Parametric inference of recombination in HIV genomes

Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational methods are needed for detecting recombinant sequences in large databases, and for inferring the parental sequences. We present a hidden Markov model to annotate a query sequence as a recombinant of a given set of aligned sequences. Parametric inference is used to determine all optimal annotations for all parameters of the model. We show that the inferred annotations recover most features of established hand-curated annotations. Thus, parametric analysis of the hidden Markov model is feasible for HIV full-length genomes, and it improves the detection and annotation of recombinant forms. All computational results, reference alignments, and C++ source code are available at http://bio.math.berkeley.edu/recombination/.Comment: 20 pages, 5 figure

Parametric Alignment of Drosophila Genomes

The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces which are suitable for Needleman--Wunsch alignment. In these alignment methods, it is standard practice to fix the parameters and to produce a single alignment for subsequent analysis by biologists. Our main result is the construction of a whole genome parametric alignment of Drosophila melanogaster and Drosophila pseudoobscura. Parametric alignment resolves the issue of robustness to changes in parameters by finding all optimal alignments for all possible parameters in a PHMM. Our alignment draws on existing heuristics for dividing whole genomes into small pieces for alignment, and it relies on advances we have made in computing convex polytopes that allow us to parametrically align non-coding regions using biologically realistic models. We demonstrate the utility of our parametric alignment for biological inference by showing that cis-regulatory elements are more conserved between Drosophila melanogaster and Drosophila pseudoobscura than previously thought. We also show how whole genome parametric alignment can be used to quantitatively assess the dependence of branch length estimates on alignment parameters. The alignment polytopes, software, and supplementary material can be downloaded at http://bio.math.berkeley.edu/parametric/.Comment: 19 pages, 3 figure

Total internal reflection Raman spectroscopy

Total internal reflection (TIR) Raman spectroscopy is an experimentally straightforward, surface-sensitive technique for obtaining chemically specific spectroscopic information from a region within approximately 100–200 nm of a surface. While TIR Raman spectroscopy has long been overshadowed by surface-enhanced Raman scattering, with modern instrumentation TIR Raman spectra can be acquired from sub-nm thick films in only a few seconds. In this review, we describe the physical basis of TIR Raman spectroscopy and illustrate the performance of the technique in the diverse fields of surfactant adsorption, liquid crystals, lubrication, polymer films and biological interfaces, including both macroscopic structures such as the surfaces of leaves, and microscopic structures such as lipid bilayers. Progress, and challenges, in using TIR Raman to obtain depth profiles with sub-diffraction resolution are described

Carpet waste, an expensive luxury we must do without!

In the U.K. the carpet industry accounts for £935 million of income each year. About 7% or £65 million of would-be extra earning is annually lost in the form of waste produced during manufacturing processes and fittings. In a recent confidential study made under the Environmental Technology Best Practice Programme landfill was identified as the main destination for most carpet waste with incineration a close second. Cost of disposal to landfill is currently estimated at about £750,000 a year. However, with increasing public concern for the environment, this figure is already rising due to introduction of large tax duties on the use of landfill. Manufacturers are consequently under pressure to reduce waste and find alternative means of utilising their waste. This paper, in the first instance, investigates the sources of waste along the entire carpet manufacturing route and assesses their quantitative measurement. It then critically reviews the current methods of dealing with processed and post consumer wastes, exploring the various methodologies applied. In conclusion the paper recommends short and long term solutions with respect to current legislative and environmental issues and calls for novel and prime quality products utilising carpet wastes as valuable raw materials rather than cheap secondary implants

Collaborate or thread the eye of the needle

Abstract: Th

Surfactant adsorption by total internal reflection Raman spectroscopy. Part III: Adsorption onto cellulose

TIR Raman spectroscopy has been used to study the adsorption of surfactants onto cellulose. The cellulose was prepared by Langmuir–Blodgett deposition of trimethylsilylcellulose onto silica followed by removal of the trimethylsilyl groups with acid to generate a hydrophilic surface. The reaction was followed in situ with Raman spectroscopy, revealing a two-step hydrolysis. Adsorption isotherms of hexadecyltrimethylammonium bromide (CTAB) and Triton X-100 (TX-100) on hydrophilic cellulose were obtained by TIR Raman scattering under quasi-equilibrium conditions where the bulk concentration was slowly but continuously varied. The isotherms of both surfactants are almost linear, in contrast to the isotherms on hydrophilic silica. The CTAB isotherm shows hysteresis depending on whether the concentration of the surfactant is increasing or decreasing due to a slow adsorption region. A mixture of TX-100 and CTAB shows ideal adsorption, in contrast to adsorption of the same mixture on silica where there is a strong cooperative interaction at low CTAB surface coverage

Electrostatically confined monolayer graphene quantum dots with orbital and valley splittings

The electrostatic confinement of massless charge carriers is hampered by Klein tunneling. Circumventing this problem in graphene mainly relies on carving out nanostructures or applying electric displacement fields to open a band gap in bilayer graphene. So far, these approaches suffer from edge disorder or insufficiently controlled localization of electrons. Here we realize an alternative strategy in monolayer graphene, by combining a homogeneous magnetic field and electrostatic confinement. Using the tip of a scanning tunneling microscope, we induce a confining potential in the Landau gaps of bulk graphene without the need for physical edges. Gating the localized states towards the Fermi energy leads to regular charging sequences with more than 40 Coulomb peaks exhibiting typical addition energies of 7-20 meV. Orbital splittings of 4-10 meV and a valley splitting of about 3 meV for the first orbital state can be deduced. These experimental observations are quantitatively reproduced by tight binding calculations, which include the interactions of the graphene with the aligned hexagonal boron nitride substrate. The demonstrated confinement approach appears suitable to create quantum dots with well-defined wave function properties beyond the reach of traditional techniques

A continuum model of gas flows with localized density variations

We discuss the kinetic representation of gases and the derivation of macroscopic equations governing the thermomechanical behavior of a dilute gas viewed at the macroscopic level as a continuous medium. We introduce an approach to kinetic theory where spatial distributions of the molecules are incorporated through a mean-free-volume argument. The new kinetic equation derived contains an extra term involving the evolution of this volume, which we attribute to changes in the thermodynamic properties of the medium. Our kinetic equation leads to a macroscopic set of continuum equations in which the gradients of thermodynamic properties, in particular density gradients, impact on diffusive fluxes. New transport terms bearing both convective and diffusive natures arise and are interpreted as purely macroscopic expansion or compression. Our new model is useful for describing gas flows that display non-local-thermodynamic-equilibrium (rarefied gas flows), flows with relatively large variations of macroscopic properties, and/or highly compressible fluid flows

Idiopathic sclerosing orbital inflammation mimicking a malignant spindle cell tumor in a dog

A dog presented with a retrobulbar mass, diagnosed histopathologically as malignant spindle cell neoplasia. Emergence of analogous findings in the contralateral orbit prompted extended immunohistochemistry of the original mass and reassignment to idiopathic sclerosing orbital inflammation. Early incisional biopsy with extended immunohistochemical analysis should be considered for canine orbital tumors

Van der Walls interaction affects wrinkle formation in two-dimensional materials

Nonlinear mechanics of solids is an exciting field that encompasses both beautiful mathematics, such as the emergence of instabilities and the formation of complex patterns, as well as multiple applications. Two-dimensional crystals and van der Waals (vdW) heterostructures allow revisiting this field on the atomic level, allowing much finer control over the parameters and offering atomistic interpretation of experimental observations. In this work, we consider the formation of instabilities consisting of radially oriented wrinkles around mono- and few-layer “bubbles” in two-dimensional vdW heterostructures. Interestingly, the shape and wavelength of the wrinkles depend not only on the thickness of the two-dimensional crystal forming the bubble, but also on the atomistic structure of the interface between the bubble and the substrate, which can be controlled by their relative orientation. We argue that the periodic nature of these patterns emanates from an energetic balance between the resistance of the top membrane to bending, which favors large wavelength of wrinkles, and the membrane-substrate vdW attraction, which favors small wrinkle amplitude. Employing the classical “Winkler foundation” model of elasticity theory, we show that the number of radial wrinkles conveys a valuable relationship between the bending rigidity of the top membrane and the strength of the vdW interaction. Armed with this relationship, we use our data to demonstrate a nontrivial dependence of the bending rigidity on the number of layers in the top membrane, which shows two different regimes driven by slippage between the layers, and a high sensitivity of the vdW force to the alignment between the substrate and the membrane