Grain boundary partitioning of Ar and He

An experimental procedure has been developed that permits measurement of the partitioning of Ar and He between crystal interiors and the intergranular medium (ITM) that surrounds them in synthetic melt-free polycrystalline diopside aggregates. ^(37)Ar and ^(4)He are introduced into the samples via neutron irradiation. As samples are crystallized under sub-solidus conditions from a pure diopside glass in a piston cylinder apparatus, noble gases diffusively equilibrate between the evolving crystal and intergranular reservoirs. After equilibration, ITM Ar and He is distinguished from that incorporated within the crystals by means of step heating analysis. An apparent equilibrium state (i.e., constant partitioning) is reached after about 20 h in the 1450 °C experiments. Data for longer durations show a systematic trend of decreasing ITM Ar (and He) with decreasing grain boundary (GB) interfacial area as would be predicted for partitioning controlled by the network of planar grain boundaries (as opposed to ITM gases distributed in discrete micro-bubbles or melt). These data yield values of GB-area-normalized partitioning, K¯^(Ar)_(ITM), with units of (Ar/m^3 of solid)/(Ar/m^2 of GB) of 6.8 x 10^3 – 2.4 x 104 m^(-1). Combined petrographic microscope, SEM, and limited TEM observation showed no evidence that a residual glass phase or grain boundary micro-bubbles dominated the ITM, though they may represent minor components. If a nominal GB thickness (δ) is assumed, and if the density of crystals and the grain boundaries are assumed equal, then a true grain boundary partition coefficient (K^(Ar)_(GB) = X^(Ar)_(crystals)/X^(Ar)_(GB) may be determined. For reasonable values of δ, K^(Ar)_(GB) is at least an order of magnitude lower than the Ar partition coefficient between diopside and melt. Helium partitioning data provide a less robust constraint with K¯^(He)_(ITM) between 4 x 10^3 and 4 x 10^4 cm^(-1), similar to the Ar partitioning data. These data suggest that an ITM consisting of nominally melt free, bubble free, tight grain boundaries can constitute a significant but not infinite reservoir, and therefore bulk transport pathway, for noble gases in fine grained portions of the crust and mantle where aqueous or melt fluids are non-wetting and of very low abundance (i.e., <0.1% fluid). Heterogeneities in grain size within dry equilibrated systems will correspond to significant differences in bulk rock noble gas content

Hard squares with negative activity

We show that the hard-square lattice gas with activity z= -1 has a number of remarkable properties. We conjecture that all the eigenvalues of the transfer matrix are roots of unity. They fall into groups (``strings'') evenly spaced around the unit circle, which have interesting number-theoretic properties. For example, the partition function on an M by N lattice with periodic boundary condition is identically 1 when M and N are coprime. We provide evidence for these conjectures from analytical and numerical arguments.Comment: 8 page

MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

Mississippian stratotypes

Working Group on the Mississippian of the U.S.A.Ope

Loop models and their critical points

Loop models have been widely studied in physics and mathematics, in problems ranging from polymers to topological quantum computation to Schramm-Loewner evolution. I present new loop models which have critical points described by conformal field theories. Examples include both fully-packed and dilute loop models with critical points described by the superconformal minimal models and the SU(2)_2 WZW models. The dilute loop models are generalized to include SU(2)_k models as well.Comment: 20 pages, 15 figure

Lattice Models with N=2 Supersymmetry

We introduce lattice models with explicit N=2 supersymmetry. In these interacting models, the supersymmetry generators Q^+ and Q^- yield the Hamiltonian H={Q^+,Q^-} on any graph. The degrees of freedom can be described as either fermions with hard cores, or as quantum dimers. The Hamiltonian of our simplest model contains a hopping term and a repulsive potential, as well as the hard-core repulsion. We discuss these models from a variety of perspectives: using a fundamental relation with conformal field theory, via the Bethe ansatz, and using cohomology methods. The simplest model provides a manifestly-supersymmetric lattice regulator for the supersymmetric point of the massless 1+1-dimensional Thirring (Luttinger) model. We discuss the ground-state structure of this same model on more complicated graphs, including a 2-leg ladder, and discuss some generalizations.Comment: 4 page

Assessing the reporting of categorised quantitative variables in observational epidemiological studies

Background One aspect to consider when reporting results of observational studies in epidemiology is how quantitative risk factors are analysed. The STROBE guidelines recommend that researchers describe how they handle quantitative variables when analysing data. For categorised quantitative variables, the authors are required to provide reasons and justifications informing their practice. We investigated and assessed the practices and reporting of categorised quantitative variables in epidemiology. Methods The assessment was based on five medical journals that publish epidemiological research. Observational studies published between April and June 2015 and investigating the relationships between quantitative exposures (or risk factors) and the outcomes were considered for assessment. A standard form was used to collect the data, and the reporting patterns amongst eligible studies were quantified and described in the results section. Results Out of 61 articles assessed for eligibility, 23 observational studies were included in the assessment. Categorisation of quantitative exposures occurred in 61% of these studies and reasons informing the practice were rarely provided. Only one article explained the choice of categorisation in the analysis. Transformation of quantitative exposures into four or five groups was common and dominant amongst studies using equally spaced categories. Dichotomisation was not popular; the practice featured in one article. Overall, the majority (86%) of the studies preferred ordered or arbitrary group categories. Other criterions used to decide categorical boundaries were based on established guidelines such as consensus statements and WHO standards. Conclusion Categorisation of continuous variables remains a dominant practice in epidemiological studies. The reasons informing the practice of categorisation within published work are limited and remains unknown in most articles. The existing STROBE guidelines could provide stronger recommendations on reporting quantitative risk factors in epidemiology. Keywords Categorisation - Quantitative or continuous variables - STOBE guidelines – Observational studie

Allosteric Conversation in the Androgen Receptor Ligand-Binding Domain Surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. Wepreviously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design. © 2012 by The Endocrie Society

Ground-state properties of a supersymmetric fermion chain

We analyze the ground state of a strongly interacting fermion chain with a supersymmetry. We conjecture a number of exact results, such as a hidden duality between weak and strong couplings. By exploiting a scale free property of the perturbative expansions, we find exact expressions for the order parameters, yielding the critical exponents. We show that the ground state of this fermion chain and another model in the same universality class, the XYZ chain along a line of couplings, are both written in terms of the same polynomials. We demonstrate this explicitly for up to N = 24 sites, and provide consistency checks for large N. These polynomials satisfy a recursion relation related to the Painlev\'e VI differential equation, and using a scale-free property of these polynomials, we derive a simple and exact formula for their limit as N goes to infinity.Comment: v2: added more information on scaling function, fixed typo

Novel APC promoter and exon 1B deletion and allelic silencing in three mutation-negative classic familial adenomatous polyposis families

BACKGROUND: The overwhelming majority (approximately 80%) of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gene. Families without detectable APC mutations are unable to benefit from the use of genetic testing for clinical management of this autosomal dominant syndrome. METHODS: We used exome sequencing and linkage analysis, coupled with second-generation sequencing of the APC locus including non-coding regions to investigate three APC mutation-negative classical FAP families. RESULTS: We identified a novel ~11 kb deletion localized 44 kb upstream of the transcription start site of APC that encompasses the APC 1B promoter and exon. This deletion was present only in affected family members of one kindred with classical FAP. Furthermore, this same deletion with identical breakpoints was found in the probands of two additional APC mutation-negative classical FAP kindreds. Phasing analysis of single nucleotide polymorphisms (SNPs) around the deletion site in the three probands showed evidence of a shared haplotype, suggesting a common founder deletion in the three kindreds. SNP analysis within the coding sequence of APC, revealed that this ~11 kb deletion was accompanied by silencing of one of the APC alleles in blood-derived RNA of affected individuals. CONCLUSIONS: These results support the causal role of a novel promoter deletion in FAP and suggest that non-coding deletions, identifiable using second-generation sequencing methods, may account for a significant fraction of APC mutation-negative classical FAP families