Testing,tracing and isolation in compartmental models

Existing compartmental mathematical modelling methods for epidemics, such as SEIR models, cannot accurately represent effects of contact tracing. This makes them inappropriate for evaluating testing and contact tracing strategies to contain an outbreak. An alternative used in practice is the application of agent- or individual-based models (ABM). However ABMs are complex, less well-understood and much more computationally expensive. This paper presents a new method for accurately including the effects of Testing, contact-Tracing and Isolation (TTI) strategies in standard compartmental models. We derive our method using a careful probabilistic argument to show how contact tracing at the individual level is reflected in aggregate on the population level. We show that the resultant SEIR-TTI model accurately approximates the behaviour of a mechanistic agent-based model at far less computational cost. The computational efficiency is such that it can be easily and cheaply used for exploratory modelling to quantify the required levels of testing and tracing, alone and with other interventions, to assist adaptive planning for managing disease outbreaks.     

Effects of two types of herbivores on the population dynamics of a perennial herb

The joint effects of multiple herbivores on their shared host plant have received increasing interest recently. The influence of herbivores on population dynamics of their host plants, especially the relative roles of different types of damage, is, however, still poorly understood. Here, we present a modelling approach, including both deterministic and stochastic matrix modelling, to be used in estimating fitness effects of multiple herbivores on perennial plants. We examined the effects and relative roles of two specialist herbivores, a pre-dispersal seed predator, Euphranta connexa, and a leaf-feeding moth, Abrostola asclepiadis, on the population dynamics and long-term fitness of their shared host plant, a long-lived perennial herb Vincetoxicum hirundinaria (Asclepiadaceae). We collected demographic data during 3 years and combined these data with the effects of natural levels of herbivory measured from the same individuals. We found that both seed predation and leaf herbivory reduced population growth of V. hirundinaria, but only very high damage levels changed the growth trend of the vigorously growing study populations from positive to negative. Demographic modelling indicated that seed predation had a greater impact on plant population growth than leaf herbivory. The effect of leaf herbivory was weaker and diminished with increasing level of seed predation. Evaluation of individual fitness components, however, suggested that leaf herbivory contributed more strongly to host plant fitness than seed predation. Our results emphasize that understanding the effects of a particular herbivore on plant population dynamics requires also knowledge on other herbivores present in the system, because the effect of a particular type of herbivory on plant population dynamics is likely to vary according to the intensity of other types of herbivory. Furthermore, evaluating herbivore impact from using individual fitness components does not necessarily reflect the long-term effects on total plant fitness.     

Modelling,abstraction, and computation in systems biology: A view from computer science

Systems biology is centrally engaged with computational modelling across multiple scales and at many levels of abstraction. Formal modelling, precise and formalised abstraction relationships, and computation also lie at the heart of computer science—and over the past decade a growing number of computer scientists have been bringing their discipline's core intellectual and computational tools to bear on biology in fascinating new ways. This paper explores some of the apparent points of contact between the two fields, in the context of a multi-disciplinary discussion on conceptual foundations of systems biology.     

Biological effects of electromagnetic fields--mechanisms for the effects of pulsed microwave radiation on protein conformation

Microwave exposure under "athermal" conditions occurs when no temperature rise can be measured by conventional thermometry. The existence of biological effects arising from the athermal exposure is still controversial, partly because of a lack of the linear dose response relation. We propose a model in which pulsed microwave radiation causes a triggering of the heat shock or stress response by altering the conformation of proteins through a transient heating of the protein and its close environment. We support this by modelling using the heat diffusion equation and show that pulsed exposure even when athermal can lead to transient temperature excursions outside the normal range. We propose that the power window phenomenon in which biological effects are observed at low power levels may be caused by an incomplete triggering of the heat shock response.     

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases. RESULTS: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3. AVAILABILITY: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/     

Effects of shear stress on endothelial cells: possible relevance for ultrasound applications

This review forms part of a series of papers resulting from a workshop on safety of ultrasound applications. The physical effects of ultrasound include generation of steady streaming in large fluid volumes, and micro-streaming around contrast bubbles. Such streaming induces shear stress acting on the vascular endothelium. This review provides a discussion on the levels of endothelial shear stress associated with diagnostic ultrasound applications, and on the biological effects of shear stress acting on the endothelial cells. Depending on vessel size and ultrasound characteristics, shear stresses associated with streaming and micro-streaming may exceed the physiological levels associated with the flow of blood by many orders of magnitude. The resulting biological effects could range anywhere from activation of normal shear stress sensors such as ion channels, damage of the endothelial surface layer, reversible perforation of the membrane, to cell detachment and lysis. The possible presence of such biological effects does not necessarily mean that the effects are harmful for the individual. However, considering the ever-increasing use of ultrasound, a further investigation into these shear stress-related effects, using both experiments and modelling, is desired. Apart from safety concerns, such effects may provide a base for strategies aimed at targeted delivery of drugs.     

Modelling the size and composition of fruit, grain and seed by process-based simulation models

Understanding what determines the size and composition of fruit, grain and seed in response to the environment and genotype is challenging, as these traits result from several linked processes controlled at different levels of organization, from the subcellular to the crop level, with subtle interactions occurring at or between the levels of organization. Process-based simulation models (PBSMs) implement algorithms to simulate metabolic and biophysical aspects of cell, tissue and organ behaviour. In this review, fruit, grain and seed PBSMs describing the main phases of growth, development and storage metabolism are discussed. From this concurrent work, it is possible to identify generic storage organ processes which can be modelled similarly for fruit, grain and seed. Spatial heterogeneity at the tissue and whole-plant level is found to be a key consideration in modelling the effects of the environment and genotype on fruit, grain and seed end-use value. In the future, PBSMs may well become the main link between studies at the molecular and whole-plant levels. To bridge this phenotype-to-genotype gap, future models need to remain plastic without becoming overparameterized.     

Effect of phytoplankton size diversity on primary productivity in the North Pacific: trait distributions under environmental variability

While most biodiversity and ecosystem functioning (BEF) studies have found positive effects of species richness on productivity, it remain unclear whether similar patterns hold for marine phytoplankton with high local richness. We use the continuous trait‐based modelling approach, which assumes infinite richness and represents diversity in terms of the variance of the size distribution, to investigate the effects of phytoplankton size diversity on productivity in a three‐dimensional ocean circulation model driven by realistic physics forcing. We find a slightly negative effect of size diversity on primary production, which we attribute to several factors including functional trait‐environment interactions, flexible stoichiometry and the saturation of productivity at low diversity levels. The benefits of trait optimisation, whereby narrow size distributions enhance productivity under relatively stable conditions, tend to dominate over those of adaptive capacity, whereby greater diversity enhances the ability of the community to respond to environmental variability.     

Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem.     

Life in a bubble: the role of the labyrinth organ in determining territory,mating and aggressive behaviours in anabantoids

As a result of long‐term climate change, regions of the ocean with low oxygen concentrations are predicted to occur more frequently and persist for longer periods of time in the future. When low levels of oxygen are present, this places additional pressure on marine organisms to meet their metabolic requirements, with implications for growth, feeding and reproduction. Extensive research has been carried out on the effects of acute hypoxia, but far less on long‐term chronic effects of low oxygen zones, especially with regard to commercially important fishes and shellfishes. To provide further understanding on how commercial species could be affected, the results of relevant experiments must support population and ecosystem models. This is not easy because individual effects are wide‐ranging; for example, studies to date have shown that low oxygen zones can affect predator–prey relationships as some species are able to tolerate low oxygen more than others. Some fishes may move away from areas until oxygen levels return to acceptable levels, while others take advantage of a reduced start response in prey fishes and remain in the area to feed. Sessile or less mobile species such as shellfishes are unable to move out of depleted oxygen zones. Some species can tolerate low oxygen levels for only short periods of time, while others are able to acclimatize. To advance the knowledge‐base further, a number of promising technological and modelling‐based developments and the role of physiological data within these, are proposed. These include advances in remote telemetry (tagging) and sensor technologies, trait‐based analyses to provide insight into how whole assemblages might respond in the future, research into long‐term adaptability of species, population and ecosystem modelling techniques and quantification of economic effects. In addition, more detailed oxygen monitoring and projections are required to better understand the likely temporal and local‐scale changes in oxygen.     

Effects of climate change and horticultural use on the spread of naturalized alien garden plants in Europe

Climate warming is supposed to enlarge the area climatically suitable to the naturalization of alien garden plants in temperate regions. However, the effects of a changing climate on the spread of naturalized ornamentals have not been evaluated by spatially and temporarily explicit range modelling at larger scales so far. Here, we assess how climate change and the frequency of cultivation interactively determine the spread of 15 ornamental plants over the 21st century in Europe. We coupled species distribution modelling with simulations of demography and dispersal to predict range dynamics of these species in annual steps across a 250 × 250 m raster of the study area. Models were run under four scenarios of climate warming and six levels of cultivation intensity. Cultivation frequency was implemented as size of the area used for planting a species. Although the area climatically suitable to the 15 species increases, on average, the area predicted to be occupied by them in 2090 shrinks under two of the three climate change scenarios. This contradiction obviously arises from dispersal limitations that were pronounced although we assumed that cultivation is spatially adapting to the changing climate. Cultivation frequency had a much stronger effect on species spread than climate change, and this effect was non‐linear. The area occupied increased sharply from low to moderate levels of cultivation intensity, but levelled off afterwards. Our simulations suggest that climate warming will not necessarily foster the spread of alien garden plants in Europe over the next decades. However, climatically suitable areas do increase and hence an invasion debt is likely accumulating. Restricting cultivation of species can be effective in preventing species spread, irrespective of how the climate develops. However, for being successful, they depend on high levels of compliance to keep propagule pressure at a low level.     

Incorporating anthropogenic effects into trophic ecology: predator–prey interactions in a human-dominated landscape

Apex predators perform important functions that regulate ecosystems worldwide. However, little is known about how ecosystem regulation by predators is influenced by human activities. In particular, how important are top-down effects of predators relative to direct and indirect human-mediated bottom-up and top-down processes? Combining data on species'' occurrence from camera traps and hunting records, we aimed to quantify the relative effects of top-down and bottom-up processes in shaping predator and prey distributions in a human-dominated landscape in Transylvania, Romania. By global standards this system is diverse, including apex predators (brown bear and wolf), mesopredators (red fox) and large herbivores (roe and red deer). Humans and free-ranging dogs represent additional predators in the system. Using structural equation modelling, we found that apex predators suppress lower trophic levels, especially herbivores. However, direct and indirect top-down effects of humans affected the ecosystem more strongly, influencing species at all trophic levels. Our study highlights the need to explicitly embed humans and their influences within trophic cascade theory. This will greatly expand our understanding of species interactions in human-modified landscapes, which compose the majority of the Earth''s terrestrial surface.     

Three perspectives on the prediction of chemical effects in ecosystems

The increasing production, use and emission of synthetic chemicals into the environment represents a major driver of global change. The large number of synthetic chemicals, limited knowledge on exposure patterns and effects in organisms and their interaction with other global change drivers hamper the prediction of effects in ecosystems. However, recent advances in biomolecular and computational methods are promising to improve our capacity for prediction. We delineate three idealised perspectives for the prediction of chemical effects: the suborganismal, organismal and ecological perspective, which are currently largely separated. Each of the outlined perspectives includes essential and complementary theories and tools for prediction but captures only part of the phenomenon of chemical effects. Links between the perspectives may foster predictive modelling of chemical effects in ecosystems and extrapolation between species. A major challenge for the linkage is the lack of data sets simultaneously covering different levels of biological organisation (here referred to as biological levels) as well as varying temporal and spatial scales. Synthesising the three perspectives, some central aspects and associated types of data seem particularly necessary to improve prediction. First, suborganism- and organism-level responses to chemicals need to be recorded and tested for relationships with chemical groups and organism traits. Second, metrics that are measurable at many biological levels, such as energy, need to be scrutinised for their potential to integrate across levels. Third, experimental data on the simultaneous response over multiple biological levels and spatiotemporal scales are required. These could be collected in nested and interconnected micro- and mesocosm experiments. Lastly, prioritisation of processes involved in the prediction framework needs to find a balance between simplification and capturing the essential complexity of a system. For example, in some cases, eco-evolutionary dynamics and interactions may need stronger consideration. Prediction needs to move from a static to a real-world eco-evolutionary view.     

Self-expanding stent modelling and radial force accuracy

Computational simulations using finite element analysis are a tool commonly used to analyse stent designs, deployment geometries and interactions between stent struts and arterial tissue. Such studies require large computational models and efforts are often made to simplify models in order to reduce computational time while maintaining reasonable accuracy. The objective of the study is focused on computational modelling and specifically aims to investigate how different methods of modelling stent–artery interactions can affect the results, computational time taken and computational size of the model. Various different models, each with increasing levels of complexity, are used to simulate this analysis, representing the many assumptions and simplifications used in other similar studies in order to determine what level of simplification will still allow for an accurate representation of stent radial force and resulting stress concentrations on the inner lining of the vessel during self-expanding stent deployment. The main conclusions of the study are that methods used in stent crimping impact on the resulting predicted radial force of the stent; that accurate representation of stent–artery interactions can only be made when modelling the full length of the stent due to the incorporation of end effects; and that modelling self-contact of the stent struts greatly impacts on the resulting stress concentrations within the stent, but that the effect of this on the unloading behaviour and resulting radial force of the stent is negligible.     

Versatile habitat conditioning by damselfish cultivating turf algae on giant clams

In this paper, a monitoring and modelling concept for ecological optimized harbour dredging and fine sediment disposal in large rivers is presented. According to the concept, first a preliminary assessment should be performed previous to the dredging and dumping procedure to derive knowledge about the current status in hydrodynamics, morphology and instream habitat quality. During the performance of the maintenance work, a high-resolution monitoring program has to be organized to measure flow velocities, the suspended sediment concentrations and the extent of the occurring plume. These data can then be compared with natural suspended sediment conditions and serve as input data for numerical sediment transport modelling. Furthermore, bathymetric surveys and biotic sampling enable the detection of possible effects of dredging and disposal in the post-dumping stage. Based on sediment transport modelling approaches, short- to mid-term developments of the sediment plume can be predicted with an additional and final habitat evaluation at the end of the project. This concept was applied and optimized during the maintenance work at the case study winter harbour Linz at the Danube River. The findings of the presented study highlight the necessity of integrated monitoring and modelling approaches for harbour dredging especially in large river systems.     

The state of plant population modelling in light of environmental change

Plant population modelling has been around since the 1970s, providing a valuable approach to understanding plant ecology from a mechanistic standpoint. It is surprising then that this area of research has not grown in prominence with respect to other approaches employed in modelling plant systems. In this review, we provide an analysis of the development and role of modelling in the field of plant population biology through an exploration of where it has been, where it is now and, in our opinion, where it should be headed. We focus, in particular, on the role plant population modelling could play in ecological forecasting, an urgent need given current rates of regional and global environmental change. We suggest that a critical element limiting the current application of plant population modelling in environmental research is the trade-off between the necessary resolution and detail required to accurately characterize ecological dynamics pitted against the goal of generality, particularly at broad spatial scales. In addition to suggestions how to overcome the current shortcoming of data on the process-level we discuss two emerging strategies that may offer a way to overcome the described limitation: (1) application of a modern approach to spatial scaling from local processes to broader levels of interaction and (2) plant functional-type modelling. Finally we outline what we believe to be needed in developing these approaches towards a ‘science of forecasting’.     

Ratio-dependent response of a temperate Australian estuarine system to sustained nitrogen loading

Classical resource- and the less studied ratio-dependent models of predator–prey relationships provide divergent predictions as to the sustained ecological effects of bottom-up forcing. While resource-dependent models, which consider only instantaneous prey density in modelling predator responses, predict community responses that are dependent on the number of trophic levels in a system, ratio-dependent models, which consider the number of prey per consumer, predict proportional increase in each level irrespective of chain length. The two models are only subtly different for systems with two or three trophic levels but in the case of four trophic levels, predict opposite effects of enrichment on primary producers. Despite the poor discriminatory power of tests of the models in systems with two or three trophic levels, field tests in estuarine and marine systems with four trophic levels have been notably absent. Sampling of phytoplankton, macroinvertebrates, invertebrate-feeding fishes, piscivorous fishes in Kooloonbung Creek, Hastings River estuary, eastern Australia, subject to over 20 years of sewage discharge, revealed increased abundances in all four trophic levels at the disturbed location relative to control sites. Increased abundance of phytoplankton at the disturbed site was counter to the predictions of resource-dependent models, which posit a reduction in the first trophic level in response to enrichment. By contrast, the increase in abundance of this first trophic level and the proportionality of increases in abundances of each of the four trophic groups to nitrogen loading provided strong support for ratio dependency. This first evidence of ratio dependence in an estuarine system with four trophic levels not only demonstrates the applicability of ecological theory which seeks to simplify the complexity of systems, but has implications for management. Although large nutrient inputs frequently induce mortality of invertebrates and fish, we have shown that smaller inputs may in fact enhance biomass of all trophic levels.     

Ecosystem engineering as an energy transfer process: a simple agent-based model

Ecosystem engineers are defined as organisms who modulate the availability of resources for themselves and other organisms by physically changing the environment. Ecosystem engineering is a well-recognised ecological interaction, but there is a limited number of general models due to the recent development of the field. Agent-based models are often used to study how organisms respond to changing environments and are suitable for modelling ecosystem engineering. To our knowledge, agent-based methodology has not yet been used to model ecosystem engineering. In this paper, we develop a simple agent-based population dynamics model of ecosystem engineering as an energy transfer process. We apply energy budget approach to conceptually explain how ecosystem engineers transfer energy to the environment and define various types of energy transfers relative to their effects on the engineers and other organisms. We simulate environments with various levels of resource abundance and compare the results of the model without ecosystem engineering agents to the model with ecosystem engineering agents. We find that in environments with higher levels of resources, the presence of ecosystem engineers increases the average carrying capacity and the strength of population fluctuations, while in environments with lower levels of resources, ecosystem engineering mitigates fluctuations, increases average carrying capacity and makes environments more resilient. Finally, we discuss about the further application of agent-based modelling for the theoretical and experimental development of the ecosystem engineering concept.