Flutamide-induced hypospadias in rats: A critical assessment.

This paper provides the first detailed description of flutamide-induced hypospadias in the rat based upon wholemount, histologic, three-dimensional reconstruction, scanning electron microscopic, and immunocytochemical analysis. The penile malformations elicited by this potent anti-androgen include a substantial proximal shift in the urethral meatus that clearly conforms to the definition of hypospadias based upon specific morphological criteria for this malformation. Through examination of the normal penile development and flutamide-induced abnormal penile development observed in prenatally oil- and flutamide-treated rats, our analysis provides insights into the morphogenetic mechanism of development of hypospadias. In this regard, a common theme in normal penile development is midline fusion of epithelia followed by removal of the epithelial seam and establishment of midline mesenchymal confluence during development of the penile urethra and prepuce, processes which are impaired as a result of prenatal flutamide treatment. The developmental processes occurring in normal penile development, through comparison with development of female external genitalia and those impaired due to prenatal flutamide treatment, are consistent with critical role of androgen receptors in normal penile development in the rat, and the specific penile abnormalities embodied in flutamide-induced rat hypospadias

Periodicity in Rank 2 Graph Algebras

Kumjian and Pask introduced an aperiodicity condition for higher rank graphs. We present a detailed analysis of when this occurs in certain rank 2 graphs. When the algebra is aperiodic, we give another proof of the simplicity of \ca(\Fth). The periodic C*-algebras are characterized, and it is shown that \ca(\Fth) \simeq \rC(\bT) \otimes \fA where \fA is a simple C*-algebra.Comment: 27 page

Wavelets and graph C∗C^*-algebras

Here we give an overview on the connection between wavelet theory and representation theory for graph $C^{\ast}$-algebras, including the higher-rank graph $C^*$-algebras of A. Kumjian and D. Pask. Many authors have studied different aspects of this connection over the last 20 years, and we begin this paper with a survey of the known results. We then discuss several new ways to generalize these results and obtain wavelets associated to representations of higher-rank graphs. In \cite{FGKP}, we introduced the "cubical wavelets" associated to a higher-rank graph. Here, we generalize this construction to build wavelets of arbitrary shapes. We also present a different but related construction of wavelets associated to a higher-rank graph, which we anticipate will have applications to traffic analysis on networks. Finally, we generalize the spectral graph wavelets of \cite{hammond} to higher-rank graphs, giving a third family of wavelets associated to higher-rank graphs

Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory (DFT) in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics, and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) can be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALBs requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale two-dimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. Employing 55,296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8,586 atoms is 90 seconds, and the time for a graphene sheet containing 11,520 atoms is 75 seconds.Comment: Submitted to The Journal of Chemical Physic

Angular sensitivity of blowfly photoreceptors: intracellular measurements and wave-optical predictions

The angular sensitivity of blowfly photoreceptors was measured in detail at wavelengths λ = 355, 494 and 588 nm. The measured curves often showed numerous sidebands, indicating the importance of diffraction by the facet lens. The shape of the angular sensitivity profile is dependent on wavelength. The main peak of the angular sensitivities at the shorter wavelengths was flattened. This phenomenon as well as the overall shape of the main peak can be quantitatively described by a wave-optical theory using realistic values for the optical parameters of the lens-photoreceptor system. At a constant response level of 6 mV (almost dark adapted), the visual acuity of the peripheral cells R1-6 is at longer wavelengths mainly diffraction limited, while at shorter wavelengths the visual acuity is limited by the waveguide properties of the rhabdomere. Closure of the pupil narrows the angular sensitivity profile at the shorter wavelengths. This effect can be fully described by assuming that the intracellular pupil progressively absorbs light from the higher order modes. In light-adapted cells R1-6 the visual acuity is mainly diffraction limited at all wavelengths.

Twisted k-graph algebras associated to Bratteli diagrams

Given a system of coverings of k-graphs, we show that the cohomology of the resulting (k+1)-graph is isomorphic to that of any one of the k-graphs in the system. We then consider Bratteli diagrams of 2-graphs whose twisted C*-algebras are matrix algebras over noncommutative tori. For such systems we calculate the ordered K-theory and the gauge-invariant semifinite traces of the resulting 3-graph C*-algebras. We deduce that every simple C*-algebra of this form is Morita equivalent to the C*-algebra of a rank-2 Bratteli diagram in the sense of Pask-Raeburn-R{\o}rdam-Sims.Comment: 28 pages, pictures prepared using tik

Non-Equilibrium Electron Transport in Two-Dimensional Nano-Structures Modeled by Green's Functions and the Finite-Element Method

We use the effective-mass approximation and the density-functional theory with the local-density approximation for modeling two-dimensional nano-structures connected phase-coherently to two infinite leads. Using the non-equilibrium Green's function method the electron density and the current are calculated under a bias voltage. The problem of solving for the Green's functions numerically is formulated using the finite-element method (FEM). The Green's functions have non-reflecting open boundary conditions to take care of the infinite size of the system. We show how these boundary conditions are formulated in the FEM. The scheme is tested by calculating transmission probabilities for simple model potentials. The potential of the scheme is demonstrated by determining non-linear current-voltage behaviors of resonant tunneling structures.Comment: 13 pages,15 figure

Designing citizen science tools for learning: lessons learnt from the iterative development of nQuire

This paper reports on a 4-year research and development case study about the design of citizen science tools for inquiry learning. It details the process of iterative pedagogy-led design and evaluation of the nQuire toolkit, a set of web-based and mobile tools scaffolding the creation of online citizen science investigations. The design involved an expert review of inquiry learning and citizen science, combined with user experience studies involving more than 200 users. These have informed a concept that we have termed ‘citizen inquiry’, which engages members of the public alongside scientists in setting up, running, managing or contributing to citizen science projects with a main aim of learning about the scientific method through doing science by interaction with others. A design-based research (DBR) methodology was adopted for the iterative design and evaluation of citizen science tools. DBR was focused on the refinement of a central concept, ‘citizen inquiry’, by exploring how it can be instantiated in educational technologies and interventions. The empirical evaluation and iteration of technologies involved three design experiments with end users, user interviews, and insights from pedagogy and user experience experts. Evidence from the iterative development of nQuire led to the production of a set of interaction design principles that aim to guide the development of online, learning-centred, citizen science projects. Eight design guidelines are proposed: users as producers of knowledge, topics before tools, mobile affordances, scaffolds to the process of scientific inquiry, learning by doing as key message, being part of a community as key message, every visit brings a reward, and value users and their time

Strong Shift Equivalence of C∗C^*-correspondences

We define a notion of strong shift equivalence for $C^*$-correspondences and show that strong shift equivalent $C^*$-correspondences have strongly Morita equivalent Cuntz-Pimsner algebras. Our analysis extends the fact that strong shift equivalent square matrices with non-negative integer entries give stably isomorphic Cuntz-Krieger algebras.Comment: 26 pages. Final version to appear in Israel Journal of Mathematic

Investigating the utility of combining Phi 29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray (TM) genotyping

Background: Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated Phi29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray(TM) genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. Results: Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray sample exclusion rate, blind to sample type, was 10.5% for MDA product compared to 5.8% for gDNA. Conclusions: We conclude that the BeadArray technology successfully produces high quality genotyping data from MDA product. The combination of these technologies improves the feasibility and efficiency of mapping common disease susceptibility genes despite limited stocks of gDNA samples