ZRT1 harbors an excess of nonsynonymous polymorphism and shows evidence of balancing selection in Saccharomyces cerevisiae

Estimates of the fraction of nucleotide substitutions driven by positive selection vary widely across different species. Accounting for different estimates of positive selection has been difficult, in part because selection on polymorphism within a species is known to obscure a signal of positive selection between species. While methods have been developed to control for the confounding effects of negative selection against deleterious polymorphism, the impact of balancing selection on estimates of positive selection has not been assessed. In Saccharomyces cerevisiae, there is no signal of positive selection within protein coding sequences as the ratio of nonsynonymous to synonymous polymorphism is higher than that of divergence. To investigate the impact of balancing selection on estimates of positive selection we examined five genes with high rates of nonsynonymous polymorphism in S. cerevisiae relative to divergence from S. paradoxus. One of the genes, a high affinity zinc transporter ZRT1, shows an elevated rate of synonymous polymorphism indicative of balancing selection. The high rate of synonymous polymorphism coincides with nonsynonymous divergence between three haplotype groups, which we find to be functionally indistinguishable. We conclude that balancing selection is not likely to be a common cause of genes harboring a large excess of nonsynonymous polymorphism in yeast

Entropy of generic quantum isolated horizons

We review our recent proposal of a method to extend the quantization of spherically symmetric isolated horizons, a seminal result of loop quantum gravity, to a phase space containing horizons of arbitrary geometry. Although the details of the quantization remain formally unchanged, the physical interpretation of the results can be quite different. We highlight several such differences, with particular emphasis on the physical interpretation of black hole entropy in loop quantum gravity.Comment: 4 pages, contribution to loops '11 conference proceedings; 2 references added, a sentence remove

Coherent states, constraint classes, and area operators in the new spin-foam models

Recently, two new spin-foam models have appeared in the literature, both motivated by a desire to modify the Barrett-Crane model in such a way that the imposition of certain second class constraints, called cross-simplicity constraints, are weakened. We refer to these two models as the FKLS model, and the flipped model. Both of these models are based on a reformulation of the cross-simplicity constraints. This paper has two main parts. First, we clarify the structure of the reformulated cross-simplicity constraints and the nature of their quantum imposition in the new models. In particular we show that in the FKLS model, quantum cross-simplicity implies no restriction on states. The deeper reason for this is that, with the symplectic structure relevant for FKLS, the reformulated cross-simplicity constraints, in a certain relevant sense, are now \emph{first class}, and this causes the coherent state method of imposing the constraints, key in the FKLS model, to fail to give any restriction on states. Nevertheless, the cross-simplicity can still be seen as implemented via suppression of intertwiner degrees of freedom in the dynamical propagation. In the second part of the paper, we investigate area spectra in the models. The results of these two investigations will highlight how, in the flipped model, the Hilbert space of states, as well as the spectra of area operators exactly match those of loop quantum gravity, whereas in the FKLS (and Barrett-Crane) models, the boundary Hilbert spaces and area spectra are different.Comment: 21 pages; statements about gamma limits made more precise, and minor phrasing change

The kernel and the injectivity of the EPRL map

In this paper we prove injectivity of the EPRL map for |\gamma|<1, filling the gap of our previous paper.Comment: 17 pages, 3 figure

Crystalline cataract caused by a heterozygous missense mutation in γD-crystallin (CRYGD)

Purpose: To describe phenotypic characteristics of two pedigrees manifesting early onset crystalline cataract with mutations in the γD-crystallin gene (CRYGD). Methods: A detailed medical history was obtained from two Caucasian pedigrees manifesting autosomal dominant congenital cataracts. Genomic DNA was extracted from saliva (DNA Genotek). Single Nucleotide Polymorphism (SNP) based genome analysis of the larger pedigree revealed linkage to an 8.2 MB region on chromosome 2q33-q35 which encompassed the crystallin-gamma gene cluster (CRYG). Exons and flanking introns of CRYGA, CRYGB, CRYGC and CRYGD were amplified and sequenced to identify disease-causing mutations. Results: A morphologically unique cataract with extensive refractile “crystals ” scattered throughout the nucleus and perinuclear cortex was found in the probands from both pedigrees. A heterozygous C→A mutation was identified at position 109 of the coding sequence (R36S of the processed protein) in exon 2 of CRYGD and this missense mutation was found to cosegregate with the disease in the larger family; this mutation was then identified in affected individuals of pedigree 2 as well. Conclusions: The heterozygous 109C→A CRYGD missense mutation is associated with a distinct crystalline cataract in two US Caucasian pedigrees. This confirms crystalline cataract formation with this mutation, as previously reported in sporadic childhood case from the Czech Republic and in members of a Chinese family

Bistatic Radar System Using Satellite-Based Transmitters with Ionospheric Compensation

A system for the passive location of non-cooperating vehicles using satellite-based transmitters with ionospheric compen­sation. The system is a light-weight, low-cost, portable, and field-deployable station to supplement deficiencies in the National Airspace System (NAS) and homeland security sur­veillance networks. The system accommodates observation modes having long integration times that potentially are greater than one second. The system utilizes satellite-based transmitters as illuminators. The passive system measures two radio waves ( e.g., a direct path and an illumination plus reflection path), and applies time-difference techniques that can compensate for the ionosphere since the ionospheric delay is applied to both signals. This also has the advantage of compensating for other uncertainties such as exist in the position of the satellite

Politics and the resilience of ecosystem services

© Cambridge University Press 2015Decisions around which ecosystem services are the focus for resilience-building initiatives, and ensuring that these choices do not lead to undesirable lock-in effects that compromise the possibility for future adaptation and change, are far from&nbsp;..

Holomorphic Factorization for a Quantum Tetrahedron

We provide a holomorphic description of the Hilbert space H(j_1,..,j_n) of SU(2)-invariant tensors (intertwiners) and establish a holomorphically factorized formula for the decomposition of identity in H(j_1,..,j_n). Interestingly, the integration kernel that appears in the decomposition formula turns out to be the n-point function of bulk/boundary dualities of string theory. Our results provide a new interpretation for this quantity as being, in the limit of large conformal dimensions, the exponential of the Kahler potential of the symplectic manifold whose quantization gives H(j_1,..,j_n). For the case n=4, the symplectic manifold in question has the interpretation of the space of "shapes" of a geometric tetrahedron with fixed face areas, and our results provide a description for the quantum tetrahedron in terms of holomorphic coherent states. We describe how the holomorphic intertwiners are related to the usual real ones by computing their overlap. The semi-classical analysis of these overlap coefficients in the case of large spins allows us to obtain an explicit relation between the real and holomorphic description of the space of shapes of the tetrahedron. Our results are of direct relevance for the subjects of loop quantum gravity and spin foams, but also add an interesting new twist to the story of the bulk/boundary correspondence.Comment: 45 pages; published versio

Physical boundary state for the quantum tetrahedron

We consider stability under evolution as a criterion to select a physical boundary state for the spinfoam formalism. As an example, we apply it to the simplest spinfoam defined by a single quantum tetrahedron and solve the associated eigenvalue problem at leading order in the large spin limit. We show that this fixes uniquely the free parameters entering the boundary state. Remarkably, the state obtained this way gives a correlation between edges which runs at leading order with the inverse distance between the edges, in agreement with the linearized continuum theory. Finally, we give an argument why this correlator represents the propagation of a pure gauge, consistently with the absence of physical degrees of freedom in 3d general relativity.Comment: 20 pages, 6 figure