Epistasis and Entropy

Epistasis is a key concept in the theory of adaptation. Indicators of epistasis are of interest for large system where systematic fitness measurements may not be possible. Some recent approaches depend on information theory. We show that considering shared entropy for pairs of loci can be misleading. The reason is that shared entropy does not imply epistasis for the pair. This observation holds true also in the absence of higher order epistasis. We discuss a refined approach for identifying pairwise interactions using entropy

Epistasis and Shapes of Fitness Landscapes

The relationship between the shape of a fitness landscape and the underlying gene interactions, or epistasis, has been extensively studied in the two-locus case. Gene interactions among multiple loci are usually reduced to two-way interactions. We present a geometric theory of shapes of fitness landscapes for multiple loci. A central concept is the genotope, which is the convex hull of all possible allele frequencies in populations. Triangulations of the genotope correspond to different shapes of fitness landscapes and reveal all the gene interactions. The theory is applied to fitness data from HIV and Drosophila melanogaster. In both cases, our findings refine earlier analyses and reveal previously undetected gene interactions.Comment: 31 pages, 7 figures; typos removed, Example 3.10 adde

The W100 pocket on HIV-1 gp120 penetrated by b12 is not a target for other CD4bs monoclonal antibodies

<p>Abstract</p> <p>Background</p> <p>The conserved CD4 binding site (CD4bs) on HIV-1 gp120 is a major target for vaccines. It is a priority to determine sites and structures within the CD4bs that are important for inclusion in vaccines. We studied a gp120 pocket penetrated by W100 of the potent CD4bs monoclonal antibody (mab), b12. We compared HIV-1 envelopes and corresponding mutants that carried blocked W100 pockets to evaluate whether other CD4bs mabs target this site.</p> <p>Findings</p> <p>All CD4bs mabs tested blocked soluble CD4 binding to gp120 consistent with their designation as CD4bs directed antibodies. All CD4bs mabs tested neutralized pseudovirions carrying NL4.3 wild type (wt) envelope. However, only b12 failed to neutralize pseudoviruses carrying mutant envelopes with a blocked W100 pocket. In addition, for CD4bs mabs that neutralized pseudovirions carrying primary envelopes, mutation of the W100 pocket had little or no effect on neutralization sensitivity.</p> <p>Conclusions</p> <p>Our data indicate that the b12 W100 pocket on gp120 is infrequently targeted by CD4bs mabs. This site is therefore not a priority for preservation in vaccines aiming to elicit antibodies targeting the CD4bs.</p

Producing organic wheat with high grain protein content: the significance of intercropping and the need for diagnostic tools

Grain quality of wheat is one of the major concerns of organic farming production. Cereal-legume intercropping may be of significance in this regard as it enhances the yield productivity and the grain protein content (GPC) of the intercropped wheat. However, fitted tools are needed for the diagnosis and management of such interspecific canopies. Our main objectives were i) to analyse the effect of intercropping and N-management on organic farming performances and ii) to analyse the relationships between N-status indicators and GPC of intercropped wheat. These objectives were assessed in winter pea–wheat intercrops in 2007 and 2009 in western France. Our study confirmed the significance of intercropping in the production of wheat with high GPC. We showed that tools for diagnosis, fitted for sole crops to manage grain yield and GPC (N nutrition index, chlorophyll meter), can be used on intercropped wheat

Dynamic analysis in the Viner model of mercantilism

This paper models the central theme of mercantilism in Jacob Viner's interpretation-power vs plenty-in a framework of modern theory of international finance. It is shown that, in the Viner model of mercantilism, a nation with strong mercantilist sentiment ends up with large foreign asset accumulation and high consumption in the long run; an import tariff leads to more foreign asset holding and more total consumption; furthermore, in the Viner model, the Harberger-Laursen-Metzler effect exists unambiguously: a permanent terms-of-trade deterioration causes a current account deficit in the short run.spirit of capitalism, social status, money, growth

Expected Bequests and Their Distribution

Based on a sample of actual bequests that is population-representative and on the subjective probability of bequests, we estimate the distribution of bequests that the older population will make. We find that the distribution is highly skewed, so that the typical baby-boom person will receive a very modest inheritance. This is partly due to the skewed distribution of wealth and partly due to the tendency of the wealthy to have fewer children. But it is also due to anticipated dissaving: we estimate that households in the age band 70-74 will bequeath just 39% of their wealth, consuming the rest before they die.

Individual differences in alpha frequency drive crossmodal illusory perception

Perception routinely integrates inputs from different senses. Stimulus temporal proximity critically determines whether or not these inputs are bound together. Despite the temporal window of integration being a widely accepted notion, its neurophysiological substrate remains unclear. Many types of common audio-visual interactions occur within a time window of -100ms [1-5]. For example, in the sound- induced double-flash illusion, when two beeps are presented within -100ms together with one flash, a second illusory flash is often perceived [2]. Due to their intrinsic rhythmic nature, brain oscillations are one candidate mechanism for gating the temporal window of integration. Interestingly, occipital alpha-band oscillations cycle on average every -100ms with peak frequencies ranging between 8-14Hz (i.e. 120-60ms cycle). Moreover, presenting a brief tone can phase-reset such oscillations in visual cortex [6, 7]. Based on these observations, we hypothesized that the duration of each alpha cycle might provide the temporal unit to bind audio-visual events. Here we first recorded EEG while participants performed the sound-induced double-flash illusion task [4] and found positive correlation between individual alpha-frequency (IAF) peak and the size of the temporal window of the illusion. Participants then performed the same task while receiving occipital transcranial alternating current stimulation (tACS), to modulate oscillatory activity [8] either at their IAF or at off-peak alpha-frequencies (IAF±2Hz). Compared to IAF tACS, IAF-2Hz and IAF+2Hz tACS respectively enlarged and shrunk the temporal window of illusion, suggesting that alpha oscillations might represent the temporal unit of visual processing that cyclically gates perception and the neurophysiological substrate promoting audio-visual interactions