Dynamic causal modelling of immune heterogeneity

An interesting inference drawn by some COVID-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection-even at the start of the current pandemic. This paper introduces a model of the immune response to a virus. This is based upon the same sort of mean-field dynamics as used in epidemiology. However, in place of the location, clinical status, and other attributes of people in an epidemiological model, we consider the state of a virus, B and T-lymphocytes, and the antibodies they generate. Our aim is to formalise some key hypotheses as to the mechanism of resistance. We present a series of simple simulations illustrating changes to the dynamics of the immune response under these hypotheses. These include attenuated viral cell entry, pre-existing cross-reactive humoral (antibody-mediated) immunity, and enhanced T-cell dependent immunity. Finally, we illustrate the potential application of this sort of model by illustrating variational inversion (using simulated data) of this model to illustrate its use in testing hypotheses. In principle, this furnishes a fast and efficient immunological assay-based on sequential serology-that provides a (1) quantitative measure of latent immunological responses and (2) a Bayes optimal classification of the different kinds of immunological response (c.f., glucose tolerance tests used to test for insulin resistance). This may be especially useful in assessing SARS-CoV-2 vaccines

Upper- and lower-limb amputees show reduced levels of eeriness for images of prosthetic hands

The uncanny phenomenon describes the feeling of unease associated with seeing an image which is close to appearing human. Prosthetic hands in particular are well-known to induce this effect. Little is known, however, about this phenomenon from the viewpoint of prosthesis users. We studied perceptions of eeriness and human-likeness for images of different types of mechanical, cosmetic, and anatomical hands in upper-limb prosthesis users (n=9), lower-limb prosthesis users (n=10), prosthetists (n=16), control participants with no prosthetic training (n=20), and control participants who were trained to use a myoelectric prosthetic hand simulator (n=23). Both the upper- and lowerlimb prosthesis user groups showed a reduced uncanny phenomenon (i.e., significantly lower levels of eeriness) for cosmetic prosthetic hands compared to the other groups, with no concomitant reduction in how these stimuli were rated in terms of human-likeness. However, a similar effect was found neither for prosthetists with prolonged visual experience of prosthetic hands, nor for the group with short-term training with the simulator. These findings in the prosthesis users therefore seem likely to be related to limb absence or prolonged experience with prostheses

Dynamic causal modelling of COVID-19 [version 1; peer review: 1 approved, 1 not approved]

This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of this model is to quantify the uncertainty that attends predictions of relevant outcomes. By assuming suitable conditional dependencies, one can model the effects of interventions (e.g., social distancing) and differences among populations (e.g., herd immunity) to predict what might happen in different circumstances. Technically, this model leverages state-of-the-art variational (Bayesian) model inversion and comparison procedures, originally developed to characterise the responses of neuronal ensembles to perturbations. Here, this modelling is applied to epidemiological populations to illustrate the kind of inferences that are supported and how the model per se can be optimised given timeseries data. Although the purpose of this paper is to describe a modelling protocol, the results illustrate some interesting perspectives on the current pandemic; for example, the nonlinear effects of herd immunity that speak to a self-organised mitigation process

Testing and tracking in the UK: A dynamic causal modelling study [version 1; peer review: 1 approved with reservations, 1 not approved]

By equipping a previously reported dynamic causal modelling of COVID-19 with an isolation state, we were able to model the effects of self-isolation consequent on testing and tracking. Specifically, we included a quarantine or isolation state occupied by people who believe they might be infected but are asymptomatic—and could only leave if they test negative. We recovered maximum posteriori estimates of the model parameters using time series of new cases, daily deaths, and tests for the UK. These parameters were used to simulate the trajectory of the outbreak in the UK over an 18-month period. Several clear-cut conclusions emerged from these simulations. For example, under plausible (graded) relaxations of social distancing, a rebound of infections is highly unlikely. The emergence of a second wave depends almost exclusively on the rate at which we lose immunity, inherited from the first wave. There exists no testing strategy that can attenuate mortality rates, other than by deferring or delaying a second wave. A testing and tracking policy—implemented at the present time—will defer any second wave beyond a time horizon of 18 months. Crucially, this deferment is within current testing capabilities (requiring an efficacy of tracing and tracking of about 20% of asymptomatic infected cases, with 50,000 tests per day). These conclusions are based upon a dynamic causal model for which we provide some construct and face validation—using a comparative analysis of the United Kingdom and Germany, supplemented with recent serological studies

Second waves, social distancing, and the spread of COVID-19 across the USA [version 2; peer review: 2 approved with reservations]

We recently described a dynamic causal model of a COVID-19 outbreak within a single region. Here, we combine several instantiations of this (epidemic) model to create a (pandemic) model of viral spread among regions. Our focus is on a second wave of new cases that may result from loss of immunity—and the exchange of people between regions—and how mortality rates can be ameliorated under different strategic responses. In particular, we consider hard or soft social distancing strategies predicated on national (Federal) or regional (State) estimates of the prevalence of infection in the population. The modelling is demonstrated using timeseries of new cases and deaths from the United States to estimate the parameters of a factorial (compartmental) epidemiological model of each State and, crucially, coupling between States. Using Bayesian model reduction, we identify the effective connectivity between States that best explains the initial phases of the outbreak in the United States. Using the ensuing posterior parameter estimates, we then evaluate the likely outcomes of different policies in terms of mortality, working days lost due to lockdown and demands upon critical care. The provisional results of this modelling suggest that social distancing and loss of immunity are the two key factors that underwrite a return to endemic equilibrium

Second waves, social distancing, and the spread of COVID-19 across the USA [version 3; peer review: 1 approved, 1 approved with reservations]

We recently described a dynamic causal model of a COVID-19 outbreak within a single region. Here, we combine several instantiations of this (epidemic) model to create a (pandemic) model of viral spread among regions. Our focus is on a second wave of new cases that may result from loss of immunity—and the exchange of people between regions—and how mortality rates can be ameliorated under different strategic responses. In particular, we consider hard or soft social distancing strategies predicated on national (Federal) or regional (State) estimates of the prevalence of infection in the population. The modelling is demonstrated using timeseries of new cases and deaths from the United States to estimate the parameters of a factorial (compartmental) epidemiological model of each State and, crucially, coupling between States. Using Bayesian model reduction, we identify the effective connectivity between States that best explains the initial phases of the outbreak in the United States. Using the ensuing posterior parameter estimates, we then evaluate the likely outcomes of different policies in terms of mortality, working days lost due to lockdown and demands upon critical care. The provisional results of this modelling suggest that social distancing and loss of immunity are the two key factors that underwrite a return to endemic equilibrium

Testing and tracking in the UK: A dynamic causal modelling study [version 2; peer review: 1 approved with reservations, 1 not approved]

By equipping a previously reported dynamic causal modelling of COVID-19 with an isolation state, we were able to model the effects of self-isolation consequent on testing and tracking. Specifically, we included a quarantine or isolation state occupied by people who believe they might be infected but are asymptomatic—and could only leave if they test negative. We recovered maximum posteriori estimates of the model parameters using time series of new cases, daily deaths, and tests for the UK. These parameters were used to simulate the trajectory of the outbreak in the UK over an 18-month period. Several clear-cut conclusions emerged from these simulations. For example, under plausible (graded) relaxations of social distancing, a rebound of infections is highly unlikely. The emergence of a second wave depends almost exclusively on the rate at which we lose immunity, inherited from the first wave. There exists no testing strategy that can attenuate mortality rates, other than by deferring or delaying a second wave. A testing and tracking policy—implemented at the present time—will defer any second wave beyond a time horizon of 18 months. Crucially, this deferment is within current testing capabilities (requiring an efficacy of tracing and tracking of about 20% of asymptomatic infected cases, with 50,000 tests per day). These conclusions are based upon a dynamic causal model for which we provide some construct and face validation—using a comparative analysis of the United Kingdom and Germany, supplemented with recent serological studies

A tool for measuring mental workload during prosthesis use: The Prosthesis Task Load Index (PROS-TLX)

When using a upper-limb prosthesis, mental, emotional, and physical effort is often experienced. These have been linked to high rates of device dissatisfaction and rejection. Therefore, understanding and quantifying the complex nature of workload experienced when using, or learning to use, a upper-limb prosthesis has practical and clinical importance for researchers and applied professionals. The aim of this paper was to design and validate a self-report measure of mental workload specific to prosthesis use (The Prosthesis Task Load Index; PROS-TLX) that encapsulates the array of mental, physical, and emotional demands often experienced by users of these devices. We first surveyed upper-limb prosthetic limb users who confirmed the importance of eight workload constructs taken from published literature and previous workload measures. These constructs were mental demands, physical demands, visual demands, conscious processing, frustration, situational stress, time pressure and device uncertainty. To validate the importance of these constructs during initial prosthesis learning, we then asked able-bodied participants to complete a coin-placement task using their anatomical hand and then using a myoelectric prosthesis simulator under low and high mental workload. As expected, using a prosthetic hand resulted in slower movements, more errors, and a greater tendency to visually fixate the hand (indexed using eye-tracking equipment). These changes in performance were accompanied by significant increases in PROS-TLX workload subscales. The scale was also found to have good convergent and divergent validity. Further work is required to validate whether the PROS-TLX can provide meaningful clinical insights to the workload experienced by clinical users of prosthetic devices

Effective immunity and second waves: a dynamic causal modelling study [version 1; peer review: 1 approved, 1 not approved]

This technical report addresses a pressing issue in the trajectory of the coronavirus outbreak; namely, the rate at which effective immunity is lost following the first wave of the pandemic. This is a crucial epidemiological parameter that speaks to both the consequences of relaxing lockdown and the propensity for a second wave of infections. Using a dynamic causal model of reported cases and deaths from multiple countries, we evaluated the evidence models of progressively longer periods of immunity. The results speak to an effective population immunity of about three months that, under the model, defers any second wave for approximately six months in most countries. This may have implications for the window of opportunity for tracking and tracing, as well as for developing vaccination programmes, and other therapeutic interventions

Individual Recognition in Domestic Cattle (Bos taurus): Evidence from 2D-Images of Heads from Different Breeds

BACKGROUND: In order to maintain cohesion of groups, social animals need to process social information efficiently. Visual individual recognition, which is distinguished from mere visual discrimination, has been studied in only few mammalian species. In addition, most previous studies used either a small number of subjects or a few various views as test stimuli. Dairy cattle, as a domestic species allow the testing of a good sample size and provide a large variety of test stimuli due to the morphological diversity of breeds. Hence cattle are a suitable model for studying individual visual recognition. This study demonstrates that cattle display visual individual recognition and shows the effect of both familiarity and coat diversity in discrimination. [br/]METHODOLOGY/PRINCIPAL FINDINGS: We tested whether 8 Prim'Holstein heifers could recognize 2D-images of heads of one cow (face, profiles, (3/4) views) from those of other cows. Experiments were based on a simultaneous discrimination paradigm through instrumental conditioning using food rewards. In Experiment 1, all images represented familiar cows (belonging to the same social group) from the Prim'Holstein breed. In Experiments 2, 3 and 4, images were from unfamiliar (unknown) individuals either from the same breed or other breeds. All heifers displayed individual recognition of familiar and unfamiliar individuals from their own breed. Subjects reached criterion sooner when recognizing a familiar individual than when recognizing an unfamiliar one (Exp 1: 3.1+/-0.7 vs. Exp 2: 5.2+/-1.2 sessions; Z = 1.99, N = 8, P = 0.046). In addition almost all subjects recognized unknown individuals from different breeds, however with greater difficulty. [br/] CONCLUSIONS/SIGNIFICANCE: Our results demonstrated that cattle have efficient individual recognition based on categorization capacities. Social familiarity improved their performance. The recognition of individuals with very different coat characteristics from the subjects was the most difficult task. These results call for studies exploring the mechanisms involved in face recognition allowing interspecies comparisons, including humans