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  1. Article ; Online: Mucociliary transport deficiency and disease progression in Syrian hamsters with SARS-CoV-2 infection

    Qian Li / Kadambari Vijaykumar / Scott E. Phillips / Shah S. Hussain / Nha V. Huynh / Courtney M. Fernandez-Petty / Jacelyn E. Peabody Lever / Jeremy B. Foote / Janna Ren / Javier Campos-Gómez / Farah Abou Daya / Nathaniel W. Hubbs / Harrison Kim / Ezinwanne Onuoha / Evan R. Boitet / Lianwu Fu / Hui Min Leung / Linhui Yu / Thomas W. Detchemendy /
    Levi T. Schaefers / Jennifer L. Tipper / Lloyd J. Edwards / Sixto M. Leal Jr. / Kevin S. Harrod / Guillermo J. Tearney / Steven M. Rowe

    JCI Insight, Vol 8, Iss

    2023  Volume 1

    Abstract: Substantial clinical evidence supports the notion that ciliary function in the airways is important in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, the extent or nature of impairment of mucociliary ...

    Abstract Substantial clinical evidence supports the notion that ciliary function in the airways is important in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, the extent or nature of impairment of mucociliary transport (MCT) in in vivo models remains unknown. We hypothesize that SARS-CoV-2 infection results in MCT deficiency in the airways of golden Syrian hamsters that precedes pathological injury in lung parenchyma. Micro-optical coherence tomography was used to quantitate functional changes in the MCT apparatus. Both genomic and subgenomic viral RNA pathological and physiological changes were monitored in parallel. We show that SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 days postinfection (dpi) in hamsters, principally due to 79% diminished airway coverage of motile cilia. Correlating quantitation of physiological, virological, and pathological changes reveals steadily descending infection from the upper airways to lower airways to lung parenchyma within 7 dpi. Our results indicate that functional deficits of the MCT apparatus are a key aspect of COVID-19 pathogenesis, may extend viral retention, and could pose a risk factor for secondary infection. Clinically, monitoring abnormal ciliated cell function may indicate disease progression. Therapies directed toward the MCT apparatus deserve further investigation.
    Keywords COVID-19 ; Medicine ; R
    Subject code 570
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher American Society for Clinical investigation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440.

    Werner, Allison Z / Clare, Rita / Mand, Thomas D / Pardo, Isabel / Ramirez, Kelsey J / Haugen, Stefan J / Bratti, Felicia / Dexter, Gara N / Elmore, Joshua R / Huenemann, Jay D / Peabody, George L / Johnson, Christopher W / Rorrer, Nicholas A / Salvachúa, Davinia / Guss, Adam M / Beckham, Gregg T

    Metabolic engineering

    2021  Volume 67, Page(s) 250–261

    Abstract: Poly(ethylene terephthalate) (PET) is the most abundantly consumed synthetic polyester and accordingly a major source of plastic waste. The development of chemocatalytic approaches for PET depolymerization to monomers offers new options for open-loop ... ...

    Abstract Poly(ethylene terephthalate) (PET) is the most abundantly consumed synthetic polyester and accordingly a major source of plastic waste. The development of chemocatalytic approaches for PET depolymerization to monomers offers new options for open-loop upcycling of PET, which can leverage biological transformations to higher-value products. To that end, here we perform four sequential metabolic engineering efforts in Pseudomonas putida KT2440 to enable the conversion of PET glycolysis products via: (i) ethylene glycol utilization by constitutive expression of native genes, (ii) terephthalate (TPA) catabolism by expression of tphA2
    MeSH term(s) Adipates ; Burkholderiales ; Ethylenes ; Hydrolases ; Phthalic Acids ; Polyethylene Terephthalates ; Pseudomonas putida/genetics ; Rhodococcus
    Chemical Substances Adipates ; Ethylenes ; Phthalic Acids ; Polyethylene Terephthalates ; 3-oxoadipic acid (1379JRA56F) ; terephthalic acid (6S7NKZ40BQ) ; Hydrolases (EC 3.-)
    Language English
    Publishing date 2021-07-12
    Publishing country Belgium
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2021.07.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Corrigendum to "Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440" [Metab. Eng. 59 (2020) 64-75].

    Bentley, Gayle J / Narayanan, Niju / Jha, Ramesh K / Salvachúa, Davinia / Elmore, Joshua R / Peabody, George L / Black, Brenna A / Ramirez, Kelsey / De Capite, Annette / Michener, William E / Werner, Allison Z / Klingeman, Dawn M / Schindel, Heidi S / Nelson, Robert / Foust, Lindsey / Guss, Adam M / Dale, Taraka / Johnson, Christopher W / Beckham, Gregg T

    Metabolic engineering

    2022  Volume 72, Page(s) 66–67

    Language English
    Publishing date 2022-03-01
    Publishing country Belgium
    Document type Journal Article ; Published Erratum
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2022.02.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Neoantigen-targeted CD8

    Puig-Saus, Cristina / Sennino, Barbara / Peng, Songming / Wang, Clifford L / Pan, Zheng / Yuen, Benjamin / Purandare, Bhamini / An, Duo / Quach, Boi B / Nguyen, Diana / Xia, Huiming / Jilani, Sameeha / Shao, Kevin / McHugh, Claire / Greer, John / Peabody, Phillip / Nayak, Saparya / Hoover, Jonathan / Said, Sara /
    Jacoby, Kyle / Dalmas, Olivier / Foy, Susan P / Conroy, Andrew / Yi, Michael C / Shieh, Christine / Lu, William / Heeringa, Katharine / Ma, Yan / Chizari, Shahab / Pilling, Melissa J / Ting, Marc / Tunuguntla, Ramya / Sandoval, Salemiz / Moot, Robert / Hunter, Theresa / Zhao, Sidi / Saco, Justin D / Perez-Garcilazo, Ivan / Medina, Egmidio / Vega-Crespo, Agustin / Baselga-Carretero, Ignacio / Abril-Rodriguez, Gabriel / Cherry, Grace / Wong, Deborah J / Hundal, Jasreet / Chmielowski, Bartosz / Speiser, Daniel E / Bethune, Michael T / Bao, Xiaoyan R / Gros, Alena / Griffith, Obi L / Griffith, Malachi / Heath, James R / Franzusoff, Alex / Mandl, Stefanie J / Ribas, Antoni

    Nature

    2023  Volume 615, Issue 7953, Page(s) 697–704

    Abstract: Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T ... ...

    Abstract Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells
    MeSH term(s) Humans ; Antigens, Neoplasm/immunology ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Immunotherapy ; Melanoma/drug therapy ; Melanoma/genetics ; Melanoma/immunology ; Melanoma/pathology ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/metabolism ; Immune Checkpoint Inhibitors/pharmacology ; Immune Checkpoint Inhibitors/therapeutic use ; HLA Antigens/immunology ; Neoplasm Metastasis ; Precision Medicine ; Gene Editing ; CRISPR-Cas Systems ; Mutation
    Chemical Substances Antigens, Neoplasm ; Receptors, Antigen, T-Cell ; Immune Checkpoint Inhibitors ; HLA Antigens ; PDCD1 protein, human
    Language English
    Publishing date 2023-03-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-05787-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The American Board of Orthopaedic Surgery Response to COVID-19.

    Wright, Rick W / Armstrong, April D / Azar, Frederick M / Bednar, Michael S / Carpenter, James E / Evans, Jack B / Flynn, John M / Garvin, Kevin L / Jacobs, Joshua J / Kang, James D / Lundy, Douglas W / Mencio, Gregory A / Murray, Peter M / Nelson, Charles L / Peabody, Terrance / Porter, Scott E / Roberson, James R / Saltzman, Charles L / Sebastianelli, Wayne J /
    Taitsman, Lisa A / Van Heest, Ann E / Martin, David F

    The Journal of the American Academy of Orthopaedic Surgeons

    2020  Volume 28, Issue 11, Page(s) e465–e468

    Abstract: The COVID-19 pandemic has disrupted every aspect of society in a way never previously experienced by our nation's orthopaedic surgeons. In response to the challenges the American Board of Orthopaedic Surgery has taken steps to adapt our Board ... ...

    Abstract The COVID-19 pandemic has disrupted every aspect of society in a way never previously experienced by our nation's orthopaedic surgeons. In response to the challenges the American Board of Orthopaedic Surgery has taken steps to adapt our Board Certification and Continuous Certification processes. These changes were made to provide flexibility for as many Candidates and Diplomates as possible to participate while maintaining our high standards. The American Board of Orthopaedic Surgery is first and foremost committed to the safety and well-being of our patients, physicians, and families while striving to remain responsive to the changing circumstances affecting our Candidates and Diplomates.
    MeSH term(s) COVID-19 ; Clinical Competence/standards ; Communicable Disease Control/methods ; Coronavirus Infections ; Education, Medical, Continuing/standards ; Education, Medical, Graduate/standards ; Female ; Humans ; Male ; Occupational Health ; Orthopedic Procedures/education ; Pandemics/prevention & control ; Pandemics/statistics & numerical data ; Patient Safety ; Pneumonia, Viral ; Safety Management ; Specialty Boards/standards ; United States
    Keywords covid19
    Language English
    Publishing date 2020-04-23
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1200524-1
    ISSN 1940-5480 ; 1067-151X
    ISSN (online) 1940-5480
    ISSN 1067-151X
    DOI 10.5435/JAAOS-D-20-00392
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440.

    Bentley, Gayle J / Narayanan, Niju / Jha, Ramesh K / Salvachúa, Davinia / Elmore, Joshua R / Peabody, George L / Black, Brenna A / Ramirez, Kelsey / De Capite, Annette / Michener, William E / Werner, Allison Z / Klingeman, Dawn M / Schindel, Heidi S / Nelson, Robert / Foust, Lindsey / Guss, Adam M / Dale, Taraka / Johnson, Christopher W / Beckham, Gregg T

    Metabolic engineering

    2020  Volume 59, Page(s) 64–75

    Abstract: Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously ... ...

    Abstract Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously engineered to produce muconate from glucose; however, periplasmic oxidation of glucose causes substantial 2-ketogluconate accumulation, reducing product yield and selectivity. Deletion of the glucose dehydrogenase gene (gcd) prevents 2-ketogluconate accumulation, but dramatically slows growth and muconate production. In this work, we employed adaptive laboratory evolution to improve muconate production in strains incapable of producing 2-ketogluconate. Growth-based selection improved growth, but reduced muconate titer. A new muconate-responsive biosensor was therefore developed to enable muconate-based screening using fluorescence activated cell sorting. Sorted clones demonstrated both improved growth and muconate production. Mutations identified by whole genome resequencing of these isolates indicated that glucose metabolism may be dysregulated in strains lacking gcd. Using this information, we used targeted engineering to recapitulate improvements achieved by evolution. Deletion of the transcriptional repressor gene hexR improved strain growth and increased the muconate production rate, and the impact of this deletion was investigated using transcriptomics. The genes gntZ and gacS were also disrupted in several evolved clones, and deletion of these genes further improved strain growth and muconate production. Together, these targets provide a suite of modifications that improve glucose conversion to muconate by P. putida in the context of gcd deletion. Prior to this work, our engineered strain lacking gcd generated 7.0 g/L muconate at a productivity of 0.07 g/L/h and a 38% yield (mol/mol) in a fed-batch bioreactor. Here, the resulting strain with the deletion of hexR, gntZ, and gacS achieved 22.0 g/L at 0.21 g/L/h and a 35.6% yield (mol/mol) from glucose in similar conditions. These strategies enabled enhanced muconic acid production and may also improve production of other target molecules from glucose in P. putida.
    MeSH term(s) Glucose/metabolism ; Metabolic Engineering ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism ; Sorbic Acid/analogs & derivatives ; Sorbic Acid/metabolism
    Chemical Substances muconic acid (3KD92ZL2KH) ; Glucose (IY9XDZ35W2) ; Sorbic Acid (X045WJ989B)
    Language English
    Publishing date 2020-01-10
    Publishing country Belgium
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2020.01.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Development of the KOOS

    Jacobs, Cale A / Peabody, Michael R / Lattermann, Christian / Vega, Jose F / Huston, Laura J / Spindler, Kurt P / Amendola, Annunziato / Andrish, Jack T / Brophy, Robert H / Dunn, Warren R / Flanigan, David C / Jones, Morgan H / Kaeding, Christopher C / Marx, Robert G / Matava, Matthew J / McCarty, Eric C / Parker, Richard D / Reinke, Emily K / Wolcott, Michelle L /
    Wolf, Brian R / Wright, Rick W / Vidal, Armando F

    The American journal of sports medicine

    2018  Volume 46, Issue 12, Page(s) 2915–2921

    Abstract: ... Joint Replacement (KOOS, JR) is a validated short-form instrument to assess patient-reported outcomes ... JR with additional KOOS items would allow for the creation of a short-form KOOS-based global knee ... to those of the IKDC.: Hypothesis: An augmented version of the KOOS, JR could be created that would demonstrate ...

    Abstract Background: The Knee injury and Osteoarthritis Outcome Score (KOOS) has demonstrated inferior psychometric properties when compared with the International Knee Documentation Committee (IKDC) subjective knee form when assessing outcomes after anterior cruciate ligament (ACL) reconstruction. The KOOS, Joint Replacement (KOOS, JR) is a validated short-form instrument to assess patient-reported outcomes (PROs) after knee arthroplasty, and the purpose of this study was to determine if augmenting the KOOS, JR with additional KOOS items would allow for the creation of a short-form KOOS-based global knee score for patients undergoing ACL reconstruction, with psychometric properties similar to those of the IKDC.
    Hypothesis: An augmented version of the KOOS, JR could be created that would demonstrate convergent validity with the IKDC but avoid the ceiling effects and limitations previously noted with several of the KOOS subscales.
    Study design: Cohort study (diagnosis); Level of evidence, 2.
    Methods: Based on preoperative and 2-year postoperative responses to the KOOS questionnaires from a sample of 1904 patients undergoing ACL reconstruction, an aggregate score combining the KOOS, JR and the 4 KOOS Quality of Life subscale questions, termed the KOOS
    Results: The newly developed KOOS
    Conclusion: The large ceiling effects limit the ability to use several of the KOOS subscales with the younger, more active ACL population. However, by creating an aggregate score from the KOOS, JR and 4 KOOS Quality of Life subscale questions, the 11-item KOOS
    MeSH term(s) Adult ; Anterior Cruciate Ligament Injuries/physiopathology ; Anterior Cruciate Ligament Injuries/surgery ; Anterior Cruciate Ligament Reconstruction/adverse effects ; Cohort Studies ; Disability Evaluation ; Female ; Humans ; Male ; Patient Reported Outcome Measures ; Program Development ; Surveys and Questionnaires
    Language English
    Publishing date 2018-08-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 197482-8
    ISSN 1552-3365 ; 0363-5465
    ISSN (online) 1552-3365
    ISSN 0363-5465
    DOI 10.1177/0363546518789619
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Seagrass Abundance Predicts Surficial Soil Organic Carbon Stocks Across the Range of Thalassia testudinum in the Western North Atlantic

    Fourqurean, James W. / Campbell, Justin E. / Rhoades, O.K. / Munson, Calvin J. / Krause, Johannes R. / Altieri, Andrew H. / Douglass, James G. / Heck, Kenneth L. / Paul, Valerie J. / Armitage, Anna R. / Barry, Savanna C. / Bethel, Enrique / Christ, Lindsey / Christianen, Marjolijn J.A. / Dodillet, Grace / Dutton, Katrina / Frazer, Thomas K. / Gaffey, Bethany M. / Glazner, Rachael /
    Goeke, Janelle A. / Grana-Valdes, Rancel / Kramer, Olivier A.A. / Linhardt, Samantha T. / Martin, Charles W. / López, Isis Gabriela Martínez / McDonald, Ashley M. / Main, Vivienne A. / Manuel, Sarah A. / Marco-Méndez, Candela / O’Brien, Duncan A. / O’Shea, Owen / Patrick, Christopher J. / Peabody, Clare / Reynolds, Laura K. / Rodriguez, Alex / Rodriguez Bravo, Lucia M. / Sang, Amanda / Sawall, Yvonne / Smulders, Fee O.H. / Thompson, Jamie E. / van Tussenbroek, Brigitta / Wied, William L. / Wilson, Sara S.

    Estuaries and coasts

    2023  Volume 46, Issue 5

    Abstract: The organic carbon (Corg) stored in seagrass meadows is globally significant and could be relevant in strategies to mitigate increasing CO2 concentration in the atmosphere. Most of that stored Corg is in the soils that underlie the seagrasses. We ... ...

    Abstract The organic carbon (Corg) stored in seagrass meadows is globally significant and could be relevant in strategies to mitigate increasing CO2 concentration in the atmosphere. Most of that stored Corg is in the soils that underlie the seagrasses. We explored how seagrass and soil characteristics vary among seagrass meadows across the geographic range of turtlegrass (Thalassia testudinum) with a goal of illuminating the processes controlling soil organic carbon (Corg) storage spanning 23° of latitude. Seagrass abundance (percent cover, biomass, and canopy height) varied by over an order of magnitude across sites, and we found high variability in soil characteristics, with Corg ranging from 0.08 to 12.59% dry weight. Seagrass abundance was a good predictor of the Corg stocks in surficial soils, and the relative importance of seagrass-derived soil Corg increased as abundance increased. These relationships suggest that first-order estimates of surficial soil Corg stocks can be made by measuring seagrass abundance and applying a linear transfer function. The relative availability of the nutrients N and P to support plant growth was also correlated with soil Corg stocks. Stocks were lower at N-limited sites than at P-limited ones, but the importance of seagrass-derived organic matter to soil Corg stocks was not a function of nutrient limitation status. This finding seemed at odds with our observation that labile standard substrates decomposed more slowly at N-limited than at P-limited sites, since even though decomposition rates were 55% lower at N-limited sites, less Corg was accumulating in the soils. The dependence of Corg stocks and decomposition rates on nutrient availability suggests that eutrophication is likely to exert a strong influence on carbon storage in seagrass meadows.
    Keywords Blue carbon ; Decomposition ; Latitudinal gradients ; Nutrient limitation ; Sediment ; Submerged aquatic vegetation
    Subject code 550
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2229170-2
    ISSN 1559-2731 ; 1559-2723
    ISSN (online) 1559-2731
    ISSN 1559-2723
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: The American Board of Orthopaedic Surgery Response to COVID-19

    Wright, Rick W / Armstrong, April D / Azar, Frederick M / Bednar, Michael S / Carpenter, James E / Evans, Jack B / Flynn, John M / Garvin, Kevin L / Jacobs, Joshua J / Kang, James D / Lundy, Douglas W / Mencio, Gregory A / Murray, Peter M / Nelson, Charles L / Peabody, Terrance / Porter, Scott E / Roberson, James R / Saltzman, Charles L / Sebastianelli, Wayne J /
    Taitsman, Lisa A / Van Heest, Ann E / Martin, David F

    J Am Acad Orthop Surg

    Abstract: The COVID-19 pandemic has disrupted every aspect of society in a way never previously experienced by our nation's orthopaedic surgeons. In response to the challenges the American Board of Orthopaedic Surgery has taken steps to adapt our Board ... ...

    Abstract The COVID-19 pandemic has disrupted every aspect of society in a way never previously experienced by our nation's orthopaedic surgeons. In response to the challenges the American Board of Orthopaedic Surgery has taken steps to adapt our Board Certification and Continuous Certification processes. These changes were made to provide flexibility for as many Candidates and Diplomates as possible to participate while maintaining our high standards. The American Board of Orthopaedic Surgery is first and foremost committed to the safety and well-being of our patients, physicians, and families while striving to remain responsive to the changing circumstances affecting our Candidates and Diplomates.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32324709
    Database COVID19

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  10. Article ; Online: The American Board of Orthopaedic Surgery Response to COVID-19

    Wright, Rick W. / Armstrong, April D. / Azar, Frederick M. / Bednar, Michael S. / Carpenter, James E. / Evans, Jack B. / Flynn, John M. / Garvin, Kevin L. / Jacobs, Joshua J. / Kang, James D. / Lundy, Douglas W. / Mencio, Gregory A. / Murray, Peter M. / Nelson, Charles L. / Peabody, Terrance / Porter, Scott E. / Roberson, James R. / Saltzman, Charles L. / Sebastianelli, Wayne J. /
    Taitsman, Lisa A. / Van Heest, Ann E. / Martin, David F.

    Journal of the American Academy of Orthopaedic Surgeons

    2020  Volume 28, Issue 11, Page(s) e465–e468

    Keywords Surgery ; Orthopedics and Sports Medicine ; covid19
    Language English
    Publisher Ovid Technologies (Wolters Kluwer Health)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1200524-1
    ISSN 1940-5480 ; 1067-151X
    ISSN (online) 1940-5480
    ISSN 1067-151X
    DOI 10.5435/jaaos-d-20-00392
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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