Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Introduction

The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.

Methods

Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.

Results

Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19.

Discussion

The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

A Time for Every Purpose: Using Time-Dependent Sensitivity Analysis to Help Understand and Manage Dynamic Ecological Systems

AbstractSensitivity analysis is often used to help understand and manage ecological systems by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time-for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act on. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life history events, and endogenously driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.

Multi-Input Multi-Output Dynamic Modelling of Type 2 Diabetes Progression

Type 2 Diabetes Mellitus (T2D) is a chronic health condition that affects millions of people globally. Early identification of risk can support preventive intervention and therefore slow down disease progression. Risk characterization is also necessary to monitor the mechanisms behind the pathology through the analysis of the interrelationships between the predictors and their time course. In this work, a multi-input multi-output Gaussian Process model is proposed to describe the evolution of different biomarkers in patients who will/will not develop T2D considering the interdependencies between outputs. The preliminary results obtained suggest that the trends in biomarkers captured by the model are coherent with the literature and with real-world data, demonstrating the value of multi-input multi-output approaches. In future developments, the proposed method could be applied to assess how the biomarkers evolve and interact with each other in groups of patients having in common one or more risk factors.

Leveraging eco-evolutionary models for gene drive risk assessment

Engineered gene drives create potential for both widespread benefits and irreversible harms to ecosystems. CRISPR-based systems of allelic conversion have rapidly accelerated gene drive research across diverse taxa, putting field trials and their necessary risk assessments on the horizon. Dynamic process-based models provide flexible quantitative platforms to predict gene drive outcomes in the context of system-specific ecological and evolutionary features. Here, we synthesize gene drive dynamic modeling studies to highlight research trends, knowledge gaps, and emergent principles, organized around their genetic, demographic, spatial, environmental, and implementation features. We identify the phenomena that most significantly influence model predictions, discuss limitations of biological complexity and uncertainty, and provide insights to promote responsible development and model-assisted risk assessment of gene drives.

A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems

Sensitivity analysis is often used to help understand and manage ecological systems, by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time-for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act upon. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life-history events, and endogenously-driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.

Dynamics of Microbial Inactivation and Acrylamide Production in High-Temperature Heat Treatments

In food processes, optimizing processing parameters is crucial to ensure food safety, maximize food quality, and minimize the formation of potentially toxigenic compounds. This research focuses on the simultaneous impacts that severe heat treatments applied to food may have on the formation of harmful chemicals and on microbiological safety. The case studies analysed consider the appearance/synthesis of acrylamide after a sterilization heat treatment for two different foods: pureed potato and prune juice, using Geobacillus stearothermophilus as an indicator. It presents two contradictory situations: on the one hand, the application of a high-temperature treatment to a low acid food with G. stearothermophilus spores causes their inactivation, reaching food safety and stability from a microbiological point of view. On the other hand, high temperatures favour the appearance of acrylamide. In this way, the two objectives (microbiological safety and acrylamide production) are opposed. In this work, we analyse the effects of high-temperature thermal treatments (isothermal conditions between 120 and 135 °C) in food from two perspectives: microbiological safety/stability and acrylamide production. After analysing both objectives simultaneously, it is concluded that, contrary to what is expected, heat treatments at higher temperatures result in lower acrylamide production for the same level of microbial inactivation. This is due to the different dynamics and sensitivities of the processes at high temperatures. These results, as well as the presented methodology, can be a basis of analysis for decision makers to design heat treatments that ensure food safety while minimizing the amount of acrylamide (or other harmful substances) produced.

A Neuron-Glial Model of Exosomal Release in the Onset and Progression of Alzheimer's Disease

Exosomes are nano-sized extracellular vesicles that perform a variety of biological functions linked to the pathogenesis of various neurodegenerative disorders. In Alzheimer's disease (AD), for examples, exosomes are responsible for the release of Aβ oligomers, and their extracellular accumulation, although the underpinning molecular machinery remains elusive. We propose a novel model for Alzheimer's Aβ accumulation based on Ca²⁺-dependent exosome release from astrocytes. Moreover, we exploit our model to assess how temperature dependence of exosome release could interact with Aβ neurotoxicity. We predict that voltage-gated Ca²⁺ channels (VGCCs) along with the transient-receptor potential M8 (TRPM8) channel are crucial molecular components in Alzheimer's progression.

Dynamical Properties and Conceptual Interpretation of Latent Change Score Models

Latent Change Score models (LCS) are a popular tool for the study of dynamics in longitudinal research. They represent processes in which the short-term dynamics have direct and indirect consequences on the long-term behavior of the system. However, this dual interpretation of the model parameters is usually overlooked in the literature, and researchers often find it difficult to see the connection between parameters and specific patterns of change. The goal of this paper is to provide a comprehensive examination of the meaning and interpretation of the parameters in LCS models. Importantly, we focus on their relation to the shape of the trajectories and explain how different specifications of the LCS model involve particular assumptions about the mechanisms of change. On a supplementary website, we present an interactive Shiny App that allows users to explore different sets of parameter values and examine their effects on the predicted trajectories. We also include fully explained code to estimate some of the most relevant specifications of the LCS model with the R-packages lavaan and OpenMx.

A Recurrent Neural-Network-Based Real-Time Dynamic Model for Soft Continuum Manipulators

This paper introduces and validates a real-time dynamic predictive model based on a neural network approach for soft continuum manipulators. The presented model provides a real-time prediction framework using neural-network-based strategies and continuum mechanics principles. A time-space integration scheme is employed to discretize the continuous dynamics and decouple the dynamic equations for translation and rotation for each node of a soft continuum manipulator. Then the resulting architecture is used to develop distributed prediction algorithms using recurrent neural networks. The proposed RNN-based parallel predictive scheme does not rely on computationally intensive algorithms; therefore, it is useful in real-time applications. Furthermore, simulations are shown to illustrate the approach performance on soft continuum elastica, and the approach is also validated through an experiment on a magnetically-actuated soft continuum manipulator. The results demonstrate that the presented model can outperform classical modeling approaches such as the Cosserat rod model while also shows possibilities for being used in practice.

Digital Cardiovascular Biomarker Responses to Transcutaneous Cervical Vagus Nerve Stimulation: State-Space Modeling, Prediction, and Simulation

Background

Transcutaneous cervical vagus nerve stimulation (tcVNS) is a promising alternative to implantable stimulation of the vagus nerve. With demonstrated potential in myriad applications, ranging from systemic inflammation reduction to traumatic stress attenuation, closed-loop tcVNS during periods of risk could improve treatment efficacy and reduce ineffective delivery. However, achieving this requires a deeper understanding of biomarker changes over time.

Objective

The aim of the present study was to reveal the dynamics of relevant cardiovascular biomarkers, extracted from wearable sensing modalities, in response to tcVNS.

Methods

Twenty-four human subjects were recruited for a randomized double-blind clinical trial, for whom electrocardiography and photoplethysmography were used to measure heart rate and photoplethysmogram amplitude responses to tcVNS, respectively. Modeling these responses in state-space, we (1) compared the biomarkers in terms of their predictability and active vs sham differentiation, (2) studied the latency between stimulation onset and measurable effects, and (3) visualized the true and model-simulated biomarker responses to tcVNS.

Results

The models accurately predicted future heart rate and photoplethysmogram amplitude values with root mean square errors of approximately one-fifth the standard deviations of the data. Moreover, (1) the photoplethysmogram amplitude showed superior predictability (P=.03) and active vs sham separation compared to heart rate; (2) a consistent delay of greater than 5 seconds was found between tcVNS onset and cardiovascular effects; and (3) dynamic characteristics differentiated responses to tcVNS from the sham stimulation.

Conclusions

This work furthers the state of the art by modeling pertinent biomarker responses to tcVNS. Through subsequent analysis, we discovered three key findings with implications related to (1) wearable sensing devices for bioelectronic medicine, (2) the dominant mechanism of action for tcVNS-induced effects on cardiovascular physiology, and (3) the existence of dynamic biomarker signatures that can be leveraged when titrating therapy in closed loop.

Trial Registration

ClinicalTrials.gov NCT02992899; https://clinicaltrials.gov/ct2/show/NCT02992899

International Registered Report Identifier (IRRID)

RR2-10.1016/j.brs.2019.08.002

Dynamic Models Supporting Personalised Chronic Disease Management through Healthcare Sensors with Interactive Process Mining

Rich streams of continuous data are available through Smart Sensors representing a unique opportunity to develop and analyse risk models in healthcare and extract knowledge from data. There is a niche for developing new algorithms, and visualisation and decision support tools to assist health professionals in chronic disease management incorporating data generated through smart sensors in a more precise and personalised manner. However, current understanding of risk models relies on static snapshots of health variables or measures, rather than ongoing and dynamic feedback loops of behaviour, considering changes and different states of patients and diseases. The rationale of this work is to introduce a new method for discovering dynamic risk models for chronic diseases, based on patients' dynamic behaviour provided by health sensors, using Process Mining techniques. Results show the viability of this method, three dynamic models have been discovered for the chronic diseases hypertension, obesity, and diabetes, based on the dynamic behaviour of metabolic risk factors associated. This information would support health professionals to translate a one-fits-all current approach to treatments and care, to a personalised medicine strategy, that fits treatments built on patients' unique behaviour thanks to dynamic risk modelling taking advantage of the amount data generated by smart sensors.

No2 Sensing with SWCNT Decorated by Nanoparticles in Temperature Pulsed Mode: Modeling and Characterization

In this paper, NO₂ sensing by means of single-wall carbon nanotubes (SWCNT) networks, decorated with nanoparticles of TiO₂ and Au, is proposed. In particular, it is shown that the performance of these materials can be enhanced using pulsed temperature mode. This sensing strategy effectiveness is theoretically and experimentally assessed. In this paper, in fact, a dynamic model for conductive gas sensors formed by networks of nanowires, considering the junctions between different wires as the main contribution to sensor conductance, and in the presence of the target gas, is presented and validated. The model accounts for variable temperature and gas concentration and sheds some light on the mechanisms leading to the sensor response improvement related to temperature pulsed working mode. It is also shown how the addition of a different material can be modeled through different surface adsorption kinetics.

Why Do We Need Computational Models of Psychological Change and Recovery, and How Should They Be Designed and Tested?

Traditional research methodologies typically assume that humans operate on the basis of an "open loop" stimulus-process-response rather than the "closed loop" control of internal state. They also average behavioral data across repeated measures rather than assess it continuously, and they draw inferences about the working of an individual from statistical group effects. As such, we propose that they are limited in their capacity to accurately identify and test for the mechanisms of change within psychological therapies. As a solution, we explain the advantages of using a closed loop functional architecture, based on an extended homeostatic model of the brain, to construct working computational models of individual clients that can be tested against real-world data. Specifically, we describe tests of a perceptual control theory (PCT) account of psychological change that combines the components of negative feedback control, hierarchies, conflict, reorganization, and awareness into a working model of psychological function, and dysfunction. In brief, psychopathology is proposed to be the loss of control experienced due to chronic, unresolved conflict between important personal goals. The mechanism of change across disorders and different psychological therapies is proposed to be the capacity for the therapist to help the client shift and sustain their awareness on the higher level goals that are driving goal conflict, for sufficiently long enough to permit a trial-and-error learning process, known as reorganization, to "stumble" upon a solution that regains control. We report on data from studies that have modeled these components both separately and in combination, and we describe the parallels with human data, such as the pattern of early gains and sudden gains within psychological therapy. We conclude with a description of our current research program that involves the following stages: (1) construct a model of the conflicting goals that are held by people with specific phobias; (2) optimize a model for each individual using their dynamic movement data from a virtual reality exposure task (VRET); (3) construct and optimize a learning parameter (reorganization) within each model using a subsequent VRET; (3) validate the model of each individual against a third VRET. The application of this methodology to robotics, attachment dynamics in childhood, and neuroimaging is discussed.

A joint modeling framework of responses and response times to assess learning outcomes

A general modeling framework of response accuracy and response times is proposed to track skill acquisition and provide additional diagnostic information on the change of latent speed in a learning environment. This framework consists of two types of models: a dynamic response model that captures the response accuracy and the change of discrete latent attribute profile upon factors such as practice, intervention effects, and other latent and observable covariates, and a dynamic response time model that describes the change of the continuous response latency due to change of latent attribute profile. These two types of models are connected through a parameter, describing the change rate of the latent speed through the learning process, and a covariate defined as a function of the latent attribute profile. A Bayesian estimation procedure is developed to calibrate the model parameters and measure the latent variables. The estimation algorithm is evaluated through several simulation studies under various conditions. The proposed models are applied to a real data set collected through a spatial rotation diagnostic assessment paired with learning tools.

Optimizing future biodiversity sampling by citizen scientists

We are currently in the midst of Earth's sixth extinction event, and measuring biodiversity trends in space and time is essential for prioritizing limited resources for conservation. At the same time, the scope of the necessary biodiversity monitoring is overwhelming funding for professional scientific monitoring. In response, scientists are increasingly using citizen science data to monitor biodiversity. But citizen science data are ‘noisy’, with redundancies and gaps arising from unstructured human behaviours in space and time. We ask whether the information content of these data can be maximized for the express purpose of trend estimation. We develop and execute a novel framework which assigns every citizen science sampling event a marginal value, derived from the importance of an observation to our understanding of overall population trends. We then make this framework predictive, estimating the expected marginal value of future biodiversity observations. We find that past observations are useful in forecasting where high-value observations will occur in the future. Interestingly, we find high value in both ‘hotspots’, which are frequently sampled locations, and ‘coldspots’, which are areas far from recent sampling, suggesting that an optimal sampling regime balances ‘hotspot’ sampling with a spread across the landscape.

Quantifying Interpersonal Dynamics for Studying Socio-Emotional Processes and Adverse Health Behaviors

OBJECTIVE

We introduce a new statistical software R package, rties, that simplifies the use of dynamic models for investigating interpersonal emotional processes. We demonstrate the package by using it to test whether emotional dynamics in romantic couples can predict, or are predicted by, shared unhealthy behaviors (SUBs).

METHODS

We use data from 74 romantic couples discussing their health behaviors. The conversations were videotaped and rated for evidence that the couples engaged in unhealthy behaviors that benefitted the relationship in some way (e.g., increasing closeness). Participants also provided video-prompted continuous recall of their emotional experience during the conversation. We use the rties package to estimate the parameters for inertia-coordination and coupled-oscillator models of the couples' emotional experience. Those parameter estimates are then used as predictors and outcomes of the couple's SUB.

RESULTS

The coupled-oscillator model accounted for 17% of the variance in unhealthy behavior, with both partner's amplification predicting higher unhealthy behavior (women: B = 0.95, SE = 0.31, t(63) = 3.06, p = .003, 95% confidence interval = 0.25-1.45; men: B = 0.9, SE = 0.29, t(63) = 3.09, p = .003, 95% confidence interval = 0.32-1.47). These results suggest that co-dysregulation, an unstable interpersonal pattern of amplified emotional oscillations is associated with more SUBs. In contrast, the dynamics assessed with inertia coordination were not associated with behavior.

CONCLUSIONS

The new rties package provides a set of relatively easy-to-use statistical models for representing and testing theories about interpersonal emotional dynamics. Our results suggest that emotional co-dysregulation may be a particularly detrimental pattern for health.

Modeling of Negative Capacitance in Ferroelectric Thin Films

The negative capacitance (NC) effect in ferroelectric thin films has attracted a great deal of attention from the material and semiconductor device communities because it could be a possible solution to the impending problems related to field-effect transistor power consumption and dynamic random-access memory charge loss. A short discussion on the fundamental premise of the NC effect is presented. A phase-field model based on the time-dependent Ginzburg-Landau (TDGL) formalism in conjunction with the Chensky-Tarasenko (C-T) formalism for multidomain configuration is then developed to reveal the subtle correlation between the domain wall motion and NC effect for different thicknesses of ferroelectric and dielectric films. When a ferroelectric film becomes thin enough, a stripe domain structure can be achieved through competition between the electrostatic energy and domain wall energy. This stripe domain structure is quite resilient to transition to a homogeneous polarization state, making it very useful for (quasi-)static NC operation. Finally, the physical implications of the numerical results are explored with analytical modeling. It is identified that the domain wall motion in the stripe domain structure remains dominated by the external field, even when the entire film is in the (quasi-)static NC state.

Review and perspective on mathematical modeling of microbial ecosystems

Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?'

QUESTION

An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.

The wear and tear on health: What is the role of occupation?

Health is well known to show a clear gradient by occupation. Although it may appear evident that occupation can affect health, there are multiple possible sources of selection that can generate a strong association, other than simply a causal effect of occupation on health. We link job characteristics to German panel data spanning 29 years to characterize occupations by their physical and psychosocial burden. Employing a dynamic model to control for factors that simultaneously affect health and selection into occupation, we find that selection into occupation accounts for at least 60% of the association. The effects of occupational characteristics such as physical strain and low job control are negative and increase with age: late-career exposure to 1 year of high physical strain and low job control is comparable to the average health decline from ageing 16 and 6 months, respectively.

Structure Determination Techniques Flex Their Muscles

A historical challenge: Gas-phase electron diffraction and single-crystal X-ray diffraction are both established techniques, but they were both pushed to their limits by the challenge posed by the highly flexible tetranitromethane molecule. New approaches had to be developed for the structure of the molecule to be elucidated.

The Contribution of Mathematical Modeling to Understanding Dynamic Aspects of Rumen Metabolism

All mechanistic rumen models cover the main drivers of variation in rumen function, which are feed intake, the differences between feedstuffs and feeds in their intrinsic rumen degradation characteristics, and fractional outflow rate of fluid and particulate matter. Dynamic modeling approaches are best suited to the prediction of more nuanced responses in rumen metabolism, and represent the dynamics of the interactions between substrates and micro-organisms and inter-microbial interactions. The concepts of dynamics are discussed for the case of rumen starch digestion as influenced by starch intake rate and frequency of feed intake, and for the case of fermentation of fiber in the large intestine. Adding representations of new functional classes of micro-organisms (i.e., with new characteristics from the perspective of whole rumen function) in rumen models only delivers new insights if complemented by the dynamics of their interactions with other functional classes. Rumen fermentation conditions have to be represented due to their profound impact on the dynamics of substrate degradation and microbial metabolism. Although the importance of rumen pH is generally acknowledged, more emphasis is needed on predicting its variation as well as variation in the processes that underlie rumen fluid dynamics. The rumen wall has an important role in adapting to rapid changes in the rumen environment, clearing of volatile fatty acids (VFA), and maintaining rumen pH within limits. Dynamics of rumen wall epithelia and their role in VFA absorption needs to be better represented in models that aim to predict rumen responses across nutritional or physiological states. For a detailed prediction of rumen N balance there is merit in a dynamic modeling approach compared to the static approaches adopted in current protein evaluation systems. Improvement is needed on previous attempts to predict rumen VFA profiles, and this should be pursued by introducing factors that relate more to microbial metabolism. For rumen model construction, data on rumen microbiomes are preferably coupled with knowledge consolidated in rumen models instead of relying on correlations with rather general aspects of treatment or animal. This helps to prevent the disregard of basic principles and underlying mechanisms of whole rumen function.

Are There Long-Run Effects of the Minimum Wage?

An empirical consensus suggests that there are small employment effects of minimum wage increases. This paper argues that these are short-run elasticities. Long-run elasticities, which may differ from short-run elasticities, are policy relevant. This paper develops a dynamic industry equilibrium model of labor demand. The model makes two points. First, long-run regressions have been misinterpreted because even if the short- and long-run employment elasticities differ, standard methods would not detect a difference using US variation. Second, the model offers a reconciliation of the small estimated short-run employment effects with the commonly found pass-through of minimum wage increases to product prices.

Angular motion estimation using dynamic models in a gyro-free inertial measurement unit

In this paper, we summarize the results of using dynamic models borrowed from tracking theory in describing the time evolution of the state vector to have an estimate of the angular motion in a gyro-free inertial measurement unit (GF-IMU). The GF-IMU is a special type inertial measurement unit (IMU) that uses only a set of accelerometers in inferring the angular motion. Using distributed accelerometers, we get an angular information vector (AIV) composed of angular acceleration and quadratic angular velocity terms. We use a Kalman filter approach to estimate the angular velocity vector since it is not expressed explicitly within the AIV. The bias parameters inherent in the accelerometers measurements' produce a biased AIV and hence the AIV bias parameters are estimated within an augmented state vector. Using dynamic models, the appended bias parameters of the AIV become observable and hence we can have unbiased angular motion estimate. Moreover, a good model is required to extract the maximum amount of information from the observation. Observability analysis is done to determine the conditions for having an observable state space model. For higher grades of accelerometers and under relatively higher sampling frequency, the error of accelerometer measurements is dominated by the noise error. Consequently, simulations are conducted on two models, one has bias parameters appended in the state space model and the other is a reduced model without bias parameters.

Bioinformatics tools in predictive ecology: applications to fisheries

There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their 'crossover potential' with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse.

Fitting dynamic models with forcing functions: application to continuous glucose monitoring in insulin therapy

The artificial pancreas is an emerging technology to treat type 1 diabetes (T1D). It has the potential to revolutionize diabetes care and improve quality of life. The system requires extensive testing, however, to ensure that it is both effective and safe. Clinical studies are resource demanding and so a principle aim is to develop an in silico population of subjects with T1D on which to conduct pre-clinical testing. This paper aims to reliably characterize the relationship between blood glucose and glucose measured by subcutaneous sensor as a major step towards this goal. Blood-and sensor-glucose are related through a dynamic model, specified in terms of differential equations. Such models can present special challenges for statistical inference, however. In this paper we make use of the BUGS software, which can accommodate a limited class of dynamic models, and it is in this context that we discuss such challenges. For example, we show how dynamic models involving forcing functions can be accommodated. To account for fluctuations away from the dynamic model that are apparent in the observed data, we assume an autoregressive structure for the residual error model. This leads to some identifiability issues but gives very good predictions of virtual data. Our approach is pragmatic and we propose a method to mitigate the consequences of such identifiability issues.