Multiscale Immune Selection and the Transmission-Diversity Feedback in Antigenically Diverse Pathogen Systems

This is the final version of the article. Available from University of Chicago Press via the DOI in this record.Antigenic diversity is commonly used by pathogens to enhance their transmission success. Within-host clonal antigenic variation helps to maintain long infectious periods, whereas high levels of allelic diversity at the population level significantly expand the pool of susceptible individuals. Diversity, however, is not necessarily a static property of a pathogen population but in many cases is generated by the very act of infection and transmission, and it is therefore expected to respond dynamically to changes in transmission and immune selection. We hypothesized that this coupling creates a positive feedback whereby infection and disease transmission promote the generation of diversity, which itself facilitates immune evasion and further infections. To investigate this link in more detail, we considered the human malaria parasite Plasmodium falciparum, one of the most important antigenically diverse pathogens. We developed an individual-based model in which antigenic diversity emerges as a dynamic property from the underlying transmission processes. Our results show that the balance between stochastic extinction and the generation of new antigenic variants is intrinsically linked to within-host and between-host immune selection. This in turn determines the level of diversity that can be maintained in a given population. Furthermore, the transmission-diversity feedback can lead to temporal lags in the response to natural or intervention-induced perturbations in transmission rates. Our results therefore have important implications for monitoring and assessing the effectiveness of disease control efforts

Predator or provider? How wild animals respond to mixed messages from humans

Wild animals encounter humans on a regular basis, but humansvary widely in their behaviour: whereas many people ignorewild animals, some people present a threat, while othersencourage animals’presence through feeding. Humans thussend mixed messages to which animals must respondappropriately to be successful. Some species appear tocircumvent this problem by discriminating among and/orsocially learning about humans, but it is not clear whethersuch learning strategies are actually beneficial in most cases.Using an individual-based model, we consider how learningrate, individual recognition (IR) of humans, and social learning(SL) affect wild animals’ability to reach an optimal avoidancestrategy when foraging in areas frequented by humans. Weshow that‘true’IR of humans could be costly. We also findthat a fast learning rate, while useful when human populationsare homogeneous or highly dangerous, can cause unwarrantedavoidance in other scenarios if animals generalize. SL reducesthis problem by allowing conspecifics to observe benigninteractions with humans. SL and a fast learning rate alsoimprove the viability of IR. These results provide an insightinto how wild animals may be affected by, and how they maycope with, contrasting human behaviour

Ten simple rules for principled simulation modelling

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On the emergence of oscillations in distributed resource allocation

We consider the problem of resource allocation in a decentralised market where users and suppliers trade for a single commodity. Due to the lack of strict concavity, convergence to the optimal solution by means of classical gradient type dynamics for the prices and demands, is not guaranteed. In the paper we explicitly characterise in this case the asymptotic behaviour of trajectories and provide an exact characterisation of the limiting oscillatory solutions. Methods of modifying the dynamics are also given, such that convergence to an optimal solution is guaranteed, without requiring additional information exchange among the users.This work was partly supported by an ERC starting grant 679774

Efficiency of hydrophobic phosphonium ionic liquids and DMSO as recyclable cellulose dissolution and regeneration media

Hydrophobic, long-chain tetraalkylphosphonium acetate salts (ionic liquids) were combined with a dipolar aprotic co-solvent, dimethylsulfoxide (DMSO), and the feasibility of these solvent systems for cellulose dissolution and regeneration was studied. A 60 : 40 w/w mixture of the ionic liquid tetraoctylphosphonium acetate ([P-8888][OAc]) and DMSO was found to dissolve up to 8 wt% cellulose, whilst trioctyl(tetradecyl) phosphonium acetate ([P-14888][OAc]) dissolved up to 3 wt% cellulose. Water (an anti-solvent for cellulose) was found to give rise to biphasic liquid-liquid systems when combined with these mixtures, yielding an upper phase rich in ionic liquid and a lower aqueous phase. The liquid-liquid equilibria of the ternary systems were experimentally determined, finding that DMSO strongly partitioned towards the aqueous phase. Thus, a process scheme involving simultaneous regeneration of cellulose and recycling of the solvent system was envisioned, and demonstrated on a large scale using [P-8888] [OAc]. A large portion of the ionic liquid (ca. 60 wt%) was directly recovered via phase separation, with a further 37 wt% being recovered from the swollen cellulose phase and residual materials, bringing recovery to 97%. XRD analysis of the recovered cellulose materials showed a loss of crystallinity and conversion from Cellulose I to Cellulose II. Non-dissolving compositions of ionic liquid and DMSO did not affect cellulose crystallinity after cellulose pulp treatment.Peer reviewe

Revised estimates of ocean-atmosphere CO2 flux are consistent with ocean carbon inventory

This is the final version. Available from the publisher via the DOI in this record.The ocean is a sink for ~25% of the atmospheric CO2 emitted by human activities, an amount in excess of 2 petagrams of carbon per year (PgC yr−1 ). Time-resolved estimates of global ocean-atmosphere CO2 flux provide an important constraint on the global carbon budget. However, previous estimates of this flux, derived from surface ocean CO2 concentrations, have not corrected the data for temperature gradients between the surface and sampling at a few meters depth, or for the effect of the cool ocean surface skin. Here we calculate a time history of ocean-atmosphere CO2 fluxes from 1992 to 2018, corrected for these effects. These increase the calculated net flux into the oceans by 0.8–0.9 PgC yr−1 , at times doubling uncorrected values. We estimate uncertainties using multiple interpolation methods, finding convergent results for fluxes globally after 2000, or over the Northern Hemisphere throughout the period. Our corrections reconcile surface uptake with independent estimates of the increase in ocean CO2 inventory, and suggest most ocean models underestimate uptake.European Space AgencyEuropean CommissionBONUS Secretariat (EEIG

Expert chess memory: Revisiting the chunking hypothesis

After reviewing the relevant theory on chess expertise, this paper re-examines experimentally the finding of Chase and Simon (1973a) that the differences in ability of chess players at different skill levels to copy and to recall positions are attributable to the experts' storage of thousands of chunks (patterned clusters of pieces) in long-term memory. Despite important differences in the experimental apparatus, the data of the present experiments regarding latencies and chess relations between successively placed pieces are highly correlated with those of Chase and Simon. We conclude that the 2-second inter-chunk interval used to define chunk boundaries is robust, and that chunks have psychological reality. We discuss the possible reasons why Masters in our new study used substantially larger chunks than the Master of the 1973 study, and extend the chunking theory to take account of the evidence for large retrieval structures (templates) in long-term memory

Liquid-state NMR analysis of nanocelluloses

Recent developments in ionic liquid electrolytes for cellulose or biomass dissolution has also allowed for high-resolution 1H and 13C NMR on very high molecular weight cellulose. This permits the development of advanced liquid-state quantitative NMR methods for characterization of unsubstituted and low degree of substitution celluloses, for example, surface-modified nanocelluloses, which are insoluble in all molecular solvents. As such, we present the use of the tetrabutylphosphonium acetate ([P4444][OAc]):DMSO-d6 electrolyte in the 1D and 2D NMR characterization of poly(methyl methacrylate) (PMMA)-grafted cellulose nanocrystals (CNCs). PMMA-g-CNCs was chosen as a difficult model to study, to illustrate the potential of the technique. The chemical shift range of [P4444][OAc] is completely upfield of the cellulose backbone signals, avoiding signal overlap. In addition, application of diffusion-editing for 1H and HSQC was shown to be effective in the discrimination between PMMA polymer graft resonances and those from low molecular weight components arising from the solvent system. The bulk ratio of methyl methacrylate monomer to anhydroglucose unit was determined using a combination of HSQC and quantitative 13C NMR. After detachment and recovery of the PMMA grafts, through methanolysis, DOSY NMR was used to determine the average self-diffusion coefficient and, hence, molecular weight of the grafts compared to self-diffusion coefficients for PMMA GPC standards. This finally led to a calculation of both graft length and graft density using liquid-state NMR techniques. In addition, it was possible to discriminate between triads and tetrads, associated with PMMA tacticity, of the PMMA still attached to the CNCs (before methanolysis). CNC reducing end and sulfate half ester resonances, from sulfuric acid hydrolysis, were also assignable. Furthermore, other biopolymers, such as hemicelluloses and proteins (silk and wool), were found to be soluble in the electrolyte media, allowing for wider application of this method beyond just cellulose analytics.Peer reviewe

Air–sea CO2 exchange in the Baltic Sea - A sensitivity analysis of the gas transfer velocity

This is the final version. Available on open access from Elsevier via the DOI in this recordAir–sea gas fluxes are commonly estimated using wind-based parametrizations of the gas transfer velocity. However, neglecting gas exchange forcing mechanisms – other than wind speed – may lead to large uncertainties in the flux estimates and the carbon budgets, in particular, in heterogeneous environments such as marginal seas and coastal areas. In this study we investigated the impact of including relevant processes to the air–sea CO flux parametrization for the Baltic Sea. We used six parametrizations of the gas transfer velocity to evaluate the effect of precipitation, water-side convection, and surfactants on the net CO flux at regional and sub-regional scale. The differences both in the mean CO fluxes and the integrated net fluxes were small between the different cases. However, the implications on the seasonal variability were shown to be significant. The inter-annual and spatial variability were also found to be associated with the forcing mechanisms evaluated in the study. In addition to wind, water-side convection was the most relevant parameter controlling the air–sea gas exchange at seasonal and inter-annual scales. The effect of precipitation and surfactants seemed negligible in terms of the inter-annual variability. The effect of water-side convection and surfactants resulted in a reduction of the downward fluxes, while precipitation was the only parameter that resulted in an enhancement of the net uptake in the Baltic Sea.BONUS Secretariat (EEIG