Signal processing for molecular and cellular biological physics:an emerging field

Recent advances in our ability to watch the molecular and cellular processes of life in action-such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer-raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied

Cornering the unphysical vertex

In the classical pure spinor worldsheet theory of AdS5xS5 there are some vertex operators which do not correspond to any physical excitations. We study their flat space limit. We find that the BRST operator of the worldsheet theory in flat space-time can be nontrivially deformed without deforming the worldsheet action. Some of these deformations describe the linear dilaton background. But the deformation corresponding to the nonphysical vertex differs from the linear dilaton in not being worldsheet parity even. The nonphysically deformed worldsheet theory has nonzero beta-function at one loop. This means that the classical Type IIB SUGRA backgrounds are not completely characterized by requiring the BRST symmetry of the classical worldsheet theory; it is also necessary to require the vanishing of the one-loop beta-function.Comment: LaTeX 40pp; v2: explained the relation to the linear dilaton background (Section 6), changes in Introduction and Abstrac

Cytonuclear introgressive swamping and species turnover of bass after an introduction

Species-specific RFLP markers from mitochondrial DNA (mtDNA) were identified and employed in conjunction with previously reported data for nuclear allozyme markers to examine the genetic consequences of an artificial introduction of spotted bass (Micropterus punctulatus) into a north Georgia reservoir originally occupied by native small mouth bass (M. dolomieui). The cytonuclear genetic data indicate that within 10-15 years following the unauthorized introduction, a reversal in these species' abundances has occurred and that more than 99% of the population sample analyzed here consists of spotted bass or products of interspecific hybridization. This demographic shift, perhaps ecologically or environmentally mediated, has been accompanied by introgressive swamping; more than 95% of the remaining small mouth bass nuclear and cytoplasmic alleles are present in individuals of hybrid ancestry. Dilocus cytonuclear disequilibria were significantly different from zero, with patterns indicative of an excess of homospecific genetic combinations (relative to expectations from single-locus allelic frequencies) and a disproportionate contribution of small mouth bass mothers to the hybrid gene pool. Results document dramatic genetic and demographic changes following the human-mediated introduction of a nonnative species

Nonabelian Faddeev-Niemi Decomposition of the SU(3) Yang-Mills Theory

Faddeev and Niemi (FN) have introduced an abelian gauge theory which simulates dynamical abelianization in Yang-Mills theory (YM). It contains both YM instantons and Wu-Yang monopoles and appears to be able to describe the confining phase. Motivated by the meson degeneracy problem in dynamical abelianization models, in this note we present a generalization of the FN theory. We first generalize the Cho connection to dynamical symmetry breaking pattern SU(N+1) -> U(N), and subsequently try to complete the Faddeev-Niemi decomposition by keeping the missing degrees of freedom. While it is not possible to write an on-shell complete FN decomposition, in the case of SU(3) theory of physical interest we find an off-shell complete decomposition for SU(3) -> U(2) which amounts to partial gauge fixing, generalizing naturally the result found by Faddeev and Niemi for the abelian scenario SU(N+1) -> U(1)^N. We discuss general topological aspects of these breakings, demonstrating for example that the FN knot solitons never exist when the unbroken gauge symmetry is nonabelian, and recovering the usual no-go theorems for colored dyons.Comment: Latex 30 page

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

published_or_final_versio

Exactly Marginal Deformations and Global Symmetries

We study the problem of finding exactly marginal deformations of N=1 superconformal field theories in four dimensions. We find that the only way a marginal chiral operator can become not exactly marginal is for it to combine with a conserved current multiplet. Additionally, we find that the space of exactly marginal deformations, also called the "conformal manifold," is the quotient of the space of marginal couplings by the complexified continuous global symmetry group. This fact explains why exactly marginal deformations are ubiquitous in N=1 theories. Our method turns the problem of enumerating exactly marginal operators into a problem in group theory, and substantially extends and simplifies the previous analysis by Leigh and Strassler. We also briefly discuss how to apply our analysis to N=2 theories in three dimensions.Comment: 23 pages, 2 figure

Divergent mathematical treatments in utility theory

In this paper I study how divergent mathematical treatments affect mathematical modelling, with a special focus on utility theory. In particular I examine recent work on the ranking of information states and the discounting of future utilities, in order to show how, by replacing the standard analytical treatment of the models involved with one based on the framework of Nonstandard Analysis, diametrically opposite results are obtained. In both cases, the choice between the standard and nonstandard treatment amounts to a selection of set-theoretical parameters that cannot be made on purely empirical grounds. The analysis of this phenomenon gives rise to a simple logical account of the relativity of impossibility theorems in economic theory, which concludes the paper

Missing Clinical Information in NHS hospital outpatient clinics: prevalence, causes and effects on patient care

In Britain over 39,000 reports were received by the National Patient Safety Agency relating to failures in documentation in 2007 and the UK Health Services Journal estimated in 2008 that over a million hospital outpatient visits each year might take place without the full record available. Despite these high numbers, the impact of missing clinical information has not been investigated for hospital outpatients in the UK.Studies in primary care in the USA have found 13.6% of patient consultations have missing clinical information, with this adversely affecting care in about half of cases, and in Australia 1.8% of medical errors were found to be due to the unavailability of clinical information.Our objectives were to assess the frequency, nature and potential impact on patient care of missing clinical information in NHS hospital outpatients and to assess the principal causes. This is the first study to present such figures for the UK and the first to look at how clinicians respond, including the associated impact on patient care