Multivariable Mendelian randomization with incomplete measurements on the exposure variables in the Hispanic Community Health Study/Study of Latinos.

Multivariable Mendelian randomization allows simultaneous estimation of direct causal effects of multiple exposure variables on an outcome. When the exposure variables of interest are quantitative omic features, obtaining complete data can be economically and technically challenging: the measurement cost is high, and the measurement devices may have inherent detection limits. In this paper, we propose a valid and efficient method to handle unmeasured and undetectable values of the exposure variables in a one-sample multivariable Mendelian randomization analysis with individual-level data. We estimate the direct causal effects with maximum likelihood estimation and develop an expectation-maximization algorithm to compute the estimators. We show the advantages of the proposed method through simulation studies and provide an application to the Hispanic Community Health Study/Study of Latinos, which has a large amount of unmeasured exposure data.

Efficacy of infliximab, abatacept, and cenicriviroc for the treatment of adults hospitalized with COVID-19 pneumonia.

A randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the efficacy of infliximab, abatacept, and cenicriviroc in treating patients hospitalized with COVID-19. The patient's clinical status was assessed daily on an 8-point ordinal scale. We evaluated the totality of evidence on the efficacy of the 3 immunomodulators by considering all possible changes in the clinical status of each patient over time. We demonstrated that infliximab accelerated improvement and reduced deterioration of clinical status when added to standard of care. There was also evidence for the benefit of abatacept. There was no evidence for the benefit of cenicriviroc.

Impact of booster vaccination interval on SARS-CoV-2 infection, hospitalization, and death.

OBJECTIVES: We investigated how booster interval affects the risks of SARS-CoV-2 infection and Covid-19-related hospitalization and death in different age groups. METHODS: We collected data on booster receipts and Covid-19 outcomes between September 22, 2021 and February 9, 2023 for 5,769,205 North Carolina residents ≥12 years of age who had completed their primary vaccination series. We related Covid-19 outcomes to baseline characteristics and booster doses through Cox regression models. RESULTS: For adults ≥65 years of age, boosting every 9 months was associated with proportionate reductions (compared with no boosting) of 18.9% (95% CI, 18.5-19.4) in the cumulative frequency of infection, 37.8% (95% CI, 35.3-40.3) in the cumulative risk of hospitalization or death, and 40.9% (95% CI, 37.2-44.7) in the cumulative risk of death at 2 years after completion of primary vaccination. The reductions were lower by boosting every 12 months and higher by boosting every 6 months. The reductions were smaller for individuals 12-64 years of age. CONCLUSION: Boosting at a shorter interval was associated with a greater reduction in Covid-19 outcomes, especially hospitalization and death. Frequent boosting conferred greater benefits for individuals aged ≥65 than for individuals aged 12-64.

A natural compound melatonin enhances the effects of Nimotuzumab via inhibiting EGFR in glioblastoma.

Sleep disorders are prevalent and debilitating symptoms in primary brain tumor patients, notably those receiving radiation therapy. Nevertheless, the relationship between sleep disorders, melatonin - a circadian rhythm regulatory hormone, and gliomas is underexplored. Melatonin exhibits various biological functions, one of them being anti-tumor activity. In the context of gliomas, often overexpressing EGFR, the humanized monoclonal antibody Nimotuzumab targets this marker. Our research discovered that variations in circadian rhythm significantly influence tumor growth in mice through impacting melatonin secretion. Harnessing proteogenomic, we identified that melatonin could inhibit the phosphorylation of EGFR and its downstream effectors, key elements in angiogenesis and tumor progression. Building on structural simulations, we propose that melatonin may amplify Nimotuzumab's anti-glioma efficacy by inhibiting EGFR TK dimerization. This proposition was validated in our in vitro and in vivo studies where melatonin synergistically augmented cytotoxicity and apoptosis in Nimotuzumab-treated glioma cells. Thus, melatonin shows promise as a beneficial addition to Nimotuzumab treatment in glioma patients.

Evaluating treatment efficacy in hospitalized COVID-19 patients, with applications to Adaptive COVID-19 Treatment Trials.

BACKGROUND: The current endpoints for therapeutic trials of hospitalized COVID-19 patients capture only part of the clinical course of a patient and have limited statistical power and robustness. METHODS: We specify proportional odds models for repeated measures of clinical status, with a common odds ratio of lower severity over time. We also specify the proportional hazards model for time to each level of improvement or deterioration of clinical status, with a common hazard ratio for overall treatment benefit. We apply these methods to Adaptive COVID-19 Treatment Trials. RESULTS: For remdesivir versus placebo, the common odds ratio was 1.48 (95% confidence interval (CI) = 1.23-1.79; p < 0.001), and the common hazard ratio was 1.27 (95% CI = 1.09-1.47; p = 0.002). For baricitinib plus remdesivir versus remdesivir alone, the common odds ratio was 1.32 (95% CI = 1.10-1.57; p = 0.002), and the common hazard ratio was 1.30 (95% CI = 1.13-1.49; p < 0.001). For interferon beta-1a plus remdesivir versus remdesivir alone, the common odds ratio was 0.95 (95% CI = 0.79-1.14; p = 0.56), and the common hazard ratio was 0.98 (95% CI = 0.85-1.12; p = 0.74). CONCLUSIONS: The proposed methods comprehensively characterize the treatment effects on the entire clinical course of a hospitalized COVID-19 patient.

Fitting the Cox proportional hazards model to big data.

The semiparametric Cox proportional hazards model, together with the partial likelihood principle, has been widely used to study the effects of potentially time-dependent covariates on a possibly censored event time. We propose a computationally efficient method for fitting the Cox model to big data involving millions of study subjects. Specifically, we perform maximum partial likelihood estimation on a small subset of the whole data and improve the initial estimator by incorporating the remaining data through one-step estimation with estimated efficient score functions. We show that the final estimator has the same asymptotic distribution as the conventional maximum partial likelihood estimator using the whole dataset but requires only a small fraction of computation time. We demonstrate the usefulness of the proposed method through extensive simulation studies and an application to the UK Biobank data.

Proportional rates models for multivariate panel count data.

Multivariate panel count data arise when there are multiple types of recurrent events, and the observation for each study subject consists of the number of recurrent events of each type between two successive examinations. We formulate the effects of potentially time-dependent covariates on multiple types of recurrent events through proportional rates models, while leaving the dependence structures of the related recurrent events completely unspecified. We employ nonparametric maximum pseudo-likelihood estimation under the working assumptions that all types of events are independent and each type of event is a nonhomogeneous Poisson process, and we develop a simple and stable EM-type algorithm. We show that the resulting estimators of the regression parameters are consistent and asymptotically normal, with a covariance matrix that can be estimated consistently by a sandwich estimator. In addition, we develop a class of graphical and numerical methods for checking the adequacy of the fitted model. Finally, we evaluate the performance of the proposed methods through simulation studies and analysis of a skin cancer clinical trial.

Mendelian randomization with incomplete measurements on the exposure in the Hispanic Community Health Study/Study of Latinos.

Mendelian randomization has been widely used to assess the causal effect of a heritable exposure variable on an outcome of interest, using genetic variants as instrumental variables. In practice, data on the exposure variable can be incomplete due to high cost of measurement and technical limits of detection. In this paper, we propose a valid and efficient method to handle both unmeasured and undetectable values of the exposure variable in one-sample Mendelian randomization analysis with individual-level data. We estimate the causal effect of the exposure variable on the outcome using maximum likelihood estimation and develop an expectation maximization algorithm for the computation of the estimator. Simulation studies show that the proposed method performs well in making inference on the causal effect. We apply our method to the Hispanic Community Health Study/Study of Latinos, a community-based prospective cohort study, and estimate the causal effect of several metabolites on phenotypes of interest.

Adaptive dynamic programming-based hierarchical decision-making of non-affine systems.

In this paper, the problem of multiplayer hierarchical decision-making problem for non-affine systems is solved by adaptive dynamic programming. Firstly, the control dynamics are obtained according to the theory of dynamic feedback and combined with the original system dynamics to construct the affine augmented system. Thus, the non-affine multiplayer system is transformed into a general affine form. Then, the hierarchical decision problem is modeled as a Stackelberg game. In the Stackelberg game, the leader makes a decision based on the information of all followers, whereas the followers do not know each other's information and only obtain their optimal control strategy based on the leader's decision. Then, the augmented system is reconstructed by a neural network (NN) using input-output data. Moreover, a single critic NN is used to approximate the value function to obtain the optimal control strategy for each player. An extra term added to the weight update law makes the initial admissible control law no longer needed. According to the Lyapunov theory, the state of the system and the error of the weights of the NN are both uniformly ultimately bounded. Finally, the feasibility and validity of the algorithm are confirmed by simulation.

Nirmatrelvir or Molnupiravir Use and Severe Outcomes From Omicron Infections.

Importance: Ritonavir-boosted nirmatrelvir and molnupiravir are currently used in the US and in other countries to treat nonhospitalized patients who have mild-to-moderate COVID-19 and who are at high risk for progression to severe disease. The associations of these 2 oral antiviral drugs with hospitalization and death resulting from infection with new SARS-CoV-2 Omicron subvariants, particularly BQ.1.1 and XBB.1.5, are unknown. Objective: To assess the association of nirmatrelvir or molnupiravir use with the risks of hospitalization and death among patients infected with new Omicron subvariants. Design, Setting, and Participants: This was a cohort study of patients who received a diagnosis of COVID-19 at Cleveland Clinic from April 1, 2022, to February 20, 2023 (during which the Omicron variant evolved from BA.2 to BA.4/BA.5, then to BQ.1/BQ.1.1, and finally to XBB/XBB.1.5) and who were at high risk of progressing to severe disease, with follow-up through 90 days after diagnosis. The final date for follow-up data collection was February 27, 2023. Exposures: Treatment with ritonavir-boosted nirmatrelvir or molnupiravir. Main Outcomes and Measures: The primary outcome was time to death. The secondary outcome was time to either hospitalization or death. The association of either nirmatrelvir or molnupiravir use with each outcome was measured by the hazard ratio (HR) adjusted for demographic factors, socioeconomic status, date of COVID-19 diagnosis, coexisting medical conditions, COVID-19 vaccination status, and previous SARS-CoV-2 infection. Results: There were 68 867 patients (29 386 [42.7%] aged ≥65 years; 26 755 [38.9%] male patients; 51 452 [74.7%] non-Hispanic White patients). Thirty of 22 594 patients treated with nirmatrelvir, 27 of 5311 patients treated with molnupiravir, and 588 of 40 962 patients who received no treatment died within 90 days of Omicron infection. The adjusted HRs of death were 0.16 (95% CI, 0.11-0.23) for nirmatrelvir and 0.23 (95% CI, 0.16-0.34) for molnupiravir. The adjusted HRs of hospitalization or death were 0.63 (95% CI, 0.59-0.68) for nirmatrelvir and 0.59 (95% CI, 0.53-0.66) for molnupiravir. The associations of both drugs with both outcomes were observed across subgroups defined by age, race and ethnicity, date of COVID-19 diagnosis, vaccination status, previous infection status, and coexisting conditions. Conclusions and Relevance: These findings suggest that the use of either nirmatrelvir or molnupiravir is associated with reductions in mortality and hospitalization in patients infected with Omicron, regardless of age, race and ethnicity, virus strain, vaccination status, previous infection status, or coexisting conditions. Both drugs can, therefore, be used to treat nonhospitalized patients who are at high risk of progressing to severe COVID-19.

Central nervous system complications in SARS-CoV-2-infected patients.

OBJECTIVE: To investigate the clinical manifestations, treatment and prognosis of COVID-19-associated central nervous system (CNS) complications. METHODS: In this single-centre observation study, we recruited patients with COVID-19-associated CNS complications at the neurology inpatient department of the Eighth Affiliated Hospital, Sun Yat-Sen University (Futian, Shenzhen) from Dec 2022 to Feb 2023. Patients were analysed for demographics, clinical manifestations, cerebrospinal fluid properties, electroencephalographic features, neuroimaging characteristics, and treatment outcome. All patients were followed-up at 1 and 2 months after discharge until Apr 2023. RESULTS: Of the 12 patients with COVID-19-associated CNS complications, the CNS symptoms occur between 0 days and 4 weeks after SARS-CoV-2 infection. The most common CNS symptoms were memory deficits (4/12, 33%), Unresponsiveness (4/12, 33%), mental and behavioural disorders (4/12, 33%). Seven of 12 cases can be categorized as probable SARS-CoV-2 encephalitis, and 5 cases can be described as brainstem encephalitis, acute disseminated encephalomyelitis, optic neuritis, multiple sclerosis or tremor probably associated with SARS-CoV-2 infection. Six patients received antiviral therapy, and 11 patients received glucocorticoid therapy, of which 3 patients received human immunoglobulin synchronously. Nine patients recovered well, two patients had residual neurological dysfunction, and one patient passed away from complications associated with tumor. CONCLUSION: In this observational study, we found that the inflammatory or immune-related complications were relatively common manifestations of COVID-19-associated CNS complications, including different phenotypes of encephalitis and CNS inflammatory demyelinating diseases. Most patients recovered well, but a few patients had significant neurological dysfunctions remaining.

Dl-3-n-butylphthalide activates Nrf2, inhibits ferritinophagy, and protects MES23.5 dopaminergic neurons from ferroptosis.

Ferroptosis, a newly identified iron-dependent form of cell death, has recently been implicated in the pathogenesis of Parkinson's disease (PD). Dl-3-n-butylphthalide (NBP) attenuates behavioral and cognitive deficits in animal models of PD. However, the potential of NBP to prevent dopaminergic neuron death by suppressing ferroptosis has rarely been explored. In this study, we aimed to investigate the effects of NBP on ferroptosis in erastin-induced dopaminergic neurons (MES23.5 cells) and the underlying mechanisms involved in these effects. Our results demonstrated that erastin significantly decreased viability of MES23.5 dopaminergic neurons in a dose-dependent manner, which was reversible by ferroptosis inhibitors. We further verified that NBP protected erastin-treated MES23.5 cells from death by inhibiting ferroptosis. Erastin increased the mitochondrial membrane density, caused lipid peroxidation, and decreased GPX4 expression in MES23.5 cells, which could be reversed by NBP preconditioning. NBP pretreatment suppressed erastin-induced labile iron accumulation and reactive oxygen species generation. Moreover, we demonstrated that erastin significantly reduced FTH expression, and pre-administration with NBP promoted Nrf2 translocation into the nucleus and increased the protein level of FTH. Additionally, the expression of LC3B-II in MES23.5 cells pretreated with NBP before administration of erastin was lower than that in cells treated with erastin alone. NBP reduced colocalization of FTH and autophagosomes in MES23.5 cells exposed to erastin. Finally, erastin gradually inhibited NCOA4 expression in a time-dependent manner, which was reversible by NBP pretreatment. Taken together, these results indicated that NBP suppressed ferroptosis via regulating FTH expression, which was achieved by promoting Nrf2 nuclear translocation and inhibiting NCOA4-mediated ferritinophagy. As such, NBP may be a promising therapeutic agent for the treatment of neurological diseases associated with ferroptosis.

Effects of COVID-19 vaccination and previous SARS-CoV-2 infection on omicron infection and severe outcomes in children under 12 years of age in the USA: an observational cohort study.

BACKGROUND: Data on the protection conferred by COVID-19 vaccination and previous SARS-CoV-2 infection against omicron (B.1.1.529) infection in young children are scarce. We aimed to estimate the time-varying effects of primary and booster COVID-19 vaccination and previous SARS-CoV-2 infection on subsequent omicron infection and severe illness (hospital admission or death) in children younger than 12 years of age. METHODS: In this observational cohort study, we obtained individual-level records on vaccination with the BNT162b2 and mRNA-1273 vaccines and clinical outcomes from the North Carolina COVID-19 Surveillance System and the COVID-19 Vaccine Management System for 1 368 721 North Carolina residents aged 11 years or younger from Oct 29, 2021 (Oct 29, 2021 for children aged 5-11 years and June 17, 2022 for children aged 0-4 years), to Jan 6, 2023. We used Cox regression to estimate the time-varying effects of primary and booster vaccination and previous infection on the risks of omicron infection, hospital admission, and death. FINDINGS: For children 5-11 years of age, the effectiveness of primary vaccination against infection, compared with being unvaccinated, was 59·9% (95% CI 58·5-61·2) at 1 month, 33·7% (32·6-34·8) at 4 months, and 14·9% (95% CI 12·3-17·5) at 10 months after the first dose. Compared with primary vaccination only, the effectiveness of a monovalent booster dose after 1 month was 24·4% (14·4-33·2) and that of a bivalent booster dose was 76·7% (45·7-90·0). The effectiveness of omicron infection against reinfection was 79·9% (78·8-80·9) after 3 months and 53·9% (52·3-55·5) after 6 months. For children 0-4 years of age, the effectiveness of primary vaccination against infection, compared with being unvaccinated, was 63·8% (57·0-69·5) at 2 months and 58·1% (48·3-66·1) at 5 months after the first dose, and the effectiveness of omicron infection against reinfection was 77·3% (75·9-78·6) after 3 months and 64·7% (63·3-66·1) after 6 months. For both age groups, vaccination and previous infection had better effectiveness against severe illness as measured by hospital admission or death as a composite endpoint than against infection. INTERPRETATION: The BNT162b2 and mRNA-1273 vaccines were effective against omicron infection and severe outcomes in children younger than 12 years, although the effectiveness decreased over time. Bivalent boosters were more effective than monovalent boosters. Immunity acquired via omicron infection was high and waned gradually over time. These findings can be used to develop effective prevention strategies against COVID-19 in children younger than 12 years. FUNDING: US National Institutes of Health.

A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data.

Mapping cell type-specific gene expression quantitative trait loci (ct-eQTLs) is a powerful way to investigate the genetic basis of complex traits. A popular method for ct-eQTL mapping is to assess the interaction between the genotype of a genetic locus and the abundance of a specific cell type using a linear model. However, this approach requires transforming RNA-seq count data, which distorts the relation between gene expression and cell type proportions and results in reduced power and/or inflated type I error. To address this issue, we have developed a statistical method called CSeQTL that allows for ct-eQTL mapping using bulk RNA-seq count data while taking advantage of allele-specific expression. We validated the results of CSeQTL through simulations and real data analysis, comparing CSeQTL results to those obtained from purified bulk RNA-seq data or single cell RNA-seq data. Using our ct-eQTL findings, we were able to identify cell types relevant to 21 categories of human traits.