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  1. Article ; Online: Multiple-Imputation Variance Estimation in Studies With Missing or Misclassified Inclusion Criteria.

    Giganti, Mark J / Shepherd, Bryan E

    American journal of epidemiology

    2020  Volume 189, Issue 12, Page(s) 1628–1632

    Abstract: In observational studies using routinely collected data, a variable with a high level of missingness or misclassification may determine whether an observation is included in the analysis. In settings where inclusion criteria are assessed after imputation, ...

    Abstract In observational studies using routinely collected data, a variable with a high level of missingness or misclassification may determine whether an observation is included in the analysis. In settings where inclusion criteria are assessed after imputation, the popular multiple-imputation variance estimator proposed by Rubin ("Rubin's rules" (RR)) is biased due to incompatibility between imputation and analysis models. While alternative approaches exist, most analysts are not familiar with them. Using partially validated data from a human immunodeficiency virus cohort, we illustrate the calculation of an imputation variance estimator proposed by Robins and Wang (RW) in a scenario where the study exclusion criteria are based on a variable that must be imputed. In this motivating example, the corresponding imputation variance estimate for the log odds was 29% smaller using the RW estimator than using the RR estimator. We further compared these 2 variance estimators with a simulation study which showed that coverage probabilities of 95% confidence intervals based on the RR estimator were too high and became worse as more observations were imputed and more subjects were excluded from the analysis. The RW imputation variance estimator performed much better and should be employed when there is incompatibility between imputation and analysis models. We provide analysis code to aid future analysts in implementing this method.
    MeSH term(s) Anti-Retroviral Agents/therapeutic use ; Cohort Studies ; HIV Infections/drug therapy ; Humans ; Observational Studies as Topic ; Software ; Statistics as Topic
    Chemical Substances Anti-Retroviral Agents
    Language English
    Publishing date 2020-07-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2937-3
    ISSN 1476-6256 ; 0002-9262
    ISSN (online) 1476-6256
    ISSN 0002-9262
    DOI 10.1093/aje/kwaa153
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Response to Drs de Grooth and Parienti.

    Giganti, Mark J / Chew, Kara W / Eron, Joseph J / Smith, Davey M / Currier, Judith S / Hughes, Michael D

    The Journal of infectious diseases

    2024  Volume 229, Issue 5, Page(s) 1596

    MeSH term(s) Humans
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Letter ; Journal Article
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiae053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Coordination of inflammatory responses in children with perinatally acquired HIV infection.

    Weinberg, Adriana / Giganti, Mark J / Sirois, Patricia A / Montepiedra, Grace / Canniff, Jennifer / Agwu, Allison / Boivin, Michael J / Kapetanovic, Suad / Abzug, Mark J

    AIDS (London, England)

    2022  Volume 36, Issue 8, Page(s) 1117–1127

    Abstract: Objective: We investigated dynamics of inflammatory biomarkers in children with perinatally acquired HIV (PHIV) who started antiretrovirals at age less than 3 years and achieved sustained virologic control (HIV plasma RNA <400 copies/ml).: Design: ... ...

    Abstract Objective: We investigated dynamics of inflammatory biomarkers in children with perinatally acquired HIV (PHIV) who started antiretrovirals at age less than 3 years and achieved sustained virologic control (HIV plasma RNA <400 copies/ml).
    Design: This was a retrospective analysis of inflammatory biomarkers in children enrolled in a randomized trial of early (<3 years of age) PI-based versus NNRTI-based regimens (P1060), who achieved sustained virologic control and participated in a neurodevelopmental follow-up study (P1104s) between ages 5 and 11 years.
    Methods: We measured 20 inflammatory biomarkers using ELISA or chemiluminescence at onset of sustained virologic control (Tc) and at P1104s entry (Te).
    Results: The 213 participants had median ages of 1.2, 1.9, and 7 years at antiretroviral initiation, Tc, and Te, respectively, with 138 on protease inhibitor-based and 74 on NNRTI-based regimens at Tc. Eighteen markers decreased and two increased from Tc to Te (Te-Tc). Biomarker subsets, particularly cytokines, the chemokine IP-10, and adhesion molecules sICAM-1 and sVCAM-1, correlated at Tc, Te, and Te-Tc. At Tc, higher biomarker levels were associated with younger age, female sex, HIV plasma RNA at least 750 000 copies/ml, lower nadir CD4 + %, lower nadir weight z scores, and NNRTI-based treatment. Greater Te-Tc biomarker declines were associated with younger age, male sex, higher Tc biomarker levels, lower nadir CD4 + %, and NNRTI-based treatment. Duration of controlled viremia and nadir height z scores showed mixed associations.
    Conclusion: Biomarker expression showed substantial coordination. Most markers decreased after virologic control. Demographic and clinical variables associated with biomarker patterns were identified. Mechanistic studies of these biomarker patterns are needed to inform interventions to control inflammation.
    MeSH term(s) Anti-HIV Agents/therapeutic use ; Anti-Retroviral Agents/therapeutic use ; Child ; Child, Preschool ; Female ; Follow-Up Studies ; HIV Infections/complications ; HIV Infections/drug therapy ; Humans ; Male ; RNA/therapeutic use ; Retrospective Studies
    Chemical Substances Anti-HIV Agents ; Anti-Retroviral Agents ; RNA (63231-63-0)
    Language English
    Publishing date 2022-04-19
    Publishing country England
    Document type Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000003229
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Systemic inflammation in pregnant women with HIV: relationship with HIV treatment regimen and preterm delivery.

    Shivakoti, Rupak / Giganti, Mark J / Lederman, Michael M / Ketchum, Rachel / Brummel, Sean / Moisi, Daniela / Dadabhai, Sufia / Moodley, Dhayendre / Violari, Avy / Chinula, Lameck / Owor, Maxensia / Gupta, Amita / Currier, Judith S / Taha, Taha E / Fowler, Mary Glenn

    AIDS (London, England)

    2024  

    Abstract: Objective: : HIV treatment regimen during pregnancy was associated with preterm delivery (PTD) in the PROMISE 1077 BF trial. Systemic inflammation among pregnant women with HIV could help explain differences in PTD by treatment regimen. We assessed ... ...

    Abstract Objective: : HIV treatment regimen during pregnancy was associated with preterm delivery (PTD) in the PROMISE 1077 BF trial. Systemic inflammation among pregnant women with HIV could help explain differences in PTD by treatment regimen. We assessed associations between inflammation, treatment regimen, and PTD.
    Design/methods: : A nested 1:1 case-control study (N = 362) was conducted within a multi-country randomized trial comparing three HIV regimens in pregnant women: zidovudine alone, or combination antiretroviral therapy (ART) with lopinavir/ritonavir and either zidovudine or tenofovir. Cases were women with PTD (<37 weeks of gestational age). The following inflammatory biomarkers were measured in plasma samples using immunoassays: soluble CD14 (sCD14) and sCD163, intestinal fatty acid-binding protein, interleukin (IL)-6, interferon γ, and tumor necrosis factor α. We fit regression models to assess associations between second trimester biomarkers (measured before ART initiation at 13-23 weeks of gestational age and 4 weeks later), treatment regimen, and PTD. We also assessed whether inflammation was a mediator in the relationship between ART regimen and PTD.
    Results: : Persistently high interleukin-6 was associated with increased PTD. Compared to zidovudine alone, the difference in biomarker concentration between week 0 and week 4 was significantly higher (p < 0.05) for both PI-based regimens. However, the estimated proportion of the ART effect on increased PTD mediated by persistently high biomarker levels was ≤5% for all biomarkers.
    Conclusions: : Persistently high IL-6 during pregnancy was associated with PTD. While PI-based ART was associated with increases in inflammation, factors other than inflammation likely explain the increased PTD in ART-based regimens compared to zidovudine alone.
    Language English
    Publishing date 2024-02-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000003877
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Safety, Efficacy, and Pharmacokinetics of Combination SARS-CoV-2 Neutralizing Monoclonal Antibodies BMS-986414 (C135-LS) and BMS-986413 (C144-LS) Administered Subcutaneously in Non-Hospitalized Persons with COVID-19 in a Phase 2 Trial.

    Corado, Katya C / Chew, Kara W / Giganti, Mark J / Mu, Ying / Fletcher, Courtney V / Currier, Judith S / Daar, Eric S / Wohl, David A / Li, Jonathan Z / Moser, Carlee B / Ritz, Justin / Javan, Arzhang Cyrus / Neytman, Gene / Caskey, Marina / Hughes, Michael D / Smith, Davey M / Eron, Joseph J

    Pathogens & immunity

    2024  Volume 9, Issue 1, Page(s) 138–155

    Abstract: Background: Outpatient COVID-19 monoclonal antibody (mAb) treatment via subcutaneous delivery, if effective, overcomes the logistical burdens of intravenous administration.: Methods: ACTIV-2/A5401 was a randomized, masked placebo-controlled platform ... ...

    Abstract Background: Outpatient COVID-19 monoclonal antibody (mAb) treatment via subcutaneous delivery, if effective, overcomes the logistical burdens of intravenous administration.
    Methods: ACTIV-2/A5401 was a randomized, masked placebo-controlled platform trial where participants with COVID-19 at low risk for progression were randomized 1:1 to subcutaneously administered BMS-986414 (C135-LS) 200 mg, plus BMS-986413 (C144-LS) 200 mg, (BMS mAbs), or placebo. Coprimary outcomes were time to symptom improvement through 28 days; nasopharyngeal SARS-CoV-2 RNA below the lower limit of quantification (LLoQ) on days 3, 7, or 14; and treatment-emergent grade 3 or higher adverse events (TEAEs) through 28 days.
    Results: A total of 211 participants (105 BMS mAbs and 106 placebo) initiated study product. Time to symptom improvement favored the active therapy but was not significant (median 8 vs 10 days,
    Conclusions: While safe, the BMS mAbs delivered subcutaneously were not effective at treating COVID-19 at low risk for progression. The lack of clinically significant activity may relate to the pharmacokinetics of subcutaneous administration of mAbs.
    Language English
    Publishing date 2024-05-06
    Publishing country United States
    Document type Journal Article
    ISSN 2469-2964
    ISSN (online) 2469-2964
    DOI 10.20411/pai.v9i1.660
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Statistical Challenges when Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials.

    Moser, Carlee B / Chew, Kara W / Giganti, Mark J / Li, Jonathan Z / Aga, Evgenia / Ritz, Justin / Greninger, Alexander L / Javan, Arzhang Cyrus / Daar, Eric S / Currier, Judith S / Eron, Joseph J / Smith, Davey M / Hughes, Michael D

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Most clinical trials evaluating COVID-19 therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal SARS-CoV-2 RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or ...

    Abstract Most clinical trials evaluating COVID-19 therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal SARS-CoV-2 RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or mixed models for repeated measures (MMRM) with single-imputation for results below assay lower limits of quantification (LLoQ). Analyzing changes in viral RNA levels with singly-imputed values can lead to biased estimates of treatment effects. In this paper, using an illustrative example from the ACTIV-2 trial, we highlight potential pitfalls of imputation when using ANCOVA or MMRM methods, and illustrate how these methods can be used when considering values <LLoQ as censored measurements. Best practices when analyzing quantitative viral RNA data should include details about the assay and its LLoQ, completeness summaries of viral RNA data, and outcomes among participants with baseline viral RNA ≥LLoQ, as well as those with viral RNA <LLoQ.<br />
    Language English
    Publishing date 2023-03-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.13.23287208
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Characterization of treatment resistance and viral kinetics in the setting of single- versus dual-active monoclonal antibodies against SARS-CoV-2.

    Choudhary, Manish C / Deo, Rinki / Evering, Teresa H / Chew, Kara W / Giganti, Mark J / Moser, Carlee / Ritz, Justin / Regan, James / Flynn, James P / Crain, Charles R / Wohl, David Alain / Currier, Judith S / Eron, Joseph J / Margolis, David / Zhu, Qing / Zhon, Lijie / Ya, Li / Greninger, Alexander L / Hughes, Michael D /
    Smith, Davey / Daar, Eric S / Li, Jonathan Z

    The Journal of infectious diseases

    2024  

    Abstract: Background: Monoclonal antibodies (mAbs) represent a crucial antiviral strategy for SARS-CoV-2 infection, but it is unclear whether combination mAbs offer a benefit over single-active mAb treatment. Amubarvimab and romlusevimab significantly reduced the ...

    Abstract Background: Monoclonal antibodies (mAbs) represent a crucial antiviral strategy for SARS-CoV-2 infection, but it is unclear whether combination mAbs offer a benefit over single-active mAb treatment. Amubarvimab and romlusevimab significantly reduced the risk of hospitalizations or death in the ACTIV-2/A5401 trial. Certain SARS-CoV-2 variants are intrinsically resistant against romlusevimab, leading to only single-active mAb therapy with amubarvimab in these variants. We evaluated virologic outcomes in individuals treated with single- versus dual-active mAbs.
    Methods: Participants were non-hospitalized adults at higher risk of clinical progression randomized to amubarvimab plus romlusevimab or placebo. Quantitative SARS-CoV-2 RNA levels and targeted S gene next-generation sequencing was performed on anterior nasal samples. We compared viral load kinetics and resistance emergence between individuals treated with effective single- versus dual-active mAbs depending on the infecting variant.
    Results: Study participants receiving single- and dual-active mAbs had similar demographics, baseline nasal viral load, symptom score, and symptom duration. Compared to single-active mAb, treatment with dual-active mAbs led to faster viral load decline at study day 3 (p < 0.001) and day 7 (p < 0.01). Treatment-emergent resistance mutations were more likely to be detected after amubarvimab plus romlusevimab treatment than placebo (2.6% vs 0%, P < 0.001), and more frequently detected in the setting of single-active compared to dual-active mAb treatment (7.2% vs 1.1%, p < 0.01). Single-active and dual-active mAb treatment resulted in similar decrease in rates of hospitalizations or death.
    Conclusion: Compared to single-active mAb therapy, dual-active mAbs led to similar clinical outcomes, but significantly faster viral load decline and a lower risk of emergent resistance.
    Language English
    Publishing date 2024-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiae192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Association Between Anterior Nasal and Plasma SARS-CoV-2 RNA Levels and Hospitalization or Death in Nonhospitalized Adults With Mild-to-Moderate COVID-19.

    Giganti, Mark J / Chew, Kara W / Eron, Joseph J / Li, Jonathan Z / Pinilla, Mauricio / Moser, Carlee / Javan, Arzhang Cyrus / Fischer, William A / Klekotka, Paul / Margolis, David / Wohl, David Alain / Coombs, Robert W / Daar, Eric S / Smith, Davey M / Currier, Judith S / Hughes, Michael D

    The Journal of infectious diseases

    2023  Volume 228, Issue Suppl 2, Page(s) S117–S125

    Abstract: Background: There is little information regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as a predictor for clinical outcomes in outpatients with mild-to-moderate coronavirus disease 2019 (COVID-19).: Methods: Anterior nasal ...

    Abstract Background: There is little information regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as a predictor for clinical outcomes in outpatients with mild-to-moderate coronavirus disease 2019 (COVID-19).
    Methods: Anterior nasal (AN) and plasma SARS-CoV-2 RNA data from 2115 nonhospitalized adults who received monoclonal antibodies (mAbs) or placebo in the ACTIV-2/A5401 trial were analyzed for associations with hospitalization or death.
    Results: One hundred two participants were hospitalized or died through 28 days of follow-up. Higher day 0 (pretreatment) AN RNA was associated with increasing risk of hospitalization/death (risk ratio [RR], 1.24 per log10 copies/mL [95% confidence interval {CI}, 1.04-1.49]) among placebo recipients, ranging from 3% to 16% for <2 to ≥6 log10 copies/mL. Although only 1% had quantifiable levels, there was a similar trend across day 0 plasma RNA categories. Higher day 3 AN RNA was associated with subsequent hospitalization/death among placebo recipients (RR, 1.42 per log10 copies/mL [95% CI, 1.00-2.03]), but not mAb recipients (RR, 1.02 per log10 copies/mL [95% CI, 0.68-1.56]). The proportion of treatment effect (reduction in hospitalizations/deaths after day 3 for mAb vs placebo) explained by day 3 AN RNA was 8%.
    Conclusions: SARS-CoV-2 RNA levels are predictive of hospitalization/death in the natural history setting, but AN RNA levels may not be a reliable surrogate marker of mAb treatment effect in COVID-19 trials. Clinical Trials Registration. NCT04518410.
    MeSH term(s) Adult ; Humans ; Antibodies, Monoclonal ; COVID-19 ; Hospitalization ; RNA, Viral ; SARS-CoV-2/genetics
    Chemical Substances Antibodies, Monoclonal ; RNA, Viral
    Language English
    Publishing date 2023-08-30
    Publishing country United States
    Document type Clinical Trial ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiad287
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Statistical Challenges When Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials.

    Moser, Carlee B / Chew, Kara W / Giganti, Mark J / Li, Jonathan Z / Aga, Evgenia / Ritz, Justin / Greninger, Alexander L / Javan, Arzhang Cyrus / Bender Ignacio, Rachel / Daar, Eric S / Wohl, David A / Currier, Judith S / Eron, Joseph J / Smith, Davey M / Hughes, Michael D

    The Journal of infectious diseases

    2023  Volume 228, Issue Suppl 2, Page(s) S101–S110

    Abstract: Most clinical trials evaluating coronavirus disease 2019 (COVID-19) therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA levels ... ...

    Abstract Most clinical trials evaluating coronavirus disease 2019 (COVID-19) therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or mixed models for repeated measures (MMRM) with single imputation for results below assay lower limits of quantification (LLoQ). Analyzing changes in viral RNA levels with singly imputed values can lead to biased estimates of treatment effects. In this article, using an illustrative example from the ACTIV-2 trial, we highlight potential pitfalls of imputation when using ANCOVA or MMRM methods, and illustrate how these methods can be used when considering values <LLoQ as censored measurements. Best practices when analyzing quantitative viral RNA data should include details about the assay and its LLoQ, completeness summaries of viral RNA data, and outcomes among participants with baseline viral RNA ≥ LLoQ, as well as those with viral RNA < LLoQ. Clinical Trials Registration. NCT04518410.<br />
    MeSH term(s) Humans ; Antiviral Agents ; Biological Assay ; COVID-19 ; RNA, Viral ; SARS-CoV-2/genetics
    Chemical Substances Antiviral Agents ; RNA, Viral
    Language English
    Publishing date 2023-08-30
    Publishing country United States
    Document type Clinical Trial ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiad285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: ACCOUNTING FOR DEPENDENT ERRORS IN PREDICTORS AND TIME-TO-EVENT OUTCOMES USING ELECTRONIC HEALTH RECORDS, VALIDATION SAMPLES, AND MULTIPLE IMPUTATION.

    Giganti, Mark J / Shaw, Pamela A / Chen, Guanhua / Bebawy, Sally S / Turner, Megan M / Sterling, Timothy R / Shepherd, Bryan E

    The annals of applied statistics

    2020  Volume 14, Issue 2, Page(s) 1045–1061

    Abstract: Data from electronic health records (EHR) are prone to errors, which are often correlated across multiple variables. The error structure is further complicated when analysis variables are derived as functions of two or more error-prone variables. Such ... ...

    Abstract Data from electronic health records (EHR) are prone to errors, which are often correlated across multiple variables. The error structure is further complicated when analysis variables are derived as functions of two or more error-prone variables. Such errors can substantially impact estimates, yet we are unaware of methods that simultaneously account for errors in covariates and time-to-event outcomes. Using EHR data from 4217 patients, the hazard ratio for an AIDS-defining event associated with a 100 cell/mm
    Language English
    Publishing date 2020-06-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2376910-5
    ISSN 1941-7330 ; 1932-6157
    ISSN (online) 1941-7330
    ISSN 1932-6157
    DOI 10.1214/20-aoas1343
    Database MEDical Literature Analysis and Retrieval System OnLINE

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