Adaptive evolution of molecular phenotypes

Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.Comment: Figures are not optimally displayed in Firefo

Non-diffusive transport in plasma turbulence: a fractional diffusion approach

Numerical evidence of non-diffusive transport in three-dimensional, resistive pressure-gradient-driven plasma turbulence is presented. It is shown that the probability density function (pdf) of test particles' radial displacements is strongly non-Gaussian and exhibits algebraic decaying tails. To model these results we propose a macroscopic transport model for the pdf based on the use of fractional derivatives in space and time, that incorporate in a unified way space-time non-locality (non-Fickian transport), non-Gaussianity, and non-diffusive scaling. The fractional diffusion model reproduces the shape, and space-time scaling of the non-Gaussian pdf of turbulent transport calculations. The model also reproduces the observed super-diffusive scaling

Simulated tomographic reconstruction of ocean features using drifting acoustic receivers and a navigated source

Author Posting. © Acoustical Society of America, 1995. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 98 (1995): 2270-2279, doi:10.1121/1.413341.Numerically simulated acoustic transmission from a single source of known position (for example, suspended from a ship) to receivers of partially known position (for example, sonobuoys dropped from the air) are used for tomographic mapping of ocean sound speed. The maps are evaluated for accuracy and utility. Grids of 16 receivers are employed, with sizes of 150, 300, and 700 km square. Ordinary statistical measures are used to evaluate the pattern similarity and thus the mapping capability of the system. For an array of 300 km square, quantitative error in the maps grows with receiver position uncertainty. The large and small arrays show lesser mapping capability than the mid-size array. Mapping errors increase with receiver position uncertainty for uncertainties less than 1000-m rms, but uncertainties exceeding that have less systematic effect on the maps. Maps of rms error of the field do not provide a complete view of the utility of the acoustic network. Features of maps are surprisingly reproducible for different navigation error levels, and give comparable information about mesoscale structures despite great variations in those levels.This work was supported by Office of Naval Research grants N00014-9l-J-1138 (Arctic Sciences )and N00014-92-I-1162 (Ocean Acoustics)

Tight local approximation results for max-min linear programs

In a bipartite max-min LP, we are given a bipartite graph \myG = (V \cup I \cup K, E), where each agent $v \in V$ is adjacent to exactly one constraint $i \in I$ and exactly one objective $k \in K$. Each agent $v$ controls a variable $x_v$. For each $i \in I$ we have a nonnegative linear constraint on the variables of adjacent agents. For each $k \in K$ we have a nonnegative linear objective function of the variables of adjacent agents. The task is to maximise the minimum of the objective functions. We study local algorithms where each agent $v$ must choose $x_v$ based on input within its constant-radius neighbourhood in \myG. We show that for every $\epsilon>0$ there exists a local algorithm achieving the approximation ratio ${\Delta_I (1 - 1/\Delta_K)} + \epsilon$. We also show that this result is the best possible -- no local algorithm can achieve the approximation ratio ${\Delta_I (1 - 1/\Delta_K)}$. Here $\Delta_I$ is the maximum degree of a vertex $i \in I$, and $\Delta_K$ is the maximum degree of a vertex $k \in K$. As a methodological contribution, we introduce the technique of graph unfolding for the design of local approximation algorithms.Comment: 16 page

An Improved Approximate Consensus Algorithm in the Presence of Mobile Faults

This paper explores the problem of reaching approximate consensus in synchronous point-to-point networks, where each pair of nodes is able to communicate with each other directly and reliably. We consider the mobile Byzantine fault model proposed by Garay '94 -- in the model, an omniscient adversary can corrupt up to $f$ nodes in each round, and at the beginning of each round, faults may "move" in the system (i.e., different sets of nodes may become faulty in different rounds). Recent work by Bonomi et al. '16 proposed a simple iterative approximate consensus algorithm which requires at least $4f+1$ nodes. This paper proposes a novel technique of using "confession" (a mechanism to allow others to ignore past behavior) and a variant of reliable broadcast to improve the fault-tolerance level. In particular, we present an approximate consensus algorithm that requires only $\lceil 7f/2\rceil + 1$ nodes, an $\lfloor f/2 \rfloor$ improvement over the state-of-the-art algorithms. Moreover, we also show that the proposed algorithm is optimal within a family of round-based algorithms

Canonically conjugate pairs and phase operators

For quantum mechanics on a lattice the position (``particle number'') operator and the quasi-momentum (``phase'') operator obey canonical commutation relations (CCR) only on a dense set of the Hilbert space. We compare exact numerical results for a particle in simple potentials on the lattice with the expectations, when the CCR are assumed to be strictly obeyed. Only for sufficiently smooth eigenfunctions this leads to reasonable results. In the long time limit the use of the CCR can lead to a qualitativel wrong dynamics even if the initial state is in the dense set.Comment: 4 pages, 5 figures. Phys. Rev. A, in pres

The Relationship Between Psychological Distress and Physical Activity Is Non-linear and Differs by Domain: a Cross-Sectional Study

Background: There is increasing evidence for the relationship between physical activity (PA), sedentary behaviour and mental health. Limited data exists on sex-specific associations. We aimed to identify associations between PA dose and domain and television time with psychological distress, including sex-stratified models. Methods: A total of 22,176 adults from the Melbourne Collaborative Cohort Study follow-up 2 cohort (2003–2007) participated in this cross-sectional study. Occupational, household, transport, leisure PA, hours watching television and psychological distress were assessed. Restricted cubic splines were used to examine the relationships between PA domains, television viewing time and psychological distress. Results: The relationships between PA and psychological distress were non-linear (p < 0.05) and differed by PA domain. There were dose-dependent, inverse associations between distress with transport (B[95% CI] = −0.39[−0.49, −0.30]) and leisure PA (B[95% CI] = −0.35[−0.46, −0.25]). The effect estimates for transport and leisure PA with distress were larger for women. For household domain, a U-shaped curve with an elongated tail was seen. Median PA was associated with lower distress compared with lower quantities (B[95% CI] = −0.12[−0.22, −0.03]); however, this association was not evident with increasing household PA. There were no clear associations between occupational PA and distress. Higher television viewing was associated with higher distress (B[95% CI] = 0.16[0.02, 0.30]). Conclusions: Increasing PA and reducing television viewing may contribute to reduced psychological distress, particularly in women. Future interventions should incorporate leisure and transport PA and decrease television viewing to assess the impact on mental health

Prediction of cholera dynamics in Haiti following the passage of Hurricane Matthew

Following the landfall of Hurricane Matthew in Haiti on October 3, 2016, an increase of suspected cholera cases was reported in both the southern part of the island (with Grande-Anse and Le Sud departments reporting 1349 and 1533 cases respectively between 5 October and 6 November) and also in the capital, Port-au-Prince (438 cases reported over the same period). The hurricane caused the displacement of about 175,000 people, the vast majority of which remained in their department of origin; however, about 10% appear to have displaced to the capital Port-au-Prince. In this context, a mass OCV vaccination campaign was planned, starting on November 8 and targeting 816,999 individuals in Grande-Anse and Le Sud. The aim of this study is to provide additional information to health actors responding to the post-hurricane cholera outbreak in Haiti. To this end, we calibrated a mechanistic model of cholera transmission on currently available data for Haiti in order to forecast the spatio-temporal dynamics of the cholera epidemic at the departmental level from November 2016 to January 2017. Model outputs have been translated into operational recommendations, with a focus on the scheduled OCV campaign