hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies

High CO2 decreases the long-term resilience of the free-living coralline algae Phymatolithon lusitanicum

Maerl/rhodolith beds are protected habitats that may be affected by ocean acidification (OA), but it is still unclear how the availability of CO2 will affect the metabolism of these organisms. Some of the inconsistencies found among OA experimental studies may be related to experimental exposure time and synergetic effects with other stressors. Here, we investigated the long-term (up to 20months) effects of OA on the production and calcification of the most common maerl species of southern Portugal, Phymatolithon lusitanicum. Both the photosynthetic and calcification rates increased with CO2 after the first 11months of the experiment, whereas respiration slightly decreased with CO2. After 20months, the pattern was reversed. Acidified algae showed lower photosynthetic and calcification rates, as well as lower accumulated growth than control algae, suggesting that a metabolic threshold was exceeded. Our results indicate that long-term exposure to high CO2 will decrease the resilience of Phymatolithon lusitanicum. Our results also show that shallow communities of these rhodoliths may be particularly at risk, while deeper rhodolith beds may become ocean acidification refuges for this biological community.Fundacao para a Ciencia e a Tecnologia [PTDC/MAR/115789/2009, SFRH/BD/76762/2011

Development of boldness and docility in yellow-bellied marmots

Peer reviewedPostprin

High-precision estimate of g4 in the 2D Ising model

We compute the renormalized four-point coupling in the 2d Ising model using transfer-matrix techniques. We greatly reduce the systematic uncertainties which usually affect this type of calculations by using the exact knowledge of several terms in the scaling function of the free energy. Our final result is g4=14.69735(3).Comment: 17 pages, revised version with minor changes, accepted for publication in Journal of Physics

Functional Forms for the Squeeze and the Time-Displacement Operators

Using Baker-Campbell-Hausdorff relations, the squeeze and harmonic-oscillator time-displacement operators are given in the form $\exp[\delta I] \exp[\alpha (x^2)]\exp[\beta(x\partial)] \exp[\gamma (\partial)^2]$, where $\alpha$, $\beta$, $\gamma$, and $\delta$ are explicitly determined. Applications are discussed.Comment: 10 pages, LaTe

Irrelevant operators in the two-dimensional Ising model

By using conformal-field theory, we classify the possible irrelevant operators for the Ising model on the square and triangular lattices. We analyze the existing results for the free energy and its derivatives and for the correlation length, showing that they are in agreement with the conformal-field theory predictions. Moreover, these results imply that the nonlinear scaling field of the energy-momentum tensor vanishes at the critical point. Several other peculiar cancellations are explained in terms of a number of general conjectures. We show that all existing results on the square and triangular lattice are consistent with the assumption that only nonzero spin operators are present.Comment: 32 pages. Added comments and reference

Explaining Myanmar's Regime Transition: The Periphery is Central

In 2010, Myanmar (Burma) held its first elections after 22 years of direct military rule. Few compelling explanations for this regime transition have emerged. This article critiques popular accounts and potential explanations generated by theories of authoritarian ‘regime breakdown’ and ‘regime maintenance’. It returns instead to the classical literature on military intervention and withdrawal. Military regimes, when not terminated by internal factionalism or external unrest, typically liberalise once they feel they have sufficiently addressed the crises that prompted their seizure of power. This was the case in Myanmar. The military intervened for fear that political unrest and ethnic-minority separatist insurgencies would destroy Myanmar’s always-fragile territorial integrity and sovereignty. Far from suddenly liberalising in 2010, the regime sought to create a ‘disciplined democracy’ to safeguard its preferred social and political order twice before, but was thwarted by societal opposition. Its success in 2010 stemmed from a strategy of coercive state-building and economic incorporation via ‘ceasefire capitalism’, which weakened and co-opted much of the opposition. Having altered the balance of forces in its favour, the regime felt sufficiently confident to impose its preferred settlement. However, the transition neither reflected total ‘victory’ for the military nor secured a genuine or lasting peace

Tethered Monte Carlo: computing the effective potential without critical slowing down

We present Tethered Monte Carlo, a simple, general purpose method of computing the effective potential of the order parameter (Helmholtz free energy). This formalism is based on a new statistical ensemble, closely related to the micromagnetic one, but with an extended configuration space (through Creutz-like demons). Canonical averages for arbitrary values of the external magnetic field are computed without additional simulations. The method is put to work in the two dimensional Ising model, where the existence of exact results enables us to perform high precision checks. A rather peculiar feature of our implementation, which employs a local Metropolis algorithm, is the total absence, within errors, of critical slowing down for magnetic observables. Indeed, high accuracy results are presented for lattices as large as L=1024.Comment: 32 pages, 8 eps figures. Corrected Eq. (36), which is wrong in the published pape

Skeletal trade-offs in coralline algae in response to ocean acidification

Ocean acidification is changing the marine environment, with potentially serious consequences for many organisms. Much of our understanding of ocean acidification effects comes from laboratory experiments, which demonstrate physiological responses over relatively short timescales. Observational studies and, more recently, experimental studies in natural systems suggest that ocean acidification will alter the structure of seaweed communities. Here, we provide a mechanistic understanding of altered competitive dynamics among a group of seaweeds, the crustose coralline algae (CCA). We compare CCA from historical experiments (1981-1997) with specimens from recent, identical experiments (2012) to describe morphological changes over this time period, which coincides with acidification of seawater in the Northeastern Pacific. Traditionally thick species decreased in thickness by a factor of 2.0-2.3, but did not experience a change in internal skeletal metrics. In contrast, traditionally thin species remained approximately the same thickness but reduced their total carbonate tissue by making thinner inter-filament cell walls. These changes represent alternative mechanisms for the reduction of calcium carbonate production in CCA and suggest energetic trade-offs related to the cost of building and maintaining a calcium carbonate skeleton as pH declines. Our classification of stress response by morphological type may be generalizable to CCA at other sites, as well as to other calcifying organisms with species-specific differences in morphological types