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1. An overview of methods for receiver operating characteristic analysis, with an application to SARS-CoV-2 vaccine-induced humoral responses in solid organ transplant recipients

Author

Dowd, Nathaniel P., Blette, Bryan, Chappell, James D., Halasa, Natasha B., and Spieker, Andrew J.

Subjects
Statistics - Methodology
Abstract

Receiver operating characteristic (ROC) analysis is a tool to evaluate the capacity of a numeric measure to distinguish between groups, often employed in the evaluation of diagnostic tests. Overall classification ability is sometimes crudely summarized by a single numeric measure such as the area under the empirical ROC curve. However, it may also be of interest to estimate the full ROC curve while leveraging assumptions regarding the nature of the data (parametric) or about the ROC curve directly (semiparametric). Although there has been recent interest in methods to conduct comparisons by way of stochastic ordering, nuances surrounding ROC geometry and estimation are not widely known in the broader scientific and statistical community. The overarching goals of this manuscript are to (1) provide an overview of existing frameworks for ROC curve estimation with examples, (2) offer intuition for and considerations regarding methodological trade-offs, and (3) supply sample R code to guide implementation. We utilize simulations to demonstrate the bias-variance trade-off across various methods. As an illustrative example, we analyze data from a recent cohort study in order to compare responses to SARS-CoV-2 vaccination between solid organ transplant recipients and healthy controls., Comment: 23 pages, 6 figures

Published
2024

2. Respiratory Syncytial Virus Prevalence and Risk Factors among Healthy Term Infants, United States

Author

Cacho, Ferdinand, Gebretsadik, Tebeb, Anderson, Larry J., Chappell, James D., Rosas-Salazar, Christian, Ortiz, Justin R., and Hartert, Tina

Subjects
Respiratory syncytial virus infection -- Statistics -- Risk factors -- Physiological aspects, Pediatric research, Health
Abstract

Respiratory syncytial virus (RSV) is a leading cause of illness in infants (1). Previous epidemiologic studies of RSV infection during infancy have focused on symptomatic illness, predominantly lower respiratory tract [...]

Published
2024

3. Resonant excitation of plasma waves in a plasma channel

Author

Ross, Aimee J., Chappell, James, van de Wetering, Johannes J., Cowley, James, Archer, Emily, Bourgeois, Nicolas, Corner, Laura, Emerson, David R., Feder, Linus, Gu, Xiao J., Jakobsson, Oscar, Jones, Harry, Picksley, Alexander, Reid, Linus, Wang, Wei-Ting, Walczak, Roman, and Hooker, Simon M.

Subjects
Physics - Accelerator Physics, Physics - Plasma Physics
Abstract

We demonstrate resonant excitation of a plasma wave by a train of short laser pulses guided in a pre-formed plasma channel, for parameters relevant to a plasma-modulated plasma accelerator (P-MoPA). We show experimentally that a train of $N \approx 10$ short pulses, of total energy $\sim 1$ J, can be guided through $110$ mm long plasma channels with on-axis densities in the range $10^{17} - 10^{18}$ cm$^{-3}$. The spectrum of the transmitted train is found to be strongly red-shifted when the plasma period is tuned to the intra-train pulse spacing. Numerical simulations are found to be in excellent agreement with the measurements and indicate that the resonantly excited plasma waves have an amplitude in the range $3$ - $10$ GV m$^{-1}$, corresponding to an accelerator stage energy gain of order $1$ GeV., Comment: 13 pages, 14 figures (including Supplemental Material)

Published
2023
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5. Resolving game theoretical dilemmas with quantum states

Author

Iqbal, Azhar, Chappell, James M., Szabo, Claudia, and Abbott, Derek

Subjects
Quantum Physics
Abstract

We present a new framework for creating a quantum version of a classical game, based on Fine's theorem. This theorem shows that for a given set of marginals, a system of Bell's inequalities constitutes both necessary and sufficient conditions for the existence of the corresponding joint probability distribution. Using Fine's theorem, we re-express both the player payoffs and their strategies in terms of a set of marginals, thus paving the way for the consideration of sets of marginals -- corresponding to entangled quantum states -- for which no corresponding joint probability distribution may exist. By harnessing quantum states and employing Positive Operator-Valued Measures (POVMs), we then consider particular quantum states that can potentially resolve dilemmas inherent in classical games., Comment: Revised

Published
2023
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6. Total and Subgenomic RNA Viral Load in Patients Infected With SARS-CoV-2 Alpha, Delta, and Omicron Variants.

Author

Dimcheff, Derek, Blair, Christopher, Zhu, Yuwei, Chappell, James, Gaglani, Manjusha, McNeal, Tresa, Ghamande, Shekhar, Steingrub, Jay, Shapiro, Nathan, Duggal, Abhijit, Busse, Laurence, Frosch, Anne, Peltan, Ithan, Hager, David, Gong, Michelle, Exline, Matthew, Khan, Akram, Wilson, Jennifer, Qadir, Nida, Ginde, Adit, Douin, David, Mohr, Nicholas, Mallow, Christopher, Martin, Emily, Johnson, Nicholas, Casey, Jonathan, Stubblefield, William, Gibbs, Kevin, Kwon, Jennie, Talbot, H, Halasa, Natasha, Grijalva, Carlos, Baughman, Adrienne, Womack, Kelsey, Hart, Kimberly, Swan, Sydney, Surie, Diya, Thornburg, Natalie, McMorrow, Meredith, Self, Wesley, and Lauring, Adam

Subjects
SARS-CoV-2, subgenomic RNA, variants of concern, viral load, Adult, Humans, SARS-CoV-2, Subgenomic RNA, COVID-19, Viral Load, RNA, RNA, Viral
Abstract

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic and subgenomic RNA levels are frequently used as a correlate of infectiousness. The impact of host factors and SARS-CoV-2 lineage on RNA viral load is unclear. METHODS: Total nucleocapsid (N) and subgenomic N (sgN) RNA levels were measured by quantitative reverse transcription polymerase chain reaction (RT-qPCR) in specimens from 3204 individuals hospitalized with coronavirus disease 2019 (COVID-19) at 21 hospitals. RT-qPCR cycle threshold (Ct) values were used to estimate RNA viral load. The impact of time of sampling, SARS-CoV-2 variant, age, comorbidities, vaccination, and immune status on N and sgN Ct values were evaluated using multiple linear regression. RESULTS: Mean Ct values at presentation for N were 24.14 (SD 4.53) for non-variants of concern, 25.15 (SD 4.33) for Alpha, 25.31 (SD 4.50) for Delta, and 26.26 (SD 4.42) for Omicron. N and sgN RNA levels varied with time since symptom onset and infecting variant but not with age, comorbidity, immune status, or vaccination. When normalized to total N RNA, sgN levels were similar across all variants. CONCLUSIONS: RNA viral loads were similar among hospitalized adults, irrespective of infecting variant and known risk factors for severe COVID-19. Total N and subgenomic RNA N viral loads were highly correlated, suggesting that subgenomic RNA measurements add little information for the purposes of estimating infectivity.

Published
2023

7. Association of Culturable-Virus Detection and Household Transmission of SARS-CoV-2, California and Tennessee, 2020-2022.

Author

Deyoe, Jessica E, Kelly, J Daniel, Grijalva, Carlos G, Bonenfant, Gaston, Lu, Scott, Anglin, Khamal, Garcia-Knight, Miguel, Pineda-Ramirez, Jesus, Hagen, Melissa Briggs, Saydah, Sharon, Abedi, Glen R, Goldberg, Sarah A, Tassetto, Michel, Zhang, Amethyst, Donohue, Kevin C, Davidson, Michelle C, Sanchez, Ruth Diaz, Djomaleu, Manuella, Mathur, Sujata, Shak, Joshua R, Deeks, Steven G, Peluso, Michael J, Chiu, Charles Y, Zhu, Yuwei, Halasa, Natasha B, Chappell, James D, Mellis, Alexandra, Reed, Carrie, Andino, Raul, Martin, Jeffrey N, Zhou, Bin, Talbot, H Keipp, Midgley, Claire M, and Rolfes, Melissa A

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Lung, Emerging Infectious Diseases, Biodefense, Prevention, Vaccine Related, Infectious Diseases, Infection, Humans, SARS-CoV-2, COVID-19, Tennessee, Family Characteristics, California, household transmission, secondary infection risk, viral culture, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

From 2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) household transmission studies (enrolling April 2020 to January 2022) with rapid enrollment and specimen collection for 14 days, 61% (43/70) of primary cases had culturable virus detected ≥6 days post-onset. Risk of secondary infection among household contacts tended to be greater when primary cases had culturable virus detected after onset. Regardless of duration of culturable virus, most secondary infections (70%, 28/40) had serial intervals

Published
2023

8. The AWAKE Run 2 programme and beyond

Author

Gschwendtner, Edda, Lotov, Konstantin, Muggli, Patric, Wing, Matthew, Agnello, Riccardo, Ahdida, Claudia Christina, Goncalves, Maria Carolina Amoedo, Andrebe, Yanis, Apsimon, Oznur, Apsimon, Robert, Arnesano, Jordan Matias, Bachmann, Anna-Maria, Barrientos, Diego, Batsch, Fabian, Bencini, Vittorio, Bergamaschi, Michele, Blanchard, Patrick, Burrows, Philip Nicholas, Buttenschön, Birger, Caldwell, Allen, Chappell, James, Chevallay, Eric, Chung, Moses, Cooke, David Andrew, Damerau, Heiko, Davut, Can, Demeter, Gabor, Dexter, Amos Christopher, Doebert, Steffen, Elverson, Francesa Ann, Farmer, John, Fasoli, Ambrogio, Fedosseev, Valentin, Fonseca, Ricardo, Furno, Ivo, Gessner, Spencer, Gorn, Aleksandr, Granados, Eduardo, Granetzny, Marcel, Graubner, Tim, Grulke, Olaf, Guran, Eloise Daria, Hafych, Vasyl, Hartin, Anthony, Henderson, James, Hüther, Mathias, Kedves, Miklos, Keeble, Fearghus, Khudiakov, Vadim, Kim, Seong-Yeol, Kraus, Florian, Krupa, Michel, Lefevre, Thibaut, Liang, Linbo, Liu, Shengli, Lopes, Nelson, Calderon, Miguel Martinez, Mazzoni, Stefano, Godoy, David Medina, Moody, Joshua, Moon, Kookjin, Guzmán, Pablo Israel Morales, Moreira, Mariana, Nechaeva, Tatiana, Nowak, Elzbieta, Pakuza, Collette, Panuganti, Harsha, Pardons, Ans, Pepitone, Kevin, Perera, Aravinda, Pucek, Jan, Pukhov, Alexander, Ramjiawan, Rebecca Louise, Rey, Stephane, Scaachi, Adam, Schmitz, Oliver, Senes, Eugenio, Silva, Fernando, Silva, Luis, Stollberg, Christine, Sublet, Alban, Swain, Catherine, Topaloudis, Athanasios, Torrado, Nuno, Tuev, Petr, Turner, Marlene, Velotti, Francesco, Verra, Livio, Verzilov, Victor, Vieira, Jorge, Vincke, Helmut, Weidl, Martin, Welsch, Carsten, Wendt, Manfred, Wiwattananon, Peerawan, Wolfenden, Joseph, Woolley, Benjamin, Wyler, Samuel, Xia, Guoxing, Yarygova, Vlada, Zepp, Michael, and Della Porta, Giovanni Zevi

Subjects
Physics - Accelerator Physics, High Energy Physics - Experiment, Physics - Plasma Physics
Abstract

Plasma wakefield acceleration is a promising technology to reduce the size of particle accelerators. Use of high energy protons to drive wakefields in plasma has been demonstrated during Run 1 of the AWAKE programme at CERN. Protons of energy 400 GeV drove wakefields that accelerated electrons to 2 GeV in under 10 m of plasma. The AWAKE collaboration is now embarking on Run 2 with the main aims to demonstrate stable accelerating gradients of 0.5-1 GV/m, preserve emittance of the electron bunches during acceleration and develop plasma sources scalable to 100s of metres and beyond. By the end of Run 2, the AWAKE scheme should be able to provide electron beams for particle physics experiments and several possible experiments have already been evaluated. This article summarises the programme of AWAKE Run 2 and how it will be achieved as well as the possible application of the AWAKE scheme to novel particle physics experiments., Comment: 21 pages, 8 figures. Submitted to Symmetry journal

Published
2022

9. Protection of mRNA vaccines against hospitalized COVID-19 in adults over the first year following authorization in the United States

Author

Tenforde, Mark W, Self, Wesley H, Zhu, Yuwei, Naioti, Eric A, Gaglani, Manjusha, Ginde, Adit A, Jensen, Kelly, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, McNeal, Tresa, Ghamande, Shekhar, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, ten Lohuis, Caitlin, Duggal, Abhijit, Wilson, Jennifer G, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Botros, Mena M, Lauring, Adam S, Shapiro, Nathan I, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Rhoads, Jillian P, Lindsell, Christopher J, Hart, Kimberly W, Turbyfill, Caitlin, Olson, Samantha, Murray, Nancy, Adams, Katherine, and Patel, Manish M

Subjects
Clinical Research, Prevention, Immunization, Vaccine Related, Good Health and Well Being, Humans, Middle Aged, COVID-19, COVID-19 Vaccines, Hospitalization, mRNA Vaccines, RNA, Messenger, SARS-CoV-2, United States, Aged, duration of protection, waning, vaccine effectiveness, mRNA, Influenza and Other Viruses in the Acutely Ill (IVY) Network, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

BackgroundCoronavirus disease 2019 (COVID-19) messenger RNA (mRNA) vaccines were authorized in the United States in December 2020. Although vaccine effectiveness (VE) against mild infection declines markedly after several months, limited understanding exists on the long-term durability of protection against COVID-19-associated hospitalization.MethodsCase-control analysis of adults (≥18 years) hospitalized at 21 hospitals in 18 states 11 March-15 December 2021, including COVID-19 case patients and reverse transcriptase-polymerase chain reaction-negative controls. We included adults who were unvaccinated or vaccinated with 2 doses of a mRNA vaccine before the date of illness onset. VE over time was assessed using logistic regression comparing odds of vaccination in cases versus controls, adjusting for confounders. Models included dichotomous time (

Published
2023

10. Absolute and Relative Vaccine Effectiveness of Primary and Booster Series of COVID-19 Vaccines (mRNA and Adenovirus Vector) Against COVID-19 Hospitalizations in the United States, December 2021–April 2022

Author

Lewis, Nathaniel M, Murray, Nancy, Adams, Katherine, Surie, Diya, Gaglani, Manjusha, Ginde, Adit A, McNeal, Tresa, Ghamande, Shekhar, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Ali, Harith, Prekker, Matthew E, Frosch, Anne E, Exline, Matthew C, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Lauring, Adam S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, Bender, William, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Chappell, James D, Halasa, Natasha, Grijalva, Carlos G, Rice, Todd W, Stubblefield, William B, Baughman, Adrienne, Lindsell, Christopher J, Hart, Kimberly W, Rhoads, Jillian P, McMorrow, Meredith L, Tenforde, Mark W, Self, Wesley H, Patel, Manish M, Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Steingrub, Jay, Kozikowski, Lori-Ann, Souza, Lesley De, Ouellette, Scott, Bolstad, Michael, Coviello, Brianna, Ciottone, Robert, Devilla, Arnaldo, Grafals, Ana, Higgins, Conor, Ottanelli, Carlo, Redman, Kimberly, Scaffidi, Douglas, Weingart, Alexander, Patel, Manish, Tenforde, Mark, Lewis, Nathaniel, Olson, Samantha, Stephenson, Meagan, McMorrow, Meredith, Tremarelli, Maraia, Turbyfill, Caitlin, Mehkri, Omar, Mitchell, Megan, Griffith, Zachary, Brennan, Connery, Ashok, Kiran, Poynter, Bryan, and Busse, Laurence

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Immunization, Biotechnology, Vaccine Related, Prevention, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Good Health and Well Being, absolute vaccine effectiveness, booster vaccine series, COVID-19, primary vaccine series, relative vaccine effectiveness, Influenza and Other Viruses in the Acutely Ill (IVY) Network, Clinical sciences, Medical microbiology
Abstract

BackgroundCoronavirus disease 2019 (COVID-19) vaccine effectiveness (VE) studies are increasingly reporting relative VE (rVE) comparing a primary series plus booster doses with a primary series only. Interpretation of rVE differs from traditional studies measuring absolute VE (aVE) of a vaccine regimen against an unvaccinated referent group. We estimated aVE and rVE against COVID-19 hospitalization in primary-series plus first-booster recipients of COVID-19 vaccines.MethodsBooster-eligible immunocompetent adults hospitalized at 21 medical centers in the United States during December 25, 2021-April 4, 2022 were included. In a test-negative design, logistic regression with case status as the outcome and completion of primary vaccine series or primary series plus 1 booster dose as the predictors, adjusted for potential confounders, were used to estimate aVE and rVE.ResultsA total of 2060 patients were analyzed, including 1104 COVID-19 cases and 956 controls. Relative VE against COVID-19 hospitalization in boosted mRNA vaccine recipients versus primary series only was 66% (95% confidence interval [CI], 55%-74%); aVE was 81% (95% CI, 75%-86%) for boosted versus 46% (95% CI, 30%-58%) for primary. For boosted Janssen vaccine recipients versus primary series, rVE was 49% (95% CI, -9% to 76%); aVE was 62% (95% CI, 33%-79%) for boosted versus 36% (95% CI, -4% to 60%) for primary.ConclusionsVaccine booster doses increased protection against COVID-19 hospitalization compared with a primary series. Comparing rVE measures across studies can lead to flawed interpretations of the added value of a new vaccination regimen, whereas difference in aVE, when available, may be a more useful metric.

Published
2023

11. Early Estimates of Bivalent mRNA Vaccine Effectiveness in Preventing COVID-19–Associated Hospitalization Among Immunocompetent Adults Aged ≥65 Years — IVY Network, 18 States, September 8–November 30, 2022

Author

Surie, Diya, DeCuir, Jennifer, Zhu, Yuwei, Gaglani, Manjusha, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, McNeal, Tresa, Ghamande, Shekhar, Gibbs, Kevin W, Files, D Clark, Hager, David N, Ali, Harith, Taghizadeh, Leyla, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Khan, Akram, Bender, William S, Duggal, Abhijit, Wilson, Jennifer G, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Kwon, Jennie H, Exline, Matthew C, Lauring, Adam S, Shapiro, Nathan I, Columbus, Cristie, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Rhoads, Jillian P, Hart, Kimberly W, Swan, Sydney A, Lewis, Nathaniel M, McMorrow, Meredith L, Self, Wesley H, and Network, IVY

Subjects
Vaccine Related, Infectious Diseases, Immunization, Biodefense, Prevention, 3.4 Vaccines, Prevention of disease and conditions, and promotion of well-being, Good Health and Well Being, Humans, Aged, COVID-19, SARS-CoV-2, COVID-19 Vaccines, Vaccine Efficacy, Hospitalization, RNA, Messenger, Vaccines, Combined, IVY Network, General & Internal Medicine
Abstract

Monovalent COVID-19 mRNA vaccines, designed against the ancestral strain of SARS-CoV-2, successfully reduced COVID-19-related morbidity and mortality in the United States and globally (1,2). However, vaccine effectiveness (VE) against COVID-19-associated hospitalization has declined over time, likely related to a combination of factors, including waning immunity and, with the emergence of the Omicron variant and its sublineages, immune evasion (3). To address these factors, on September 1, 2022, the Advisory Committee on Immunization Practices recommended a bivalent COVID-19 mRNA booster (bivalent booster) dose, developed against the spike protein from ancestral SARS-CoV-2 and Omicron BA.4/BA.5 sublineages, for persons who had completed at least a primary COVID-19 vaccination series (with or without monovalent booster doses) ≥2 months earlier (4). Data on the effectiveness of a bivalent booster dose against COVID-19 hospitalization in the United States are lacking, including among older adults, who are at highest risk for severe COVID-19-associated illness. During September 8-November 30, 2022, the Investigating Respiratory Viruses in the Acutely Ill (IVY) Network§ assessed effectiveness of a bivalent booster dose received after ≥2 doses of monovalent mRNA vaccine against COVID-19-associated hospitalization among immunocompetent adults aged ≥65 years. When compared with unvaccinated persons, VE of a bivalent booster dose received ≥7 days before illness onset (median = 29 days) against COVID-19-associated hospitalization was 84%. Compared with persons who received ≥2 monovalent-only mRNA vaccine doses, relative VE of a bivalent booster dose was 73%. These early findings show that a bivalent booster dose provided strong protection against COVID-19-associated hospitalization in older adults and additional protection among persons with previous monovalent-only mRNA vaccination. All eligible persons, especially adults aged ≥65 years, should receive a bivalent booster dose to maximize protection against COVID-19 hospitalization this winter season. Additional strategies to prevent respiratory illness, such as masking in indoor public spaces, should also be considered, especially in areas where COVID-19 community levels are high (4,5).

Published
2022

12. Comparison of test-negative and syndrome-negative controls in SARS-CoV-2 vaccine effectiveness evaluations for preventing COVID-19 hospitalizations in the United States

Author

Turbyfill, Caitlin, Adams, Katherine, Tenforde, Mark W, Murray, Nancy L, Gaglani, Manjusha, Ginde, Adit A, McNeal, Tresa, Ghamande, Shekhar, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Frosch, Anne E, Exline, Matthew C, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Lauring, Adam S, Khan, Akram, Busse, Laurence W, Lohuis, Caitlin C ten, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Kwon, Jennie H, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Stubblefield, William B, Baughman, Adrienne, Rhoads, Jillian P, Lindsell, Christopher J, Hart, Kimberly W, McMorrow, Meredith, Surie, Diya, Self, Wesley H, and Patel, Manish M

Subjects
Prevention, Lung, Pneumonia & Influenza, Immunization, Clinical Research, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Vaccine Related, Rehabilitation, Good Health and Well Being, Humans, Adult, United States, Influenza, Human, COVID-19 Vaccines, SARS-CoV-2, COVID-19, COVID-19 Testing, Vaccine Efficacy, Case-Control Studies, Influenza Vaccines, Hospitalization, Syndrome, Test-negative, Vaccine effectiveness, Case-control study, Control groups, Research design, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
Abstract

BackgroundTest-negative design (TND) studies have produced validated estimates of vaccine effectiveness (VE) for influenza vaccine studies. However, syndrome-negative controls have been proposed for differentiating bias and true estimates in VE evaluations for COVID-19. To understand the use of alternative control groups, we compared characteristics and VE estimates of syndrome-negative and test-negative VE controls.MethodsAdults hospitalized at 21 medical centers in 18 states March 11-August 31, 2021 were eligible for analysis. Case patients had symptomatic acute respiratory infection (ARI) and tested positive for SARS-CoV-2. Control groups were test-negative patients with ARI but negative SARS-CoV-2 testing, and syndrome-negative controls were without ARI and negative SARS-CoV-2 testing. Chi square and Wilcoxon rank sum tests were used to detect differences in baseline characteristics. VE against COVID-19 hospitalization was calculated using logistic regression comparing adjusted odds of prior mRNA vaccination between cases hospitalized with COVID-19 and each control group.Results5811 adults (2726 cases, 1696 test-negative controls, and 1389 syndrome-negative controls) were included. Control groups differed across characteristics including age, race/ethnicity, employment, previous hospitalizations, medical conditions, and immunosuppression. However, control-group-specific VE estimates were very similar. Among immunocompetent patients aged 18-64 years, VE was 93 % (95 % CI: 90-94) using syndrome-negative controls and 91 % (95 % CI: 88-93) using test-negative controls.ConclusionsDespite demographic and clinical differences between control groups, the use of either control group produced similar VE estimates across age groups and immunosuppression status. These findings support the use of test-negative controls and increase confidence in COVID-19 VE estimates produced by test-negative design studies.

Published
2022

13. Ascertainment of vaccination status by self‐report versus source documentation: Impact on measuring COVID‐19 vaccine effectiveness

Author

Stephenson, Meagan, Olson, Samantha M, Self, Wesley H, Ginde, Adit A, Mohr, Nicholas M, Gaglani, Manjusha, Shapiro, Nathan I, Gibbs, Kevin W, Hager, David N, Prekker, Matthew E, Gong, Michelle N, Steingrub, Jay S, Peltan, Ithan D, Martin, Emily T, Reddy, Raju, Busse, Laurence W, Duggal, Abhijit, Wilson, Jennifer G, Qadir, Nida, Mallow, Christopher, Kwon, Jennie H, Exline, Matthew C, Chappell, James D, Lauring, Adam S, Baughman, Adrienne, Lindsell, Christopher J, Hart, Kimberly W, Lewis, Nathaniel M, Patel, Manish M, Tenforde, Mark W, and Investigators, IVY Network

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Immunization, Vaccine Related, Clinical Research, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Good Health and Well Being, Adult, COVID-19, COVID-19 Vaccines, Documentation, Humans, Pandemics, RNA, Messenger, SARS-CoV-2, Self Report, Vaccination, Vaccine Efficacy, concordance, registry, self-report, vaccine effectiveness, IVY Network Investigators, Public Health and Health Services, Virology, Clinical sciences, Epidemiology
Abstract

BackgroundDuring the COVID-19 pandemic, self-reported COVID-19 vaccination might facilitate rapid evaluations of vaccine effectiveness (VE) when source documentation (e.g., immunization information systems [IIS]) is not readily available. We evaluated the concordance of COVID-19 vaccination status ascertained by self-report versus source documentation and its impact on VE estimates.MethodsHospitalized adults (≥18 years) admitted to 18 U.S. medical centers March-June 2021 were enrolled, including COVID-19 cases and SARS-CoV-2 negative controls. Patients were interviewed about COVID-19 vaccination. Abstractors simultaneously searched IIS, medical records, and other sources for vaccination information. To compare vaccination status by self-report and documentation, we estimated percent agreement and unweighted kappa with 95% confidence intervals (CIs). We then calculated VE in preventing COVID-19 hospitalization of full vaccination (2 doses of mRNA product ≥14 days prior to illness onset) independently using data from self-report or source documentation.ResultsOf 2520 patients, 594 (24%) did not have self-reported vaccination information to assign vaccination group; these patients tended to be more severely ill. Among 1924 patients with both self-report and source documentation information, 95.0% (95% CI: 93.9-95.9%) agreement was observed, with a kappa of 0.9127 (95% CI: 0.9109-0.9145). VE was 86% (95% CI: 81-90%) by self-report data only and 85% (95% CI: 81-89%) by source documentation data only.ConclusionsApproximately one-quarter of hospitalized patients could not provide self-report COVID-19 vaccination status. Among patients with self-report information, there was high concordance with source documented status. Self-report may be a reasonable source of COVID-19 vaccination information for timely VE assessment for public health action.

Published
2022

14. Effectiveness of the Ad26.COV2.S (Johnson & Johnson) COVID-19 Vaccine for Preventing COVID-19 Hospitalizations and Progression to High Disease Severity in the United States

Author

Lewis, Nathaniel M, Self, Wesley H, Gaglani, Manjusha, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Ghamande, Shekhar A, McNeal, Tresa A, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, amuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Busse, Laurence W, Lohuis, Caitlin C ten, Duggal, bhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Lauring, Adam S, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Rhoads, Jillian P, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Adams, Katherine, Patel, Manish M, Tenforde, Mark W, and Collaborators, IVY Network

Subjects
Rare Diseases, Immunization, Clinical Research, Prevention, Vaccine Related, 3.4 Vaccines, Prevention of disease and conditions, and promotion of well-being, Good Health and Well Being, Ad26COVS1, Adult, COVID-19, COVID-19 Vaccines, Hospitalization, Humans, Influenza Vaccines, Influenza, Human, Severity of Illness Index, United States, vaccine effectiveness, viral vector vaccines, IVY Network Collaborators, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Background . Adults in the United States (US) began receiving the adenovirus vector coronavirus disease 2019 (COVID-19) vaccine, Ad26.COV2.S (Johnson & Johnson [Janssen]), in February 2021. We evaluated Ad26.COV2.S vaccine effectiveness (VE) against COVID-19 hospitalization and high disease severity during the first 10 months of its use. Methods . In a multicenter case-control analysis of US adults (≥18 years) hospitalized 11 March to 15 December 2021, we estimated VE against susceptibility to COVID-19 hospitalization (VEs), comparing odds of prior vaccination with a single dose Ad26.COV2.S vaccine between hospitalized cases with COVID-19 and controls without COVID-19. Among hospitalized patients with COVID-19, we estimated VE against disease progression (VEp) to death or invasive mechanical ventilation (IMV), comparing odds of prior vaccination between patients with and without progression. Results . After excluding patients receiving mRNA vaccines, among 3979 COVID-19 case-patients (5% vaccinated with Ad26.COV2.S) and 2229 controls (13% vaccinated with Ad26.COV2.S), VEs of Ad26.COV2.S against COVID-19 hospitalization was 70% (95% confidence interval [CI]: 63-75%) overall, including 55% (29-72%) among immunocompromised patients, and 72% (64-77%) among immunocompetent patients, for whom VEs was similar at 14-90 days (73% [59-82%]), 91-180 days (71% [60-80%]), and 181-274 days (70% [54-81%]) postvaccination. Among hospitalized COVID-19 case-patients, VEp was 46% (18-65%) among immunocompetent patients. Conclusions . The Ad26.COV2.S COVID-19 vaccine reduced the risk of COVID-19 hospitalization by 72% among immunocompetent adults without waning through 6 months postvaccination. After hospitalization for COVID-19, vaccinated immunocompetent patients were less likely to require IMV or die compared to unvaccinated immunocompetent patients.

Published
2022

15. Assessment and mitigation of bias in influenza and COVID-19 vaccine effectiveness analyses — IVY Network, September 1, 2022–March 30, 2023

Author

Lewis, Nathaniel M., Harker, Elizabeth J., Leis, Aleda, Zhu, Yuwei, Talbot, H. Keipp, Grijalva, Carlos G., Halasa, Natasha, Chappell, James D., Johnson, Cassandra A., Rice, Todd W., Casey, Jonathan D., Lauring, Adam S., Gaglani, Manjusha, Ghamande, Shekhar, Columbus, Cristie, Steingrub, Jay S., Shapiro, Nathan I., Duggal, Abhijit, Felzer, Jamie, Prekker, Matthew E., Peltan, Ithan D., Brown, Samuel M., Hager, David N., Gong, Michelle N., Mohamed, Amira, Exline, Matthew C., Khan, Akram, Wilson, Jennifer G., Mosier, Jarrod, Qadir, Nida, Chang, Steven Y., Ginde, Adit A., Mohr, Nicholas M., Mallow, Christopher, Harris, Estelle S., Johnson, Nicholas J., Srinivasan, Vasisht, Gibbs, Kevin W., Kwon, Jennie H., Vaughn, Ivana A., Ramesh, Mayur, Safdar, Basmah, DeCuir, Jennifer, Surie, Diya, Dawood, Fatimah S., Ellington, Sascha, Self, Wesley H., and Martin, Emily T.

Published
2025
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20. Effectiveness of mRNA Vaccines Against COVID-19 Hospitalization by Age and Chronic Medical Conditions Burden Among Immunocompetent US Adults, March-August 2021

Author

Lewis, Nathaniel M, Naioti, Eric A, Self, Wesley H, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Gaglani, Manjusha, Ghamande, Shekhar A, McNeal, Tresa A, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Henning, Daniel J, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Hubel, Kinsley, Hough, Catherine L, Busse, Laurence W, Lohuis, Caitlin C ten, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra J, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Halasa, Natasha, Chappell, James D, Lauring, Adam S, Grijalva, Carlos G, Rice, Todd W, Rhoads, Jillian P, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Schrag, Stephanie J, Kobayashi, Miwako, Verani, Jennifer R, Patel, Manish M, Tenforde, Mark W, Collaborators, IVY Network, McNeal, Tresa, Ghamande, Shekhar, Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Settele, Natalie, Ettlinger, Jason, Priest, Elisa, Thomas, Jennifer, Arroliga, Alejandro, Beeram, Madhava, Kindle, Ryan, Kozikowski, Lori-Ann, De Souza, Lesley, Ouellette, Scott, Thornton-Thompson, Sherell, Tyler, Patrick, Mehkri, Omar, Mitchell, Meg, Brennan, Connery, Ashok, Kiran, Poynter, Bryan, Stanley, Nicholas, Hendrickson, Audrey, Caspers, Sean, Scharber, Tyler, Jorgensen, Jeffrey, Bowers, Robert, King, Jennifer, Aston, Valerie, Armbruster, Brent, Rothman, Richard E, Nair, Rahul, Chen, Jen-Ting, Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, and Khan, Maryiam

Subjects
Immunization, Aging, Vaccine Related, Good Health and Well Being, Adult, COVID-19, COVID-19 Vaccines, Chronic Disease, Hospitalization, Humans, Vaccines, Synthetic, mRNA Vaccines, chronic medical conditions, preexisting conditions, vaccine effectiveness, IVY Network Collaborators, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Vaccine effectiveness (VE) against COVID-19 hospitalization was evaluated among immunocompetent adults (≥18 years) during March-August 2021 using a case-control design. Among 1669 hospitalized COVID-19 cases (11% fully vaccinated) and 1950 RT-PCR-negative controls (54% fully vaccinated), VE was 96% (95% confidence interval [CI], 93%-98%) among patients with no chronic medical conditions and 83% (95% CI, 76%-88%) among patients with ≥ 3 categories of conditions. VE was similar between those aged 18-64 years versus ≥65 years (P > .05). VE against severe COVID-19 was very high among adults without chronic conditions and lessened with increasing comorbidity burden.

Published
2022

21. Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States

Author

Tenforde, Mark W, Patel, Manish M, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Gaglani, Manjusha, McNeal, Tresa, Ghamande, Shekhar, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Exline, Matthew C, Gong, Michelle N, Mohamed, Amira, Henning, Daniel J, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, Ten Lohuis, Caitlin C, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Gershengorn, Hayley B, Babcock, Hilary M, Kwon, Jennie H, Halasa, Natasha, Chappell, James D, Lauring, Adam S, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Olson, Samantha M, Stephenson, Meagan, Schrag, Stephanie J, Kobayashi, Miwako, Verani, Jennifer R, and Self, Wesley H

Subjects
Pneumonia & Influenza, Immunization, Biodefense, Vaccine Related, Clinical Research, Lung, Infectious Diseases, Emerging Infectious Diseases, Pneumonia, Prevention, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Infection, Good Health and Well Being, Adult, COVID-19, COVID-19 Vaccines, Hospitalization, Humans, Middle Aged, RNA, SARS-CoV-2, United States, mRNA Vaccines, vaccine effectiveness, mRNA vaccines, hospitalized, immunocompromised, Influenza and Other Viruses in the Acutely Ill (IVY) Network, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

BackgroundAs severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination coverage increases in the United States, there is a need to understand the real-world effectiveness against severe coronavirus disease 2019 (COVID-19) and among people at increased risk for poor outcomes.MethodsIn a multicenter case-control analysis of US adults hospitalized March 11-May 5, 2021, we evaluated vaccine effectiveness to prevent COVID-19 hospitalizations by comparing odds of prior vaccination with a messenger RNA (mRNA) vaccine (Pfizer-BioNTech or Moderna) between cases hospitalized with COVID-19 and hospital-based controls who tested negative for SARS-CoV-2.ResultsAmong 1212 participants, including 593 cases and 619 controls, median age was 58 years, 22.8% were Black, 13.9% were Hispanic, and 21.0% had immunosuppression. SARS-CoV-2 lineage B0.1.1.7 (Alpha) was the most common variant (67.9% of viruses with lineage determined). Full vaccination (receipt of 2 vaccine doses ≥14 days before illness onset) had been received by 8.2% of cases and 36.4% of controls. Overall vaccine effectiveness was 87.1% (95% confidence interval [CI], 80.7-91.3). Vaccine effectiveness was similar for Pfizer-BioNTech and Moderna vaccines, and highest in adults aged 18-49 years (97.4%; 95% CI, 79.3-9.7). Among 45 patients with vaccine-breakthrough COVID hospitalizations, 44 (97.8%) were ≥50 years old and 20 (44.4%) had immunosuppression. Vaccine effectiveness was lower among patients with immunosuppression (62.9%; 95% CI,20.8-82.6) than without immunosuppression (91.3%; 95% CI, 85.6-94.8).ConclusionDuring March-May 2021, SARS-CoV-2 mRNA vaccines were highly effective for preventing COVID-19 hospitalizations among US adults. SARS-CoV-2 vaccination was beneficial for patients with immunosuppression, but effectiveness was lower in the immunosuppressed population.

Published
2022

22. A flexible design platform for Si/SiGe exchange-only qubits with low disorder

Author

Ha, Wonill, Ha, Sieu D., Choi, Maxwell D., Tang, Yan, Schmitz, Adele E., Levendorf, Mark P., Lee, Kangmu, Chappell, James M., Adams, Tower S., Hulbert, Daniel R., Acuna, Edwin, Noah, Ramsey S., Matten, Justine W., Jura, Michael P., Wright, Jeffrey A., Rakher, Matthew T., and Borselli, Matthew G.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

Spin-based silicon quantum dots are an attractive qubit technology for quantum information processing with respect to coherence time, control, and engineering. Here we present an exchange-only Si qubit device platform that combines the throughput of CMOS-like wafer processing with the versatility of direct-write lithography. The technology, which we coin "SLEDGE," features dot-shaped gates that are patterned simultaneously on one topographical plane and subsequently connected by vias to interconnect metal lines. The process design enables non-trivial layouts as well as flexibility in gate dimensions, material selection, and additional device features such as for rf qubit control. We show that the SLEDGE process has reduced electrostatic disorder with respect to traditional overlapping gate devices with lift-off metallization, and we present spin coherent exchange oscillations and single qubit blind randomized benchmarking data.

Published
2021
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23. Immunophenotypic predictors of influenza vaccine immunogenicity in pediatric hematopoietic cell transplant recipients

Author

Naik, Swati, Williams, Christopher, Russo, Michael, Goyal, Rakesh, Blum, Samantha, Shoemaker, Lauren, Lacombe, Kirsten, Smith, Hannah, Allison, Kim J., Truong, Kenny, Dvorak, Christopher, Hamdan, Lubna, Batarseh, Einas, Haddadin, Zaid, Stewart, Laura S., Stahl, Anna, Potter, Molly, Rahman, Herdi, McHenry, Rendie, Bender, Margaret, Barto, Shari, Amarin, Justin Z., Dulek, Daniel E., Simmons, Joshua, Hayek, Haya, Chappell, James D., Nochowicz, Cindy Hager, Kitko, Carrie L., Schuster, Jennifer E., Muñoz, Flor M., Bocchini, Claire E., Moulton, Elizabeth A., Coffin, Susan E., Freedman, Jason L., Ardura, Monica I., Wattier, Rachel L., Maron, Gabriela, Grimley, Michael, Paulsen, Grant, Danziger-Isakov, Lara, Carpenter, Paul A., Englund, Janet A., Halasa, Natasha B., Spieker, Andrew J., and Kalams, Spyros A.

Published
2024
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24. SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis

Author

Raglow, Zoe, Surie, Diya, Chappell, James D, Zhu, Yuwei, Martin, Emily T, Kwon, Jennie H, Frosch, Anne E, Mohamed, Amira, Gilbert, Julie, Bendall, Emily E, Bahr, Auden, Halasa, Natasha, Talbot, H Keipp, Grijalva, Carlos G, Baughman, Adrienne, Womack, Kelsey N, Johnson, Cassandra, Swan, Sydney A, Koumans, Emilia, McMorrow, Meredith L, Harcourt, Jennifer L, Atherton, Lydia J, Burroughs, Ashley, Thornburg, Natalie J, Self, Wesley H, and Lauring, Adam S

Published
2024
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25. Effectiveness of a Third Dose of Pfizer-BioNTech and Moderna Vaccines in Preventing COVID-19 Hospitalization Among Immunocompetent and Immunocompromised Adults — United States, August–December 2021

Author

Tenforde, Mark W, Patel, Manish M, Gaglani, Manjusha, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, McNeal, Tresa, Ghamande, Shekhar, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, Duggal, Abhijit, Wilson, Jennifer G, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Botros, Mena, Lauring, Adam S, Shapiro, Nathan I, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Rhoads, Jillian P, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Naioti, Eric A, Adams, Katherine, Lewis, Nathaniel M, Surie, Diya, McMorrow, Meredith L, Self, Wesley H, Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Kindle, Ryan, Kozikowski, Lori-Ann, De Souza, Lesley, Ouellette, Scott, Thornton-Thompson, Sherell, Mehkri, Omar, Ashok, Kiran, Gole, Susan, King, Alexander, Poynter, Bryan, ten Lohuis, Caitlin, Stanley, Nicholas, Hendrickson, Audrey, Caspers, Sean, Tordsen, Walker, Kaus, Olivia, Scharber, Tyler, Jorgensen, Jeffrey, Bowers, Robert, King, Jennifer, Aston, Valerie, Rothman, Richard E, Ali, Harith, Nair, Rahul, Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, Khan, Maryiam, So, Preston, Krol, Olivia, Martinez, Jesus, Zouyed, Zachary, Acosta, Michael, and Bazyarboroujeni, Reihaneh

Subjects
Immunization, Infectious Diseases, Prevention, Vaccine Related, Clinical Research, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Good Health and Well Being, 2019-nCoV Vaccine mRNA-1273, Adult, Aged, BNT162 Vaccine, COVID-19, Female, Hospitalization, Humans, Immunization, Secondary, Immunocompetence, Immunocompromised Host, Male, Middle Aged, SARS-CoV-2, United States, Vaccine Efficacy, IVY Network, General & Internal Medicine
Abstract

COVID-19 mRNA vaccines (BNT162b2 [Pfizer-BioNTech] and mRNA-1273 [Moderna]) provide protection against infection with SARS-CoV-2, the virus that causes COVID-19, and are highly effective against COVID-19-associated hospitalization among eligible persons who receive 2 doses (1,2). However, vaccine effectiveness (VE) among persons with immunocompromising conditions* is lower than that among immunocompetent persons (2), and VE declines after several months among all persons (3). On August 12, 2021, the Food and Drug Administration (FDA) issued an emergency use authorization (EUA) for a third mRNA vaccine dose as part of a primary series ≥28 days after dose 2 for persons aged ≥12 years with immunocompromising conditions, and, on November 19, 2021, as a booster dose for all adults aged ≥18 years at least 6 months after dose 2, changed to ≥5 months after dose 2 on January 3, 2022 (4,5,6). Among 2,952 adults (including 1,385 COVID-19 case-patients and 1,567 COVID-19-negative controls) hospitalized at 21 U.S. hospitals during August 19-December 15, 2021, effectiveness of mRNA vaccines against COVID-19-associated hospitalization was compared between adults eligible for but who had not received a third vaccine dose (1,251) and vaccine-eligible adults who received a third dose ≥7 days before illness onset (312). Among 1,875 adults without immunocompromising conditions (including 1,065 [57%] unvaccinated, 679 [36%] 2-dose recipients, and 131 [7%] 3-dose [booster] recipients), VE against COVID-19 hospitalization was higher among those who received a booster dose (97%; 95% CI = 95%-99%) compared with that among 2-dose recipients (82%; 95% CI = 77%-86%) (p

Published
2022

26. Clinical severity of, and effectiveness of mRNA vaccines against, covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: prospective observational study

Author

Lauring, Adam S, Tenforde, Mark W, Chappell, James D, Gaglani, Manjusha, Ginde, Adit A, McNeal, Tresa, Ghamande, Shekhar, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Exline, Matthew C, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, Ten Lohuis, Caitlin C, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Halasa, Natasha, Grijalva, Carlos G, Rice, Todd W, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Rhoads, Jillian P, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Adams, Katherine, Schrag, Stephanie J, Olson, Samantha M, Kobayashi, Miwako, Verani, Jennifer R, Patel, Manish M, and Self, Wesley H

Subjects
Genetics, Immunization, Clinical Research, Prevention, Vaccine Related, Comparative Effectiveness Research, Good Health and Well Being, COVID-19, COVID-19 Vaccines, Case-Control Studies, Hospitalization, Humans, Immunization Schedule, Prospective Studies, SARS-CoV-2, Severity of Illness Index, United States, Influenza and Other Viruses in the Acutely Ill (IVY) Network, Clinical Sciences, Public Health and Health Services, General & Internal Medicine
Abstract

ObjectivesTo characterize the clinical severity of covid-19 associated with the alpha, delta, and omicron SARS-CoV-2 variants among adults admitted to hospital and to compare the effectiveness of mRNA vaccines to prevent hospital admissions related to each variant.DesignCase-control study.Setting21 hospitals across the United States.Participants11 690 adults (≥18 years) admitted to hospital: 5728 with covid-19 (cases) and 5962 without covid-19 (controls). Patients were classified into SARS-CoV-2 variant groups based on viral whole genome sequencing, and, if sequencing did not reveal a lineage, by the predominant circulating variant at the time of hospital admission: alpha (11 March to 3 July 2021), delta (4 July to 25 December 2021), and omicron (26 December 2021 to 14 January 2022).Main outcome measuresVaccine effectiveness calculated using a test negative design for mRNA vaccines to prevent covid-19 related hospital admissions by each variant (alpha, delta, omicron). Among patients admitted to hospital with covid-19, disease severity on the World Health Organization's clinical progression scale was compared among variants using proportional odds regression.ResultsEffectiveness of the mRNA vaccines to prevent covid-19 associated hospital admissions was 85% (95% confidence interval 82% to 88%) for two vaccine doses against the alpha variant, 85% (83% to 87%) for two doses against the delta variant, 94% (92% to 95%) for three doses against the delta variant, 65% (51% to 75%) for two doses against the omicron variant; and 86% (77% to 91%) for three doses against the omicron variant. In-hospital mortality was 7.6% (81/1060) for alpha, 12.2% (461/3788) for delta, and 7.1% (40/565) for omicron. Among unvaccinated patients with covid-19 admitted to hospital, severity on the WHO clinical progression scale was higher for the delta versus alpha variant (adjusted proportional odds ratio 1.28, 95% confidence interval 1.11 to 1.46), and lower for the omicron versus delta variant (0.61, 0.49 to 0.77). Compared with unvaccinated patients, severity was lower for vaccinated patients for each variant, including alpha (adjusted proportional odds ratio 0.33, 0.23 to 0.49), delta (0.44, 0.37 to 0.51), and omicron (0.61, 0.44 to 0.85).ConclusionsmRNA vaccines were found to be highly effective in preventing covid-19 associated hospital admissions related to the alpha, delta, and omicron variants, but three vaccine doses were required to achieve protection against omicron similar to the protection that two doses provided against the delta and alpha variants. Among adults admitted to hospital with covid-19, the omicron variant was associated with less severe disease than the delta variant but still resulted in substantial morbidity and mortality. Vaccinated patients admitted to hospital with covid-19 had significantly lower disease severity than unvaccinated patients for all the variants.

Published
2022

27. Effectiveness of mRNA Vaccination in Preventing COVID-19–Associated Invasive Mechanical Ventilation and Death — United States, March 2021–January 2022

Author

Tenforde, Mark W, Self, Wesley H, Gaglani, Manjusha, Ginde, Adit A, Douin, David J, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, McNeal, Tresa, Ghamande, Shekhar, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Frosch, Anne E, Gong, Michelle N, Mohamed, Amira, Johnson, Nicholas J, Srinivasan, Vasisht, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, Duggal, Abhijit, Wilson, Jennifer G, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Botros, Mena, Lauring, Adam S, Shapiro, Nathan I, Halasa, Natasha, Chappell, James D, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Rhoads, Jillian P, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Adams, Katherine, Surie, Diya, McMorrow, Meredith L, Patel, Manish M, and Network, IVY

Subjects
Clinical Research, Prevention, Vaccine Related, Immunization, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Good Health and Well Being, 2019-nCoV Vaccine mRNA-1273, BNT162 Vaccine, COVID-19, Hospital Mortality, Humans, Respiration, Artificial, United States, Vaccine Efficacy, IVY Network, General & Internal Medicine
Abstract

COVID-19 mRNA vaccines (BNT162b2 [Pfizer-BioNTech] and mRNA-1273 [Moderna]) are effective at preventing COVID-19-associated hospitalization (1-3). However, how well mRNA vaccines protect against the most severe outcomes of these hospitalizations, including invasive mechanical ventilation (IMV) or death is uncertain. Using a case-control design, mRNA vaccine effectiveness (VE) against COVID-19-associated IMV and in-hospital death was evaluated among adults aged ≥18 years hospitalized at 21 U.S. medical centers during March 11, 2021-January 24, 2022. During this period, the most commonly circulating variants of SARS-CoV-2, the virus that causes COVID-19, were B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Previous vaccination (2 or 3 versus 0 vaccine doses before illness onset) in prospectively enrolled COVID-19 case-patients who received IMV or died within 28 days of hospitalization was compared with that among hospitalized control patients without COVID-19. Among 1,440 COVID-19 case-patients who received IMV or died, 307 (21%) had received 2 or 3 vaccine doses before illness onset. Among 6,104 control-patients, 4,020 (66%) had received 2 or 3 vaccine doses. Among the 1,440 case-patients who received IMV or died, those who were vaccinated were older (median age = 69 years), more likely to be immunocompromised* (40%), and had more chronic medical conditions compared with unvaccinated case-patients (median age = 55 years; immunocompromised = 10%; p

Published
2022

28. Controlled density-downramp injection in a beam-driven plasma wakefield accelerator

Author

Knetsch, Alexander, Sheeran, Bridget, Boulton, Lewis, Niknejadi, Pardis, Põder, Kristjan, Schaper, Lucas, Zeng, Ming, Bohlen, Simon, Boyle, Gregory, Brümmer, Theresa, Chappell, James, D'Arcy, Richard, Diederichs, Severin, Foster, Brian, Garland, Matthew James, Caminal, Pau Gonzalez, Hidding, Bernhard, Libov, Vladislav, Lindstrøm, Carl Andreas, de la Ossa, Alberto Martinez, Meisel, Martin, Parikh, Trupen, Schmidt, Bernhard, Schröder, Sarah, Tauscher, Gabriele, Wesch, Stephan, Winkler, Paul, Wood, Jonathan, and Osterhoff, Jens

Subjects
Physics - Accelerator Physics, Physics - Plasma Physics
Abstract

This paper describes the utilization of beam-driven plasma wakefield acceleration to implement a high-quality plasma cathode via density-downramp injection in a short injector stage at the FLASHForward facility at DESY. Electron beams with charge of up to 105 pC and energy spread of a few percent were accelerated by a tunable effective accelerating field of up to 2.7 GV/m. The plasma cathode was operated drift-free with very high injection efficiency. Sources of jitter, the emittance and divergence of the resulting beam were investigated and modeled, as were strategies for performance improvements that would further increase the wide-ranging applications for a plasma cathode with the demonstrated operational stability, Comment: 11 pages, 9 figures

Published
2020
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30. Experimental study of long timescale plasma wakefield evolution

Author

Chappell, James

Abstract

Over the last century, particle accelerators have significantly enhanced our understanding of the fundamental nature of the universe and, as such, have become ubiquitous tools within society. The continued search for explanations of phenomena beyond our current best models motivates the proposal of ever-larger and more expensive particle accelerators. However, the economic impact of building and operating such machines potentially casts doubt on their delivery. The exploration of alternative acceleration concepts that can potentially provide a reduction in the size and cost of these machines has therefore seen a significant growth in interest over the past few decades. One such acceleration concept is that of plasma-based wakefield acceleration where high-intensity particle or laser beams strongly perturb a plasma and, in doing so, generate fields in their wake that can be used to accelerate charged particles. This is an attractive concept as plasmas can support accelerating fields multiple orders of magnitude larger than those provided in conventional accelerators, potentially reducing the accelerating length by similar scales. While rapid progress has recently been made with regards to high-quality acceleration in plasma, comparatively little effort has been applied to the study of the frequency at which this is possible. The measurements presented in this thesis study the evolution of a plasma as the energy imparted into it via the wakefield acceleration process dissipates. Such detailed measurements allow determination of the fundamental mechanisms that will limit high-repetition-rate operation of plasma-based accelerators. As such, these measurements represent a significant first step towards the demonstration of plasma-based acceleration at frequencies comparable to those provided by state-of-the-art conventional accelerators, helping to define the achievable luminosity of future facilities that rely on such technology.

Published
2021

31. Sustained Effectiveness of Pfizer-BioNTech and Moderna Vaccines Against COVID-19 Associated Hospitalizations Among Adults — United States, March–July 2021

Author

Tenforde, Mark W, Self, Wesley H, Naioti, Eric A, Ginde, Adit A, Douin, David J, Olson, Samantha M, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, Gaglani, Manjusha, McNeal, Tresa, Ghamande, Shekhar, Shapiro, Nathan I, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Henning, Daniel J, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, ten Lohuis, Caitlin C, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Halasa, Natasha, Chappell, James D, Lauring, Adam S, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Stephenson, Meagan, Schrag, Stephanie J, Kobayashi, Miwako, Verani, Jennifer R, Patel, Manish M, Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Settele, Natalie, Ettlinger, Jason, Priest, Elisa, Thomas, Jennifer, Arroliga, Alejandro, Beeram, Madhava, Kindle, Ryan, Kozikowski, Lori-Ann, De Souza, Lesley, Ouellette, Scott, Thornton-Thompson, Sherell, Tyler, Patrick, Mehkri, Omar, Ashok, Kiran, Gole, Susan, King, Alexander, Poynter, Bryan, Stanley, Nicholas, Hendrickson, Audrey, Maruggi, Ellen, Scharber, Tyler, Jorgensen, Jeffrey, Bowers, Robert, King, Jennifer, Aston, Valerie, Armbruster, Brent, Rothman, Richard E, Nair, Rahul, Chen, Jen-Ting Tina, Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, Khan, Maryiam, and So, Preston

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Immunization, Clinical Research, Biodefense, Vaccine Related, Prevention, 3.4 Vaccines, 6.1 Pharmaceuticals, Prevention of disease and conditions, and promotion of well-being, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, Adolescent, Adult, Aged, COVID-19, COVID-19 Vaccines, Female, Hospitalization, Humans, Male, Middle Aged, Time Factors, United States, Vaccination, Vaccines, Synthetic, Young Adult, IVY Network Investigators, IVY Network, General & Internal Medicine
Abstract

Real-world evaluations have demonstrated high effectiveness of vaccines against COVID-19-associated hospitalizations (1-4) measured shortly after vaccination; longer follow-up is needed to assess durability of protection. In an evaluation at 21 hospitals in 18 states, the duration of mRNA vaccine (Pfizer-BioNTech or Moderna) effectiveness (VE) against COVID-19-associated hospitalizations was assessed among adults aged ≥18 years. Among 3,089 hospitalized adults (including 1,194 COVID-19 case-patients and 1,895 non-COVID-19 control-patients), the median age was 59 years, 48.7% were female, and 21.1% had an immunocompromising condition. Overall, 141 (11.8%) case-patients and 988 (52.1%) controls were fully vaccinated (defined as receipt of the second dose of Pfizer-BioNTech or Moderna mRNA COVID-19 vaccines ≥14 days before illness onset), with a median interval of 65 days (range = 14-166 days) after receipt of second dose. VE against COVID-19-associated hospitalization during the full surveillance period was 86% (95% confidence interval [CI] = 82%-88%) overall and 90% (95% CI = 87%-92%) among adults without immunocompromising conditions. VE against COVID-19- associated hospitalization was 86% (95% CI = 82%-90%) 2-12 weeks and 84% (95% CI = 77%-90%) 13-24 weeks from receipt of the second vaccine dose, with no significant change between these periods (p = 0.854). Whole genome sequencing of 454 case-patient specimens found that 242 (53.3%) belonged to the B.1.1.7 (Alpha) lineage and 74 (16.3%) to the B.1.617.2 (Delta) lineage. Effectiveness of mRNA vaccines against COVID-19-associated hospitalization was sustained over a 24-week period, including among groups at higher risk for severe COVID-19; ongoing monitoring is needed as new SARS-CoV-2 variants emerge. To reduce their risk for hospitalization, all eligible persons should be offered COVID-19 vaccination.

Published
2021

32. Comparative Effectiveness of Moderna, Pfizer-BioNTech, and Janssen (Johnson & Johnson) Vaccines in Preventing COVID-19 Hospitalizations Among Adults Without Immunocompromising Conditions — United States, March–August 2021

Author

Self, Wesley H, Tenforde, Mark W, Rhoads, Jillian P, Gaglani, Manjusha, Ginde, Adit A, Douin, David J, Olson, Samantha M, Talbot, H Keipp, Casey, Jonathan D, Mohr, Nicholas M, Zepeski, Anne, McNeal, Tresa, Ghamande, Shekhar, Gibbs, Kevin W, Files, D Clark, Hager, David N, Shehu, Arber, Prekker, Matthew E, Erickson, Heidi L, Gong, Michelle N, Mohamed, Amira, Henning, Daniel J, Steingrub, Jay S, Peltan, Ithan D, Brown, Samuel M, Martin, Emily T, Monto, Arnold S, Khan, Akram, Hough, Catherine L, Busse, Laurence W, ten Lohuis, Caitlin C, Duggal, Abhijit, Wilson, Jennifer G, Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y, Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M, Kwon, Jennie H, Exline, Matthew C, Halasa, Natasha, Chappell, James D, Lauring, Adam S, Grijalva, Carlos G, Rice, Todd W, Jones, Ian D, Stubblefield, William B, Baughman, Adrienne, Womack, Kelsey N, Lindsell, Christopher J, Hart, Kimberly W, Zhu, Yuwei, Mills, Lisa, Lester, Sandra N, Stumpf, Megan M, Naioti, Eric A, Kobayashi, Miwako, Verani, Jennifer R, Thornburg, Natalie J, Patel, Manish M, Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Seattle, Natalie, Ettlinger, Jason, Priest, Elisa, Thomas, Jennifer, Arroliga, Alejandro, Beeram, Madhava, Kindle, Ryan, Kozikowski, Lori-Ann, De Souza, Lesley, Ouellette, Scott, Thornton-Thompson, Sherell, Mehkri, Omar, Ashok, Kiran, Gole, Susan, King, Alexander, Poynter, Bryan, Stanley, Nicholas, Hendrickson, Audrey, Maruggi, Ellen, Scharber, Tyler, Jorgensen, Jeffrey, Bowers, Robert, King, Jennifer, Aston, Valerie, Armbruster, Brent, Rothman, Richard E, Nair, Rahul, Chen, Jen-Ting Tina, Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, and Khan, Maryiam

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Immunization, Vaccine Related, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Infection, Good Health and Well Being, Adolescent, Adult, Aged, COVID-19, COVID-19 Vaccines, Female, Hospitalization, Humans, Immunocompromised Host, Male, Middle Aged, United States, Vaccines, Synthetic, Young Adult, IVY Network, General & Internal Medicine
Abstract

Three COVID-19 vaccines are authorized or approved for use among adults in the United States (1,2). Two 2-dose mRNA vaccines, mRNA-1273 from Moderna and BNT162b2 from Pfizer-BioNTech, received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA) in December 2020 for persons aged ≥18 years and aged ≥16 years, respectively. A 1-dose viral vector vaccine (Ad26.COV2 from Janssen [Johnson & Johnson]) received EUA in February 2021 for persons aged ≥18 years (3). The Pfizer-BioNTech vaccine received FDA approval for persons aged ≥16 years on August 23, 2021 (4). Current guidelines from FDA and CDC recommend vaccination of eligible persons with one of these three products, without preference for any specific vaccine (4,5). To assess vaccine effectiveness (VE) of these three products in preventing COVID-19 hospitalization, CDC and collaborators conducted a case-control analysis among 3,689 adults aged ≥18 years who were hospitalized at 21 U.S. hospitals across 18 states during March 11-August 15, 2021. An additional analysis compared serum antibody levels (anti-spike immunoglobulin G [IgG] and anti-receptor binding domain [RBD] IgG) to SARS-CoV-2, the virus that causes COVID-19, among 100 healthy volunteers enrolled at three hospitals 2-6 weeks after full vaccination with the Moderna, Pfizer-BioNTech, or Janssen COVID-19 vaccine. Patients with immunocompromising conditions were excluded. VE against COVID-19 hospitalizations was higher for the Moderna vaccine (93%; 95% confidence interval [CI] = 91%-95%) than for the Pfizer-BioNTech vaccine (88%; 95% CI = 85%-91%) (p = 0.011); VE for both mRNA vaccines was higher than that for the Janssen vaccine (71%; 95% CI = 56%-81%) (all p

Published
2021

33. A compact electron injector for the EIC based on plasma wakefields driven by the RHIC-EIC proton beam

Author

Chappell, James, Caldwell, Allen, and Wing, Matthew

Subjects
Physics - Plasma Physics, High Energy Physics - Experiment, Physics - Accelerator Physics
Abstract

Initial simulations investigating using the RHIC-EIC proton beam as the drive beam in a plasma wakefield acceleration experiment are presented. The proton beam enters the plasma and undergoes self-modulation, forming a series of microbunches. These microbunches resonantly drive electron density perturbations within the plasma, exciting a longitudinal electric field with accelerating gradients in excess of $\mathrm{GVm^{-1}}$. Injecting electrons into the resulting wakefield offers an efficient method for accelerating electron bunches for use in the proposed EIC collider., Comment: 6 pages, 3 figures, submitted as proceedings for the XXVII International Workshop on Deep-Inelastic Scattering and Related Subjects (DIS2019)

Published
2019

34. Comparison of mRNA vaccine effectiveness against COVID-19-associated hospitalization by vaccination source: Immunization information systems, electronic medical records, and self-report—IVY Network, February 1–August 31, 2022

Author

Surie, Diya, Bonnell, Levi N., DeCuir, Jennifer, Gaglani, Manjusha, McNeal, Tresa, Ghamande, Shekhar, Steingrub, Jay S., Shapiro, Nathan I., Busse, Laurence W., Prekker, Matthew E., Peltan, Ithan D., Brown, Samuel M., Hager, David N., Ali, Harith, Gong, Michelle N., Mohamed, Amira, Khan, Akram, Wilson, Jennifer G., Qadir, Nida, Chang, Steven Y., Ginde, Adit A., Huynh, David, Mohr, Nicholas M., Mallow, Christopher, Martin, Emily T., Lauring, Adam S., Johnson, Nicholas J., Casey, Jonathan D., Gibbs, Kevin W., Kwon, Jennie H., Baughman, Adrienne, Chappell, James D., Hart, Kimberly W., Grijalva, Carlos G., Rhoads, Jillian P., Swan, Sydney A., Keipp Talbot, H., Womack, Kelsey N., Zhu, Yuwei, Tenforde, Mark W., Adams, Katherine, Self, Wesley H., and McMorrow, Meredith L.

Published
2023
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36. Effectiveness of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccination Against SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 Lineage Hospitalization and a Comparison of Clinical Severity — IVY Network, 26 Hospitals, October 18, 2023–March 9, 2024

Author

Ma, Kevin C., primary, Surie, Diya, additional, Lauring, Adam S., additional, Martin, Emily T., additional, Leis, Aleda M., additional, Papalambros, Leigh, additional, Gaglani, Manjusha, additional, Columbus, Christie, additional, Gottlieb, Robert L., additional, Ghamande, Shekhar, additional, Peltan, Ithan D., additional, Brown, Samuel M., additional, Ginde, Adit A., additional, Mohr, Nicholas M., additional, Gibbs, Kevin W., additional, Hager, David N., additional, Saeed, Safa, additional, Prekker, Matthew E., additional, Gong, Michelle Ng, additional, Mohamed, Amira, additional, Johnson, Nicholas J., additional, Srinivasan, Vasisht, additional, Steingrub, Jay S., additional, Khan, Akram, additional, Hough, Catherine L., additional, Duggal, Abhijit, additional, Wilson, Jennifer G., additional, Qadir, Nida, additional, Chang, Steven Y., additional, Mallow, Christopher, additional, Kwon, Jennie H., additional, Parikh, Bijal, additional, Exline, Matthew C., additional, Vaughn, Ivana A., additional, Ramesh, Mayur, additional, Safdar, Basmah, additional, Mosier, Jarrod, additional, Harris, Estelle S., additional, Shapiro, Nathan I., additional, Felzer, Jamie, additional, Zhu, Yuwei, additional, Grijalva, Carlos G., additional, Halasa, Natasha, additional, Chappell, James D., additional, Womack, Kelsey N., additional, Rhoads, Jillian P., additional, Baughman, Adrienne, additional, Swan, Sydney A., additional, Johnson, Cassandra A., additional, Rice, Todd W., additional, Casey, Jonathan D., additional, Blair, Paul W., additional, Han, Jin H., additional, Ellington, Sascha, additional, Lewis, Nathaniel M., additional, Thornburg, Natalie, additional, Paden, Clinton R., additional, Atherton, Lydia J., additional, Self, Wesley H., additional, Dawood, Fatimah S., additional, and DeCuir, Jennifer, additional

Published
2024
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37. Neutralizing COVID-19 Convalescent Plasma in Adults Hospitalized With COVID-19: A Blinded, Randomized, Placebo-Controlled Trial

Author

Self, Wesley H., Wheeler, Allison P., Stewart, Thomas G., Schrager, Harry, Mallada, Jason, Thomas, Christopher B., Cataldo, Vince D., O’Neal, Hollis R., Jr., Shapiro, Nathan I., Higgins, Conor, Ginde, Adit A., Chauhan, Lakshmi, Johnson, Nicholas J., Henning, Daniel J., Jaiswal, Stuti J., Mammen, Manoj J., Harris, Estelle S., Pannu, Sonal R., Laguio-Vila, Maryrose, El Atrouni, Wissam, de Wit, Marjolein, Hoda, Daanish, Cohn, Claudia S., McWilliams, Carla, Shanholtz, Carl, Jones, Alan E., Raval, Jay S., Mucha, Simon, Ipe, Tina S., Qiao, Xian, Schrantz, Stephen J., Shenoy, Aarthi, Fremont, Richard D., Brady, Eric J., Carnahan, Robert H., Chappell, James D., Crowe, James E., Jr., Denison, Mark R., Gilchuk, Pavlo, Stevens, Laura J., Sutton, Rachel E., Thomsen, Isaac, Yoder, Sandra M., Bistran-Hall, Amanda J., Casey, Jonathan D., Lindsell, Christopher J., Wang, Li, Pulley, Jill M., Rhoads, Jillian P., Bernard, Gordon R., and Rice, Todd W.

Published
2022
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38. Interim Effectiveness of Updated 2023-2024 (Monovalent XBB.1.5) COVID-19 Vaccines Against COVID-19-Associated Emergency Department and Urgent Care Encounters and Hospitalization Among Immunocompetent Adults Aged [greater than or equal to]18 Years--VISION and IVY Networks, September 2023- January 2024

Author

DeCuir, Jennifer, Payne, Amanda B., Self, Wesley H., Rowley, Elizabeth A.K., Dascomb, Kristin, DeSilva, Malini B., Irving, Stephanie A., Grannis, Shaun J., Ong, Toan C., Klein, Nicola P., Weber, Zachary A., Reese, Sarah E., Ball, Sarah W., Barron, Michelle A., Naleway, Allison L., Dixon, Brian E., Essien, Inih, Bride, Daniel, Natarajan, Karthik, Fireman, Bruce, Shah, Ami B., Okwuazi, Erica, Wiegand, Ryan, Zhu, Yuwei, Lauring, Adam S., Martin, Emily T., Gaglani, Manjusha, Peltan, Ithan D., Brown, Samuel M., Ginde, Adit A., Mohr, Nicholas M., Gibbs, Kevin W., Hager, David N., Prekker, Matthew, Mohamed, Amira, Srinivasan, Vasisht, Steingrub, Jay S., Khan, Akram, Busse, Laurence W., Duggal, Abhijit, Wilson, Jennifer G., Chang, Steven Y., Mallow, Christopher, Kwon, Jennie H., Exline, Matthew C., Columbus, Cristie, Vaughn, Ivana A., Safdar, Basmah, Mosier, Jarrod M., Harris, Estelle S., Casey, Jonathan D., Chappell, James D., Grijalva, Carlos G., Swan, Sydney A., Johnson, Cassandra, Lewis, Nathaniel M., Ellington, Sascha, Adams, Katherine, Tenforde, Mark W., Paden, Clinton R., Dawood, Fatimah S., Fleming-Dutra, Katherine E., Surie, Diya, and Link-Gelles, Ruth

Subjects
Vaccination, Medical research, Medicine, Experimental, Hospitals -- Emergency service, Emergency medicine, Adults, Vaccines, Health, Vanderbilt University. Medical Center
Abstract

Introduction On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 COVID-19 vaccination with a monovalent XBB.1.5--derived vaccine for all persons aged [greater than or equal to]6 [...]

Published
2024

40. Hilbert's forgotten equation, the equivalence principle and velocity dependence of free fall

Author

Berkahn, David L., Chappell, James M., and Abbott, Derek

Subjects
Physics - General Physics, 83-02, 83C25
Abstract

Referring to the behavior of accelerating objects in special relativity, and applying the principle of equivalence, one expects that the coordinate acceleration of point masses under gravity will be velocity dependent. Then, using the Schwarzschild solution, we analyze the similar case of masses moving on timelike geodesics, which reproduces a little known result by Hilbert from 1917, describing this dependence. We find that the relativistic correction term for the acceleration based on general relativity differs by a factor of two from the simpler acceleration arguments in flat space. As we might expect from the general theory, the velocity dependence can be removed by a suitable coordinate transformation, such as the Painlev{\'e}-Gullstrand coordinate system. The validity of this approach is supported by previous authors who have demonstrated vacuum solutions to general relativity producing true flat space metrics for uniform gravitational fields. We suggest explicit experiments could be undertaken to test the property of velocity dependence., Comment: 14 pages, no figures

Published
2017
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41. Rotavirus Vaccine Effectiveness Against Severe Acute Gastroenteritis: 2009-2022.

Author

Diallo, Alpha Oumar, Wikswo, Mary E., Sulemana, Iddrisu, Sahni, Leila C., Boom, Julie A., Ramani, Sasirekha, Selvarangan, Rangaraj, Moffatt, Mary E., Harrison, Christopher J., Halasa, Natasha, Chappell, James, Stewart, Laura, Staat, Mary Allen, Schlaudecker, Elizabeth, Quigley, Christina, Klein, Eileen J., Englund, Janet A., Zerr, Danielle M., Weinberg, Geoffrey A., and Szilagyi, Peter G.

Published
2024
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43. Influenza virus shedding and symptoms: Dynamics and implications from a multi-season household transmission study

Author

Morris, Sinead E, primary, Nguyen, Huong Q, additional, Grijalva, Carlos G, additional, Hanson, Kayla E, additional, Zhu, Yuwei, additional, Biddle, Jessica E, additional, Meece, Jennifer K, additional, Halasa, Natasha B, additional, Chappell, James D, additional, Mellis, Alexandra M, additional, Reed, Carrie, additional, Biggerstaff, Matthew, additional, Belongia, Edward A, additional, Talbot, H Keipp, additional, and Rolfes, Melissa A, additional

Published
2024
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44. Stabilized coronavirus spike stem elicits a broadly protective antibody

Author

Hsieh, Ching-Lin, Werner, Anne P., Leist, Sarah R., Stevens, Laura J., Falconer, Ester, Goldsmith, Jory A., Chou, Chia-Wei, Abiona, Olubukola M., West, Ande, Westendorf, Kathryn, Muthuraman, Krithika, Fritch, Ethan J., Dinnon, Kenneth H., III, Schäfer, Alexandra, Denison, Mark R., Chappell, James D., Baric, Ralph S., Graham, Barney S., Corbett, Kizzmekia S., and McLellan, Jason S.

Published
2021
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45. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

Author

Kim, Daniel S., Risca, Viviana I., Reynolds, David L., Chappell, James, Rubin, Adam J., Jung, Namyoung, Donohue, Laura K. H., Lopez-Pajares, Vanessa, Kathiria, Arwa, Shi, Minyi, Zhao, Zhixin, Deep, Harsh, Sharmin, Mahfuza, Rao, Deepti, Lin, Shin, Chang, Howard Y., Snyder, Michael P., Greenleaf, William J., Kundaje, Anshul, and Khavari, Paul A.

Published
2021
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46. Generalizing the Lorentz transformations

Author

Chappell, James M., Berkahn, David L., Iannella, Nicolangelo, Hartnett, John G., Iqbal, Azhar, and Abbott, Derek

Subjects
Physics - General Physics, J.2
Abstract

In this paper we develop a framework allowing a natural extension of the Lorentz transformations. To begin, we show that by expanding conventional four-dimensional spacetime to eight-dimensions that a natural generalization is indeed obtained. We then find with these generalized coordinate transformations acting on Maxwell's equations that the electromagnetic field transformations are nevertheless unchanged. We find further, that if we assume the absence of magnetic monopoles, in accordance with Maxwell's theory, our generalized transformations are then restricted to be the conventional ones. While the conventional Lorentz transformations are indeed recovered from our framework, we nevertheless provide a new perspective into why the Lorentz transformations are constrained to be the conventional ones. Also, this generalized framework may assist in explaining several unresolved questions in electromagnetism as well as to be able to describe quasi magnetic monopoles found in spin-ice systems., Comment: 9 pages, no figures

Published
2016

50. A brief study of time

Author

Chappell, James M., Hartnett, John G., Iqbal, Azhar, Iannella, Nicolangelo, and Abbott, Derek

Subjects
Physics - General Physics
Abstract

Understanding the nature of time remains a key unsolved problem in science. Newton in the Principia asserted an absolute universal time that {\it `flows equably'}. Hamilton then proposed a mathematical unification of space and time within the framework of the quaternions that ultimately lead to the famous Minkowski formulation in 1908 using four-vectors. The Minkowski framework is found to provide a versatile formalism for describing the relationship between space and time in accordance with relativistic principles, but nevertheless fails to provide deeper insights into the physical origin of time and its properties. In this paper we begin with a recognition of the fundamental role played by three-dimensional space in physics that we model using the Clifford algebra multivector. From this geometrical foundation we are then able to identify a plausible origin for our concept of time. This geometrical perspective also allows us to make a key topological distinction between time and space, with time being a point-like quantity. The multivector then allows a generalized unification of time and space within a Minkowski-like description., Comment: 17 pages, 0 figures

Published
2015

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