Close Packing of Atoms, Geometric Frustration and the Formation of Heterogeneous States in Crystals

To describe structural peculiarities in inhomogeneous media caused by the tendency to the close packing of atoms a formalism based on the using of the Riemann geometry methods (which were successfully applied lately to the description of structures of quasicrystals and glasses) is developed. Basing on this formalism we find in particular the criterion of stability of precipitates of the Frank-Kasper phases in metallic systems. The nature of the ''rhenium effect'' in W-Re alloys is discussed.Comment: 14 pages, RevTex, 2 PostScript figure

Shock Wave Structure in a Strongly Nonlinear Granular Lattice with Viscous Dissipation

The shock wave structure in a one-dimensional lattice (e.g. granular chain) with a power law dependence of force on displacement between particles with viscous dissipation is considered and compared to the corresponding long wave approximation. A dissipative term depending on the relative velocity between neighboring particles is included in the discrete model to investigate its influence on the shape of steady shock profiles. The critical viscosity coefficient is obtained from the long-wave approximation for arbitrary values of the exponent n and denotes the transition from an oscillatory to a monotonic shock profile in stronly nonlinear systems. The expression for the critical viscosity coefficient converges to the known equation for the critical viscosity in the weakly nonlinear case. Values of viscosity based on this expression are comparable to the values obtained in the numerical analysis of a discrete particle lattice with a Herzian contact interaction corresponding to n = 3/2. An initial disturbance in a discrete system approaches a stationary shock profile after traveling a short distance that is comparable to the width of the leading pulse of a stationary shock front. The shock front width is minimized when the viscosity is equal to its critical value.Comment: 20 pages, 6 figure

2-{[2,8-Bis(trifluoro­meth­yl)quinolin-4-yl](hy­droxy)meth­yl}piperidin-1-ium 3-amino-5-nitro­benzoate sesquihydrate

The asymmetric unit of the title salt solvate, C17H17F6N2O+·C7H5N2O4 −·1.5H2O, comprises a piperidin-1-ium cation, a 3-amino-5-nitro­benzoate anion, and three fractionally occupied [i.e. 0.414 (3), 0.627 (6) and 0.459 (5)] disordered water mol­ecules of solvation. The cation has an L shape with a C—C—C—C torsion angle of −102.9 (3)° for the atoms linking the quinolinyl group to the rest of the cation. In the anion, the carboxyl­ate and nitro groups are essentially coplanar with the benzene ring [O—C—C—C torsion angle = 179.7 (2)° and O—N—C—C torsion angle = −3.9 (3)°]. In the crystal, extensive O—H⋯O, O—H⋯F and N—H⋯·O hydrogen bonding leads to the formation of a layer in the ab plane

(R*,S*)-(±)-1-(2-{[2,8-Bis(trifluoromethyl)quinolin-4-yl](hydroxy)methyl}piperidin-1-yl)ethanone methanol monosolvate

The title mefloquine derivative has been crystallized as its 1:1 methanol solvate, C19H18F6N2O2·CH3OH. Each of the meth­ine­hydroxyl residue [the C—C—C—O torsion angle is −16.35 (17) °] and the piperidinyl group [distorted chair conformation] lies to one side of the quinolinyl ring system. The hydroxyl and carbonyl groups lie to either side of the mol­ecule, enabling their participation in inter­molecular inter­actions. Thus, the hydroxyl and carbonyl groups of two centrosymmetrically related mol­ecules are bridged by two methanol mol­ecules via O—H⋯O hydrogen bonds, leading to a four-mol­ecule aggregate. These are linked into a supra­molecular chain along the a axis via C—H⋯O inter­actions involving the hydroxyl-O atom. The chains assemble into layers that inter­digitate along the c axis being connected by C—H⋯F inter­actions

Where is the UK's pollinator biodiversity? The importance of urban areas for flower-visiting insects

Insect pollinators provide a crucial ecosystem service, but are under threat. Urban areas could be important for pollinators, though their value relative to other habitats is poorly known. We compared pollinator communities using quantified flower-visitation networks in 36 sites (each 1 km2) in three landscapes: urban, farmland and nature reserves. Overall, flower-visitor abundance and species richness did not differ significantly between the three landscape types. Bee abundance did not differ between landscapes, but bee species richness was higher in urban areas than farmland. Hoverfly abundance was higher in farmland and nature reserves than urban sites, but species richness did not differ significantly. While urban pollinator assemblages were more homogeneous across space than those in farmland or nature reserves, there was no significant difference in the numbers of rarer species between the three landscapes. Network-level specialization was higher in farmland than urban sites. Relative to other habitats, urban visitors foraged from a greater number of plant species (higher generality) but also visited a lower proportion of available plant species (higher specialization), both possibly driven by higher urban plant richness. Urban areas are growing, and improving their value for pollinators should be part of any national strategy to conserve and restore pollinators

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Non-singular screw dislocations as the Coulomb gas with smoothed out coupling and the renormalization of the shear modulus

A field theory is developed for a thermodynamical description of array of parallel non-singular screw dislocations in elastic cylinder. The partition function of the system is considered in the functional integral form. Self-energy of the dislocation cores is chosen in the form suggested by the gauge-translational model of non-singular screw dislocation. It is shown that the system of the dislocations is equivalent to the two-dimensional Coulomb gas. The coupling potential is prevented from a short-distance divergency since the core energies are taken into account. Two-point correlation functions of the stress components are obtained. Renormalization of the shear modulus caused by the presence of the dislocations is studied in the approximation of non-interacting dislocation dipoles. It is demonstrated that the finite size of the dislocation cores results in a modification of the renormalization law.Comment: 20 pages, LaTe

Reporting HIV in Papua New Guinea: Trends and Omissions from 2000 to 2010

This article presents the findings from a longitudinal content analysis on the reporting of HIV (Human Immunodeficiency Virus) in Papua New Guinea’s two national newspapers—The National and Post-Courier—in 2000, 2005 and 2010. The authors tried to answer two key questions: Did press coverage of the disease increase and did the topics change or remain the same? Data from the content analysis showed that coverage of the disease increased significantly during the ten-year study period, and that the framing of the disease moved beyond representing HIV as purely a health story to one that was linked to socio-economic conditions and cultural practices. The feature stories gradually showed more sensitivity to people living with HIV, while they recognised and challenged the social stigma still associated with the disease in much of the countr

The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry

The closest tensors of higher symmetry classes are derived in explicit form for a given elasticity tensor of arbitrary symmetry. The mathematical problem is to minimize the elastic length or distance between the given tensor and the closest elasticity tensor of the specified symmetry. Solutions are presented for three distance functions, with particular attention to the Riemannian and log-Euclidean distances. These yield solutions that are invariant under inversion, i.e., the same whether elastic stiffness or compliance are considered. The Frobenius distance function, which corresponds to common notions of Euclidean length, is not invariant although it is simple to apply using projection operators. A complete description of the Euclidean projection method is presented. The three metrics are considered at a level of detail far greater than heretofore, as we develop the general framework to best fit a given set of moduli onto higher elastic symmetries. The procedures for finding the closest elasticity tensor are illustrated by application to a set of 21 moduli with no underlying symmetry.Comment: 48 pages, 1 figur

Diverse CRISPRs Evolving in Human Microbiomes

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR–associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes