Bayesian inference for the onset time and epidemiological characteristics of emerging infectious diseases.

Background: Emerging infectious diseases pose a significant threat to global public health. Timely detection and response are crucial in mitigating the spread of such epidemics. Inferring the onset time and epidemiological characteristics is vital for accelerating early interventions, but accurately predicting these parameters in the early stages remains challenging. Methods: We introduce a Bayesian inference method to fit epidemic models to time series data based on state-space modeling, employing a stochastic Susceptible-Exposed-Infectious-Removed (SEIR) model for transmission dynamics analysis. Our approach uses the particle Markov chain Monte Carlo (PMCMC) method to estimate key epidemiological parameters, including the onset time, the transmission rate, and the recovery rate. The PMCMC algorithm integrates the advantageous aspects of both MCMC and particle filtering methodologies to yield a computationally feasible and effective means of approximating the likelihood function, especially when it is computationally intractable. Results: To validate the proposed method, we conduct case studies on COVID-19 outbreaks in Wuhan, Shanghai and Nanjing, China, respectively. Using early-stage case reports, the PMCMC algorithm accurately predicted the onset time, key epidemiological parameters, and the basic reproduction number. These findings are consistent with empirical studies and the literature. Conclusion: This study presents a robust Bayesian inference method for the timely investigation of emerging infectious diseases. By accurately estimating the onset time and essential epidemiological parameters, our approach is versatile and efficient, extending its utility beyond COVID-19.

Accessing the syndemic of COVID-19 and malaria intervention in Africa.

BACKGROUND: The pandemic of the coronavirus disease 2019 (COVID-19) has caused substantial disruptions to health services in the low and middle-income countries with a high burden of other diseases, such as malaria in sub-Saharan Africa. The aim of this study is to assess the impact of COVID-19 pandemic on malaria transmission potential in malaria-endemic countries in Africa. METHODS: We present a data-driven method to quantify the extent to which the COVID-19 pandemic, as well as various non-pharmaceutical interventions (NPIs), could lead to the change of malaria transmission potential in 2020. First, we adopt a particle Markov Chain Monte Carlo method to estimate epidemiological parameters in each country by fitting the time series of the cumulative number of reported COVID-19 cases. Then, we simulate the epidemic dynamics of COVID-19 under two groups of NPIs: (1) contact restriction and social distancing, and (2) early identification and isolation of cases. Based on the simulated epidemic curves, we quantify the impact of COVID-19 epidemic and NPIs on the distribution of insecticide-treated nets (ITNs). Finally, by treating the total number of ITNs available in each country in 2020, we evaluate the negative effects of COVID-19 pandemic on malaria transmission potential based on the notion of vectorial capacity. RESULTS: We conduct case studies in four malaria-endemic countries, Ethiopia, Nigeria, Tanzania, and Zambia, in Africa. The epidemiological parameters (i.e., the basic reproduction number [Formula: see text] and the duration of infection [Formula: see text]) of COVID-19 in each country are estimated as follows: Ethiopia ([Formula: see text], [Formula: see text]), Nigeria ([Formula: see text], [Formula: see text]), Tanzania ([Formula: see text], [Formula: see text]), and Zambia ([Formula: see text], [Formula: see text]). Based on the estimated epidemiological parameters, the epidemic curves simulated under various NPIs indicated that the earlier the interventions are implemented, the better the epidemic is controlled. Moreover, the effect of combined NPIs is better than contact restriction and social distancing only. By treating the total number of ITNs available in each country in 2020 as a baseline, our results show that even with stringent NPIs, malaria transmission potential will remain higher than expected in the second half of 2020. CONCLUSIONS: By quantifying the impact of various NPI response to the COVID-19 pandemic on malaria transmission potential, this study provides a way to jointly address the syndemic between COVID-19 and malaria in malaria-endemic countries in Africa. The results suggest that the early intervention of COVID-19 can effectively reduce the scale of the epidemic and mitigate its impact on malaria transmission potential.

Risk assessment of malaria transmission at the border area of China and Myanmar.

BACKGROUND: In order to achieve the goal of malaria elimination, the Chinese government launched the National Malaria Elimination Programme in 2010. However, as a result of increasing cross-border population movements, the risk of imported malaria cases still exists at the border areas of China, resulting in a potential threat of local transmission. The focus of this paper is to assess the Plasmodium vivax incidences in Tengchong, Yunnan Province, at the border areas of China and Myanmar. METHODS: Time series of P. vivax incidences in Tengchong from 2006 to 2010 are collected from the web-based China Information System for Disease Control and Prevention, which are further separated into time series of imported and local cases. First, the seasonal and trend decomposition are performed on time series of imported cases using Loess method. Then, the impact of climatic factors on the local transmission of P. vivax is assessed using both linear regression models (LRM) and generalized additive models (GAM). Specifically, the notion of vectorial capacity (VCAP) is used to estimate the transmission potential of P. vivax at different locations, which is calculated based on temperature and rainfall collected from China Meteorological Administration. RESULTS: Comparing with Ruili County, the seasonal pattern of imported cases in Tengchong is different: Tengchong has only one peak, while Ruili has two peaks during each year. This may be due to the different cross-border behaviors of peoples in two locations. The vectorial capacity together with the imported cases and the average humidity, can well explain the local incidences of P. vivax through both LRM and GAM methods. Moreover, the maximum daily temperature is verified to be more suitable to calculate VCAP than the minimal and average temperature in Tengchong County. CONCLUSION: To achieve malaria elimination in China, the assessment results in this paper will provide further guidance in active surveillance and control of malaria at the border areas of China and Myanmar.

Reputation-Based Investment Helps to Optimize Group Behaviors in Spatial Lattice Networks.

Encouraging cooperation among selfish individuals is crucial in many real-world systems, where individuals' collective behaviors can be analyzed using evolutionary public goods game. Along this line, extensive studies have shown that reputation is an effective mechanism to investigate the evolution of cooperation. In most existing studies, participating individuals in a public goods game are assumed to contribute unconditionally into the public pool, or they can choose partners based on a common reputation standard (e.g., preferences or characters). However, to assign one reputation standard for all individuals is impractical in many real-world deployment. In this paper, we introduce a reputation tolerance mechanism that allows an individual to select its potential partners and decide whether or not to contribute an investment to the public pool based on its tolerance to other individuals' reputation. Specifically, an individual takes part in a public goods game only if the number of participants with higher reputation exceeds the value of its tolerance. Moreover, in this paper, an individual's reputation can increase or decrease in a bounded interval based on its historical behaviors. We explore the principle that how the reputation tolerance and conditional investment mechanisms can affect the evolution of cooperation in spatial lattice networks. Our simulation results demonstrate that a larger tolerance value can achieve an environment that promote the cooperation of participants.

Concurrent negotiation and coordination for grid resource coallocation.

Bolstering resource coallocation is essential for realizing the Grid vision, because computationally intensive applications often require multiple computing resources from different administrative domains. Given that resource providers and consumers may have different requirements, successfully obtaining commitments through concurrent negotiations with multiple resource providers to simultaneously access several resources is a very challenging task for consumers. The impetus of this paper is that it is one of the earliest works that consider a concurrent negotiation mechanism for Grid resource coallocation. The concurrent negotiation mechanism is designed for 1) managing (de)commitment of contracts through one-to-many negotiations and 2) coordination of multiple concurrent one-to-many negotiations between a consumer and multiple resource providers. The novel contributions of this paper are devising 1) a utility-oriented coordination (UOC) strategy, 2) three classes of commitment management strategies (CMSs) for concurrent negotiation, and 3) the negotiation protocols of consumers and providers. Implementing these ideas in a testbed, three series of experiments were carried out in a variety of settings to compare the following: 1) the CMSs in this paper with the work of others in a single one-to-many negotiation environment for one resource where decommitment is allowed for both provider and consumer agents; 2) the performance of the three classes of CMSs in different resource market types; and 3) the UOC strategy with the work of others [e.g., the patient coordination strategy (PCS )] for coordinating multiple concurrent negotiations. Empirical results show the following: 1) the UOC strategy achieved higher utility, faster negotiation speed, and higher success rates than PCS for different resource market types; and 2) the CMS in this paper achieved higher final utility than the CMS in other works. Additionally, the properties of the three classes of CMSs in different kinds of resource markets are also verified.