Lack of weight gain and increased mortality during and after treatment among adults with drug-resistant tuberculosis in Georgia, 2009-2020.

Background: While low body mass index (BMI) is associated with poor tuberculosis (TB) treatment outcomes, the impact of weight gain during TB treatment is unclear. To address this knowledge gap, we assessed if lack of weight gain is associated with all-cause mortality during and after TB treatment. Methods: We conducted a retrospective cohort study among adults with newly diagnosed multi- or extensively drug-resistant (M/XDR) pulmonary TB in Georgia between 2009-2020. The exposure was a change in BMI during the first 3-6 months of TB treatment. All-cause mortality during and after TB treatment was assessed using the National Death Registry. We used competing-risk Cox proportional hazard models to estimate adjusted hazard ratios (aHR) between BMI change and all-cause mortality. Results: Among 720 adult participants, 21% had low BMI (<18.5 kg/m2) at treatment initiation and 9% died either during (n=16) or after treatment (n=50). During the first 3-6 months of TB treatment, 17% lost weight and 14% had no weight change. Among 479 adults with normal baseline BMI ( ≥18.5-24.9 kg/m2), weight loss was associated with an increased risk of death during TB treatment (aHR=5.25; 95%CI: 1.31-21.10). Among 149 adults with a low baseline BMI, no change in BMI was associated with increased post-TB treatment mortality (aHR=4.99; 95%CI: 1.25-19.94). Conclusions: Weight loss during TB treatment (among those with normal baseline BMI) or no weight gain (among those with low baseline BMI) was associated with increased rates of all-cause mortality. Our findings suggest that scaling up weight management interventions among those with M/XDR TB may be beneficial.

Evaluating the forecasting performance of ensemble sub-epidemic frameworks and other time series models for the 2022-2023 mpox epidemic.

During the 2022-2023 unprecedented mpox epidemic, near real-time short-term forecasts of the epidemic's trajectory were essential in intervention implementation and guiding policy. However, as case levels have significantly decreased, evaluating model performance is vital to advancing the field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention and Our World in Data teams, we generated retrospective sequential weekly forecasts for Brazil, Canada, France, Germany, Spain, the United Kingdom, the United States and at the global scale using an auto-regressive integrated moving average (ARIMA) model, generalized additive model, simple linear regression, Facebook's Prophet model, as well as the sub-epidemic wave and n-sub-epidemic modelling frameworks. We assessed forecast performance using average mean squared error, mean absolute error, weighted interval scores, 95% prediction interval coverage, skill scores and Winkler scores. Overall, the n-sub-epidemic modelling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best most frequently. The n-sub-epidemic and spatial-wave frameworks considerably improved in average forecasting performance relative to the ARIMA model (greater than 10%) for all performance metrics. Findings further support sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases.

SpatialWavePredict: a tutorial-based primer and toolbox for forecasting growth trajectories using the ensemble spatial wave sub-epidemic modeling framework.

BACKGROUND: Dynamical mathematical models defined by a system of differential equations are typically not easily accessible to non-experts. However, forecasts based on these types of models can help gain insights into the mechanisms driving the process and may outcompete simpler phenomenological growth models. Here we introduce a friendly toolbox, SpatialWavePredict, to characterize and forecast the spatial wave sub-epidemic model, which captures diverse wave dynamics by aggregating multiple asynchronous growth processes and has outperformed simpler phenomenological growth models in short-term forecasts of various infectious diseases outbreaks including SARS, Ebola, and the early waves of the COVID-19 pandemic in the US. RESULTS: This tutorial-based primer introduces and illustrates a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using an ensemble spatial wave sub-epidemic model based on ordinary differential equations. Scientists, policymakers, and students can use the toolbox to conduct real-time short-term forecasts. The five-parameter epidemic wave model in the toolbox aggregates linked overlapping sub-epidemics and captures a rich spectrum of epidemic wave dynamics, including oscillatory wave behavior and plateaus. An ensemble strategy aims to improve forecasting performance by combining the resulting top-ranked models. The toolbox provides a tutorial for forecasting time-series trajectories, including the full uncertainty distribution derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. CONCLUSIONS: We have developed the first comprehensive toolbox to characterize and forecast time-series data using an ensemble spatial wave sub-epidemic wave model. As an epidemic situation or contagion occurs, the tools presented in this tutorial can facilitate policymakers to guide the implementation of containment strategies and assess the impact of control interventions. We demonstrate the functionality of the toolbox with examples, including a tutorial video, and is illustrated using daily data on the COVID-19 pandemic in the USA.

Campus climate impacts on sexual violence: a Bayesian comparison of undergraduate and community colleges.

OBJECTIVE: Sexual violence is endemic on college campuses. Four-year campuses present high-risk environments for sexual violence and heavy episodic drinking is a robust risk factor for victimization. However, limited literature exists on sexual violence at two-year institutions, with most research focused on four-year campuses. We examined whether campus climates affect sexual violence prevalence rates. PARTICIPANTS: Sexual misconduct campus climate data from two-year and four-year campus students. METHODS: We used Bayesian logistic regressions to compare sexual victimization odds between two- and four-year campuses. RESULTS: Four-year students were twice as likely to have experienced sexual victimization and 2.5 times more likely to engage in heavy episodic drinking compared to two-year students. The risk of sexual victimization associated with heavy episodic drinking was reliably similar across campus types. CONCLUSIONS: Campus climates reliably impact student's risk of sexual victimization. Based on these findings, two- and four-year campuses may need to implement distinct prevention services.

Parameter estimation and forecasting with quantified uncertainty for ordinary differential equation models using QuantDiffForecast: A MATLAB toolbox and tutorial.

Mathematical models based on systems of ordinary differential equations (ODEs) are frequently applied in various scientific fields to assess hypotheses, estimate key model parameters, and generate predictions about the system's state. To support their application, we present a comprehensive, easy-to-use, and flexible MATLAB toolbox, QuantDiffForecast, and associated tutorial to estimate parameters and generate short-term forecasts with quantified uncertainty from dynamical models based on systems of ODEs. We provide software ( https://github.com/gchowell/paramEstimation_forecasting_ODEmodels/) and detailed guidance on estimating parameters and forecasting time-series trajectories that are characterized using ODEs with quantified uncertainty through a parametric bootstrapping approach. It includes functions that allow the user to infer model parameters and assess forecasting performance for different ODE models specified by the user, using different estimation methods and error structures in the data. The tutorial is intended for a diverse audience, including students training in dynamic systems, and will be broadly applicable to estimate parameters and generate forecasts from models based on ODEs. The functions included in the toolbox are illustrated using epidemic models with varying levels of complexity applied to data from the 1918 influenza pandemic in San Francisco. A tutorial video that demonstrates the functionality of the toolbox is included.

SubEpiPredict: A tutorial-based primer and toolbox for fitting and forecasting growth trajectories using the ensemble n-sub-epidemic modeling framework.

An ensemble n-sub-epidemic modeling framework that integrates sub-epidemics to capture complex temporal dynamics has demonstrated powerful forecasting capability in previous works. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. In this tutorial paper, we introduce and illustrate SubEpiPredict, a user-friendly MATLAB toolbox for fitting and forecasting time series data using an ensemble n-sub-epidemic modeling framework. The toolbox can be used for model fitting, forecasting, and evaluation of model performance of the calibration and forecasting periods using metrics such as the weighted interval score (WIS). We also provide a detailed description of these methods including the concept of the n-sub-epidemic model, constructing ensemble forecasts from the top-ranking models, etc. For the illustration of the toolbox, we utilize publicly available daily COVID-19 death data at the national level for the United States. The MATLAB toolbox introduced in this paper can be very useful for a wider group of audiences, including policymakers, and can be easily utilized by those without extensive coding and modeling backgrounds.

GrowthPredict: A toolbox and tutorial-based primer for fitting and forecasting growth trajectories using phenomenological growth models.

Simple dynamic modeling tools can help generate real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. This tutorial-based primer introduces and illustrates GrowthPredict, a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to a broad audience, including students training in mathematical biology, applied statistics, and infectious disease modeling, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 1-parameter exponential growth model and the 2-parameter generalized-growth model, which have proven useful in characterizing and forecasting the ascending phase of epidemic outbreaks. It also includes the 2-parameter Gompertz model, the 3-parameter generalized logistic-growth model, and the 3-parameter Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks. We provide detailed guidance on forecasting time-series trajectories and available software ( https://github.com/gchowell/forecasting_growthmodels ), including the full uncertainty distribution derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. This tutorial and toolbox can be broadly applied to characterizing and forecasting time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can help create forecasts to guide policy regarding implementing control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and the examples use publicly available data on the monkeypox (mpox) epidemic in the USA.

Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14th, 2022, through February 26th, 2023.

In May 2022, public health officials noted an unprecedented surge in mpox cases in non-endemic countries worldwide. As the epidemic accelerated, multi-model forecasts of the epidemic's trajectory were critical in guiding the implementation of public health interventions and determining policy. As the case levels have significantly decreased as of early September 2022, evaluating model performance is essential to advance the growing field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention (CDC) and Our World in Data (OWID) teams through the week of January 26th, 2023, we generated retrospective sequential weekly forecasts (e.g., 1-4-weeks) for Brazil, Canada, France, Germany, Spain, the United Kingdom, the USA, and at the global scale using models that require minimal input data including the auto-regressive integrated moving average (ARIMA), general additive model (GAM), simple linear regression (SLR), Facebook's Prophet model, as well as the sub-epidemic wave (spatial-wave) and n-sub-epidemic modeling frameworks. We assess forecast performance using average mean squared error (MSE), mean absolute error (MAE), weighted interval score (WIS), 95% prediction interval coverage (95% PI coverage), and skill scores. Average Winkler scores were used to calculate skill scores for 95% PI coverage. Overall, the n-sub-epidemic modeling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best across all forecasting horizons for most locations regarding average MSE, MAE, WIS, and 95% PI coverage. However, many locations had multiple models performing equally well for the average 95% PI coverage. The n-sub-epidemic and spatial-wave frameworks improved considerably in average MSE, MAE, and WIS, and Winkler scores (95% PI coverage) relative to the ARIMA model. Findings lend further support to sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases.

Nonpharmaceutical Interventions in Georgia: Public Health Implications.

OBJECTIVES: As coronavirus disease 2019 (COVID-19) spread, many states implemented nonpharmaceutical interventions in the absence of effective therapies with varying degrees of success. Our aim was to evaluate restrictions comparing two regions of Georgia and their impact on outcomes as measured by confirmed illness and deaths. METHODS: Using The New York Times COVID-19 incidence data and mandate information from various web sites, we examined trends in cases and deaths using joinpoint analysis at the region and county level before and after the implementation of a mandate. RESULTS: We found that rates of cases and deaths showed the greatest decrease in acceleration after the simultaneous implementation of a statewide shelter-in-place for vulnerable populations combined with social distancing for businesses and limiting gatherings to <10 people. County-level shelters-in-place, business closures, limits on gatherings to <10, and mask mandates showed significant case rate decreases after a county implemented them. School closures had no consistent effect on either outcome. CONCLUSIONS: Our findings indicate that protecting vulnerable populations, implementing social distancing, and mandating masks may be effective countermeasures to containment while mitigating the economic and psychosocial effects of strict shelters-in-place and business closures. In addition, states should consider allowing local municipalities the flexibility to enact nonpharmaceutical interventions that are more or less restrictive than the state-level mandates under some conditions in which the data indicate it is necessary to protect communities from disease or undue economic burden.

A MATLAB toolbox to fit and forecast growth trajectories using phenomenological growth models: Application to epidemic outbreaks.

Background: Simple dynamic modeling tools can be useful for generating real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. Results: In this tutorial-based primer, we introduce and illustrate a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to various audiences, including students training in time-series forecasting, dynamic growth modeling, parameter estimation, parameter uncertainty and identifiability, model comparison, performance metrics, and forecast evaluation, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 2-parameter generalized-growth model, which has proved useful to characterize and forecast the ascending phase of epidemic outbreaks, and the Gompertz model as well as the 3-parameter generalized logistic-growth model and the Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks.The toolbox provides a tutorial for forecasting time-series trajectories that include the full uncertainty distribution, derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. Conclusions: We have developed the first comprehensive toolbox to characterize and forecast time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can facilitate policymaking to guide the implementation of control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and is illustrated using weekly data on the monkeypox epidemic in the USA.

Nonlinear function-on-scalar regression via functional universal approximation.

We consider general nonlinear function-on-scalar (FOS) regression models, where the functional response depends on multiple scalar predictors in a general unknown nonlinear form. Existing methods either assume specific model forms (e.g., additive models) or directly estimate the nonlinear function in a space with dimension equal to the number of scalar predictors, which can only be applied to models with a few scalar predictors. To overcome these shortcomings, motivated by the classic universal approximation theorem used in neural networks, we develop a functional universal approximation theorem which can be used to approximate general nonlinear FOS maps and can be easily adopted into the framework of functional data analysis. With this theorem and utilizing smoothness regularity, we develop a novel method to fit the general nonlinear FOS regression model and make predictions. Our new method does not make any specific assumption on the model forms, and it avoids the direct estimation of nonlinear functions in a space with dimension equal to the number of scalar predictors. By estimating a sequence of bivariate functions, our method can be applied to models with a relatively large number of scalar predictors. The good performance of the proposed method is demonstrated by empirical studies on various simulated and real datasets.

Real-time forecasting the trajectory of monkeypox outbreaks at the national and global levels, July-October 2022.

BACKGROUND: Beginning May 7, 2022, multiple nations reported an unprecedented surge in monkeypox cases. Unlike past outbreaks, differences in affected populations, transmission mode, and clinical characteristics have been noted. With the existing uncertainties of the outbreak, real-time short-term forecasting can guide and evaluate the effectiveness of public health measures. METHODS: We obtained publicly available data on confirmed weekly cases of monkeypox at the global level and for seven countries (with the highest burden of disease at the time this study was initiated) from the Our World in Data (OWID) GitHub repository and CDC website. We generated short-term forecasts of new cases of monkeypox across the study areas using an ensemble n-sub-epidemic modeling framework based on weekly cases using 10-week calibration periods. We report and assess the weekly forecasts with quantified uncertainty from the top-ranked, second-ranked, and ensemble sub-epidemic models. Overall, we conducted 324 weekly sequential 4-week ahead forecasts across the models from the week of July 28th, 2022, to the week of October 13th, 2022. RESULTS: The last 10 of 12 forecasting periods (starting the week of August 11th, 2022) show either a plateauing or declining trend of monkeypox cases for all models and areas of study. According to our latest 4-week ahead forecast from the top-ranked model, a total of 6232 (95% PI 487.8, 12,468.0) cases could be added globally from the week of 10/20/2022 to the week of 11/10/2022. At the country level, the top-ranked model predicts that the USA will report the highest cumulative number of new cases for the 4-week forecasts (median based on OWID data: 1806 (95% PI 0.0, 5544.5)). The top-ranked and weighted ensemble models outperformed all other models in short-term forecasts. CONCLUSIONS: Our top-ranked model consistently predicted a decreasing trend in monkeypox cases on the global and country-specific scale during the last ten sequential forecasting periods. Our findings reflect the potential impact of increased immunity, and behavioral modification among high-risk populations.

An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA.

We analyze an ensemble of n-sub-epidemic modeling for forecasting the trajectory of epidemics and pandemics. These ensemble modeling approaches, and models that integrate sub-epidemics to capture complex temporal dynamics, have demonstrated powerful forecasting capability. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. We systematically assess their calibration and short-term forecasting performance in short-term forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022. We compare their performance with two commonly used statistical ARIMA models. The best fit sub-epidemic model and three ensemble models constructed using the top-ranking sub-epidemic models consistently outperformed the ARIMA models in terms of the weighted interval score (WIS) and the coverage of the 95% prediction interval across the 10-, 20-, and 30-day short-term forecasts. In our 30-day forecasts, the average WIS ranged from 377.6 to 421.3 for the sub-epidemic models, whereas it ranged from 439.29 to 767.05 for the ARIMA models. Across 98 short-term forecasts, the ensemble model incorporating the top four ranking sub-epidemic models (Ensemble(4)) outperformed the (log) ARIMA model 66.3% of the time, and the ARIMA model, 69.4% of the time in 30-day ahead forecasts in terms of the WIS. Ensemble(4) consistently yielded the best performance in terms of the metrics that account for the uncertainty of the predictions. This framework can be readily applied to investigate the spread of epidemics and pandemics beyond COVID-19, as well as other dynamic growth processes found in nature and society that would benefit from short-term predictions.

Investigating oral health among individuals with depression: NHANES 2015-2016.

Objectives: Depression is highly prevalent across populations, yet studies on its contribution to oral health are lacking. Therefore, our goal is to examine the association of depression and oral health problems (preventative care, access to dental care, and oral condition in relation to quality of life) controlling for sociodemographic and chronic disease indicators (CDI). Methods: 5,992 respondents' data 18+ years old were analyzed from the 2015-2016 National Health and Nutrition Examination Survey (NHANES). The independent variable of interest was depression symptoms status. Oral health outcomes were the dependent variables. We used the Patient Health Questionnaire-9 (PHQ-9) for depression and the Oral Health Questionnaire (OHQ) to measure oral health outcomes. Covariates included sociodemographics (age, education, sex, race/ethnicity, and income) and CDI included current smoking, diabetes, and body mass index. All data were weighted using 2 years sample weight. Results: The mean age of respondents was 47.22 years (45.97-48.46) and 46% were males. Participants with depression present 6.93%, and females 63.85% were higher than males 36.15%.Participants with depression have significantly low income 43.10% than others p value < 0.0001. After adjusting for sociodemographics and CDI, participants who have depression were more prone to report fair/poor oral condition [aOR = 1.91 (1.29-2.84)], oral pain [aOR = 2.66 (1.91-3.71)], and difficulty accessing needed dental care [aOR = 2.52 (1.96-3.24)] than others. Having depression was associated with poor oral health perceptions [aOR = 2.10 (1.41-3.13)], and having difficulty at job/school because of their oral health [aOR = 2.85 (1.90-4.26)]. Conclusion: Based on the empirical evidence provided by our study, there is an association between depression and oral health outcomes and oral health-related quality of life.

Investigating COVID-19 transmission and mortality differences between indigenous and non-indigenous populations in Mexico.

OBJECTIVES: Indigenous populations have been disproportionately affected during pandemics. We investigated COVID-19 mortality estimates among indigenous and non-indigenous populations at national and sub-national levels in Mexico. METHODS: We obtained data from the Ministry of Health, Mexico, on 2,173,036 laboratory-confirmed RT-PCR positive COVID-19 cases and 238,803 deaths. We estimated mortality per 1000 person-weeks, mortality rate ratio (RR) among indigenous vs. non-indigenous groups, and hazard ratio (HR) for COVID-19 deaths across four waves of the pandemic, from February 2020 to March 2022. We also assessed differences in the reproduction number (Rt). RESULTS: The mortality rate among indigenous populations of Mexico was 68% higher than that of non-indigenous groups. Out of 32 federal entities, 23 exhibited higher mortality rates among indigenous groups (P < 0.05 in 13 entities). The fourth wave showed the highest RR (2.40). The crude HR was 1.67 (95% CI: 1.62, 1.72), which decreased to 1.08 (95% CI: 1.04, 1.11) after controlling for other covariates. During the intense fourth wave, the Rt among the two groups was comparable. CONCLUSION: Indigenous status is a significant risk factor for COVID-19 mortality in Mexico. Our findings may reflect disparities in non-pharmaceutical (e.g., handwashing and using facemasks), and COVID-19 vaccination interventions among indigenous and non-indigenous populations in Mexico.

An ensemble n -sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA.

We analyze an ensemble of n -sub-epidemic modeling for forecasting the trajectory of epidemics and pandemics. These ensemble modeling approaches, and models that integrate sub-epidemics to capture complex temporal dynamics, have demonstrated powerful forecasting capability. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. We systematically assess their calibration and short-term forecasting performance in short-term forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022. We compare their performance with two commonly used statistical ARIMA models. The best fit sub-epidemic model and three ensemble models constructed using the top-ranking sub-epidemic models consistently outperformed the ARIMA models in terms of the weighted interval score (WIS) and the coverage of the 95% prediction interval across the 10-, 20-, and 30-day short-term forecasts. In the 30-day forecasts, the average WIS ranged from 377.6 to 421.3 for the sub-epidemic models, whereas it ranged from 439.29 to 767.05 for the ARIMA models. Across 98 short-term forecasts, the ensemble model incorporating the top four ranking sub-epidemic models (Ensemble(4)) outperformed the (log) ARIMA model 66.3% of the time, and the ARIMA model 69.4% of the time in 30-day ahead forecasts in terms of the WIS. Ensemble(4) consistently yielded the best performance in terms of the metrics that account for the uncertainty of the predictions. This framework could be readily applied to investigate the spread of epidemics and pandemics beyond COVID-19, as well as other dynamic growth processes found in nature and society that would benefit from short-term predictions. Summary: The COVID-19 pandemic has highlighted the urgent need to develop reliable tools to forecast the trajectory of epidemics and pandemics in near real-time. We describe and apply an ensemble n -sub-epidemic modeling framework for forecasting the trajectory of epidemics and pandemics. We systematically assess its calibration and short-term forecasting performance in weekly 10-30 days ahead forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022 and compare its performance with two different statistical ARIMA models. This framework demonstrated reliable forecasting performance and substantially outcompeted the ARIMA models. The forecasting performance was consistently best for the ensemble sub-epidemic models incorporating a higher number of top-ranking sub-epidemic models. The ensemble model incorporating the top four ranking sub-epidemic models consistently yielded the best performance, particularly in terms of the coverage rate of the 95% prediction interval and the weighted interval score. This framework can be applied to forecast other growth processes found in nature and society including the spread of information through social media.

An investigation of spatial-temporal patterns and predictions of the coronavirus 2019 pandemic in Colombia, 2020-2021.

Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicate disease containment, with Rt<1.0 as of October 31, 2021. On the forecasting front, the sub-epidemic model performs best at capturing the 30-day ahead COVID-19 trajectory compared to the Richards and generalized logistic growth model. Nevertheless, the spatial variability in the incidence rate patterns across different departments can be grouped into four distinct clusters. As the case incidence surged in July 2020, an increase in mobility patterns was also observed. On the contrary, a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued, indicating the pandemic fatigue in the country.

Restricted function-on-function linear regression model.

The usual function-on-function linear regression model depicts the association between functional variables in the whole rectangular region and the value of response curve at any point is influenced by the entire trajectory of the predictor curve. But in addition to this, there are cases where the value of the response curve at a point is only influenced by the value of the predictor curve in a subregion, such as the historical relationship and the short-term association. We will consider the restricted function-on-function regression model, where the value of response curve at any point is influenced by a subtrajectory of the predictor. We have two major purposes. First, we propose a novel estimation procedure that is more accurate and computational efficient for the restricted function-on-function model with a given subregion. Second, as the subregion is seldom specified in practice, we propose a subregion selection procedure that can lead to models with better interpretation and predictive performance. Algorithms are developed for both model estimation and subregion selection.

Geospatial Variability in Excess Death Rates during the COVID-19 Pandemic in Mexico: Examining Socio Demographic, Climate and Population Health Characteristics.

OBJECTIVES: This study examined how socio-demographic, climate and population health characteristics shaped the geospatial variability in excess mortality patterns during the COVID-19 pandemic in Mexico. METHODS: We used Serfling regression models to estimate all-cause excess mortality rates for all 32 Mexican states. The association between socio-demographic, climate, health indicators and excess mortality rates were determined using multiple linear regression analyses. Functional data analysis characterized clusters of states with distinct excess mortality growth rate curves. RESULTS: The overall all-cause excess deaths rate during the COVID-19 pandemic in Mexico until April 10, 2021 was estimated at 39.66 per 10 000 population. The lowest excess death rates were observed in southeastern states including Chiapas (12.72) and Oaxaca (13.42), whereas Mexico City had the highest rate (106.17), followed by Tlaxcala (51.99). We found a positive association of excess mortality rates with aging index, marginalization index, and average household size (P < 0.001) in the final adjusted model (Model R2=77%). We identified four distinct clusters with qualitatively similar excess mortality curves. CONCLUSION: Central states exhibited the highest excess mortality rates, whereas the distribution of aging index, marginalization index, and average household size explained the variability in excess mortality rates across Mexico.

Transmission dynamics and forecasts of the COVID-19 pandemic in Mexico, March-December 2020.

Mexico has experienced one of the highest COVID-19 mortality rates in the world. A delayed implementation of social distancing interventions in late March 2020 and a phased reopening of the country in June 2020 has facilitated sustained disease transmission in the region. In this study we systematically generate and compare 30-day ahead forecasts using previously validated growth models based on mortality trends from the Institute for Health Metrics and Evaluation for Mexico and Mexico City in near real-time. Moreover, we estimate reproduction numbers for SARS-CoV-2 based on the methods that rely on genomic data as well as case incidence data. Subsequently, functional data analysis techniques are utilized to analyze the shapes of COVID-19 growth rate curves at the state level to characterize the spatiotemporal transmission patterns of SARS-CoV-2. The early estimates of the reproduction number for Mexico were estimated between Rt ~1.1-1.3 from the genomic and case incidence data. Moreover, the mean estimate of Rt has fluctuated around ~1.0 from late July till end of September 2020. The spatial analysis characterizes the state-level dynamics of COVID-19 into four groups with distinct epidemic trajectories based on epidemic growth rates. Our results show that the sequential mortality forecasts from the GLM and Richards model predict a downward trend in the number of deaths for all thirteen forecast periods for Mexico and Mexico City. However, the sub-epidemic and IHME models perform better predicting a more realistic stable trajectory of COVID-19 mortality trends for the last three forecast periods (09/21-10/21, 09/28-10/27, 09/28-10/27) for Mexico and Mexico City. Our findings indicate that phenomenological models are useful tools for short-term epidemic forecasting albeit forecasts need to be interpreted with caution given the dynamic implementation and lifting of social distancing measures.