Daphnias: from the individual based model to the large population equation

The class of deterministic 'Daphnia' models treated by Diekmann et al. (J Math Biol 61: 277-318, 2010) has a long history going back to Nisbet and Gurney (Theor Pop Biol 23: 114-135, 1983) and Diekmann et al. (Nieuw Archief voor Wiskunde 4: 82-109, 1984). In this note, we formulate the individual based models (IBM) supposedly underlying those deterministic models. The models treat the interaction between a general size-structured consumer population ('Daphnia') and an unstructured resource ('algae'). The discrete, size and age-structured Daphnia population changes through births and deaths of its individuals and throught their aging and growth. The birth and death rates depend on the sizes of the individuals and on the concentration of the algae. The latter is supposed to be a continuous variable with a deterministic dynamics that depends on the Daphnia population. In this model setting we prove that when the Daphnia population is large, the stochastic differential equation describing the IBM can be approximated by the delay equation featured in (Diekmann et al., l.c.)

Overview on METEOSAT geometrical image data processing

Digital Images acquired from the geostationary METEOSAT satellites are processed and disseminated at ESA's European Space Operations Centre in Darmstadt, Germany. Their scientific value is mainly dependent on their radiometric quality and geometric stability. This paper will give an overview on the image processing activities performed at ESOC, concentrating on the geometrical restoration and quality evaluation. The performance of the rectification process for the various satellites over the past years will be presented and the impacts of external events as for instance the Pinatubo eruption in 1991 will be explained. Special developments both in hard and software, necessary to cope with demanding tasks as new image resampling or to correct for spacecraft anomalies, are presented as well. The rotating lens of MET-5 causing severe geometrical image distortions is an example for the latter

Second look at the spread of epidemics on networks

In an important paper, M.E.J. Newman claimed that a general network-based stochastic Susceptible-Infectious-Removed (SIR) epidemic model is isomorphic to a bond percolation model, where the bonds are the edges of the contact network and the bond occupation probability is equal to the marginal probability of transmission from an infected node to a susceptible neighbor. In this paper, we show that this isomorphism is incorrect and define a semi-directed random network we call the epidemic percolation network that is exactly isomorphic to the SIR epidemic model in any finite population. In the limit of a large population, (i) the distribution of (self-limited) outbreak sizes is identical to the size distribution of (small) out-components, (ii) the epidemic threshold corresponds to the phase transition where a giant strongly-connected component appears, (iii) the probability of a large epidemic is equal to the probability that an initial infection occurs in the giant in-component, and (iv) the relative final size of an epidemic is equal to the proportion of the network contained in the giant out-component. For the SIR model considered by Newman, we show that the epidemic percolation network predicts the same mean outbreak size below the epidemic threshold, the same epidemic threshold, and the same final size of an epidemic as the bond percolation model. However, the bond percolation model fails to predict the correct outbreak size distribution and probability of an epidemic when there is a nondegenerate infectious period distribution. We confirm our findings by comparing predictions from percolation networks and bond percolation models to the results of simulations. In an appendix, we show that an isomorphism to an epidemic percolation network can be defined for any time-homogeneous stochastic SIR model.Comment: 29 pages, 5 figure

Connectivity, neutral theories and the assessment of species vulnerability to global change in temperate estuaries

One of the main adaptation strategies to global change scenarios, aiming to preserve ecosystem functioning and biodiversity, is to maximise ecosystem resilience. The resilience of a species metapopulation can be improved by facilitating connectivity between local populations, which will prevent demographic stochasticity and inbreeding. The objective of this investigation is to estimate the degree of connectivity among estuarine species along the north-eastern Iberian coast, in order to assess community vulnerability to global change scenarios. To address this objective, two connectivity proxy types have been used based upon genetic and ecological drift processes: 1) DNA markers for the bivalve cockle (Cerastoderma edule) and seagrass Zostera noltei, and 2) the decrease in the number of species shared between two sites with geographic distance; neutral biodiversity theory predicts that dispersal limitation modulates this decrease, and this has been explored in estuarine plants and macroinvertebrates. Results indicate dispersal limitation for both saltmarsh plants and seagrass beds community and Z. noltei populations; this suggests they are especially vulnerable to expected climate changes on their habitats. In contrast, unstructured spatial pattern found in macroinvertebrate communities and in C. edule genetic populations in the area suggests that estuarine soft-bottom macroinvertebrates with planktonic larval dispersal strategies may have a high resilience capacity to moderate changes within their habitats. Our findings can help environmental managers to prioritise the most vulnerable species and habitats to be restored

Inverse design approach to x-ray quantum optics with Mössbauer nuclei in thin-film cavities

Thin-film cavities containing layers of Mössbauer nuclei have been demonstrated to be a rich platform for x-ray quantum optics. At low excitation, these systems can be described by effective few-level schemes, thereby providing tunable artificial quantum systems at hard x-ray energies. With the recent advent of an ab initio theory, a numerically efficient description of these systems is now possible. On this basis, we introduce the inverse design and develop a comprehensive optimization for an archetype system with a single resonant layer, corresponding to an artificial two-level scheme. We discover a number of qualitative insights into x-ray photonic environments for nuclei that will likely impact the design of future x-ray cavities and thereby improve their performance. The presented methods readily generalize beyond the two-level case and thus provide a clear perspective towards the inverse design of more advanced tunable x-ray quantum optical level schemes

Rabifier2: an improved bioinformatic classifier of Rab GTPases

SUMMARY: The Rab family of small GTPases regulates and provides specificity to the endomembrane trafficking system; each Rab subfamily is associated with specific pathways. Thus, characterization of Rab repertoires provides functional information about organisms and evolution of the eukaryotic cell. Yet, the complex structure of the Rab family limits the application of existing methods for protein classification. Here, we present a major redesign of the Rabifier, a bioinformatic pipeline for detection and classification of Rab GTPases. It is more accurate, significantly faster than the original version and is now open source, both the code and the data, allowing for community participation. AVAILABILITY AND IMPLEMENTATION: Rabifier and RabDB are freely available through the web at http://rabdb.org. The Rabifier package can be downloaded from the Python Package Index at https://pypi.python.org/pypi/rabifier, the source code is available at Github https://github.com/evocell/rabifier

Population growth in discrete time: a renewal equation oriented survey

Traditionally, population models distinguish individuals on the basis of their current state. Given a distribution, a discrete time model then specifies (precisely in deterministic models, probabilistically in stochastic models) the population distribution at the next time point. The renewal equation alternative concentrates on newborn individuals and the model specifies the production of offspring as a function of age. This has two advantages: (i) as a rule, there are far fewer birth states than individual states in general, so the dimension is often low; (ii) it relates seamlessly to the next-generation matrix and the basic reproduction number. Here we start from the renewal equation for the births and use results of Feller and Thieme to characterise the asymptotic large time behaviour. Next we explicitly elaborate the relationship between the two bookkeeping schemes. This allows us to transfer the characterisation of the large time behaviour to traditional structured-population models

Size-structured populations: immigration, (bi)stability and the net growth rate

We consider a class of physiologically structured population models, a first order nonlinear partial differential equation equipped with a nonlocal boundary condition, with a constant external inflow of individuals. We prove that the linearised system is governed by a quasicontraction semigroup. We also establish that linear stability of equilibrium solutions is governed by a generalized net reproduction function. In a special case of the model ingredients we discuss the nonlinear dynamics of the system when the spectral bound of the linearised operator equals zero, i.e. when linearisation does not decide stability. This allows us to demonstrate, through a concrete example, how immigration might be beneficial to the population. In particular, we show that from a nonlinearly unstable positive equilibrium a linearly stable and unstable pair of equilibria bifurcates. In fact, the linearised system exhibits bistability, for a certain range of values of the external inflow, induced potentially by All\'{e}e-effect.Comment: to appear in Journal of Applied Mathematics and Computin

Variability of Contact Process in Complex Networks

We study numerically how the structures of distinct networks influence the epidemic dynamics in contact process. We first find that the variability difference between homogeneous and heterogeneous networks is very narrow, although the heterogeneous structures can induce the lighter prevalence. Contrary to non-community networks, strong community structures can cause the secondary outbreak of prevalence and two peaks of variability appeared. Especially in the local community, the extraordinarily large variability in early stage of the outbreak makes the prediction of epidemic spreading hard. Importantly, the bridgeness plays a significant role in the predictability, meaning the further distance of the initial seed to the bridgeness, the less accurate the predictability is. Also, we investigate the effect of different disease reaction mechanisms on variability, and find that the different reaction mechanisms will result in the distinct variabilities at the end of epidemic spreading.Comment: 6 pages, 4 figure

Experimental pig-to-pig transmission dynamics for African swine fever virus, Georgia 2007/1 strain

African swine fever virus (ASFV) continues to cause outbreaks in domestic pigs and wild boar in Eastern European countries. To gain insights into its transmission dynamics, we estimated the pig-to-pig basic reproduction number (R 0) for the Georgia 2007/1 ASFV strain using a stochastic susceptible-exposed-infectious-recovered (SEIR) model with parameters estimated from transmission experiments. Models showed that R 0 is 2·8 [95% confidence interval (CI) 1·3–4·8] within a pen and 1·4 (95% CI 0·6–2·4) between pens. The results furthermore suggest that ASFV genome detection in oronasal samples is an effective diagnostic tool for early detection of infection. This study provides quantitative information on transmission parameters for ASFV in domestic pigs, which are required to more effectively assess the potential impact of strategies for the control of between-farm epidemic spread in European countries.ISSN:0950-2688ISSN:1469-440