A%224CYG4DMK%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Girinathan%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGirinathan%2C%20Brintha%20P.%2C%20Nicholas%20DiBenedetto%2C%20Jay%20N.%20Worley%2C%20Johann%20Peltier%2C%20Mario%20L.%20Arrieta-Ortiz%2C%20Selva%20Rupa%20Christinal%20Immanuel%2C%20Richard%20Lavin%2C%20et%20al.%202021.%20%26%23x201C%3BIn%26%23xA0%3BVivo%20Commensal%20Control%20of%20Clostridioides%20Difficile%20Virulence.%26%23x201D%3B%20%3Ci%3ECell%20Host%20%26amp%3B%20Microbe%3C%5C%2Fi%3E%2C%20S1931-3128%2821%2900423-6.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.chom.2021.09.007%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.chom.2021.09.007%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D4CYG4DMK%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22In%5Cu00a0vivo%20commensal%20control%20of%20Clostridioides%20difficile%20virulence%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Brintha%20P.%22%2C%22lastName%22%3A%22Girinathan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicholas%22%2C%22lastName%22%3A%22DiBenedetto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jay%20N.%22%2C%22lastName%22%3A%22Worley%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Johann%22%2C%22lastName%22%3A%22Peltier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mario%20L.%22%2C%22lastName%22%3A%22Arrieta-Ortiz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Selva%20Rupa%20Christinal%22%2C%22lastName%22%3A%22Immanuel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Richard%22%2C%22lastName%22%3A%22Lavin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mary%20L.%22%2C%22lastName%22%3A%22Delaney%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christopher%20K.%22%2C%22lastName%22%3A%22Cummins%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Maria%22%2C%22lastName%22%3A%22Hoffman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yan%22%2C%22lastName%22%3A%22Luo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Narjol%22%2C%22lastName%22%3A%22Gonzalez-Escalona%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Allard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20B.%22%2C%22lastName%22%3A%22Onderdonk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Georg%20K.%22%2C%22lastName%22%3A%22Gerber%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Abraham%20L.%22%2C%22lastName%22%3A%22Sonenshein%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nitin%20S.%22%2C%22lastName%22%3A%22Baliga%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Dupuy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lynn%22%2C%22lastName%22%3A%22Bry%22%7D%5D%2C%22abstractNote%22%3A%22Leveraging%20systems%20biology%20approaches%2C%20we%20illustrate%20how%20metabolically%20distinct%20species%20of%20Clostridia%20protect%20against%20or%20worsen%20Clostridioides%20difficile%20infection%20in%20mice%20by%20modulating%20the%20pathogen%27s%20colonization%2C%20growth%2C%20and%20virulence%20to%20impact%20host%20survival.%20Gnotobiotic%20mice%20colonized%20with%20the%20amino%20acid%20fermenter%20Paraclostridium%5Cu00a0bifermentans%20survive%20infection%20with%20reduced%20disease%20severity%2C%20while%20mice%20colonized%20with%20the%20butyrate-producer%2C%20Clostridium%20sardiniense%2C%20succumb%20more%20rapidly.%20Systematic%20in%5Cu00a0vivo%20analyses%20revealed%20how%20each%20commensal%20alters%20the%20gut-nutrient%20environment%20to%20modulate%20the%20pathogen%27s%20metabolism%2C%20gene%20regulatory%20networks%2C%20and%20toxin%20production.%20Oral%20administration%20of%20P.%5Cu00a0bifermentans%20rescues%20conventional%2C%20clindamycin-treated%20mice%20from%20lethal%20C.%5Cu00a0difficile%20infection%20in%20a%20manner%20similar%20to%20that%20of%20monocolonized%20animals%2C%20thereby%20supporting%20the%20therapeutic%20potential%20of%20this%20commensal%20species.%20Our%20findings%20lay%20the%20foundation%20for%20mechanistically%20informed%20therapies%20to%20counter%20C.%5Cu00a0difficile%20disease%20using%20systems%20biology%20approaches%20to%20define%20host-commensal-pathogen%20interactions%20in%5Cu00a0vivo.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.chom.2021.09.007%22%2C%22ISSN%22%3A%221934-6069%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A34%3A28Z%22%7D%7D%2C%7B%22key%22%3A%2225DQJ9W2%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Giurgea%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGiurgea%2C%20Luca%20T.%2C%20Jae-Keun%20Park%2C%20K.A.%20Walters%2C%20Kelsey%20Scherler%2C%20Adriana%20Cervantes-Medina%2C%20Ashley%20Freeman%2C%20Luz%20Angela%20Rosas%2C%20John%20C.%20Kash%2C%20Jeffery%20K.%20Taubenberger%2C%20and%20Matthew%20J.%20Memoli.%202021.%20%26%23x201C%3BThe%20Effect%20of%20Calcium%20and%20Magnesium%20on%20Activity%2C%20Immunogenicity%2C%20and%20Efficacy%20of%20a%20Recombinant%20N1%5C%2FN2%20Neuraminidase%20Vaccine.%26%23x201D%3B%20%3Ci%3ENPJ%20Vaccines%3C%5C%2Fi%3E%206%20%281%29%3A%2048.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41541-021-00310-x%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41541-021-00310-x%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D25DQJ9W2%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DRYDDQFCQ%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22The%20effect%20of%20calcium%20and%20magnesium%20on%20activity%2C%20immunogenicity%2C%20and%20efficacy%20of%20a%20recombinant%20N1%5C%2FN2%20neuraminidase%20vaccine%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luca%20T.%22%2C%22lastName%22%3A%22Giurgea%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jae-Keun%22%2C%22lastName%22%3A%22Park%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22K.A.%22%2C%22lastName%22%3A%22Walters%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kelsey%22%2C%22lastName%22%3A%22Scherler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adriana%22%2C%22lastName%22%3A%22Cervantes-Medina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ashley%22%2C%22lastName%22%3A%22Freeman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luz%20Angela%22%2C%22lastName%22%3A%22Rosas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%20C.%22%2C%22lastName%22%3A%22Kash%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffery%20K.%22%2C%22lastName%22%3A%22Taubenberger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20J.%22%2C%22lastName%22%3A%22Memoli%22%7D%5D%2C%22abstractNote%22%3A%22Despite%20the%20importance%20of%20immunity%20against%20neuraminidase%20%28NA%29%2C%20NA%20content%20and%20immunogenicity%20are%20neglected%20in%20current%20influenza%20vaccines.%20To%20address%20this%2C%20a%20recombinant%20N1%5C%2FN2%20NA%20vaccine%20%28NAV%29%20was%20developed.%20Stability%20assays%20were%20used%20to%20determine%20optimal%20temperature%20and%20buffer%20conditions%20for%20vaccine%20storage.%20The%20effect%20of%20divalent%20cation-related%20enhancement%20of%20NA%20stability%20and%20activity%20on%20N1%20and%20N2%20immunogenicity%20and%20efficacy%20against%20viral%20challenge%20was%20assessed.%20Differences%20in%20activity%20between%20N1%20and%20N2%20and%20cation-related%20activity%20enhancement%20did%20not%20translate%20into%20differences%20in%20immunogenicity%20or%20efficacy.%20NAV-vaccinated%20mice%20showed%20robust%20antibody%20titers%20against%20N1%20and%20N2%2C%20and%20after%20challenge%20with%20influenza%20A%20%28H1N1%29%20virus%2C%20decreased%20viral%20titers%20and%20decreased%20antiviral%20and%20inflammatory%20responses%20by%20transcriptomic%20analysis.%20These%20findings%20provide%20guidance%20for%20optimal%20storage%20and%20assessment%20of%20NA-based%20vaccines%20and%20confirm%20the%20importance%20of%20NA%20in%20influenza%20vaccination%20strategies%20in%20attenuating%20viral%20replication%20and%20limiting%20inflammatory%20responses%20necessary%20to%20clear%20infection.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41541-021-00310-x%22%2C%22ISSN%22%3A%222059-0105%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T00%3A22%3A51Z%22%7D%7D%2C%7B%22key%22%3A%22FDRGXX7K%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Giurgea%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGiurgea%2C%20Luca%20T.%2C%20Adriana%20Cervantes-Medina%2C%20K.A.%20Walters%2C%20Kelsey%20Scherler%2C%20Alison%20Han%2C%20Lindsay%20M.%20Czajkowski%2C%20Holly%20Ann%20Baus%2C%20et%20al.%202021.%20%26%23x201C%3BSex%20Differences%20in%20Influenza%3A%20The%20Challenge%20Study%20Experience.%26%23x201D%3B%20%3Ci%3EThe%20Journal%20of%20Infectious%20Diseases%3C%5C%2Fi%3E%2C%20jiab422.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Finfdis%5C%2Fjiab422%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1093%5C%2Finfdis%5C%2Fjiab422%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DFDRGXX7K%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DNNWPFXAC%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Sex%20Differences%20in%20Influenza%3A%20The%20Challenge%20Study%20Experience%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luca%20T.%22%2C%22lastName%22%3A%22Giurgea%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adriana%22%2C%22lastName%22%3A%22Cervantes-Medina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22K.A.%22%2C%22lastName%22%3A%22Walters%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kelsey%22%2C%22lastName%22%3A%22Scherler%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alison%22%2C%22lastName%22%3A%22Han%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lindsay%20M.%22%2C%22lastName%22%3A%22Czajkowski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Holly%20Ann%22%2C%22lastName%22%3A%22Baus%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sally%22%2C%22lastName%22%3A%22Hunsberger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sabra%20L.%22%2C%22lastName%22%3A%22Klein%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%20C.%22%2C%22lastName%22%3A%22Kash%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeffery%20K.%22%2C%22lastName%22%3A%22Taubenberger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20J.%22%2C%22lastName%22%3A%22Memoli%22%7D%5D%2C%22abstractNote%22%3A%22BACKGROUND%3A%20Preclinical%20animal%20studies%20and%20retrospective%20human%20studies%20suggest%20that%20adult%20females%20have%20worse%20outcomes%20from%20influenza%20than%20males.%20Prospective%20studies%20in%20humans%20are%20missing.%5CnMETHODS%3A%20Data%20from%20164%20healthy%20volunteers%20who%20underwent%20Influenza%20A%5C%2FCalifornia%5C%2F04%5C%2F2009%5C%2FH1N1%20challenge%20were%20compiled%20to%20compare%20differences%20between%20sexes.%20Baseline%20characteristics%2C%20including%20hormone%20levels%2C%20hemagglutination-inhibition%20%28HAI%29%20titers%2C%20neuraminidase-inhibition%20titers%20%28NAI%29%2C%20and%20outcomes%20after%20challenge%20were%20compared.%20Linear%20and%20logistic%20regression%20models%20were%20built%20to%20determine%20significant%20predictor%20variables%20with%20respect%20to%20outcomes%20of%20interest.%5CnRESULTS%3A%20Hemagglutination-inhibition%20%28HAI%29%20titers%20were%20similar%20between%20the%20sexes%2C%20but%20neuraminidase-inhibition%20titers%20%28NAI%29%20were%20higher%20in%20males%20than%20females%20at%204-weeks%20and%208-weeks%20post-challenge.%20Females%20were%20more%20likely%20to%20have%20symptoms%20%28mean%200.96%20vs%200.80%2C%20p%3D.003%29%20and%20to%20have%20a%20higher%20number%20of%20symptoms%20%28median%203%20vs%204%2C%20p%3D.011%29%20than%20males.%20Linear%20and%20logistic%20regression%20models%20showed%20that%20pre-challenge%20NAI%20titers%2C%20but%20not%20HAI%20titers%20or%20sex%20hormone%20levels%2C%20were%20predictive%20of%20all%20shedding%20and%20symptom%20outcomes%20of%20interest.%5CnCONCLUSIONS%3A%20Females%20in%20our%20cohorts%20were%20more%20likely%20to%20be%20symptomatic%20and%20to%20have%20a%20higher%20number%20of%20symptoms%20than%20males.%20NAI%20titers%20predicted%20all%20outcomes%20of%20interest%20and%20may%20explain%20differential%20outcomes%20between%20the%20sexes.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1093%5C%2Finfdis%5C%2Fjiab422%22%2C%22ISSN%22%3A%221537-6613%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T00%3A26%3A26Z%22%7D%7D%2C%7B%22key%22%3A%22QJL89Q2W%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Gnanavel%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGnanavel%2C%20Mutharasu%2C%20Akshaya%20Murugesan%2C%20Saravanan%20Konda%20Mani%2C%20Olli%20Yli-Harja%2C%20and%20Meenakshisundaram%20Kandhavelu.%202021.%20%26%23x201C%3BIdentifying%20the%20MiRNA%20Signature%20Association%20with%20Aging-Related%20Senescence%20in%20Glioblastoma.%26%23x201D%3B%20%3Ci%3EInternational%20Journal%20of%20Molecular%20Sciences%3C%5C%2Fi%3E%2022%20%282%29.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fijms22020517%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fijms22020517%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DQJL89Q2W%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DR65SVYSX%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Identifying%20the%20miRNA%20Signature%20Association%20with%20Aging-Related%20Senescence%20in%20Glioblastoma%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mutharasu%22%2C%22lastName%22%3A%22Gnanavel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Akshaya%22%2C%22lastName%22%3A%22Murugesan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Saravanan%22%2C%22lastName%22%3A%22Konda%20Mani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Olli%22%2C%22lastName%22%3A%22Yli-Harja%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Meenakshisundaram%22%2C%22lastName%22%3A%22Kandhavelu%22%7D%5D%2C%22abstractNote%22%3A%22Glioblastoma%20%28GBM%29%20is%20the%20most%20common%20malignant%20brain%20tumor%20and%20its%20malignant%20phenotypic%20characteristics%20are%20classified%20as%20grade%20IV%20tumors.%20Molecular%20interactions%2C%20such%20as%20protein-protein%2C%20protein-ncRNA%2C%20and%20protein-peptide%20interactions%20are%20crucial%20to%20transfer%20the%20signaling%20communications%20in%20cellular%20signaling%20pathways.%20Evidences%20suggest%20that%20signaling%20pathways%20of%20stem%20cells%20are%20also%20activated%2C%20which%20helps%20the%20propagation%20of%20GBM.%20Hence%2C%20it%20is%20important%20to%20identify%20a%20common%20signaling%20pathway%20that%20could%20be%20visible%20from%20multiple%20GBM%20gene%20expression%20data.%20microRNA%20signaling%20is%20considered%20important%20in%20GBM%20signaling%2C%20which%20needs%20further%20validation.%20We%20performed%20a%20high-throughput%20analysis%20using%20micro%20array%20expression%20profiles%20from%20574%20samples%20to%20explore%20the%20role%20of%20non-coding%20RNAs%20in%20the%20disease%20progression%20and%20unique%20signaling%20communication%20in%20GBM.%20A%20series%20of%20computational%20methods%20involving%20miRNA%20expression%2C%20gene%20ontology%20%28GO%29%20based%20gene%20enrichment%2C%20pathway%20mapping%2C%20and%20annotation%20from%20metabolic%20pathways%20databases%2C%20and%20network%20analysis%20were%20used%20for%20the%20analysis.%20Our%20study%20revealed%20the%20physiological%20roles%20of%20many%20known%20and%20novel%20miRNAs%20in%20cancer%20signaling%2C%20especially%20concerning%20signaling%20in%20cancer%20progression%20and%20proliferation.%20Overall%2C%20the%20results%20revealed%20a%20strong%20connection%20with%20stress%20induced%20senescence%2C%20significant%20miRNA%20targets%20for%20cell%20cycle%20arrest%2C%20and%20many%20common%20signaling%20pathways%20to%20GBM%20in%20the%20network.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3390%5C%2Fijms22020517%22%2C%22ISSN%22%3A%221422-0067%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A19%3A43Z%22%7D%7D%2C%7B%22key%22%3A%227LG6K79S%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Grasberger%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGrasberger%2C%20Helmut%2C%20Andrew%20T.%20Magis%2C%20Elisa%20Sheng%2C%20Matthew%20P.%20Conomos%2C%20Min%20Zhang%2C%20Lea%20S.%20Garzotto%2C%20Guoqing%20Hou%2C%20et%20al.%202021.%20%26%23x201C%3BDUOX2%20Variants%20Associate%20with%20Preclinical%20Disturbances%20in%20Microbiota-Immune%20Homeostasis%20and%20Increased%20Inflammatory%20Bowel%20Disease%20Risk.%26%23x201D%3B%20%3Ci%3EThe%20Journal%20of%20Clinical%20Investigation%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1172%5C%2FJCI141676%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1172%5C%2FJCI141676%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D7LG6K79S%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DDDIN8SZR%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22DUOX2%20variants%20associate%20with%20preclinical%20disturbances%20in%20microbiota-immune%20homeostasis%20and%20increased%20inflammatory%20bowel%20disease%20risk%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Helmut%22%2C%22lastName%22%3A%22Grasberger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20T.%22%2C%22lastName%22%3A%22Magis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elisa%22%2C%22lastName%22%3A%22Sheng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20P.%22%2C%22lastName%22%3A%22Conomos%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Min%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lea%20S.%22%2C%22lastName%22%3A%22Garzotto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guoqing%22%2C%22lastName%22%3A%22Hou%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shrinivas%22%2C%22lastName%22%3A%22Bishu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hiroko%22%2C%22lastName%22%3A%22Nagao-Kitamoto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mohamad%22%2C%22lastName%22%3A%22El-Zataari%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sho%22%2C%22lastName%22%3A%22Kitamoto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nobuhiko%22%2C%22lastName%22%3A%22Kamada%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ryan%22%2C%22lastName%22%3A%22Stidham%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yasutada%22%2C%22lastName%22%3A%22Akiba%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jonathan%22%2C%22lastName%22%3A%22Kaunitz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yael%22%2C%22lastName%22%3A%22Haberman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Subra%22%2C%22lastName%22%3A%22Kugathasan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lee%20A.%22%2C%22lastName%22%3A%22Denson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gilbert%20S.%22%2C%22lastName%22%3A%22Omenn%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22John%20Y.%22%2C%22lastName%22%3A%22Kao%22%7D%5D%2C%22abstractNote%22%3A%22A%20primordial%20gut-epithelial%20innate%20defense%20response%20is%20the%20release%20of%20hydrogen%20peroxide%20by%20dual%20NADPH%20oxidase%20%28DUOX%29.%20In%20inflammatory%20bowel%20disease%20%28IBD%29%2C%20a%20condition%20characterized%20by%20an%20imbalanced%20gut%20microbiota-immune%20homeostasis%2C%20DUOX2%20isoenzyme%20is%20the%20highest%20induced%20gene.%20Performing%20multi-omic%20analyses%20using%202%2C872%20human%20participants%20of%20a%20wellness%20program%2C%20we%20detected%20a%20substantial%20burden%20of%20rare%20protein-altering%20DUOX2%20gene%20variants%20of%20unknown%20physiologic%20significance%20%28155%20unique%20variants%20with%20allele%20frequency%20%3C%201%25%3B%2012.9%25%20carrier%20rate%29.%20We%20identified%20a%20significant%20association%20between%20these%20rare%20loss-of-function%20variants%20and%20increased%20plasma%20levels%20of%20interleukin-17C%20%28FDR%3D2.6e-5%29%2C%20which%20is%20induced%20also%20in%20mucosal%20biopsies%20of%20IBD%20patients.%20DUOX2%20deficient%20mice%20replicated%20increased%20IL17C%20induction%20in%20the%20intestine%2C%20with%20outlier%20high%20Il17c%20expression%20linked%20to%20the%20mucosal%20expansion%20of%20specific%20Proteobacteria%20pathobionts.%20Integrated%20microbiota%5C%2Fhost%20gene%20expression%20analyses%20in%20IBD%20patients%20corroborated%20IL17C%20as%20a%20marker%20for%20epithelial%20activation%20by%20gram-negative%20bacteria.%20Finally%2C%20the%20impact%20of%20DUOX2%20variants%20on%20IL17C%20induction%20provided%20a%20rationale%20for%20variant%20stratification%20in%20case-control%20studies%20that%20substantiated%20DUOX2%20as%20an%20IBD%20risk%20gene%20%28pooled%20OR%20%3D%201.54%20%5B95%25%20CI%201.09-2.18%5D%3B%20P%20%3D%207.1e-4%29.%20Thus%2C%20our%20study%20identifies%20an%20association%20of%20deleterious%20DUOX2%20variants%20with%20a%20preclinical%20hallmark%20of%20disturbed%20microbiota-immune%20homeostasis%20that%20appears%20to%20precede%20the%20manifestation%20of%20IBD.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1172%5C%2FJCI141676%22%2C%22ISSN%22%3A%221558-8238%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A21%3A39Z%22%7D%7D%2C%7B%22key%22%3A%22QKQ8LWAH%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Groussin%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGroussin%2C%20Mathieu%2C%20Mathilde%20Poyet%2C%20Ainara%20Sistiaga%2C%20Sean%20M.%20Kearney%2C%20Katya%20Moniz%2C%20Mary%20Noel%2C%20Jeff%20Hooker%2C%20et%20al.%202021.%20%26%23x201C%3BElevated%20Rates%20of%20Horizontal%20Gene%20Transfer%20in%20the%20Industrialized%20Human%20Microbiome.%26%23x201D%3B%20%3Ci%3ECell%3C%5C%2Fi%3E%20184%20%288%29%3A%202053-2067.e18.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.cell.2021.02.052%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.cell.2021.02.052%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DQKQ8LWAH%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DMRJLUFSB%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Elevated%20rates%20of%20horizontal%20gene%20transfer%20in%20the%20industrialized%20human%20microbiome%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mathieu%22%2C%22lastName%22%3A%22Groussin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mathilde%22%2C%22lastName%22%3A%22Poyet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ainara%22%2C%22lastName%22%3A%22Sistiaga%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20M.%22%2C%22lastName%22%3A%22Kearney%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Katya%22%2C%22lastName%22%3A%22Moniz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mary%22%2C%22lastName%22%3A%22Noel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jeff%22%2C%22lastName%22%3A%22Hooker%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sean%20M.%22%2C%22lastName%22%3A%22Gibbons%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laure%22%2C%22lastName%22%3A%22Segurel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alain%22%2C%22lastName%22%3A%22Froment%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rihlat%20Said%22%2C%22lastName%22%3A%22Mohamed%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alain%22%2C%22lastName%22%3A%22Fezeu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vanessa%20A.%22%2C%22lastName%22%3A%22Juimo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Lafosse%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Francis%20E.%22%2C%22lastName%22%3A%22Tabe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Catherine%22%2C%22lastName%22%3A%22Girard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Deborah%22%2C%22lastName%22%3A%22Iqaluk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Le%20Thanh%20Tu%22%2C%22lastName%22%3A%22Nguyen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22B.%20Jesse%22%2C%22lastName%22%3A%22Shapiro%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jenni%22%2C%22lastName%22%3A%22Lehtim%5Cu00e4ki%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lasse%22%2C%22lastName%22%3A%22Ruokolainen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pinja%20P.%22%2C%22lastName%22%3A%22Kettunen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tommi%22%2C%22lastName%22%3A%22Vatanen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shani%22%2C%22lastName%22%3A%22Sigwazi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Audax%22%2C%22lastName%22%3A%22Mabulla%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Manuel%22%2C%22lastName%22%3A%22Dom%5Cu00ednguez-Rodrigo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yvonne%20A.%22%2C%22lastName%22%3A%22Nartey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Adwoa%22%2C%22lastName%22%3A%22Agyei-Nkansah%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amoako%22%2C%22lastName%22%3A%22Duah%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yaw%20A.%22%2C%22lastName%22%3A%22Awuku%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kenneth%20A.%22%2C%22lastName%22%3A%22Valles%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shadrack%20O.%22%2C%22lastName%22%3A%22Asibey%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mary%20Y.%22%2C%22lastName%22%3A%22Afihene%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lewis%20R.%22%2C%22lastName%22%3A%22Roberts%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amelie%22%2C%22lastName%22%3A%22Plymoth%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charles%20A.%22%2C%22lastName%22%3A%22Onyekwere%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Roger%20E.%22%2C%22lastName%22%3A%22Summons%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ramnik%20J.%22%2C%22lastName%22%3A%22Xavier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%20J.%22%2C%22lastName%22%3A%22Alm%22%7D%5D%2C%22abstractNote%22%3A%22Industrialization%20has%20impacted%20the%20human%20gut%20ecosystem%2C%20resulting%20in%20altered%20microbiome%20composition%20and%20diversity.%20Whether%20bacterial%20genomes%20may%20also%20adapt%20to%20the%20industrialization%20of%20their%20host%20populations%20remains%20largely%20unexplored.%20Here%2C%20we%20investigate%20the%20extent%20to%20which%20the%20rates%20and%20targets%20of%20horizontal%20gene%20transfer%20%28HGT%29%20vary%20across%20thousands%20of%20bacterial%20strains%20from%2015%20human%20populations%20spanning%20a%20range%20of%20industrialization.%20We%20show%20that%20HGTs%20have%20accumulated%20in%20the%20microbiome%20over%20recent%20host%20generations%20and%20that%20HGT%20occurs%20at%20high%20frequency%20within%20individuals.%20Comparison%20across%20human%20populations%20reveals%20that%20industrialized%20lifestyles%20are%20associated%20with%20higher%20HGT%20rates%20and%20that%20the%20functions%20of%20HGTs%20are%20related%20to%20the%20level%20of%20host%20industrialization.%20Our%20results%20suggest%20that%20gut%20bacteria%20continuously%20acquire%20new%20functionality%20based%20on%20host%20lifestyle%20and%20that%20high%20rates%20of%20HGT%20may%20be%20a%20recent%20development%20in%20human%20history%20linked%20to%20industrialization.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.cell.2021.02.052%22%2C%22ISSN%22%3A%221097-4172%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A17%3A23Z%22%7D%7D%2C%7B%22key%22%3A%22HWR58LIU%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Guo%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EGuo%2C%20Zhili%2C%20Hanjun%20Cheng%2C%20Zhonghan%20Li%2C%20Shiqun%20Shao%2C%20Priyanka%20Sarkar%2C%20Siwen%20Wang%2C%20Rohit%20Chaudhuri%2C%20et%20al.%202021.%20%26%23x201C%3BSingle-Cell%20Profiling%20of%20Fatty%20Acid%20Uptake%20Using%20Surface-Immobilized%20Dendrimers.%26%23x201D%3B%20%3Ci%3EJournal%20of%20the%20American%20Chemical%20Society%3C%5C%2Fi%3E%20143%20%2829%29%3A%2011191%26%23x2013%3B98.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Fjacs.1c05103%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Fjacs.1c05103%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DHWR58LIU%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Single-Cell%20Profiling%20of%20Fatty%20Acid%20Uptake%20Using%20Surface-Immobilized%20Dendrimers%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhili%22%2C%22lastName%22%3A%22Guo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hanjun%22%2C%22lastName%22%3A%22Cheng%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zhonghan%22%2C%22lastName%22%3A%22Li%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shiqun%22%2C%22lastName%22%3A%22Shao%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Priyanka%22%2C%22lastName%22%3A%22Sarkar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Siwen%22%2C%22lastName%22%3A%22Wang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rohit%22%2C%22lastName%22%3A%22Chaudhuri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicole%20G.%22%2C%22lastName%22%3A%22Perkins%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fei%22%2C%22lastName%22%3A%22Ji%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wei%22%2C%22lastName%22%3A%22Wei%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Min%22%2C%22lastName%22%3A%22Xue%22%7D%5D%2C%22abstractNote%22%3A%22We%20present%20a%20chemical%20approach%20to%20profile%20fatty%20acid%20uptake%20in%20single%20cells.%20We%20use%20azide-modified%20analogues%20to%20probe%20the%20fatty%20acid%20influx%20and%20surface-immobilized%20dendrimers%20with%20dibenzocyclooctyne%20%28DBCO%29%20groups%20for%20detection.%20A%20competition%20between%20the%20fatty%20acid%20probes%20and%20BHQ2-azide%20quencher%20molecules%20generates%20fluorescence%20signals%20in%20a%20concentration-dependent%20manner.%20By%20integrating%20this%20method%20onto%20a%20microfluidics-based%20multiplex%20protein%20analysis%20platform%2C%20we%20resolved%20the%20relationships%20between%20fatty%20acid%20influx%2C%20oncogenic%20signaling%20activities%2C%20and%20cell%20proliferation%20in%20single%20glioblastoma%20cells.%20We%20found%20that%20p70S6K%20and%204EBP1%20differentially%20correlated%20with%20fatty%20acid%20uptake.%20We%20validated%20that%20cotargeting%20p70S6K%20and%20fatty%20acid%20metabolism%20synergistically%20inhibited%20cell%20proliferation.%20Our%20work%20provided%20the%20first%20example%20of%20studying%20fatty%20acid%20metabolism%20in%20the%20context%20of%20protein%20signaling%20at%20single-cell%20resolution%20and%20generated%20new%20insights%20into%20cancer%20biology.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1021%5C%2Fjacs.1c05103%22%2C%22ISSN%22%3A%221520-5126%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A30%3A59Z%22%7D%7D%2C%7B%22key%22%3A%2242AIHZFT%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Haak%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHaak%2C%20Victoria%20M.%2C%20Sui%20Huang%2C%20and%20Dipak%20Panigrahy.%202021.%20%26%23x201C%3BDebris-Stimulated%20Tumor%20Growth%3A%20A%20Pandora%26%23x2019%3Bs%20Box%3F%26%23x201D%3B%20%3Ci%3ECancer%20Metastasis%20Reviews%3C%5C%2Fi%3E%2040%20%283%29%3A%20791%26%23x2013%3B801.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs10555-021-09998-8%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs10555-021-09998-8%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D42AIHZFT%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DJHG3X7KT%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Debris-stimulated%20tumor%20growth%3A%20a%20Pandora%27s%20box%3F%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Victoria%20M.%22%2C%22lastName%22%3A%22Haak%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sui%22%2C%22lastName%22%3A%22Huang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dipak%22%2C%22lastName%22%3A%22Panigrahy%22%7D%5D%2C%22abstractNote%22%3A%22Current%20cancer%20therapies%20aim%20at%20eradicating%20cancer%20cells%20from%20the%20body.%20However%2C%20killing%20cells%20generates%20cell%20%5C%22debris%5C%22%20which%20can%20promote%20tumor%20progression.%20Thus%2C%20therapy%20can%20be%20a%20double-edged%20sword.%20Specifically%2C%20injury%20and%20debris%20generated%20by%20cancer%20therapies%2C%20including%20chemotherapy%2C%20radiation%2C%20and%20surgery%2C%20may%20offset%20their%20benefit%20by%20promoting%20the%20secretion%20of%20pro-tumorigenic%20factors%20%28e.g.%2C%20eicosanoid-driven%20cytokines%29%20that%20stimulate%20regrowth%20and%20metastasis%20of%20surviving%20cells.%20The%20debris%20produced%20by%20cytotoxic%20cancer%20therapy%20can%20also%20contribute%20to%20a%20tumor%20microenvironment%20that%20promotes%20tumor%20progression%20and%20recurrence.%20Although%20not%20well%20understood%2C%20several%20molecular%20mechanisms%20have%20been%20implicated%20in%20debris-stimulated%20tumor%20growth%20that%20we%20review%20here%2C%20such%20as%20the%20involvement%20of%20extracellular%20vesicles%2C%20exosomal%20miR-194-5p%2C%20Bax%2C%20Bak%2C%20Smac%2C%20HMGB1%2C%20cytokines%2C%20and%20caspase-3.%20We%20discuss%20the%20cases%20of%20pancreatic%20and%20other%20cancer%20types%20where%20debris%20promotes%20postoperative%20tumor%20recurrence%20and%20metastasis%2C%20thus%20offering%20a%20new%20opportunity%20to%20prevent%20cancer%20progression%20intrinsically%20linked%20to%20treatment%20by%20stimulating%20resolution%20of%20tumor-promoting%20debris.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1007%5C%2Fs10555-021-09998-8%22%2C%22ISSN%22%3A%221573-7233%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A39%3A01Z%22%7D%7D%2C%7B%22key%22%3A%22EEGTGZ6W%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Haiman%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHaiman%2C%20Zachary%20B.%2C%20Daniel%20C.%20Zielinski%2C%20Yuko%20Koike%2C%20James%20T.%20Yurkovich%2C%20and%20Bernhard%20O.%20Palsson.%202021.%20%26%23x201C%3BMASSpy%3A%20Building%2C%20Simulating%2C%20and%20Visualizing%20Dynamic%20Biological%20Models%20in%20Python%20Using%20Mass%20Action%20Kinetics.%26%23x201D%3B%20%3Ci%3EPLoS%20Computational%20Biology%3C%5C%2Fi%3E%2017%20%281%29%3A%20e1008208.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pcbi.1008208%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.pcbi.1008208%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DEEGTGZ6W%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DN2ZRS8KW%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22MASSpy%3A%20Building%2C%20simulating%2C%20and%20visualizing%20dynamic%20biological%20models%20in%20Python%20using%20mass%20action%20kinetics%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zachary%20B.%22%2C%22lastName%22%3A%22Haiman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%20C.%22%2C%22lastName%22%3A%22Zielinski%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yuko%22%2C%22lastName%22%3A%22Koike%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20T.%22%2C%22lastName%22%3A%22Yurkovich%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bernhard%20O.%22%2C%22lastName%22%3A%22Palsson%22%7D%5D%2C%22abstractNote%22%3A%22Mathematical%20models%20of%20metabolic%20networks%20utilize%20simulation%20to%20study%20system-level%20mechanisms%20and%20functions.%20Various%20approaches%20have%20been%20used%20to%20model%20the%20steady%20state%20behavior%20of%20metabolic%20networks%20using%20genome-scale%20reconstructions%2C%20but%20formulating%20dynamic%20models%20from%20such%20reconstructions%20continues%20to%20be%20a%20key%20challenge.%20Here%2C%20we%20present%20the%20Mass%20Action%20Stoichiometric%20Simulation%20Python%20%28MASSpy%29%20package%2C%20an%20open-source%20computational%20framework%20for%20dynamic%20modeling%20of%20metabolism.%20MASSpy%20utilizes%20mass%20action%20kinetics%20and%20detailed%20chemical%20mechanisms%20to%20build%20dynamic%20models%20of%20complex%20biological%20processes.%20MASSpy%20adds%20dynamic%20modeling%20tools%20to%20the%20COnstraint-Based%20Reconstruction%20and%20Analysis%20Python%20%28COBRApy%29%20package%20to%20provide%20an%20unified%20framework%20for%20constraint-based%20and%20kinetic%20modeling%20of%20metabolic%20networks.%20MASSpy%20supports%20high-performance%20dynamic%20simulation%20through%20its%20implementation%20of%20libRoadRunner%3A%20the%20Systems%20Biology%20Markup%20Language%20%28SBML%29%20simulation%20engine.%20Three%20examples%20are%20provided%20to%20demonstrate%20how%20to%20use%20MASSpy%3A%20%281%29%20a%20validation%20of%20the%20MASSpy%20modeling%20tool%20through%20dynamic%20simulation%20of%20detailed%20mechanisms%20of%20enzyme%20regulation%3B%20%282%29%20a%20feature%20demonstration%20using%20a%20workflow%20for%20generating%20ensemble%20of%20kinetic%20models%20using%20Monte%20Carlo%20sampling%20to%20approximate%20missing%20numerical%20values%20of%20parameters%20and%20to%20quantify%20biological%20uncertainty%2C%20and%20%283%29%20a%20case%20study%20in%20which%20MASSpy%20is%20utilized%20to%20overcome%20issues%20that%20arise%20when%20integrating%20experimental%20data%20with%20the%20computation%20of%20functional%20states%20of%20detailed%20biological%20mechanisms.%20MASSpy%20represents%20a%20powerful%20tool%20to%20address%20challenges%20that%20arise%20in%20dynamic%20modeling%20of%20metabolic%20networks%2C%20both%20at%20small%20and%20large%20scales.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1371%5C%2Fjournal.pcbi.1008208%22%2C%22ISSN%22%3A%221553-7358%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A20%3A41Z%22%7D%7D%2C%7B%22key%22%3A%22WVI3KSHJ%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Hansell%20and%20Orellana%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHansell%2C%20Dennis%20A.%2C%20and%20M%26%23xF3%3Bnica%20V.%20Orellana.%202021.%20%26%23x201C%3BDissolved%20Organic%20Matter%20in%20the%20Global%20Ocean%3A%20A%20Primer.%26%23x201D%3B%20%3Ci%3EGels%20%28Basel%2C%20Switzerland%29%3C%5C%2Fi%3E%207%20%283%29%3A%20128.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fgels7030128%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.3390%5C%2Fgels7030128%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DWVI3KSHJ%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DD3A2WRUF%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Dissolved%20Organic%20Matter%20in%20the%20Global%20Ocean%3A%20A%20Primer%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dennis%20A.%22%2C%22lastName%22%3A%22Hansell%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22M%5Cu00f3nica%20V.%22%2C%22lastName%22%3A%22Orellana%22%7D%5D%2C%22abstractNote%22%3A%22Marine%20dissolved%20organic%20matter%20%28DOM%29%20holds%20~660%20billion%20metric%20tons%20of%20carbon%2C%20making%20it%20one%20of%20Earth%27s%20major%20carbon%20reservoirs%20that%20is%20exchangeable%20with%20the%20atmosphere%20on%20annual%20to%20millennial%20time%20scales.%20The%20global%20ocean%20scale%20dynamics%20of%20the%20pool%20have%20become%20better%20illuminated%20over%20the%20past%20few%20decades%2C%20and%20those%20are%20very%20briefly%20described%20here.%20What%20is%20still%20far%20from%20understood%20is%20the%20dynamical%20control%20on%20this%20pool%20at%20the%20molecular%20level%3B%20in%20the%20case%20of%20this%20Special%20Issue%2C%20the%20role%20of%20microgels%20is%20poorly%20known.%20This%20manuscript%20provides%20the%20global%20context%20of%20a%20large%20pool%20of%20marine%20DOM%20upon%20which%20those%20missing%20insights%20can%20be%20built.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.3390%5C%2Fgels7030128%22%2C%22ISSN%22%3A%222310-2861%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A34%3A01Z%22%7D%7D%2C%7B%22key%22%3A%22A8EH97UB%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Hernandez-Boussard%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHernandez-Boussard%2C%20Tina%2C%20Paul%20Macklin%2C%20Emily%20J.%20Greenspan%2C%20Amy%20L.%20Gryshuk%2C%20Eric%20Stahlberg%2C%20Tanveer%20Syeda-Mahmood%2C%20and%20Ilya%20Shmulevich.%202021.%20%26%23x201C%3BDigital%20Twins%20for%20Predictive%20Oncology%20Will%20Be%20a%20Paradigm%20Shift%20for%20Precision%20Cancer%20Care.%26%23x201D%3B%20%3Ci%3ENature%20Medicine%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41591-021-01558-5%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41591-021-01558-5%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DA8EH97UB%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Digital%20twins%20for%20predictive%20oncology%20will%20be%20a%20paradigm%20shift%20for%20precision%20cancer%20care%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tina%22%2C%22lastName%22%3A%22Hernandez-Boussard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Paul%22%2C%22lastName%22%3A%22Macklin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Emily%20J.%22%2C%22lastName%22%3A%22Greenspan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Amy%20L.%22%2C%22lastName%22%3A%22Gryshuk%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eric%22%2C%22lastName%22%3A%22Stahlberg%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tanveer%22%2C%22lastName%22%3A%22Syeda-Mahmood%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ilya%22%2C%22lastName%22%3A%22Shmulevich%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41591-021-01558-5%22%2C%22ISSN%22%3A%221546-170X%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-12-06T17%3A30%3A59Z%22%7D%7D%2C%7B%22key%22%3A%22FTRVUVC2%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Huang%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHuang%2C%20Sui.%202021.%20%26%23x201C%3BReconciling%20Non-Genetic%20Plasticity%20with%20Somatic%20Evolution%20in%20Cancer.%26%23x201D%3B%20%3Ci%3ETrends%20in%20Cancer%3C%5C%2Fi%3E.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.trecan.2020.12.007%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.trecan.2020.12.007%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DFTRVUVC2%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Reconciling%20Non-Genetic%20Plasticity%20with%20Somatic%20Evolution%20in%20Cancer%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sui%22%2C%22lastName%22%3A%22Huang%22%7D%5D%2C%22abstractNote%22%3A%22Post-treatment%20progression%20of%20tumors%20is%20commonly%20explained%20by%20somatic%20Darwinian%20evolution%20%28i.e.%2C%20selection%20of%20cells%20carrying%20genetic%20mutations%20that%20create%20more%20aggressive%20cell%20traits%29.%20But%20cancer%20genome%20and%20transcriptome%20analyses%20now%20paint%20a%20picture%20far%20more%20complex%2C%20prompting%20us%20to%20see%20beyond%20the%20Darwinian%20scheme%3A%20non-genetic%20cell%20phenotype%20plasticity%20explained%20by%20alternative%20stable%20gene%20expression%20states%20%28%27attractors%27%29%2C%20may%20also%20produce%20aggressive%20phenotypes%20that%20can%20be%20selected%20for%2C%20without%20mutations.%20Worse%2C%20treatment%20may%20even%20induce%20cell%20state%20transitions%20into%20more%20malignant%20attractors.%20We%20review%20recent%20evidence%20for%20non-genetic%20mechanisms%20of%20progression%2C%20explain%20the%20theoretical%20foundation%20of%20attractor%20transitions%20behind%20treatment-induced%20increase%20of%20aggressiveness%2C%20and%20provide%20a%20framework%20for%20unifying%20genetic%20and%20non-genetic%20dynamics%20in%20tumor%20progression.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.trecan.2020.12.007%22%2C%22ISSN%22%3A%222405-8025%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A20%3A58Z%22%7D%7D%2C%7B%22key%22%3A%22H5FPB39P%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Huang%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHuang%2C%20Sui.%202021.%20%26%23x201C%3BShould%20Biophysics%20Study%20Nonphysical%20Quantities%20of%20Biological%20Systems%3F%20Take%20Max%20Delbr%26%23xFC%3Bck%20for%20Inspiration.%26%23x201D%3B%20%3Ci%3EBiophysics%20Reviews%3C%5C%2Fi%3E%202%20%284%29%3A%20040401.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0079700%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0079700%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DH5FPB39P%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DTAVAWDU6%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Should%20biophysics%20study%20nonphysical%20quantities%20of%20biological%20systems%3F%20Take%20Max%20Delbr%5Cu00fcck%20for%20inspiration%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sui%22%2C%22lastName%22%3A%22Huang%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1063%5C%2F5.0079700%22%2C%22ISSN%22%3A%222688-4089%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222022-01-31T17%3A52%3A30Z%22%7D%7D%2C%7B%22key%22%3A%227MVSBWI9%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Hwang%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EHwang%2C%20Yu%20Jin%2C%20Seung%20Jae%20Hyeon%2C%20Younghee%20Kim%2C%20Sungsu%20Lim%2C%20Min%20Young%20Lee%2C%20Jieun%20Kim%2C%20Ashwini%20M.%20Londhe%2C%20et%20al.%202021.%20%26%23x201C%3BModulation%20of%20SETDB1%20Activity%20by%20APQ%20Ameliorates%20Heterochromatin%20Condensation%2C%20Motor%20Function%2C%20and%20Neuropathology%20in%20a%20Huntington%26%23x2019%3Bs%20Disease%20Mouse%20Model.%26%23x201D%3B%20%3Ci%3EJournal%20of%20Enzyme%20Inhibition%20and%20Medicinal%20Chemistry%3C%5C%2Fi%3E%2036%20%281%29%3A%20856%26%23x2013%3B68.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1080%5C%2F14756366.2021.1900160%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1080%5C%2F14756366.2021.1900160%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3D7MVSBWI9%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DN5ZRBVGC%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Modulation%20of%20SETDB1%20activity%20by%20APQ%20ameliorates%20heterochromatin%20condensation%2C%20motor%20function%2C%20and%20neuropathology%20in%20a%20Huntington%27s%20disease%20mouse%20model%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yu%20Jin%22%2C%22lastName%22%3A%22Hwang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Seung%20Jae%22%2C%22lastName%22%3A%22Hyeon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Younghee%22%2C%22lastName%22%3A%22Kim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sungsu%22%2C%22lastName%22%3A%22Lim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Min%20Young%22%2C%22lastName%22%3A%22Lee%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jieun%22%2C%22lastName%22%3A%22Kim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ashwini%20M.%22%2C%22lastName%22%3A%22Londhe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lizaveta%22%2C%22lastName%22%3A%22Gotina%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yunha%22%2C%22lastName%22%3A%22Kim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ae%20Nim%22%2C%22lastName%22%3A%22Pae%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yong%20Seo%22%2C%22lastName%22%3A%22Cho%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jihye%22%2C%22lastName%22%3A%22Seong%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hyemyung%22%2C%22lastName%22%3A%22Seo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yun%20Kyung%22%2C%22lastName%22%3A%22Kim%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hyunah%22%2C%22lastName%22%3A%22Choo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Hoon%22%2C%22lastName%22%3A%22Ryu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sun-Joon%22%2C%22lastName%22%3A%22Min%22%7D%5D%2C%22abstractNote%22%3A%22The%20present%20study%20describes%20evaluation%20of%20epigenetic%20regulation%20by%20a%20small%20molecule%20as%20the%20therapeutic%20potential%20for%20treatment%20of%20Huntington%27s%20disease%20%28HD%29.%20We%20identified%205-allyloxy-2-%28pyrrolidin-1-yl%29quinoline%20%28APQ%29%20as%20a%20novel%20SETDB1%5C%2FESET%20inhibitor%20using%20a%20combined%20in%20silico%20and%20in%5Cu00a0vitro%20cell%20based%20screening%20system.%20APQ%20reduced%20SETDB1%20activity%20and%20H3K9me3%20levels%20in%20a%20HD%20cell%20line%20model.%20In%20particular%2C%20not%20only%20APQ%20reduced%20H3K9me3%20levels%20in%20the%20striatum%20but%20it%20also%20improved%20motor%20function%20and%20neuropathological%20symptoms%20such%20as%20neuronal%20size%20and%20activity%20in%20HD%20transgenic%20%28YAC128%29%20mice%20with%20minimal%20toxicity.%20Using%20H3K9me3-ChIP%20and%20genome-wide%20sequencing%2C%20we%20also%20confirmed%20that%20APQ%20modulates%20H3K9me3-landscaped%20epigenomes%20in%20YAC128%20mice.%20These%20data%20provide%20that%20APQ%2C%20a%20novel%20small%20molecule%20SETDB1%20inhibitor%2C%20coordinates%20H3K9me-dependent%20heterochromatin%20remodelling%20and%20can%20be%20an%20epigenetic%20drug%20for%20treating%20HD%2C%20leading%20with%20hope%20in%20clinical%20trials%20of%20HD.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1080%5C%2F14756366.2021.1900160%22%2C%22ISSN%22%3A%221475-6374%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-06-04T19%3A16%3A06Z%22%7D%7D%2C%7B%22key%22%3A%22HHA8VC7D%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Idso%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EIdso%2C%20Matthew%20N.%2C%20Bert%20T.%20Lai%2C%20Heather%20D.%20Agnew%2C%20and%20James%20R.%20Heath.%202021.%20%26%23x201C%3BProtein%20Catalyzed%20Capture%20%28PCC%29%20Agents%20for%20Antigen%20Targeting.%26%23x201D%3B%20%3Ci%3EMethods%20in%20Molecular%20Biology%20%28Clifton%2C%20N.J.%29%3C%5C%2Fi%3E%202371%3A177%26%23x2013%3B91.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2F978-1-0716-1689-5_10%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2F978-1-0716-1689-5_10%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DHHA8VC7D%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Protein%20Catalyzed%20Capture%20%28PCC%29%20Agents%20for%20Antigen%20Targeting%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthew%20N.%22%2C%22lastName%22%3A%22Idso%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bert%20T.%22%2C%22lastName%22%3A%22Lai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Heather%20D.%22%2C%22lastName%22%3A%22Agnew%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20R.%22%2C%22lastName%22%3A%22Heath%22%7D%5D%2C%22abstractNote%22%3A%22The%20protein%20catalyzed%20capture%20agent%20%28PCC%29%20method%20is%20a%20powerful%20combinatorial%20screening%20strategy%20for%20discovering%20synthetic%20macrocyclic%20peptide%20ligands%2C%20called%20PCCs%2C%20to%20designated%20protein%20epitopes.%20The%20foundational%20concept%20of%20the%20PCC%20method%20is%20the%20use%20of%20in%20situ%20click%20chemistry%20to%20survey%20large%20combinatorial%20libraries%20of%20peptides%20for%20ligands%20to%20designated%20biological%20targets.%20State-of-the-art%20PCC%20screens%20integrate%20synthetic%20libraries%20of%20constrained%20macrocyclic%20peptides%20with%20epitope-specific%20targeting%20strategies%20to%20identify%20high-affinity%20%28%3C100%5Cu00a0nM%29%20binders%20de%20novo.%20Automated%20instrumentation%20can%20accelerate%20PCC%20discovery%20to%20a%20rapid%202-week%20timeframe.%20Here%2C%20we%20describe%20methods%20to%20perform%20combinatorial%20screens%20that%20yield%20epitope-targeted%20PCCs.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1007%5C%2F978-1-0716-1689-5_10%22%2C%22ISSN%22%3A%221940-6029%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-10-14T23%3A29%3A16Z%22%7D%7D%2C%7B%22key%22%3A%22DW9A42GT%22%2C%22library%22%3A%7B%22id%22%3A2323737%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Immanuel%20et%20al.%22%2C%22parsedDate%22%3A%222021%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%3EImmanuel%2C%20Selva%20Rupa%20Christinal%2C%20Avinash%20D.%20Ghanate%2C%20Dharmeshkumar%20S.%20Parmar%2C%20Ritu%20Yadav%2C%20Riya%20Uthup%2C%20Venkateswarlu%20Panchagnula%2C%20and%20Anu%20Raghunathan.%202021.%20%26%23x201C%3BIntegrated%20Genetic%20and%20Metabolic%20Landscapes%20Predict%20Vulnerabilities%20of%20Temozolomide%20Resistant%20Glioblastoma%20Cells.%26%23x201D%3B%20%3Ci%3ENPJ%20Systems%20Biology%20and%20Applications%3C%5C%2Fi%3E%207%20%281%29%3A%202.%20%3Ca%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41540-020-00161-7%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1038%5C%2Fs41540-020-00161-7%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D2323737%26amp%3Bitem_key%3DDW9A42GT%27%3ECite%3C%5C%2Fa%3E%20%20%3Ca%20title%3D%27Download%27%20class%3D%27zp-DownloadURL%27%20href%3D%27https%3A%5C%2F%5C%2Fisbscience.org%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.dl.php%3Fapi_user_id%3D2323737%26amp%3Bdlkey%3DAC5D7PB3%26amp%3Bcontent_type%3Dapplication%5C%2Fpdf%27%3EDownload%3C%5C%2Fa%3E%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Integrated%20genetic%20and%20metabolic%20landscapes%20predict%20vulnerabilities%20of%20temozolomide%20resistant%20glioblastoma%20cells%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Selva%20Rupa%20Christinal%22%2C%22lastName%22%3A%22Immanuel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Avinash%20D.%22%2C%22lastName%22%3A%22Ghanate%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dharmeshkumar%20S.%22%2C%22lastName%22%3A%22Parmar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ritu%22%2C%22lastName%22%3A%22Yadav%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Riya%22%2C%22lastName%22%3A%22Uthup%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Venkateswarlu%22%2C%22lastName%22%3A%22Panchagnula%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Anu%22%2C%22lastName%22%3A%22Raghunathan%22%7D%5D%2C%22abstractNote%22%3A%22Metabolic%20reprogramming%20and%20its%20molecular%20underpinnings%20are%20critical%20to%20unravel%20the%20duality%20of%20cancer%20cell%20function%20and%20chemo-resistance.%20Here%2C%20we%20use%20a%20constraints-based%20integrated%20approach%20to%20delineate%20the%20interplay%20between%20metabolism%20and%20epigenetics%2C%20hardwired%20in%20the%20genome%2C%20to%20shape%20temozolomide%20%28TMZ%29%20resistance.%20Differential%20metabolism%20was%20identified%20in%20response%20to%20TMZ%20at%20varying%20concentrations%20in%20both%20the%20resistant%20neurospheroidal%20%28NSP%29%20and%20the%20susceptible%20%28U87MG%29%20glioblastoma%20cell-lines.%20The%20genetic%20basis%20of%20this%20metabolic%20adaptation%20was%20characterized%20by%20whole%20exome%20sequencing%20that%20identified%20mutations%20in%20signaling%20pathway%20regulators%20of%20growth%20and%20energy%20metabolism.%20Remarkably%2C%20our%20integrated%20approach%20identified%20rewiring%20in%20glycolysis%2C%20TCA%20cycle%2C%20malate%20aspartate%20shunt%2C%20and%20oxidative%20phosphorylation%20pathways.%20The%20differential%20killing%20of%20TMZ%20resistant%20NSP%20by%20Rotenone%20at%20low%20concentrations%20with%20an%20IC50%20value%20of%205%5Cu2009nM%2C%20three%20orders%20of%20magnitude%20lower%20than%20for%20U87MG%20that%20exhibited%20an%20IC50%20value%20of%201.8%5Cu2009mM%20was%20thus%20identified%20using%20our%20integrated%20systems-based%20approach.%22%2C%22date%22%3A%222021%22%2C%22language%22%3A%22eng%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41540-020-00161-7%22%2C%22ISSN%22%3A%222056-7189%22%2C%22url%22%3A%22%22%2C%22collections%22%3A%5B%222RQKSFR5%22%5D%2C%22dateModified%22%3A%222021-03-05T20%3A19%3A49Z%22%7D%7D%5D%7D
Aguadé-Gorgorió, Guim, Stuart Kauffman, and Ricard Solé. 2021. “Transition Therapy: Tackling the Ecology of Tumor Phenotypic Plasticity.” Bulletin of Mathematical Biology 84 (1): 24. https://doi.org/10.1007/s11538-021-00970-9. Cite Download
Akbari, Amir, James T. Yurkovich, Daniel C. Zielinski, and Bernhard O. Palsson. 2021. “The Quantitative Metabolome Is Shaped by Abiotic Constraints.” Nature Communications 12 (1): 3178. https://doi.org/10.1038/s41467-021-23214-9. Cite Download
Arrieta-Ortiz, Mario L., Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, et al. 2021. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe, S1931-3128(21)00424-8. https://doi.org/10.1016/j.chom.2021.09.008. Cite
Azer, Karim, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, et al. 2021. “History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.” Frontiers in Physiology 12:637999. https://doi.org/10.3389/fphys.2021.637999. Cite Download
Baloni, Priyanka, Wikum Dinalankara, John C. Earls, Theo A. Knijnenburg, Donald Geman, Luigi Marchionni, and Nathan D. Price. 2021. “Identifying Personalized Metabolic Signatures in Breast Cancer.” Metabolites 11 (1): 20. https://doi.org/10.3390/metabo11010020. Cite Download
Baloni, Priyanka, Cory C. Funk, Ben Readhead, and Nathan D. Price. 2021. “Systems Modeling of Metabolic Dysregulation in Neurodegenerative Diseases.” Current Opinion in Pharmacology 60:59–65. https://doi.org/10.1016/j.coph.2021.06.012. Cite
Bandeira, Nuno, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno. 2021. “Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future.” Molecular & Cellular Proteomics: MCP 20:100071. https://doi.org/10.1016/j.mcpro.2021.100071. Cite Download
Banerjee, Ushashi, Priyanka Baloni, Amit Singh, and Nagasuma Chandra. 2021. “Immune Subtyping in Latent Tuberculosis.” Frontiers in Immunology 12. https://doi.org/10.3389/fimmu.2021.595746. Cite Download
Bastard, Paul, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Jérémy Manry, Eleftherios Michailidis, et al. 2021. “Autoantibodies Neutralizing Type I IFNs Are Present in ~4% of Uninfected Individuals over 70 Years Old and Account for ~20% of COVID-19 Deaths.” Science Immunology 6 (62): eabl4340. https://doi.org/10.1126/sciimmunol.abl4340. Cite Download
Bobe, Jason R., Brandon L. Jutras, Elizabeth J. Horn, Monica E. Embers, Allison Bailey, Robert L. Moritz, Ying Zhang, et al. 2021. “Recent Progress in Lyme Disease and Remaining Challenges.” Frontiers in Medicine 8:666554. https://doi.org/10.3389/fmed.2021.666554. Cite Download
Brand, Marjorie, and Jeffrey A. Ranish. 2021. “Proteomic/Transcriptomic Analysis of Erythropoiesis.” Current Opinion in Hematology 28 (3): 150–57. https://doi.org/10.1097/MOH.0000000000000647. Cite
Cheng, Hanjun, Zhonghan Li, Zhili Guo, Shiqun Shao, Li Mo, Wei Wei, and Min Xue. 2021. “Single-Cell Profiling of D-2-Hydroxyglutarate Using Surface-Immobilized Resazurin Analogs.” Biosensors & Bioelectronics 190:113368. https://doi.org/10.1016/j.bios.2021.113368. Cite
Cobb, David W., Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, and Vasant Muralidharan. 2021. “A Redox-Active Crosslinker Reveals an Essential and Inhibitable Oxidative Folding Network in the Endoplasmic Reticulum of Malaria Parasites.” PLoS Pathogens 17 (2): e1009293. https://doi.org/10.1371/journal.ppat.1009293. Cite Download
Corpas, Manuel, Stephan Beck, Gustavo Glusman, and Mahsa Shabani. 2021. “Editorial: Personal Genomes: Accessing, Sharing, and Interpretation.” Frontiers in Genetics 12:687584. https://doi.org/10.3389/fgene.2021.687584. Cite Download
Crouser, Elliott D., Mark W. Julian, Sabahattin Bicer, Vikas Ghai, Taek-Kyun Kim, Lisa A. Maier, May Gillespie, Nabeel Y. Hamzeh, and Kai Wang. 2021. “Circulating Exosomal MicroRNA Expression Patterns Distinguish Cardiac Sarcoidosis from Myocardial Ischemia.” PloS One 16 (1): e0246083. https://doi.org/10.1371/journal.pone.0246083. Cite Download
D, Park, Anisuzzaman Asm, Magis At, Chen G, Xie M, Zhang G, Behera M, et al. 2021. “Discovery of Small Molecule Bak Activator for Lung Cancer Therapy.” Theranostics 11 (17). https://doi.org/10.7150/thno.60349. Cite Download
D’Agnillo, Felice, K.A. Walters, Yongli Xiao, Zong-Mei Sheng, Kelsey Scherler, Jaekeun Park, Sebastian Gygli, et al. 2021. “Lung Epithelial and Endothelial Damage, Loss of Tissue Repair, Inhibition of Fibrinolysis, and Cellular Senescence in Fatal COVID-19.” Science Translational Medicine 13 (620): eabj7790. https://doi.org/10.1126/scitranslmed.abj7790. Cite Download
Dai, Chengzhen L., Sergey A. Kornilov, Ryan T. Roper, Hannah Cohen-Cline, Kathleen Jade, Brett Smith, James R. Heath, et al. 2021. “Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciab154. Cite Download
Dai, Chengxin, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, et al. 2021. “A Proteomics Sample Metadata Representation for Multiomics Integration and Big Data Analysis.” Nature Communications 12 (1): 5854. https://doi.org/10.1038/s41467-021-26111-3. Cite
Day, JA, CM Ludwig, and NS Baliga. 2021. “Cultivating Environmental Sustainable Food through a Community Ambassador Program.” Clearing: Journal of Community-Based Environmental Literacy Education Winter Edition:12–16. Cite
Day, Jessica A., Christian Diener, Anne E. Otwell, Kourtney E. Tams, Brad Bebout, Angela M. Detweiler, Michael D. Lee, et al. 2021. “Lettuce (Lactuca Sativa) Productivity Influenced by Microbial Inocula under Nitrogen-Limited Conditions in Aquaponics.” PloS One 16 (2): e0247534. https://doi.org/10.1371/journal.pone.0247534. Cite Download
Deutsch, Eric W., Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, et al. 2021. “Universal Spectrum Identifier for Mass Spectra.” Nature Methods 18 (7): 768–70. https://doi.org/10.1038/s41592-021-01184-6. Cite Download
Deutsch, Eric W., Gilbert S. Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K. Palaniappan, Natasha Letunica, et al. 2021. “Advances and Utility of the Human Plasma Proteome.” Journal of Proteome Research 20 (12): 5241–63. https://doi.org/10.1021/acs.jproteome.1c00657. Cite
Diaz, George A, Alyssa B Christensen, Tobias Pusch, Delaney Goulet, Shu-Ching Chang, Gary L Grunkemeier, Paul A McKelvey, et al. 2021. “Remdesivir and Mortality in Patients With Coronavirus Disease 2019.” Clinical Infectious Diseases, ciab698. https://doi.org/10.1093/cid/ciab698. Cite Download
Diener, Christian, Anna C. H. Hoge, Sean M. Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L. Moritz, Susan E. Erdman, and Sean M. Gibbons. 2021. “Non-Responder Phenotype Reveals Apparent Microbiome-Wide Antibiotic Tolerance in the Murine Gut.” Communications Biology 4 (1): 316. https://doi.org/10.1038/s42003-021-01841-8. Cite Download
Doan, Phuong, Phung Nguyen, Akshaya Murugesan, Kumar Subramanian, Saravanan Konda Mani, Vignesh Kalimuthu, Bobin George Abraham, et al. 2021. “Targeting Orphan G Protein-Coupled Receptor 17 with T0 Ligand Impairs Glioblastoma Growth.” Cancers 13 (15): 3773. https://doi.org/10.3390/cancers13153773. Cite Download
Doan, Phuong, Phung Nguyen, Akshaya Murugesan, Nuno R. Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2021. “Alkylaminophenol and GPR17 Agonist for Glioblastoma Therapy: A Combinational Approach for Enhanced Cell Death Activity.” Cells 10 (8): 1975. https://doi.org/10.3390/cells10081975. Cite Download
Dokic, Anja, Eliza Peterson, Mario L. Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin Baliga, and Apoorva Bhatt. 2021. “Mycobacterium Abscessus Biofilms Produce an Extracellular Matrix and Have a Distinct Mycolic Acid Profile.” Cell Surface (Amsterdam, Netherlands) 7:100051. https://doi.org/10.1016/j.tcsw.2021.100051. Cite Download
Doty, Raymond T., Xiaowei Yan, Changting Meng, Christopher Lausted, Qiang Tian, and Janis L. Abkowitz. 2021. “Single-Cell Analysis of Erythropoiesis in Rpl11 Haploinsufficient Mice Reveals Insight into the Pathogenesis of Diamond Blackfan Anemia.” Experimental Hematology. https://doi.org/10.1016/j.exphem.2021.02.010. Cite
Emmert-Streib, Frank, Kalifa Manjang, Matthias Dehmer, Olli Yli-Harja, and Anssi Auvinen. 2021. “Are There Limits in Explainability of Prognostic Biomarkers? Scrutinizing Biological Utility of Established Signatures.” Cancers 13 (20): 5087. https://doi.org/10.3390/cancers13205087. Cite Download
Fecho, Karamarie, James Balhoff, Chris Bizon, William E. Byrd, Sui Hang, David Koslicki, Stefano E. Rensi, et al. 2021. “Application of MCAT Questions as a Testing Tool and Evaluation Metric for Knowledge Graph-Based Reasoning Systems.” Clinical and Translational Science. https://doi.org/10.1111/cts.13021. Cite Download
Fedorov, Andrey, William J. R. Longabaugh, David Pot, David A. Clunie, Steve Pieper, Hugo J. W. L. Aerts, André Homeyer, et al. 2021. “NCI Imaging Data Commons.” Cancer Research 81 (16): 4188–93. https://doi.org/10.1158/0008-5472.CAN-21-0950. Cite Download
Ghiselli, Fabrizio, André Gomes-Dos-Santos, Coen M. Adema, Manuel Lopes-Lima, Joel Sharbrough, and Jeffrey L. Boore. 2021. “Molluscan Mitochondrial Genomes Break the Rules.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 376 (1825): 20200159. https://doi.org/10.1098/rstb.2020.0159. Cite
Gibbs, David L., Boris Aguilar, Vésteinn Thorsson, Alexander V. Ratushny, and Ilya Shmulevich. 2021. “Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer.” Frontiers in Genetics 12:667382. https://doi.org/10.3389/fgene.2021.667382. Cite Download
Girinathan, Brintha P., Nicholas DiBenedetto, Jay N. Worley, Johann Peltier, Mario L. Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Richard Lavin, et al. 2021. “In Vivo Commensal Control of Clostridioides Difficile Virulence.” Cell Host & Microbe, S1931-3128(21)00423-6. https://doi.org/10.1016/j.chom.2021.09.007. Cite
Giurgea, Luca T., Jae-Keun Park, K.A. Walters, Kelsey Scherler, Adriana Cervantes-Medina, Ashley Freeman, Luz Angela Rosas, John C. Kash, Jeffery K. Taubenberger, and Matthew J. Memoli. 2021. “The Effect of Calcium and Magnesium on Activity, Immunogenicity, and Efficacy of a Recombinant N1/N2 Neuraminidase Vaccine.” NPJ Vaccines 6 (1): 48. https://doi.org/10.1038/s41541-021-00310-x. Cite Download
Giurgea, Luca T., Adriana Cervantes-Medina, K.A. Walters, Kelsey Scherler, Alison Han, Lindsay M. Czajkowski, Holly Ann Baus, et al. 2021. “Sex Differences in Influenza: The Challenge Study Experience.” The Journal of Infectious Diseases, jiab422. https://doi.org/10.1093/infdis/jiab422. Cite Download
Gnanavel, Mutharasu, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2021. “Identifying the MiRNA Signature Association with Aging-Related Senescence in Glioblastoma.” International Journal of Molecular Sciences 22 (2). https://doi.org/10.3390/ijms22020517. Cite Download
Grasberger, Helmut, Andrew T. Magis, Elisa Sheng, Matthew P. Conomos, Min Zhang, Lea S. Garzotto, Guoqing Hou, et al. 2021. “DUOX2 Variants Associate with Preclinical Disturbances in Microbiota-Immune Homeostasis and Increased Inflammatory Bowel Disease Risk.” The Journal of Clinical Investigation. https://doi.org/10.1172/JCI141676. Cite Download
Groussin, Mathieu, Mathilde Poyet, Ainara Sistiaga, Sean M. Kearney, Katya Moniz, Mary Noel, Jeff Hooker, et al. 2021. “Elevated Rates of Horizontal Gene Transfer in the Industrialized Human Microbiome.” Cell 184 (8): 2053-2067.e18. https://doi.org/10.1016/j.cell.2021.02.052. Cite Download
Guo, Zhili, Hanjun Cheng, Zhonghan Li, Shiqun Shao, Priyanka Sarkar, Siwen Wang, Rohit Chaudhuri, et al. 2021. “Single-Cell Profiling of Fatty Acid Uptake Using Surface-Immobilized Dendrimers.” Journal of the American Chemical Society 143 (29): 11191–98. https://doi.org/10.1021/jacs.1c05103. Cite
Haak, Victoria M., Sui Huang, and Dipak Panigrahy. 2021. “Debris-Stimulated Tumor Growth: A Pandora’s Box?” Cancer Metastasis Reviews 40 (3): 791–801. https://doi.org/10.1007/s10555-021-09998-8. Cite Download
Haiman, Zachary B., Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, and Bernhard O. Palsson. 2021. “MASSpy: Building, Simulating, and Visualizing Dynamic Biological Models in Python Using Mass Action Kinetics.” PLoS Computational Biology 17 (1): e1008208. https://doi.org/10.1371/journal.pcbi.1008208. Cite Download
Hansell, Dennis A., and Mónica V. Orellana. 2021. “Dissolved Organic Matter in the Global Ocean: A Primer.” Gels (Basel, Switzerland) 7 (3): 128. https://doi.org/10.3390/gels7030128. Cite Download
Hernandez-Boussard, Tina, Paul Macklin, Emily J. Greenspan, Amy L. Gryshuk, Eric Stahlberg, Tanveer Syeda-Mahmood, and Ilya Shmulevich. 2021. “Digital Twins for Predictive Oncology Will Be a Paradigm Shift for Precision Cancer Care.” Nature Medicine. https://doi.org/10.1038/s41591-021-01558-5. Cite
Huang, Sui. 2021. “Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer.” Trends in Cancer. https://doi.org/10.1016/j.trecan.2020.12.007. Cite
Huang, Sui. 2021. “Should Biophysics Study Nonphysical Quantities of Biological Systems? Take Max Delbrück for Inspiration.” Biophysics Reviews 2 (4): 040401. https://doi.org/10.1063/5.0079700. Cite Download
Hwang, Yu Jin, Seung Jae Hyeon, Younghee Kim, Sungsu Lim, Min Young Lee, Jieun Kim, Ashwini M. Londhe, et al. 2021. “Modulation of SETDB1 Activity by APQ Ameliorates Heterochromatin Condensation, Motor Function, and Neuropathology in a Huntington’s Disease Mouse Model.” Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 856–68. https://doi.org/10.1080/14756366.2021.1900160. Cite Download
Idso, Matthew N., Bert T. Lai, Heather D. Agnew, and James R. Heath. 2021. “Protein Catalyzed Capture (PCC) Agents for Antigen Targeting.” Methods in Molecular Biology (Clifton, N.J.) 2371:177–91. https://doi.org/10.1007/978-1-0716-1689-5_10. Cite
Immanuel, Selva Rupa Christinal, Avinash D. Ghanate, Dharmeshkumar S. Parmar, Ritu Yadav, Riya Uthup, Venkateswarlu Panchagnula, and Anu Raghunathan. 2021. “Integrated Genetic and Metabolic Landscapes Predict Vulnerabilities of Temozolomide Resistant Glioblastoma Cells.” NPJ Systems Biology and Applications 7 (1): 2. https://doi.org/10.1038/s41540-020-00161-7. Cite Download
