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Abstract Drug overdose deaths continue to increase in the United States for all major drug categories. Over the past two decades the total number of overdose fatalities has increased more than fivefold; since 2013 the surge in overdose rates is primarily driven by fentanyl and methamphetamines. Different drug categories and factors such as age, gender, and ethnicity are associated with different overdose mortality characteristics that may also change in time. For example, the average age at death from a drug overdose has decreased from 1940 to 1990 while the overall mortality rate has steadily increased. To provide insight into the population-level dynamics of drug overdose mortality, we develop an age-structured model for drug addiction. Using an augmented ensemble Kalman filter (EnKF), we show through a simple example how our model can be combined with synthetic observation data to estimate mortality rate and an age-distribution parameter. Finally, we use an EnKF to combine our model with observation data on overdose fatalities in the United States from 1999 to 2020 to forecast the evolution of overdose trends and estimate model parameters. 

We examine trends in drug overdose deaths by race, gender, and geography in the United States during the period 2013–2020. Race and gender specific crude rates were extracted from the final National Vital Statistics System multiple cause-of-death mortality files for several jurisdictions and used to calculate the male-to-female ratios of crude rates between 2013 and 2020. We established 2013–2019 temporal trends for four major drug types: psychostimulants with addiction potential (T43.6, such as methamphetamines); heroin (T40.1); natural and semi-synthetic opioids (T40.2, such as those contained in prescription pain-killers); synthetic opioids (T40.4, such as fentanyl and its derivatives) through a quadratic regression and determined whether changes in the pandemic year 2020 were statistically significant. We also identified which race, gender and states were most impacted by drug overdose deaths. Nationwide, the year 2020 saw statistically significant increases in overdose deaths from all drug categories except heroin, surpassing predictions based on 2013–2019 trends. Crude rates for Black individuals of both genders surpassed those for White individuals for fentanyl and psychostimulants in 2018, creating a gap that widened through 2020. In some regions, mortality among White persons decreased while overdose deaths for Black persons kept rising. The largest 2020 mortality statistic is for Black males in the District of Columbia, with a record 134 overdose deaths per 100,000 due to fentanyl, 9.4 times more than the fatality rate among White males. Male overdose crude rates in 2020 remain larger than those of females for all drug categories except in Idaho, Utah and Arkansas where crude rates of overdose deaths by natural and semisynthetic opioids for females exceeded those of males. Drug prevention, mitigation and no-harm strategies should include racial, geographical and gender-specific efforts, to better identify and serve at-risk groups. 

Hematopoiesis has been studied via stem cell labeling using barcodes, viral integration sites (VISs), or in situ methods. Subsequent proliferation and differentiation preserve the tag identity, thus defining a clone of mature cells across multiple cell type or lineages. By tracking the population of clones, measured within samples taken at discrete time points, we infer physiological parameters associated with a hybrid stochastic-deterministic mathematical model of hematopoiesis. We analyze clone population data from Koelle et al. ( Koelle et al., 2017 ) and compare the states of clones (mean and variance of their abundances) and the state-space density of clones with the corresponding quantities predicted from our model. Comparing our model to the tagged granulocyte populations, we find parameters (stem cell carrying capacity, stem cell differentiation rates, and the proliferative potential of progenitor cells, and sample sizes) that provide reasonable fits in three out of four animals. Even though some observed features cannot be quantitatively reproduced by our model, our analyses provides insight into how model parameters influence the underlying mechanisms in hematopoiesis. We discuss additional mechanisms not incorporated in our model. 

The specificity of T cells is that each T cell has only one T cell receptor (TCR). A T cell clone represents a collection of T cells with the same TCR sequence. Thus, the number of different T cell clones in an organism reflects the number of different T cell receptors (TCRs) that arise from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution, are important factors in immune functions. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. We describe the heterogeneous steady-state population of naive T cells (those that have not yet been antigenically triggered) by using a mean-field model of a regulated birth-death-immigration process. After accounting for random sampling, we investigate how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or “clone counts”). By using reasonable physiological parameter values and fitting predicted clone counts to experimentally sampled clone abundances, we show that realistic levels of heterogeneity in immigration rates cause very little change to predicted clone-counts, but that modest heterogeneity in proliferation rates can generate the observed clone abundances. Our analysis provides constraints among physiological parameters that are necessary to yield predictions that qualitatively match the data. Assumptions of the model and potentially other important mechanistic factors are discussed. 

We develop a statistical model for the testing of disease prevalence in a population. The model assumes a binary test result, positive or negative, but allows for biases in sample selection and both type I (false positive) and type II (false negative) testing errors. Our model also incorporates multiple test types and is able to distinguish between retesting and exclusion after testing. Our quantitative framework allows us to directly interpret testing results as a function of errors and biases. By applying our testing model to COVID-19 testing data and actual case data from specific jurisdictions, we are able to estimate and provide uncertainty quantification of indices that are crucial in a pandemic, such as disease prevalence and fatality ratios. This article is part of the theme issue ‘Data science approach to infectious disease surveillance’. 

We examine patterns of reported crime in Santa Monica, California before and after the passage of Proposition 47, a 2014 initiative that reclassified some non-violent felonies as misdemeanors. We also investigate impacts of the opening of four new light rail stations in 2016 and of increased community-based policing starting in late 2018. Our statistical analyses of reclassified crimes—larceny, fraud, possession of narcotics, forgery, receiving/possessing stolen property—and non-reclassified ones are based on publicly available reported crime data from 2006 to 2019. These analyses examine reported crime at various levels: city-wide, within eight neighborhoods, and within a 450-meter radius of the new transit stations. Monthly reported reclassified crimes increased city-wide by approximately 15% after enactment of Proposition 47, with a significant drop observed in late 2018. Downtown exhibited the largest overall surge. Reported non-reclassified crimes fell overall by approximately 9%. Areas surrounding two new train stations, including Downtown, saw significant increases in reported crime after train service began. While reported reclassified crimes increased after passage of Proposition 47, non-reclassified crimes, for the most part, decreased or stayed constant, suggesting that Proposition 47 may have impacted reported crime in Santa Monica. Reported crimes decreased in late 2018 concurrent with the adoption of new community-based policing measures. Follow-up studies needed to confirm long-term trends may be challenging due to the COVID-19 pandemic that drastically changed societal conditions. While our research detects changes in reported crime, it does not provide causative explanations. Our work, along with other considerations relevant to public utility, respect for human rights, and existence of socioeconomic disparities, may be useful to law enforcement and policymakers to assess the overall effect of Proposition 47. 

Abstract Factors such as varied definitions of mortality, uncertainty in disease prevalence, and biased sampling complicate the quantification of fatality during an epidemic. Regardless of the employed fatality measure, the infected population and the number of infection-caused deaths need to be consistently estimated for comparing mortality across regions. We combine historical and current mortality data, a statistical testing model, and an SIR epidemic model, to improve estimation of mortality. We find that the average excess death across the entire US from January 2020 until February 2021 is 9 $$\%$$ % higher than the number of reported COVID-19 deaths. In some areas, such as New York City, the number of weekly deaths is about eight times higher than in previous years. Other countries such as Peru, Ecuador, Mexico, and Spain exhibit excess deaths significantly higher than their reported COVID-19 deaths. Conversely, we find statistically insignificant or even negative excess deaths for at least most of 2020 in places such as Germany, Denmark, and Norway. 

The COVID-19 pandemic has unleashed multiple public health, socio-economic, and institutional crises. Measures taken to slow the spread of the virus have fostered significant strain between authorities and citizens, leading to waves of social unrest and anti-government demonstrations. We study the temporal nature of pandemic-related disorder events as tallied by the “COVID-19 Disorder Tracker” initiative by focusing on the three countries with the largest number of incidents, India, Israel, and Mexico. By fitting Poisson and Hawkes processes to the stream of data, we find that disorder events are inter-dependent and self-excite in all three countries. Geographic clustering confirms these features at the subnational level, indicating that nationwide disorders emerge as the convergence of meso-scale patterns of self-excitation. Considerable diversity is observed among countries when computing correlations of events between subnational clusters; these are discussed in the context of specific political, societal and geographic characteristics. Israel, the most territorially compact and where large scale protests were coordinated in response to government lockdowns, displays the largest reactivity and the shortest period of influence following an event, as well as the strongest nationwide synchrony. In Mexico, where complete lockdown orders were never mandated, reactivity and nationwide synchrony are lowest. Our work highlights the need for authorities to promote local information campaigns to ensure that livelihoods and virus containment policies are not perceived as mutually exclusive.