A Bovine Babesiosis Model with Dispersion

Bovine Babesiosis (BB) is a tick borne parasitic disease with worldwide over 1.3 billion bovines at potential risk of being infected. The disease, also called tick fever, causes significant mortality from infection by the protozoa upon exposure to infected ticks. An important factor in the spread of the disease is the dispersion or migration of cattle as well as ticks. In this paper, we study the effect of this factor. We introduce a number, $\mathcal{P}$ , a “proliferation index,” which plays the same role as the basic reproduction number $\mathcal{R}_{0}$ with respect to the stability/instability of the disease-free equilibrium, and observe that $\mathcal{P}$ decreases as the dispersion coefficients increase. We prove, mathematically, that if $\mathcal{P}>1$ then the tick fever will remain endemic. We also consider the case where the birth rate of ticks undergoes seasonal oscillations. Based on data from Colombia, South Africa, and Brazil, we use the model to determine the effectiveness of several intervention schemes to control the progression of BB.     

Sensory uncertainty and stick balancing at the fingertip

The effects of sensory input uncertainty, $\varepsilon $ , on the stability of time-delayed human motor control are investigated by calculating the minimum stick length, $\ell _\mathrm{crit}$ , that can be stabilized in the inverted position for a given time delay, $\tau $ . Five control strategies often discussed in the context of human motor control are examined: three time-invariant controllers [proportional–derivative, proportional–derivative–acceleration (PDA), model predictive (MP) controllers] and two time-varying controllers [act-and-wait (AAW) and intermittent predictive controllers]. The uncertainties of the sensory input are modeled as a multiplicative term in the system output. Estimates based on the variability of neural spike trains and neural population responses suggest that $\varepsilon \approx 7$ –13 %. It is found that for this range of uncertainty, a tapped delay-line type of MP controller is the most robust controller. In particular, this controller can stabilize inverted sticks of the length balanced by expert stick balancers (0.25–0.5 m when $\tau \approx 0.08$  s). However, a PDA controller becomes more effective when $\varepsilon > 15\,\%$ . A comparison between $\ell _\mathrm{crit}$ for human stick balancing at the fingertip and balancing on the rubberized surface of a table tennis racket suggest that friction likely plays a role in balance control. Measurements of $\ell _\mathrm{crit},\,\tau $ , and a variability of the fluctuations in the vertical displacement angle, an estimate of $\varepsilon $ , may make it possible to study the changes in control strategy as motor skill develops.     

Quantifying interspecific spatial overlap in aquatic macrophyte communities

Levins’s asymmetrical α index quantifies between species overlap over resources more realistically than similar-purpose single-value indices. The associated community-wide \(\bar \alpha\) index expresses the degree of “species packing”. Both indices were formulated upon competing animal (i.e., mobile) organisms and are independent of population densities. However, overlap over resources for nonmobile organisms such as plants may have an impact even below carrying capacity. The proposed \(\hat \alpha\) index, based on Levins’s α index, quantifies spatial overlap for plants integrating information on species spatial distribution and crowding conditions. The \(\hat \alpha\) index is specifically designed for plant distribution data collected in discrete plots with density expressed as percent coverage (%cover) of substratum. We also propose a community-wide \({\hat \alpha_{\text{c}}}\) index, conceptually analogous to \(\bar \alpha\) , but furnished with a measure of dispersion (se \({\hat \alpha_{\text{c}}}\) ). Species importance within the community is inferred from comparisons of pairwise \(\hat \alpha\) ’s with \({\hat \alpha_{\text{c}}}\) . The \(\hat \alpha\) and \({\hat \alpha_{\text{c}}}\) indices correlate closely and exponentially with plant density, and correct apparent over- and underestimations of interaction intensity at low and very high crowding by Levins’s α and \(\bar \alpha\) , respectively. Index application to aquatic plant communities gave results consistent with within-community and general ecological patterns, suggesting a high potential of the proposed \(\hat \alpha\) and \({\hat \alpha_{\text{c}}}\) indices in basic and applied macrophyte ecological studies and management.     

Declarative platform for high-performance network traffic analytics

This paper presents Scalanytics, a declarative platform that supports high-performance application layer analysis of network traffic. Scalanytics uses (1) stateful network packet processing techniques for extracting application layer data from network packets, (2) a declarative rule-based language called Analog for compactly specifying analysis pipelines from reusable modules, and (3) a task-stealing architecture for processing network packets at high throughput within these pipelines, by leveraging multi-core processing capabilities in a load-balanced manner without the need for explicit performance profiling. In a cluster of machines, Scalanytics further improves throughput through the use of a consistent-hashing based load partitioning strategy. Our evaluation on a 16-core machine demonstrate that Scalanytics achieves up to 11.4 \(\times \) improvement in throughput compared with the best uniprocessor implementation. Moreover, Scalanytics outperforms the Bro intrusion detection system by an order of magnitude when used for analyzing SMTP traffic. We further observed increased throughput when running Scalanytics pipelines across multiple machines.     

DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance

Scientific data analytics in high-performance computing environments has been evolving along with the advancement of computing capabilities. With the onset of exascale computing, the increasing gap between compute performance and I/O bandwidth has rendered the traditional post-simulation processing a tedious process. Despite the challenges due to increased data production, there exists an opportunity to benefit from “cheap” computing power to perform query-driven exploration and visualization during simulation time. To accelerate such analyses, applications traditionally augment, post-simulation, raw data with large indexes, which are then repeatedly utilized for data exploration. However, the generation of current state-of-the-art indexes involves a compute- and memory-intensive processing, thus rendering them inapplicable in an in situ context. In this paper we propose DIRAQ, a parallel in situ, in network data encoding and reorganization technique that enables the transformation of simulation output into a query-efficient form, with negligible runtime overhead to the simulation run. DIRAQ’s effective core-local, precision-based encoding approach incorporates an embedded compressed index that is 3–6 \(\times \) smaller than current state-of-the-art indexing schemes. Its data-aware index adjustmentation improves performance of group-level index layout creation by up to 35 % and reduces the size of the generated index by up to 27 %. Moreover, DIRAQ’s in network index merging strategy enables the creation of aggregated indexes that speed up spatial-context query responses by up to \(10\times \) versus alternative techniques. DIRAQ’s topology-, data-, and memory-aware aggregation strategy results in efficient I/O and yields overall end-to-end encoding and I/O time that is less than that required to write the raw data with MPI collective I/O.     

Quasi equilibrium,variance effective size and fixation index for populations with substructure

In this paper, we develop a method for computing the variance effective size \(N_{eV}\) , the fixation index \(F_{ST}\) and the coefficient of gene differentiation \(G_{ST}\) of a structured population under equilibrium conditions. The subpopulation sizes are constant in time, with migration and reproduction schemes that can be chosen with great flexibility. Our quasi equilibrium approach is conditional on non-fixation of alleles. This is of relevance when migration rates are of a larger order of magnitude than the mutation rates, so that new mutations can be ignored before equilibrium balance between genetic drift and migration is obtained. The vector valued time series of subpopulation allele frequencies is divided into two parts; one corresponding to genetic drift of the whole population and one corresponding to differences in allele frequencies among subpopulations. We give conditions under which the first two moments of the latter, after a simple standardization, are well approximated by quantities that can be explicitly calculated. This enables us to compute approximations of the quasi equilibrium values of \(N_{eV}\) , \(F_{ST}\) and \(G_{ST}\) . Our findings are illustrated for several reproduction and migration scenarios, including the island model, stepping stone models and a model where one subpopulation acts as a demographic reservoir. We also make detailed comparisons with a backward approach based on coalescence probabilities.     

Approximating the dynamics of communicating cells in a diffusive medium by ODEs—homogenization with localization

Bacteria may change their behavior depending on the population density. Here we study a dynamical model in which cells of radius $R$ within a diffusive medium communicate with each other via diffusion of a signalling substance produced by the cells. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration $u$ of the signalling substance, coupled with $N$ ODEs for the masses $a_i$ of the substance within each cell. We show that for small $R$ the model can be approximated by a hierarchy of models, namely first a system of $N$ coupled delay ODEs, and in a second step by $N$ coupled ODEs. We give some illustrations of the dynamics of the approximate model.     

Fishermen’s Profits Maximization: Case of Generalized Nash Equilibrium of a Non-symmetrical Game

In the present paper, we consider a bio-economic equilibrium model which describes the dynamics of a fish population fished by several fishermen seeking to maximize their profits. Each fisherman tries to find the fishing effort which maximizes his profit at biological equilibrium without any consultation with others, but all of them have to respect two constraints: (1) the sustainable management of the resources ; and (2) the preservation of the biodiversity. With all these considerations, our problem leads to a generalized Nash equilibrium problem. The objective is to show that even when a fisherman \(i\) provides a fishing effort equal to twice the fishing effort of a fisherman \(j\) , then the profit of fisherman \(i\) is not necessarily double that of fisherman \(j\) .     

The Basic Reproduction Number for Cellular SIR Networks

The basic reproduction number \(R_0\) is the average number of new infections produced by a typical infective individual in the early stage of an infectious disease, following the introduction of few infective individuals in a completely susceptible population. If \(R_0<1\) , then the disease dies, whereas for \(R_0>1\) the infection can invade the host population and persist. This threshold quantity is well studied for SIR compartmental or mean field models based on ordinary differential equations, and a general method for its computation has been proposed by van den Driessche and Watmough. We concentrate here on SIR epidemiological models that take into account the contact network N underlying the transmission of the disease. In this context, it is generally admitted that \(R_{0}\) can be approximated by the average number \(R_{2,3}\) of infective individuals of generation three produced by an infective of generation two. We give here a simple analytic formula of \(R_{2,3}\) for SIR cellular networks. Simulations on two-dimensional cellular networks with von Neumann and Moore neighborhoods show that \(R_{2,3}\) can be used to capture a threshold phenomenon related the dynamics of SIR cellular network and confirm the good quality of the simple approach proposed recently by Aparicio and Pascual for the particular case of Moore neighborhood.     

Individual-Based Model for Quorum Sensing with Background Flow

Quorum sensing is a wide-spread mode of cell–cell communication among bacteria in which cells release a signalling substance at a low rate. The concentration of this substance allows the bacteria to gain information about population size or spatial confinement. We consider a model for \(N\) cells which communicate with each other via a signalling substance in a diffusive medium with a background flow. The model consists of an initial boundary value problem for a parabolic PDE describing the exterior concentration \(u\) of the signalling substance, coupled with \(N\) ODEs for the masses \(a_i\) of the substance within each cell. The cells are balls of radius \(R\) in \(\mathbb {R} ^3\) , and under some scaling assumptions we formally derive an effective system of \(N\) ODEs describing the behaviour of the cells. The reduced system is then used to study the effect of flow on communication in general, and in particular for a number of geometric configurations.     

Exact formulas for the variance of several balance indices under the Yule model

One of the main applications of balance indices is in tests of null models of evolutionary processes. The knowledge of an exact formula for a statistic of a balance index, holding for any number $n$ of leaves, is necessary in order to use this statistic in tests of this kind involving trees of any size. In this paper we obtain exact formulas for the variance under the Yule model of the Sackin, the Colless and the total cophenetic indices of binary rooted phylogenetic trees with $n$ leaves.     

Cellular systems as graphs

The definition of an (M,R) is formulated in a way that emphasizes its mathematical properties. Neglecting interactions between the components, it is shown that:

1. An (M,R) contains only one non-reestablishable component.
2. If an (M,R) contains only one non-reestablishable component, then that component is central.

Examples are given to illustrate the biological significance of these two results. The notion of “lag-independence” is introduced, and it is shown that if a system possesses only one non-reestablishable component which is “lag-independent” then all components are lag-independent. The concepts of reestablishability, centrality and lag-independence are applied in order to suggest various criteria for optimal organization of (M,R).     

Quantifying the risk of mis-estimating correlation significance of climate–tree growth relationships

In dendroecology, sampling effort has a strong influence of both regional chronology properties and climate–tree growth relationships assessment. Recent studies evidenced that decreasing sample size leads to a weakening of the bootstrapped correlation coefficients ( ${\text{BCC}}$ BCC ). The present analysis focused on the risk of mis-estimating the significance of population ${\text{BCC}}\,\left( {{\text{BCC}}_{\text{POP}} } \right)$ BCC ( BCC POP ) from a sample of N trees, and then proposed an approach to detect and correct mis-estimations using the properties of the sample. The sample size effect and the limits of the correction were illustrated from 840 individual growth chronologies of Corsican pine (Pinus nigra Arnold ssp. laricio Poiret var. Corsicana) sampled in Western France. The 840 trees were used to assess the population characteristics, and the effect of sampling effort was investigated through a simulation approach based on a resampling procedure of N trees amongst 840 (N ? [5; 50]). Our results evidenced that the risk strongly varied amongst the climatic regressors. The highest risks were evidenced for significant ${\text{BCC}}_{\text{POP}}$ BCC POP , with a percentage of mis-estimation ranging from 25 to 80. On the contrary, small samples allowed providing an reliable estimation of the significance of non-significant ${\text{BCC}}_{\text{POP}}$ BCC POP . To a lesser extent, the risk slightly decreased with increasing N, according to a negative exponential trend. The detection and correction method was found relevant to detect mis-estimation only for significant ${\text{BCC}}_{\text{POP}}$ BCC POP ; otherwise, the ${\text{BCC}}_{\text{POP}}$ BCC POP significance was generally overestimated.     

Probing the specificity of gamma-glutamylamine cyclotransferase: an enzyme involved in the metabolism of transglutaminase-catalyzed protein crosslinks

γ-Glutamylamine cyclotransferase (gGACT) catalyzes the intramolecular cyclization of a variety of l-γ-glutamylamines producing 5-oxo-l-proline and free amines. Its substrate specificity implicates it in the downstream metabolism of transglutaminase products, and is distinct from that of γ-glutamyl cyclotransferase which acts on l-γ-glutamyl amino acids. To elucidate the mechanism by which gGACT distinguishes between l-γ-glutamylamine and amino acid substrates, the specificity of the rabbit kidney enzyme for the amide region of substrates was probed through the kinetic analysis of a series of l-γ-glutamylamines. The isodipeptide N ^?-(l-γ-glutamyl)-l-lysine 1 was used as a reference. The kinetic constants of the l-γ-glutamyl derivative of n-butylamine 7, were nearly identical to those of 1. Introduction of a methyl or carboxylate group on the carbon adjacent to the side-chain amide nitrogen in l-γ-glutamylamine substrates resulted in a dramatic decrease in substrate properties for gGACT thus providing an explanation of why gGACT does not act on l-γ-glutamyl amino acids except for l-γ-glutamylglycine. Placement of substituents on carbons further removed from the side-chain amide nitrogen in l-γ-glutamylamines restored activity for gGACT, and l-γ-glutamylneohexylamine 19 had a higher specificity constant (k _cat /K _m) than 1. gGACT did not exhibit any stereospecificity in the amide region of l-γ-glutamylamine substrates. In addition, analogues (26–30) with heteroatom substitutions for the γ methylene position of the l-γ-glutamyl moiety were examined. Several thiocarbamoyl derivatives of l-cysteine (28–30) were excellent substrates for gGACT.     

Modulation of the cAMP Response by G\alpha _i and G\beta \gamma : A Computational Study of G Protein Signaling in Immune Cells

Cyclic AMP is important for the resolution of inflammation, as it promotes anti-inflammatory signaling in several immune cell lines. In this paper, we present an immune cell specific model of the cAMP signaling cascade, paying close attention to the specific isoforms of adenylyl cyclase (AC) and phosphodiesterase that control cAMP production and degradation, respectively, in these cells. The model describes the role that G protein subunits, including G \(\alpha _s\) , G \(\alpha _i\) , and G \(\beta \gamma \) , have in regulating cAMP production. Previously, G \(\alpha _i\) activation has been shown to increase the level of cAMP in certain immune cell types. This increase in cAMP is thought to be mediated by \(\beta \gamma \) subunits which are released upon G \(\alpha \) activation and can directly stimulate specific isoforms of AC. We conduct numerical experiments in order to explore the mechanisms through which G \(\alpha _i\) activation can increase cAMP production. An important conclusion of our analysis is that the relative abundance of different G protein subunits is an essential determinant of the cAMP profile in immune cells. In particular, our model predicts that limited availability of \(\beta \gamma \) subunits may both \((i)\) enable immune cells to link inflammatory G \(\alpha _i\) signaling to anti-inflammatory cAMP production thereby creating a balanced immune response to stimulation with low concentrations of PGE2, and \((ii)\) prohibit robust anti-inflammatory cAMP signaling in response to stimulation with high concentrations of PGE2.     

A thermomechanical framework for reconciling the effects of ultraviolet radiation exposure time and wavelength on connective tissue elasticity

Augmentation of the mechanical properties of connective tissue using ultraviolet (UV) radiation—by targeting collagen cross-linking in the tissue at predetermined UV exposure time \((t)\) and wavelength \((\lambda )\) —has been proposed as a therapeutic method for supporting the treatment for structural-related injuries and pathologies. However, the effects of \(\lambda \) and \(t\) on the tissue elasticity, namely elastic modulus \((E)\) and modulus of resilience \((u_\mathrm{Y})\) , are not entirely clear. We present a thermomechanical framework to reconcile the \(t\) - and \(\lambda \) -related effects on \(E\) and \(u_\mathrm{Y}\) . The framework addresses (1) an energy transfer model to describe the dependence of the absorbed UV photon energy, \(\xi \) , per unit mass of the tissue on \(t\) and \(\lambda \) , (2) an intervening thermodynamic shear-related parameter, \(G\) , to quantify the extent of UV-induced cross-linking in the tissue, (3) a threshold model for the \(G\) versus \(\xi \) relationship, characterized by   \(t_\mathrm{C}\) —the critical \(t\) underpinning the association of \(\xi \) with \(G\) —and (4) the role of \(G\) in the tissue elasticity. We hypothesized that \(G\) regulates \(E\) (UV-stiffening hypothesis) and \(u_\mathrm{Y}\) (UV-resilience hypothesis). The framework was evaluated with the support from data derived from tensile testing on isolated ligament fascicles, treated with two levels of \(\lambda \) (365 and 254 nm) and three levels of \(t\) (15, 30 and 60 min). Predictions from the energy transfer model corroborated the findings from a two-factor analysis of variance of the effects of \(t\) and \(\lambda \) treatments. Student’s t test revealed positive change in \(E\) and \(u_\mathrm{Y}\) with increases in \(G\) —the findings lend support to the hypotheses, implicating the implicit dependence of UV-induced cross-links on \(t\) and \(\lambda \) for directing tissue stiffness and resilience. From a practical perspective, the study is a step in the direction to establish a UV irradiation treatment protocol for effective control of exogenous cross-linking in connective tissues.     

d-Ser-containing humanin shows promotion of fibril formation

Humanin (HN), a peptide of 24 amino acid residues, suppresses the neuronal cell death that is induced by the gene products of Alzheimer’s disease. HN contains two Ser residues at positions 7 and 14. Because the proportion of d-Ser isomerized from l-Ser in proteins appears to increase as cellular organs age, we explored the structural effects of the isomerization of each Ser residue in HN. By using a thioflavin-T assay to detect fibril formation, we found that an HN derivative that contained two isomerized d-Ser residues had a greater tendency to form fibrils than did wild-type HN or HNs containing single d-Ser residues. A previous report showed that HN containing two d-Ser residues exerts neuroprotective activity. Our data, therefore, suggest that the fibril formation by HN that contains two d-Ser residues may promote HN neuroprotective activity.     

Approximation of sojourn-times via maximal couplings: motif frequency distributions

Sojourn-times provide a versatile framework to assess the statistical significance of motifs in genome-wide searches even under non-Markovian background models. However, the large state spaces encountered in genomic sequence analyses make the exact calculation of sojourn-time distributions computationally intractable in long sequences. Here, we use coupling and analytic combinatoric techniques to approximate these distributions in the general setting of Polish state spaces, which encompass discrete state spaces. Our approximations are accompanied with explicit, easy to compute, error bounds for total variation distance. Broadly speaking, if \({\mathsf{T}}_n\) is the random number of times a Markov chain visits a certain subset \({\mathsf{T}}\) of states in its first \(n\) transitions, then we can usually approximate the distribution of \({\mathsf{T}}_n\) for \(n\) of order \((1-\alpha )^{-m}\) , where \(m\) is the largest integer for which the exact distribution of \({\mathsf{T}}_m\) is accessible and \(0\le \alpha \le 1\) is an ergodicity coefficient associated with the probability transition kernel of the chain. This gives access to approximations of sojourn-times in the intermediate regime where \(n\) is perhaps too large for exact calculations, but too small to rely on Normal approximations or stationarity assumptions underlying Poisson and compound Poisson approximations. As proof of concept, we approximate the distribution of the number of matches with a motif in promoter regions of C. elegans. Mathematical properties of the proposed ergodicity coefficients and connections with additive functionals of homogeneous Markov chains as well as ergodicity of non-homogeneous Markov chains are also explored.     

Notes on some African hepatic genera 1–5

The present study deals with five genera of hepatics in Africa, Isotachis Mitt., Anastrophyllum (Spruce) Steph., Tritomaria Schiffn. ex Loeske, Gymnocoleopsis (Schust.) Schust. and Lophozia (Dum.) Dum. All African populations of the genus Isotachis Mitt. are considered to be one species, I. aubertii (Schwaegr.) Mitt. Four species of Anastrophyllum (Spruce) Steph. (s.l.), A. auritum (Lehm.) Steph., A. piligerum (Nees) Spruce, A. subcomplicatum (Lehm. et Lindenb.) Steph. and A. minutum (Schreb.) Schust., and two species of Tritomaria Schiffn. et Loeske, T. camerunensis S. Arnell and T. exsecta (Schrad.) Schiffn. ex Loeske occur in Africa. Gymmocoleopsis multiflora (Steph.) Schust. represents a genus and species hitherto unreported for the African flora. Finally, five Lophozia (Dum.) Dum. species, L. argentina (Steph.) Schust., L. capensis S. Arnell, L. decolorans (Limpr.) Steph., L. hedbergii S. Arnell and L. tristaniana (S. Arnell) Váňa, are reported from central and southern Africa; two of these (L. argentina (Steph.) Schust. and L. decolorans (Limpr.) Steph.) represent the first reports from Africa.     

Pareto genealogies arising from a Poisson branching evolution model with selection

We study a class of coalescents derived from a sampling procedure out of $N$ i.i.d. Pareto $\left( \alpha \right) $ random variables, normalized by their sum, including $\beta $ –size-biasing on total length effects ( $\beta <\alpha $ ). Depending on the range of $\alpha ,$ we derive the large $N$ limit coalescents structure, leading either to a discrete-time Poisson-Dirichlet $ \left(\alpha ,-\beta \right) \Xi -$ coalescent ( $\alpha \in \left[ 0,1\right) $ ), or to a family of continuous-time Beta $\left( 2-\alpha ,\alpha -\beta \right) \Lambda -$ coalescents ( $\alpha \in \left[ 1,2\right) $ ), or to the Kingman coalescent ( $\alpha \ge 2$ ). We indicate that this class of coalescent processes (and their scaling limits) may be viewed as the genealogical processes of some forward in time evolving branching population models including selection effects. In such constant-size population models, the reproduction step, which is based on a fitness-dependent Poisson Point Process with scaling power-law $\left( \alpha \right) $ intensity, is coupled to a selection step consisting of sorting out the $N$ fittest individuals issued from the reproduction step.