Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response

© 2014. Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes

On graviton non-Gaussianities during inflation

We consider the most general three point function for gravitational waves produced during a period of exactly de Sitter expansion. The de Sitter isometries constrain the possible shapes to only three: two preserving parity and one violating parity. These isometries imply that these correlation functions should be conformal invariant. One of the shapes is produced by the ordinary gravity action. The other shape is produced by a higher derivative correction and could be as large as the gravity contribution. The parity violating shape does not contribute to the bispectrum [1106.3228, 1108.0175], even though it is present in the wavefunction. We also introduce a spinor helicity formalism to describe de Sitter gravitational waves with circular polarization. These results also apply to correlation functions in Anti-de Sitter space. They also describe the general form of stress tensor correlation functions, in momentum space, in a three dimensional conformal field theory. Here all three shapes can arise, including the parity violating one.Comment: 51 pages, v2: Corrected statement about parity violation in the gravitational wave bispectrum. Some other changes and references adde

Tracking Dehydration Mechanisms in Crystalline Hydrates with Molecular Dynamics Simulations

Dehydration of crystalline solids is a widespread phenomenon, yet the fundamental mechanisms by which dehydration occurs is not properly understood. This arises due to technical limitations in studying such fast processes with sufficient sensitivity, nevertheless understanding dehydration pathways is critical for designing optimal properties for materials, particularly in the case of pharmaceutical solids. The computational methods presented here allow for accurate determination of the dehydrated species' crystal structure and to develop an understanding of the mechanism of dehydration at the molecular level. This work also highlights the critical role of explicitly taking into account the dynamical aspect of molecules using computational techniques, rather then relying on static energy minimization approaches. Specifically, the crystalline active pharmaceutical agent naproxen sodium, and its hydrates, is studied in silico using density functional theory and molecular dynamics, ultimately elucidating the face-specific dehydration mechanisms and revealing highly complex diffusion and nucleation behaviour. Additionally, the results indicate that the method is a viable way to explore dehydration pathways and predict new dehydrated crystal structures.A.S.L, K.E.J and J.R. gratefully acknowledges the Villum Foundation (Denmark) for financial support (project No. VKR023111). M.T.R. and J.A.Z. would like to acknowledge funding from the U.K. Engineering and Physical Sciences Research Council (EP/N022769/1)

Neuromodulation and the role of electrodiagnostic techniques

Electrodiagnostic techniques have been utilized in surgery since the early 1960s. These techniques have been primarily used in neurosurgery; however, with the introduction of neuromodulation for voiding dysfunction, these techniques have now found their way into the field of female pelvic medicine. This article will review techniques applicable to evaluate pelvic floor function as it relates to neuromodulation. It will also review the literature describing how these techniques are used to help determine appropriate candidates as well as improve surgical outcomes. A PubMed search was conducted using the terms neuromodulation, Interstim, electrodiagnosis, electrodiagnostic techniques, electromyography with limits to the pelvic floor, and voiding dysfunction. Eight articles and three abstracts were found that directly related to the use of electrodiagnostic techniques as they apply to neuromodulation. Electrodiagnostic techniques may play a role in helping predict appropriate candidates for neuromodulation as well as improve surgical outcomes

A road to reality with topological superconductors

Topological states of matter are a source of low-energy quasiparticles, bound to a defect or propagating along the surface. In a superconductor these are Majorana fermions, described by a real rather than a complex wave function. The absence of complex phase factors promises protection against decoherence in quantum computations based on topological superconductivity. This is a tutorial style introduction written for a Nature Physics focus issue on topological matter.Comment: pre-copy-editing, author-produced version of the published paper: 4 pages, 2 figure

Individual Eigenvalue Distributions for the Wilson Dirac Operator

We derive the distributions of individual eigenvalues for the Hermitian Wilson Dirac Operator D5 as well as for real eigenvalues of the Wilson Dirac Operator DW. The framework we provide is valid in the epsilon regime of chiral perturbation theory for any number of flavours Nf and for non-zero low energy constants W6, W7, W8. It is given as a perturbative expansion in terms of the k-point spectral density correlation functions and integrals thereof, which in some cases reduces to a Fredholm Pfaffian. For the real eigenvalues of DW at fixed chirality nu this expansion truncates after at most nu terms for small lattice spacing "a". Explicit examples for the distribution of the first and second eigenvalue are given in the microscopic domain as a truncated expansion of the Fredholm Pfaffian for quenched D5, where all k-point densities are explicitly known from random matrix theory. For the real eigenvalues of quenched DW at small "a" we illustrate our method by the finite expansion of the corresponding Fredholm determinant of size nu.Comment: 20 pages, 5 figures; v2: typos corrected, refs added and discussion of W6 and W7 extende

Sub-logarithmic Distributed Oblivious RAM with Small Block Size

Oblivious RAM (ORAM) is a cryptographic primitive that allows a client to securely execute RAM programs over data that is stored in an untrusted server. Distributed Oblivious RAM is a variant of ORAM, where the data is stored in $m>1$ servers. Extensive research over the last few decades have succeeded to reduce the bandwidth overhead of ORAM schemes, both in the single-server and the multi-server setting, from $O(\sqrt{N})$ to $O(1)$. However, all known protocols that achieve a sub-logarithmic overhead either require heavy server-side computation (e.g. homomorphic encryption), or a large block size of at least $\Omega(\log^3 N)$. In this paper, we present a family of distributed ORAM constructions that follow the hierarchical approach of Goldreich and Ostrovsky [GO96]. We enhance known techniques, and develop new ones, to take better advantage of the existence of multiple servers. By plugging efficient known hashing schemes in our constructions, we get the following results: 1. For any $m\geq 2$, we show an $m$-server ORAM scheme with $O(\log N/\log\log N)$ overhead, and block size $\Omega(\log^2 N)$. This scheme is private even against an $(m-1)$-server collusion. 2. A 3-server ORAM construction with $O(\omega(1)\log N/\log\log N)$ overhead and a block size almost logarithmic, i.e. $\Omega(\log^{1+\epsilon}N)$. We also investigate a model where the servers are allowed to perform a linear amount of light local computations, and show that constant overhead is achievable in this model, through a simple four-server ORAM protocol

Ash generation and distribution from the April-May 2010 eruption of Eyjafjallajökull, Iceland

The 39-day long eruption at the summit of Eyjafjallajökull volcano in April–May 2010 was of modest size but ash was widely dispersed. By combining data from ground surveys and remote sensing we show that the erupted material was 4.8±1.2·1011 kg (benmoreite and trachyte, dense rock equivalent volume 0.18±0.05 km3). About 20% was lava and water-transported tephra, 80% was airborne tephra (bulk volume 0.27 km3) transported by 3–10 km high plumes. The airborne tephra was mostly fine ash (diameter <1000 µm). At least 7·1010 kg (70 Tg) was very fine ash (<28 µm), several times more than previously estimated via satellite retrievals. About 50% of the tephra fell in Iceland with the remainder carried towards south and east, detected over ~7 million km2 in Europe and the North Atlantic. Of order 1010 kg (2%) are considered to have been transported longer than 600–700 km with <108 kg (<0.02%) reaching mainland Europe