Tuning and Development of an Individual-Based Model of the Herring Spawning Migration

Norwegian spring spawning herring is a migratory pelagic fish stock that seasonally navigates between distant locations in the Norwegian Sea. The spawning migration takes place between late winter and early spring. In this article, we present an individual-based model that simulated the spawning migration, which was tuned and validated against observation data. Individuals were modelled on a continuous grid coupled to a physical oceanographic model. We explore the development of individual model states in relation to local environmental conditions and predict the distribution and abundance of individuals in the Norwegian Sea for selected years (2015–2020). Individuals moved position mainly according to the prevailing coastal current. A tuning procedure was used to minimize the deviations between model and survey estimates at specific time stamps. Furthermore, 4 separate scenarios were simulated to ascertain the sensitivity of the model to initial conditions. Subsequently, one scenario was evaluated and compared with catch data in 5 day periods within the model time frame. Agreement between model and catch data varies throughout the season and between years. Regardless, emergent properties of the migration are identifiable that match observations, particularly migration trajectories that run perpendicular to deep bathymetry and counter the prevailing current. The model developed is efficient to implement and can be extended to generate multiple realizations of the migration path. This model, in combination with various sources of fisheries-dependent data, can be applied to improve real-time estimates of fish distributions.

Commercial DNA tests and police investigations: a broad bioethical perspective

Over 30 million people worldwide have taken a commercial at-home DNA test, because they were interested in their genetic ancestry, disease predisposition or inherited traits. Yet, these consumer DNA data are also increasingly used for a very different purpose: to identify suspects in criminal investigations. By matching a suspect’s DNA with DNA from a suspect’s distant relatives who have taken a commercial at-home DNA test, law enforcement can zero in on a perpetrator. Such forensic use of consumer DNA data has been performed in over 200 criminal investigations. However, this practice of so-called investigative genetic genealogy (IGG) raises ethical concerns. In this paper, we aim to broaden the bioethical analysis on IGG by showing the limitations of an individual-based model. We discuss two concerns central in the debate: privacy and informed consent. However, we argue that IGG raises pressing ethical concerns that extend beyond these individual-focused issues. The very nature of the genetic information entails that relatives may also be affected by the individual customer’s choices. In this respect, we explore to what extent the ethical approach in the biomedical genetic context on consent and consequences for relatives can be helpful for the debate on IGG. We argue that an individual-based model has significant limitations in an IGG context. The ethical debate is further complicated by the international, transgenerational and commercial nature of IGG. We conclude that IGG should not only be approached as an individual but also—and perhaps primarily—as a collective issue.

PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.

Facility-based HIV self-testing strategies may substantially increase number of men and youth tested for HIV in Malawi: results from a data-driven individual-based model

BackgroundMalawi is rapidly closing the gap in achieving the UNAIDS 95-95-95 targets, with 90% of people living with HIV in Malawi aware of their status. As we approach epidemic control, interventions to improve coverage will become more costly. There is therefore an urgent need to identify innovative and low-cost strategies to maintain and increase testing coverage without diverting resources from other HIV services.MethodsA data-driven individual-based model was parameterized with data from a community-representative survey (sociodemographic, health service utilization, HIV testing history) of men and youth in Malawi (data collected 08/2019). 79 different strategies for the implementation of HIV self-testing (HIVST) and provider-initiated-testing-and-counselling at the outpatient department (OPD) were evaluated. Outcomes included percent of men/youth tested for HIV in a 12-month period, cost-effectiveness, and human resource requirements. Testing yield was assumed to be constant across the scenarios.FindingsFacility-based HIVST offered year-round resulted in the greatest increase in proportion of men and youth tested in the OPD (from 45% to 72%-83%), was considered cost-saving for HIVST kit priced at $1.00, and generally reduced required personnel as compared to the status quo. At higher HIVST kit prices, and more relaxed eligibility criteria, all scenarios that considered year-round HIVST in the OPD remained on the cost-effectiveness frontier.InterpretationFacility-based HIVST is a cost-effective strategy to increase the proportion of men/youth tested for HIV and decreases the human resource requirements for HIV testing in the OPD-providing additional health care worker time for other priority health care activities.FundingFCDO; USAID

Stable Coexistence in a Field-Calibrated Individual-Based Model of Mangrove Forest Dynamics Caused by Inter-Specific Crown Plasticity

(1,2) In this theoretical study, we apply MesoFON, a field-calibrated individual-based model of mangrove forest dynamics, and its Lotka–Volterra interpretations to address two questions: (a) Do the dynamics of two identical red mangrove species that compete for light resources and avoid inter-specific competition by lateral crown displacement follow the predictions of classical competition theory or resource competition theory? (b) Which mechanisms drive the dynamics in the presence of inter-specific crown plasticity when local competition is combined with global or with localized seed dispersal? (3) In qualitative support of classical competition theory, the two species can stably coexist within MesoFON. However, the total standing stock at equilibrium matched the carrying capacity of the single species. Therefore, a “non-overyielding” Lotka–Volterra model rather than the classic one approximated best the observed behavior. Mechanistically, inter-specific crown plasticity moved heterospecific trees apart and pushed conspecifics together. Despite local competition, the community exhibited mean-field dynamics with global dispersal. In comparison, localized dispersal slowed down the dynamics by diminishing the strength of intra-/inter-specific competition and their difference due to a restriction in the competitive race to the mean-field that prevails between conspecific clusters. (4) As the outcome in field-calibrated IBMs is mediated by the competition for resources, we conclude that classical competition mechanisms can override those of resource competition, and more species are likely to successfully coexist within communities.