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 rationale, 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.
ABSTRACT
Herbivory is a fundamental process that controls primary producer abundance and regulates energy and nutrient flows to higher trophic levels. Despite the recent proliferation of small‐scale ...studies on herbivore effects on aquatic plants, there remains limited understanding of the factors that control consumer regulation of vascular plants in aquatic ecosystems. Our current knowledge of the regulation of primary producers has hindered efforts to understand the structure and functioning of aquatic ecosystems, and to manage such ecosystems effectively. We conducted a global meta‐analysis of the outcomes of plant–herbivore interactions using a data set comprised of 326 values from 163 studies, in order to test two mechanistic hypotheses: first, that greater negative changes in plant abundance would be associated with higher herbivore biomass densities; second, that the magnitude of changes in plant abundance would vary with herbivore taxonomic identity. We found evidence that plant abundance declined with increased herbivore density, with plants eliminated at high densities. Significant between‐taxa differences in impact were detected, with insects associated with smaller reductions in plant abundance than all other taxa. Similarly, birds caused smaller reductions in plant abundance than echinoderms, fish, or molluscs. Furthermore, larger reductions in plant abundance were detected for fish relative to crustaceans. We found a positive relationship between herbivore species richness and change in plant abundance, with the strongest reductions in plant abundance reported for low herbivore species richness, suggesting that greater herbivore diversity may protect against large reductions in plant abundance. Finally, we found that herbivore–plant nativeness was a key factor affecting the magnitude of herbivore impacts on plant abundance across a wide range of species assemblages. Assemblages comprised of invasive herbivores and native plant assemblages were associated with greater reductions in plant abundance compared with invasive herbivores and invasive plants, native herbivores and invasive plants, native herbivores and mixed‐nativeness plants, and native herbivores and native plants. By contrast, assemblages comprised of native herbivores and invasive plants were associated with lower reductions in plant abundance compared with both mixed‐nativeness herbivores and native plants, and native herbivores and native plants. However, the effects of herbivore–plant nativeness on changes in plant abundance were reduced at high herbivore densities. Our mean reductions in aquatic plant abundance are greater than those reported in the literature for terrestrial plants, but lower than aquatic algae. Our findings highlight the need for a substantial shift in how biologists incorporate plant–herbivore interactions into theories of aquatic ecosystem structure and functioning. Currently, the failure to incorporate top‐down effects continues to hinder our capacity to understand and manage the ecological dynamics of habitats that contain aquatic plants.
The purpose of this study was to develop and test a new continuous measure for rural health disparities research that characterizes geographic areas according to a perspective of access to resources. ...We call the measure Isolation and anticipate it will be useful as an alternative to commonly used rural classification schemes (e.g., the Census Bureau's measure). Following the best known standards for measuring rurality, it captures the trade-off between access to resource-rich, high-population-density areas and the cost of travel to those areas; thus even intrinsically low-resource areas may have high access to nearby resources. Validity was tested with proxies such as distance to hospitals, physician availability, and access to high quality food. The Isolation scale demonstrated good construct validity (i.e., both convergent and criterion validity). Fit statistics indicated that, compared to other commonly-used urban/rural definitions, the Isolation scale was the best overall measure when predicting several proxies for rurality, even when categorized. We also show that the measure does a substantially better job at explaining national health outcome data at the state level. This new continuous Isolation scale shows considerable promise for improving our conceptualization, theorization, and measurement of the features of rurality that are pertinent to rural health disparities research, and can also be useful to policy makers who may find value in using isolation thresholds that are most relevant to their policy planning needs.
•Existing US urban/rural measures are limited for health research use.•A new Isolation measure accounts for location and distance from population centers.•Isolation is superior for explaining actual access to health related resources.•Isolation is superior for explaining the distribution of health outcomes.•Isolation is a measurement step forward for rural health disparities research.
Drivers of environmental change are causing novel combinations of pressures on ecological systems. Prediction in ecology often uses understanding of past conditions to make predictions to the future, ...but such an approach can breakdown when future conditions have not previously been encountered. Individual‐based models (IBMs) consider ecological systems as arising from the adaptive behavior and fates of individuals and have potential to provide more reliable predictions. To demonstrate potential, we review a lineage of related IBMs addressing the effects of environmental change on waterbirds, comprising 53 case studies of 28 species in 32 sites in 9 countries, using the Drivers‐Pressures‐State‐Impact‐Response (DPSIR) environmental management framework. Each case study comprises the predictions of an IBM on the effects of one or more drivers of environmental change on one or more bird species. Drivers exert a pressure on the environment which is represented in the IBMs as changes in either area or time available for feeding, the quality of habitat, or the energetic cost of living within an environment. Birds in the IBMs adapt to increased pressure by altering their behavioral state, defined as their location, diet, and the proportion of time spent feeding. If the birds are not able to compensate behaviorally, they suffer a physiological impact, determined by a decrease in body energy reserves, increased mortality, or decreased ability to migrate. Each case study assesses the impact of alternative drivers and potential ways to mitigate impacts to advise appropriate conservation management responses. We overview the lessons learned from the case studies and highlight the opportunities of using IBMs to inform conservation management for other species. Key findings indicate that understanding the behavioral and physiological processes that determine whether or not birds survive following a change in their environment is vital, so that mitigation measures can be better targeted. This is especially important where multiple hazards exist so that sensitivities and worse‐case scenarios can be better understood. Increasing the involvement of stakeholders to help inform and shape model development is encouraged and can lead to better representation of the modeled system and wider understanding and support for the final model.
This paper describes an individual-based model, MORPH, that has been designed to predict the effect of environmental change on foraging animal populations. The key assumptions of MORPH are that ...individuals within populations behave in order to maximise their perceived fitness, but that perceived fitness may not always be positively related to the actual chances of survival and reproduction. MORPH has been parameterised for coastal birds on several European sites and predicted the effect of environmental change, caused by factors such as habitat loss, disturbance from humans and sea-level rise, on the survival and body condition of these species. However, MORPH contains a basic framework to describe animal physiology and foraging behaviour, and the distribution and abundance of the resources required by these animals. Therefore, MORPH is not restricted to coastal birds, and is potentially applicable to a wider range of systems. To be applied to a forager system, MORPH requires parameters describing (i) the distribution of the food supply and how food quality and abundance changes through time; (ii) the rate at which foragers consume food given the abundance of food and competitors; (iii) the amount of food the forager must consume each day to survive; (iv) the distribution and seasonal changes in other factors which influence the foraging behaviour and survival of foragers. The purpose of this paper is to (i) describe MORPH, (ii) give examples of its application, (iii) describe the types of systems to which MORPH can be applied, and (iv) publish its source code and a user guide.
Autism spectrum disorders (ASD) are a group of related neurodevelopmental syndromes with complex genetic etiology.
1
We identified a de novo chromosome 7q inversion disrupting
Autism susceptibility ...candidate 2 (
AUTS2) and
Contactin Associated Protein-Like 2 (
CNTNAP2) in a child with cognitive and social delay. We focused our initial analysis on
CNTNAP2 based on our demonstration of disruption of
Contactin 4 (
CNTN4) in a patient with ASD;
2
the recent finding of rare homozygous mutations in
CNTNAP2 leading to intractable seizures and autism;
3
and in situ and biochemical analyses reported herein that confirm expression in relevant brain regions and demonstrate the presence of CNTNAP2 in the synaptic plasma membrane fraction of rat forebrain lysates. We comprehensively resequenced
CNTNAP2 in 635 patients and 942 controls. Among patients, we identified a total of 27 nonsynonymous changes; 13 were rare and unique to patients and 8 of these were predicted to be deleterious by bioinformatic approaches and/or altered residues conserved across all species. One variant at a highly conserved position, I869T, was inherited by four affected children in three unrelated families, but was not found in 4010 control chromosomes (p = 0.014). Overall, this resequencing data demonstrated a modest nonsignificant increase in the burden of rare variants in cases versus controls. Nonethless, when viewed in light of two independent studies published in this issue of
AJHG showing a relationship between ASD and common
CNTNAP2 alleles,
4,5
the cytogenetic and mutation screening data suggest that rare variants may also contribute to the pathophysiology of ASD, but place limits on the magnitude of this contribution.
Ecosystem‐based management of fisheries aims to allow sustainable use of fished stocks while keeping impacts upon ecosystems within safe ecological limits. Both the FAO Code of Conduct for ...Responsible Fisheries and the Aichi Biodiversity Targets promote these aims. We evaluate implementation of ecosystem‐based management in six case‐study fisheries in which potential indirect impacts upon bird or mammal predators of fished stocks are well publicized and well studied. In particular, we consider the components needed to enable management strategies to respond to information from predator monitoring. Although such information is available in all case‐studies, only one has a reference point defining safe ecological limits for predators and none has a method to adjust fishing activities in response to estimates of the state of the predator population. Reference points for predators have been developed outside the fisheries management context, but adoption by fisheries managers is hindered a lack of clarity about management objectives and uncertainty about how fishing affects predator dynamics. This also hinders the development of adjustment methods because these generally require information on the state of ecosystem variables relative to reference points. Nonetheless, most of the case‐studies include precautionary measures to limit impacts on predators. These measures are not used tactically and therefore risk excessive restrictions on sustainable use. Adoption of predator reference points to inform tactical adjustment of precautionary measures would be an appropriate next step towards ecosystem‐based management.
Access to high‐quality food is critical for long‐distance migrants to provide energy for migration and arrival at breeding grounds in good condition. We studied effects of changing abundance and ...availability of a marine food, common eelgrass (Zostera marina L.), on an arctic‐breeding, migratory goose, black brant (Brant bernicla nigricans Lawrence 1846), at a key non‐breeding site, Bahía San Quintín, Mexico. Eelgrass, the primary food of brant, is consumed when exposed by the tide or within reach from the water's surface. Using an individual‐based model, we predicted effects of observed changes (1991–2013) in parameters influencing food abundance and availability: eelgrass biomass (abundance), eelgrass shoot length (availability, as longer shoots more within reach), brant population size (availability, as competition greater with more birds), and sea level (availability, as less food within reach when sea level higher). The model predicted that the ability to gain enough energy to migrate was most strongly influenced by eelgrass biomass (threshold January biomass for migration = 60 g m−2 dry mass). Conversely, annual variation in population size (except for 1998), was relatively low, and variation in eelgrass shoot length and sea level were not strongly related to ability to migrate. We used observed data on brant body mass at Bahía San Quintín and annual survival to test for effects of eelgrass biomass in the real system. The lowest observed values of body mass and survival were in years when biomass was below 60 g m−2, although in some years of low biomass body mass and/or survival was higher. This suggests that the real birds may have some capacity to compensate to meet their energy demands when eelgrass biomass is low. We discuss consequences for brant population trends and conservation.
We studied effects of annual changes in abundance and availability of a marine food, common eelgrass (Zostera marina), on an arctic‐breeding, migratory goose, black brant (Brant bernicla nigricans), at a key non‐breeding site, Bahía San Quintín, Mexico. Using an individual‐based model, we predicted that the ability to gain enough energy to migrate was most strongly influenced by eelgrass biomass, rather than eelgrass shoot length, brant population size or sea level. We compare these predictions to observations from the real system and discuss consequences for brant population trends and conservation.
Introduction: Previous literature has highlighted athletes as a population that is particularly vulnerable to a range of psychiatric symptoms and disorders. Although psychotherapy and pharmacological ...interventions have been demonstrated as clinically effective for athletes in isolation, the potential for a combination of such approaches (integrative treatment) as superior to either modality is of increasing interest and importance. Specifically, the athlete population may benefit from an integrative approach since it faces unique factors and implications for treatment, including but not limited to doping regulations, performance modulation secondary to psychiatric medication, and particular barriers to adherence (e.g., personality factors, athlete-specific schedules, stigma). Methods: To retrieve relevant articles for our review, we searched five electronic databases (PubMed (MEDLINE), SportDiscus via EBSCO, PSycINFO viaProQuest, Scopus and Cochrane). Athletes were defined as those competing at professional, Olympic, or collegiate/university levels. Results: We seek to highlight clinically relevant factors, conceptual models, rationales and examples of an integrative approach so as to set the stage for future literature aiming to investigate such a topic on both theoretical and experimental levels. Conclusion: Ultimately, our review seeks to provide a rationale for systematically assessing factors for and against combination therapy for each athlete, a risk benefit analysis aimed at providing a clinically effective and parsimonious intervention strategy, which may include the use of one or multiple intervention modalities. Such a strategy will ideally facilitate positive outcomes for athletes’ personal functioning which may consequently maintain or augment their athletic performance, initiating a positive feedback loop of optimal functioning.
Understanding plant community responses to combinations of biotic and abiotic factors is critical for predicting ecosystem response to environmental change. However, studies of plant community ...regulation have seldom considered how responses to such factors vary with the different phases of the plant growth cycle. To address this deficit we studied an aquatic plant community in an ecosystem subject to gradients in mute swan (Cygnus olor) herbivory, riparian shading, water temperature and distance downstream of the river source. We quantified abundance, species richness, evenness, flowering and dominance in relation to biotic and abiotic factors during the growth-, peak-, and recession-phases of the plant growth cycle. We show that the relative importance of biotic and abiotic factors varied between plant community properties and between different phases of the plant growth cycle. Herbivory became more important during the later phases of peak abundance and recession due to an influx of swans from adjacent pasture fields. Shading by riparian vegetation also had a greater depressing effect on biomass in later seasons, probably due to increased leaf abundance reducing light intensity reaching the aquatic plants. The effect of temperature on community diversity varied between upstream and downstream sites by altering the relative competitiveness of species at these sites. These results highlight the importance of seasonal patterns in the regulation of plant community structure and function by multiple factors.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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