Compressed Genotyping

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, largely due to the relatively tedious and expensive process of DNA sequencing. Since the genetic polymorphisms that underlie these disorders are relatively rare in the human population, the presence or absence of a disease-linked polymorphism can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies, and assembled a mathematical framework that has some important distinctions from 'traditional' compressed sensing ideas in order to address different biological and technical constraints.Comment: Submitted to IEEE Transaction on Information Theory - Special Issue on Molecular Biology and Neuroscienc

Necessary and sufficient conditions for non-perturbative equivalences of large N orbifold gauge theories

Large N coherent state methods are used to study the relation between U(N) gauge theories containing adjoint representation matter fields and their orbifold projections. The classical dynamical systems which reproduce the large N limits of the quantum dynamics in parent and daughter orbifold theories are compared. We demonstrate that the large N dynamics of the parent theory, restricted to the subspace invariant under the orbifold projection symmetry, and the large N dynamics of the daughter theory, restricted to the untwisted sector invariant under "theory space'' permutations, coincide. This implies equality, in the large N limit, between appropriately identified connected correlation functions in parent and daughter theories, provided the orbifold projection symmetry is not spontaneously broken in the parent theory and the theory space permutation symmetry is not spontaneously broken in the daughter. The necessity of these symmetry realization conditions for the validity of the large N equivalence is unsurprising, but demonstrating the sufficiency of these conditions is new. This work extends an earlier proof of non-perturbative large N equivalence which was only valid in the phase of the (lattice regularized) theories continuously connected to large mass and strong coupling.Comment: 21 page, JHEP styl

Small volume expansion of almost supersymmetric large N theories

We consider the small-volume dynamics of nonsupersymmetric orbifold and orientifold field theories defined on a three-torus, in a test of the claimed planar equivalence between these models and appropriate supersymmetric ``parent models". We study one-loop effective potentials over the moduli space of flat connections and find that planar equivalence is preserved for suitable averages over the moduli space. On the other hand, strong nonlinear effects produce local violations of planar equivalence at special points of moduli space. In the case of orbifold models, these effects show that the "twisted" sector dominates the low-energy dynamics.Comment: 20 pages, 3 figures; added references, minor change

Tuning continua and keyboard layouts

Previous work has demonstrated the existence of keyboard layouts capable of maintaining consistent fingerings across a parametrized family of tunings. This paper describes the general principles underlying layouts that are invariant in both transposition and tuning. Straightforward computational methods for determining appropriate bases for a regular temperament are given in terms of a row-reduced matrix for the temperament-mapping. A concrete description of the range over which consistent fingering can be maintained is described by the valid tuning range. Measures of the resulting keyboard layouts allow direct comparison of the ease with which various chordal and scalic patterns can be fingered as a function of the keyboard geometry. A number of concrete examples illustrate the generality of the methods and their applicability to a wide variety of commas and temperaments, tuning continua and keyboard layouts

A MIDI sequencer that widens access to the compositional possibilities of novel tunings

We present a new Dynamic Tonality MIDI sequencer, Hex, that aims to make sequencing music in and across a large variety of novel tunings as straightforward as sequencing in twelve-tone equal temperament. It replaces the piano roll used in conventional MIDI sequencers with a two-dimensional lattice roll in order to enable the intuitive visualization and dynamic manipulation of tuning. In conventional piano roll sequencers, a piano keyboard is displayed on the left side of the window, and white and black note lanes extend horizontally to the right, into which a user can draw a sequence of notes. Similarly, in Hex, a button lattice is displayed in its own pane on the left side of the window, and horizontal lines are drawn from the center of each note to the right. These lines function as generalized note lanes, just like in piano roll sequencers, but with the added benefit that each note lane's height is always proportional to its pitch, even if the user changes the tuning. The presence of the button lattice on the left side of the window illustrates exactly which buttons a performer would play in order to replicate the sequence when playing a physical button lattice instrument

Hamiltonian light-front field theory within an AdS/QCD basis

Non-perturbative Hamiltonian light-front quantum field theory presents opportunities and challenges that bridge particle physics and nuclear physics. Fundamental theories, such as Quantum Chromodynmamics (QCD) and Quantum Electrodynamics (QED) offer the promise of great predictive power spanning phenomena on all scales from the microscopic to cosmic scales, but new tools that do not rely exclusively on perturbation theory are required to make connection from one scale to the next. We outline recent theoretical and computational progress to build these bridges and provide illustrative results for nuclear structure and quantum field theory. As our framework we choose light-front gauge and a basis function representation with two-dimensional harmonic oscillator basis for transverse modes that corresponds with eigensolutions of the soft-wall AdS/QCD model obtained from light-front holography.Comment: To appear in the proceedings of Light-Cone 2009: Relativistic Hadronic and Particle Physics, July 8-13, 2009, Sao Jose dos Campos, Brazi

Expression of factor V by resident macrophages boosts host defense in the peritoneal cavity

Macrophages resident in different organs express distinct genes, but understanding how this diversity fits into tissue-specific features is limited. Here, we show that selective expression of coagulation factor V (FV) by resident peritoneal macrophages in mice promotes bacterial clearance in the peritoneal cavity and serves to facilitate the well-known but poorly understood macrophage disappearance reaction. Intravital imaging revealed that resident macrophages were nonadherent in peritoneal fluid during homeostasis. Bacterial entry into the peritoneum acutely induced macrophage adherence and associated bacterial phagocytosis. However, optimal control of bacterial expansion in the peritoneum also required expression of FV by the macrophages to form local clots that effectively brought macrophages and bacteria in proximity and out of the fluid phase. Thus, acute cellular adhesion and resident macrophage-induced coagulation operate independently and cooperatively to meet the challenges of a unique, open tissue environment. These events collectively account for the macrophage disappearance reaction in the peritoneal cavity

Supernovae as a probe of particle physics and cosmology

It has very recently been demonstrated by Csaki, Kaloper and Terning (CKT) that the faintness of supernovae at high redshift can be accommodated by mixing of a light axion with the photon in the presence of an intergalactic magnetic field, as opposed to the usual explanation of an accelerating universe by a dark energy component. In this paper we analyze further aspects of the CKT mechanism and its generalizations. The CKT mechanism also passes various cosmological constraints from the fluctuations of the CMB and the formation of structure at large scales, without requiring an accelerating phase in the expansion of the Universe. We investigate the statistical significance of current supernova data for pinning down the different components of the cosmological energy-momentum tensor and for probing physics beyond the standard models.Comment: 17 pages, LaTeX, 4 figures; v2: typos corrected, minor changes, references added; v3: updated figures, details regarding fits include

A tubo-ovarian abscess mimicking an appendiceal abscess: a rare presentation of Streptococcus agalactiae.

A tubo-ovarian abscess (TOA) is a relatively rare medical complication that results from an untreated/unrecognized ascending pelvic infection of the female genital tract. In a right-sided TOA, this clinical entity may mimic appendicitis on computed tomography (CT). In addition, both disease processes can present with pelvic pain, leukocytosis and fever. We present the case of a 47-year-old female with mid right-sided abdominal pain that was diagnosed on CT scan with an appendiceal abscess. She underwent CT-guided percutaneous drainage with interventional radiology. On Day 8, a CT limited study involving a contrast injection was performed to evaluate for abscess resolution. The contrast within the drain filled the fallopian tube, endometrial cavity and contralateral fallopian tube. These findings demonstrated that the initial diagnosis actually represented a TOA. To the authors\u27 knowledge, this is the only reported case involving a TOA secondary to Streptococcus agalactiae (GBS) mimicking an appendicitis with abscess formation

N=1 Supersymmetric Product Group Theories in the Coulomb Phase

We study the low-energy behavior of N=1 supersymmetric gauge theories with product gauge groups SU(N)^M and M chiral superfields transforming in the fundamental representation of two of the SU(N) factors. These theories are in the Coulomb phase with an unbroken U(1)^(N-1) gauge group. For N >= 3, M >= 3 the theories are chiral. The low-energy gauge kinetic functions can be obtained from hyperelliptic curves which we derive by considering various limits of the theories. We present several consistency checks of the curves including confinement through the addition of mass perturbations and other limits.Comment: 22 pages, LaTeX, minor changes. Eqs. (20) and (42) correcte