The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities. Published by AIP Publishing

The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism

© 2020, University of Surrey. All rights reserved. The Overview, Design concepts and Details (ODD) protocol for describing Individual-and Agent-Based Models (ABMs) is now widely accepted and used to document such models in journal articles. As a standardized document for providing a consistent, logical and readable account of the structure and dynamics of ABMs, some research groups also find it useful as a workflow for model design. Even so, there are still limitations to ODD that obstruct its more widespread adoption. Such limitations are discussed and addressed in this paper: the limited availability of guidance on how to use ODD; the length of ODD documents; limitations of ODD for highly complex models; lack of sufficient details of many ODDs to enable reimplementation without access to the model code; and the lack of provision for sections in the document structure covering model design ratio-nale, the model’s underlying narrative, and the means by which the model’s fitness for purpose is evaluated. We document the steps we have taken to provide better guidance on: structuring complex ODDs and an ODD summary for inclusion in a journal article (with full details in supplementary material; Table 1); using ODD to point readers to relevant sections of the model code; update the document structure to include sections on model rationale and evaluation. We also further advocate the need for standard descriptions of simulation experiments and argue that ODD can in principle be used for any type of simulation model. Thereby ODD would provide a lingua franca for simulation modelling

Mechano‐Optical Characterization of Extrusion Flow Instabilities in Styrene‐Butadiene Rubbers: Investigating the Influence of Molecular Properties and Die Geometry

The extrusion flow instabilities of two commercial styrene-butadiene rubbers are investigated as they vary in isomer content (1,4-cis, 1,4-trans, and 1,2 con- formation) of the butadiene monomer and the molecular architecture (linear, branched). The investigated samples have similar multimodal molecular weight distribution. Two geometries of extrusion dies, slit and round capillary, are compared in terms of the type and the spatial characteristics of the flow instabilities. The latter are quantified using three methods: a highly pressure sensitive slit die, online and offline optical analysis. The highly pressure- sensitive slit die has three piezoelectric pressure transducers (Δt ≈ 10−3 s and Δp ≈ 10−5 bar) placed along the die length. The characteristic frequency (fChar.) of the flow instabilities follows a power law behavior as a function of shear\ua0rate to a 0.5 power for both materials, f Char. ∝ γ app.. A qualitative model is used\ua0to predict the spatial characteristic wavelength (λ) of the flow instabilities from round capillary to slit dies and vice versa. Slip velocities (Vs) are used to quantify the slippage at slit and round capillary dies as well

Predicting impacts of chemicals from organisms to ecosystem service delivery: A case study of endocrine disruptor effects on trout

We demonstrate how mechanistic modeling can be used to predict whether and how biological responses to chemicals at (sub)organismal levels in model species (i.e., what we typically measure) translate into impacts on ecosystem service delivery (i.e., what we care about). We consider a hypothetical case study of two species of trout, brown trout (Salmo trutta; BT) and greenback cutthroat trout (Oncorhynchus clarkii stomias; GCT). These hypothetical populations live in a high-altitude river system and are exposed to human-derived estrogen (17α‑ethinyl estradiol, EE2), which is the bioactive estrogen in many contraceptives. We use the individual based model in STREAM to explore how seasonally varying concentrations of EE2 could influence male spawning and sperm quality. Resulting impacts on trout recruitment and the consequences of such for anglers and for the continued viability of populations of GCT (the state fish of Colorado) are explored. in STREAM incorporates seasonally varying river flow and temperature, fishing pressure, the influence of EE2 on species-specific demography, and inter-specific competition. The model facilitates quantitative exploration of the relative importance of endocrine disruption and inter-species competition on trout population dynamics. Simulations predicted constant EE2 loading to have more impacts on GCT than BT. However, increasing removal of BT by anglers can enhance the persistence of GCT and offset some of the negative effects of EE2. We demonstrate how models that quantitatively link impacts of chemicals and other stressors on individual survival, growth, and reproduction to consequences for populations and ecosystem service delivery, can be coupled with ecosystem service valuation. The approach facilitates interpretation of toxicity data in an ecological context and gives beneficiaries of ecosystem services amore explicit role in management decisions. Although challenges remain, this type of approach may be particularly helpful for site-specific risk assessments and those in which trade offs and synergies among ecosystem services need to be considered

A rigorous approach to investigating common assumptions about disease transmission: Process algebra as an emerging modelling methodology for epidemiology

Changing scale, for example the ability to move seamlessly from an individual-based model to a population-based model, is an important problem in many fields. In this paper we introduce process algebra as a novel solution to this problem in the context of models of infectious disease spread. Process algebra allows us to describe a system in terms of the stochastic behaviour of individuals, and is a technique from computer science. We review the use of process algebra in biological systems, and the variety of quantitative and qualitative analysis techniques available. The analysis illustrated here solves the changing scale problem: from the individual behaviour we can rigorously derive equations to describe the mean behaviour of the system at the level of the population. The biological problem investigated is the transmission of infection, and how this relates to individual interaction

A multilevel analytical framework for studying cultural evolution in prehistoric hunter-gatherer societies

Over the past decade, a major debate has taken place on the underpinnings of cultural changes in human societies. A growing array of evidence in behavioural and evolutionary biology has revealed that social connectivity among populations and within them affects, and is affected by, culture. Yet the interplay between prehistoric hunter-gatherer social structure and cultural transmission has typically been overlooked. Interestingly, the archaeological record contains large data sets, allowing us to track cultural changes over thousands of years: they thus offer a unique opportunity to shed light on long‐term cultural transmission processes

Global food security and food riots – an agent-based modelling approach

Due to negative consequences of climate change for agriculture and food production shocks affecting different areas of the world, the past two decades saw the conditions of global food security increasingly worsen. This has resulted in negative consequences for the world economy, partly causing international food price spikes and social upheavals. In this paper we present statistical findings along with a preliminary version of an original agent-based model called the Dawe Global Security Model that simulates the global food market and the political fragility of countries. The model simulates the effects of food insecurity on international food prices and how these, coupled with national political fragility and international food trade can, in turn, increase the probability of food riots in countries. The agents in the model are the 213 countries of the world whose characteristics reflect empirical data and the international trade of food is also simulated based on real trade partnerships and data. The model has been informed, calibrated and validated using real data and the results of these procedures are presented in the paper. To further test the model we also present the model’s forecasts for the near future in terms of food prices and incidence of food riots. The Dawe Global Security Model can be used to test scenarios on the evolution of shocks to global food production and analyse consequences for food riots. Further developments of the model can include national responses to food crises to investigate how countries can influence the spread of global food crises

Indicated Truancy Interventions: Effects on School Attendance Among Chronic Truant Students.

BACKGROUNDTruancy is a significant problem in the U.S. and in other countries around the world. Truancy has been linked to serious immediate and far-reaching consequences for youth, families, and schools and communities, leading researchers, practitioners, and policy makers to try to understand and to address the problem. Although numerous and significant steps have been taken at the local, state, and national levels to reduce truancy, the rates of truancy have at best remained stable or at worst been on the rise, depending on the indicator utilized to assess truancy rates. The costs and impact of chronic truancy are significant, with both short- and long-term implications for the truant youth as well as for the family, school, and community. Although several narrative reviews and one meta-analysis of attendance and truancy interventions have attempted to summarize the extant research, there are a number of limitations to these reviews. It is imperative that we systematically synthesize and examine the evidence base to provide a comprehensive picture of interventions that are being utilized to intervene with chronic truants, to identify interventions that are effective and ineffective, and to identify gaps and areas in which more research needs to be conducted to better inform practice and policy.OBJECTIVESThe main objective of this systematic review was to examine the effects of interventions on school attendance to inform policy, practice, and research. The questions guiding this study were: 1) Do truancy programs with a goal of increasing student attendance for truant youth affect school attendance behaviors of elementary and secondary students with chronic attendance problems?2) Are there differences in the effects of school-based, clinic/community-based, and court-based programs?3) Are some modalities (i.e., family, group, multimodal) more effective than others in increasing student attendance? SEARCH STRATEGYA systematic and comprehensive search process was employed to locate all possible studies between 1990 and 2009, with every effort made to include both published and unpublished studies to minimize publication bias. A wide range of electronic bibliographic databases and research registers was searched, websites of relevant research centers and groups were mined for possible reports, over 200 e-mails and letters were sent to programs listed in large databases of truancy programs compiled by the National Center for School Engagement and the National Dropout Prevention Center, and contact with researchers in the field of truancy and absenteeism was attempted. In addition, we examined reference lists of all previous reviews as well as citations in research reports for potential studies.SELECTION CRITERIAStudies eligible for this review were required to meet several eligibility criteria. Studies must have utilized a randomized, quasi-experimental, or single-group pre-posttest design with the aim of evaluating the effectiveness of interventions with a stated primary goal of increasing student attendance (or decreasing absenteeism) among chronic truant students. Studies must have measured an attendance outcome and reported sufficient data to calculate an effect size. Finally, studies must have been published between 1990 and 2009 in the United States, United Kingdom, Australia, or Canada. DATA COLLECTION AND ANALYSISA total of 28 studies, reported in 26 reports, met final eligibility criteria and were included in this review and meta-analysis. Of the studies that were included, 5 utilized a randomized design (RCT), 11 utilized a quasi-experimental design (QED), and 12 utilized a single group pre-posttest design (SGPP). All eligible studies were coded using a structured coding instrument, with 20% of studies coded by a second coder. Descriptive analysis was conducted to examine and describe data related to the characteristics of the included studies. Analysis of the mean effect size, the heterogeneity of effect sizes, and the relationship between effect size and methodological and substantive characteristics of the interventions was also conducted separately for the RCT/QED studies and the SGPP studies. The effect sizes were calculated using the standardized mean difference effect size statistic, correcting for small sample size using Hedges’ g (Hedges, 1992). Assuming a mixed effects model, the analog to the ANOVA and bivariate meta-regression frameworks were used to examine potential moderating variables related to study, participant, and intervention characteristics. RESULTSThe meta-analytic findings demonstrated a significant overall positive and moderate mean effect of interventions on attendance outcomes. The mean effect size for interventions examined in the included RCT studies was .57 and the mean effect size for the QED studies was .43. No significant differences were observed between the RCT and QED studies in the magnitude of the treatment effect (Qb= .28, p \u3e.05). The mean effect size of interventions examined using an SGPP design was .95. A moderate effect on attendance outcomes is encouraging; however, the overall mean effect size is masked by a large amount of heterogeneity, indicating significant variance in effect sizes between studies. Moderator analyses found no significant differences in mean effects between studies on any moderating variable tested. No differences were found between school-, court-, or community-based programs or between different modalities of programs. The duration of the intervention also did not demonstrate any association with effect size. Collaborative programs and multimodal interventions produced statistically similar effects on attendance as non-collaborative and single-modality programs, which runs counter to the prevailing beliefs and recommendations for best practices in truancy reduction found in the literature.Other significant findings from this study relate to methodological shortcomings, the absence of important variables as well as gaps in the evidence base. These findings include the lack of inclusion of minority students and a lack of reporting and statistical analysis of demographic variables, particularly race/ethnicity and socioeconomic status (SES). Given that race and SES have been linked to absenteeism, the absence of this data was surprising. The majority of studies also lacked adequate descriptions of the interventions, making replication of the intervention difficult, and failed to measure and report long-term outcomes. AUTHORS’ CONCLUSIONSOverall, the findings from this study suggest that chronic truant students benefit from interventions targeting attendance behaviors; thus it is important and worthwhile to intervene with chronic truant youth. Given the minimal differences in effects across program types and modalities, no one program type or modality stands out as being more effective than any other. Although no statistically significant differences in effects were found between types and modalities of interventions included in this review, there was a lack of available evidence to support the general belief (and popular “best-practice” recommendations) that collaborative and multimodal interventions are more effective than programs that are not collaborative and single modal interventions. Due to the small sample size and large heterogeneity between studies and within groups of studies, caution must be used when interpreting and applying the findings from this meta-analysis. Overall, the studies included in the review improved attendance by an average of 4.69 days, almost a full school week. However, although the interventions included in this study were, overall, found to be effective, the mean rates of absenteeism at posttest in most studies remained above acceptable levels. This finding indicates the need for additional work and research. Developing more effective interventions and policies as well as studying outcomes of interventions, particularly with vulnerable and at-risk populations, is crucial to combating absenteeism. The gaps and deficiencies identified in this study also affirm the need for increasing and strengthening the evidence base on which current policies and practices rest. Although additional outcome research is necessary, more of the same is not sufficient. Significant improvements in the quality of truancy intervention research are required and identified gaps need to be addressed. Recommendations to improve the quality and fill gaps in truancy intervention research are discussed here. In addition, given the significant and pervasive deficiencies in the extant research, a critical analysis of the practices, assumptions, and sociopolitical contexts underlying truancy intervention research seems warranted