A gillespie algorithm for non-markovian stochastic processes

The Gillespie algorithm provides statistically exact methods for simulating stochastic dynamics modeled as interacting sequences of discrete events including systems of biochemical reactions or earthquake occurrences, networks of queuing processes or spiking neurons, and epidemic and opinion formation processes on social networks. Empirically, the inter-event times of various phenomena obey long-tailed distributions. The Gillespie algorithm and its variants either assume Poisson processes (i.e., exponentially distributed inter-event times), use particular functions for time courses of the event rate, or work for non-Poissonian renewal processes, including the case of long-tailed distributions of inter-event times, but at a high computational cost. In the present study, we propose an innovative Gillespie algorithm for renewal processes on the basis of the Laplace transform. The algorithm makes use of the fact that a class of point processes is represented as a mixture of Poisson processes with different event rates. The method is applicable to multivariate renewal processes whose survival function of inter-event times is completely monotone. It is an exact algorithm and works faster than a recently proposed Gillespie algorithm for general renewal processes, which is exact only in the limit of infinitely many processes. We also propose a method to generate sequences of event times with a tunable amount of positive correlation between inter-event times. We demonstrate our algorithm with exact simulations of epidemic processes on networks, finding that a realistic amount of positive correlation in inter-event times only slightly affects the epidemic dynamics

Clustering of chronic hepatitis B screening intentions in social networks of Moroccan immigrants in the Netherlands

Background Early detection, identification, and treatment of chronic hepatitis B through screening is vital for those at increased risk, e.g. born in hepatitis B endemic countries. In the Netherlands, Moroccan immigrants show low participation rates in health-related screening programmes. Since social networks influence health behaviour, we investigated whether similar screening intentions for chronic hepatitis B cluster within social networks of Moroccan immigrants. Methods We used respondent-driven sampling (RDS) where each participant ("recruiter") was asked to complete a questionnaire and to recruit three Moroccans ("recruitees") from their social network. Logistic regression analyses were used to analyse whether the recruiters' intention to request a screening test was similar to the intention of their recruitees. Results We sampled 354 recruiter-recruitee pairs: for 154 pairs both participants had a positive screening intention, for 68 pairs both had a negative screening intention, and the remaining 132 pairs had a discordant intention to request a screening test. A tie between a recruiter and recruitee was associated with having the same screening intention, after correction for sociodemographic variables (OR 1.70 [1.15-2.51]). Conclusions The findings of our pilot study show clustering of screening intention among individuals in the same network. This provides opportunities for social network interventions to encourage participation in hepatitis B screening initiatives

Dynamics of air transport networks: A review from a complex systems perspective

Air transport systems are highly dynamic at temporal scales from minutes to years. This dynamic behavior not only characterizes the evolution of the system but also affect the system's functioning. Understanding the evolutionary mechanisms is thus fundamental in order to better design optimal air transport networks that benefits companies, passengers and the environment. In this review, we briefly present and discuss the state-of-the-art on time-evolving air transport networks. We distinguish the structural analysis of sequences of network snapshots, ideal for long-term network evolution (e.g. annual evolution), and temporal paths, preferred for short-term dynamics (e.g. hourly evolution). We emphasize that most previous research focused on the first modeling approach (i.e. long-term) whereas only a few studies look at high-resolution temporal paths. We conclude the review highlighting that much research remains to be done, both to apply already available methods and to develop new measures for temporal paths on air transport networks. In particular, we identify that the study of delays, network resilience and optimization of resources (aircraft and crew) are critical topics

Applications and recruitment performance of web-based respondent-driven sampling: Scoping review

Background: Web-based respondent-driven sampling is a novel sampling method for the recruitment of participants for generating population estimates, studying social network characteristics, and delivering health interventions. However, the application, barriers and facilitators, and recruitment performance of web-based respondent-driven sampling have not yet been systematically investigated. Objective: Our objectives were to provide an overview of published research using web-based respondent-driven sampling and to investigate factors related to the recruitment performance of web-based respondent-driven sampling. Methods: We conducted a scoping review on web-based respondent-driven sampling studies published between 2000 and 2019. We used the process evaluation of complex interventions framework to gain insights into how web-based respondent-driven sampling was implemented, what mechanisms of impact drove recruitment, what the role of context was in the study, and how these components together influenced the recruitment performance of web-based respondent-driven sampling. Results: We included 18 studies from 8 countries (high- and low-middle income countries), in which web-based respondent-driven sampling was used for making population estimates (n=12), studying social network characteristics (n=3), and delivering health-related interventions (n=3). Studies used web-based respondent-driven sampling to recruit between 19 and 3448 participants from a variety of target populations. Studies differed greatly in the number of seeds recruited, the proportion of successfully recruiting participants, the number of recruitment waves, the type of incentives offered to participants, and the duration of data collection. Studies that recruited relatively more seeds, through online platforms, and with less rigorous selection procedures reported relatively low percentages of successfully recruiting seeds. Studies that did not offer at least one guaranteed material incentive reported relatively fewer waves and lower percentages of successfully recruiting participants. The time of data collection was shortest in studies with university students. Conclusions: Web-based respondent-driven sampling can be successfully applied to recruit individuals for making population estimates, studying social network characteristics, and delivering health interventions. In general, seed and peer recruitment may be enhanced by rigorously selecting and motivating seeds, offering at least one guaranteed material incentive, and facilitating adequate recruitment options regarding the target population's online connectedness and communication behavior. Potential trade-offs should be taken into account when implementing web-based respondent-driven sampling, such as having less opportunities to implement rigorous seed selection procedures when recruiting many seeds, as well as issues around online rather than physical participation, such as the risk of cheaters participating repeatedly

Clustering of chronic hepatitis B screening intentions in social networks of Moroccan immigrants in the Netherlands

Background: Early detection, identification, and treatment of chronic hepatitis B through screening is vital for those at increased risk, e.g. born in hepatitis B endemic countries. In the Netherlands, Moroccan immigrants show low participation rates in health-related screening programmes. Since social networks influence health behaviour, we investigated whether similar screening intentions for chronic hepatitis B cluster within social networks of Moroccan immigrants. Methods: We used respondent-driven sampling (RDS) where each participant ("recruiter") was asked to complete a questionnaire and to recruit three Moroccans ("recruitees") from their social network. Logistic regression analyses were used to analyse whether the recruiters' intention to request a screening test was similar to the intention of their recruitees. Results: We sampled 354 recruiter-recruitee pairs: For 154 pairs both participants had a positive screening intention, for 68 pairs both had a negative screening intention, and the remaining 132 pairs had a discordant intention to request a screening test. A tie between a recruiter and recruitee was associated with having the same screening intention, after correction for sociodemographic variables (OR 1.70 [1.15-2.51]). Conclusions: The findings of our pilot study show clustering of screening intention among individuals in the same network. This provides opportunities for social network interventions to encourage participation in hepatitis B screening initiatives

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora