Mutual information for examining correlations in DNA

This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we explore their use comparing DNA sequences from a variety of sources. Using software for performing in silico mutations, we also consider evolutionary events leading to long range correlations and analyse these correlations using the techniques presented. Comparisons are made between these virtual sequences, randomly generated sequences, and real sequences. We also explore correlations in chromosomes from different species.Comment: 8 pages, 3 figure

Dynamic polarization of graphene by moving external charges: random phase approximation

We evaluate the stopping and image forces on a charged particle moving parallel to a doped sheet of graphene by using the dielectric response formalism for graphene's $\pi$-electron bands in the random phase approximation (RPA). The forces are presented as functions of the particle speed and the particle distance for a broad range of charge-carrier densities in graphene. A detailed comparison with the results from a kinetic equation model reveal the importance of inter-band single-particle excitations in the RPA model for high particle speeds. We also consider the effects of a finite gap between graphene and a supporting substrate, as well as the effects of a finite damping rate that is included through the use of Mermin's procedure. The damping rate is estimated from a tentative comparison of the Mermin loss function with a HREELS experiment. In the limit of low particle speeds, several analytical results are obtained for the friction coefficient that show an intricate relationship between the charge-carrier density, the damping rate, and the particle distance, which may be relevant to surface processes and electrochemistry involving graphene.Comment: 14 pages, 10 figures, accepted for publication in Phys. Rev.

Bubbles in a minority game setting with real financial data

© 2005 COPYRIGHT SPIE--The International Society for Optical Engineering Copyright 2005 Society of Photo-Optical Instrumentation Engineers. This paper was published in Complex Systems, edited by Axel Bender, Proc. of SPIE Vol. 6039, 60390C and is made available as an electronic reprint with permission of SPIE. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.It is a well observed fact that markets follow both positive and/or negative trends, crashes and bubble effects. In general a strong positive trend is followed by a crash--a famous example of these effects was seen in the recent crash on the NASDAQ (April 2000) and prior to the crash in the Hong Kong market, which was associated with the Asian crisis in the early 1994. In this paper we use real market data coupled into a minority game with different payoff functions to study the dynamics and the location of financial bubbles.Frédéric D.R. Bonnet, Andrew Allison, and Derek Abbot

Effect of Brief Biofeedback via a Smartphone App on Stress Recovery: Randomized Experimental Study.

BACKGROUND:Smartphones are often vilified for negatively influencing well-being and contributing to stress. However, these devices may, in fact, be useful in times of stress and, in particular, aid in stress recovery. Mobile apps that deliver evidence-based techniques for stress reduction, such as heart rate variability biofeedback (HRVB) training, hold promise as convenient, accessible, and effective stress-reducing tools. Numerous mobile health apps that may potentially aid in stress recovery are available, but very few have demonstrated that they can influence health-related physiological stress parameters (eg, salivary biomarkers of stress). The ability to recover swiftly from stress and reduce physiological arousal is particularly important for long-term health, and thus, it is imperative that evidence is provided to demonstrate the effectiveness of stress-reducing mobile health apps in this context. OBJECTIVE:The purpose of this research was to investigate the physiological and psychological effects of using a smartphone app for HRVB training following a stressful experience. The efficacy of the gamified Breather component of the Happify mobile health app was examined in an experimental setting. METHODS:In this study, participants (N=140) underwent a laboratory stressor and were randomly assigned to recover in one of three ways: with no phone present, with a phone present, with the HRBV game. Those in the no phone condition had no access to their phone. Those in the phone present condition had their phone but did not use it. Those in the HRVB game condition used the serious game Breather on the Happify app. Stress recovery was assessed via repeated measures of salivary alpha amylase, cortisol, and self-reported acute stress (on a 1-100 scale). RESULTS:Participants in the HRVB game condition had significantly lower levels of salivary alpha amylase during recovery than participants in the other conditions (F2,133=3.78, P=.03). There were no significant differences among the conditions during recovery for salivary cortisol levels or self-reported stress. CONCLUSIONS:These results show that engaging in a brief HRVB training session on a smartphone reduces levels of salivary alpha amylase following a stressful experience, providing preliminary evidence for the effectiveness of Breather in improving physiological stress recovery. Given the known ties between stress recovery and future well-being, this study provides a possible mechanism by which gamified biofeedback apps may lead to better health

Algebraic arctic curves in the domain-wall six-vertex model

The arctic curve, i.e. the spatial curve separating ordered (or `frozen') and disordered (or `temperate) regions, of the six-vertex model with domain wall boundary conditions is discussed for the root-of-unity vertex weights. In these cases the curve is described by algebraic equations which can be worked out explicitly from the parametric solution for this curve. Some interesting examples are discussed in detail. The upper bound on the maximal degree of the equation in a generic root-of-unity case is obtained.Comment: 15 pages, no figures; v2: metadata correcte

Microstructural characterisation of biocompatible sol-gel derived vanadium doped TiO2 on Ti substrates

Sol-gel derived pure titania is compared with vanadium and / or aluminium modified titania deposited by spin coating on pure titanium substrates annealed at 300C and 650C. Reflection high-energy electron diffraction indicated the presence of anatase from the surface layers of samples annealed at 300C with a transition to rutile with increasing annealing temperature and addition of vanadium. Cross-sectional transmission electron microscopy indicated a gradation of Ti-O phases through the layer with the dominant presence of rutile. Aluminium was found to inhibit grain growth while vanadium promoted crystallisation

Two Weeks of Ischemic Conditioning Improves Walking Speed and Reduces Neuromuscular Fatigability in Chronic Stroke Survivors

This pilot study examined whether ischemic conditioning (IC), a noninvasive, cost-effective, and easy-to-administer intervention, could improve gait speed and paretic leg muscle function in stroke survivors. We hypothesized that 2 wk of IC training would increase self-selected walking speed, increase paretic muscle strength, and reduce neuromuscular fatigability in chronic stroke survivors. Twenty-two chronic stroke survivors received either IC or IC Sham on their paretic leg every other day for 2 wk (7 total sessions). IC involved 5-min bouts of ischemia, repeated five times, using a cuff inflated to 225 mmHg on the paretic thigh. For IC Sham, the cuff inflation pressure was 10 mmHg. Self-selected walking speed was assessed using the 10-m walk test, and paretic leg knee extensor strength and fatigability were assessed using a Biodex dynamometer. Self-selected walking speed increased in the IC group (0.86 ± 0.21 m/s pretest vs. 1.04 ± 0.22 m/s posttest, means ± SD; P\u3c 0.001) but not in the IC Sham group (0.92 ± 0.47 m/s pretest vs. 0.96 ± 0.46 m/s posttest; P= 0.25). Paretic leg maximum voluntary contractions were unchanged in both groups (103 ± 57 N·m pre-IC vs. 109 ± 65 N·m post-IC; 103 ± 59 N·m pre-IC Sham vs. 108 ± 67 N·m post-IC Sham; P = 0.81); however, participants in the IC group maintained a submaximal isometric contraction longer than participants in the IC Sham group (278 ± 163 s pre-IC vs. 496 ± 313 s post-IC, P = 0.004; 397 ± 203 s pre-IC Sham vs. 355 ± 195 s post-IC Sham; P = 0.46). The results from this pilot study thus indicate that IC training has the potential to improve walking speed and paretic muscle fatigue resistance poststroke

Radiative association and inverse predissociation of oxygen atoms

The formation of \mbox{O}_2 by radiative association and by inverse predissociation of ground state oxygen atoms is studied using quantum-mechanical methods. Cross sections, emission spectra, and rate coefficients are presented and compared with prior experimental and theoretical results. At temperatures below 1000~K radiative association occurs by approach along the $1\,{}^3\Pi_u$ state of \mbox{O}_2 and above 1000~K inverse predissociation through the \mbox{B}\,{}^3\Sigma_u^- state is the dominant mechanism. This conclusion is supported by a quantitative comparison between the calculations and data obtained from hot oxygen plasma spectroscopy.Comment: submitted to Phys. Rev. A (Sept. 7., 1994), 19 pages, 4 figures, latex (revtex3.0 and epsf.sty

Friction force on slow charges moving over supported graphene

We provide a theoretical model that describes the dielectric coupling of a 2D layer of graphene, represented by a polarization function in the Random Phase Approximation, and a semi-infinite 3D substrate, represented by a surface response function in a non-local formulation. We concentrate on the role of the dynamic response of the substrate for low-frequency excitations of the combined graphene-substrate system, which give rise to the stopping force on slowly moving charges above graphene. A comparison of the dielectric loss function with experimental HREELS data for graphene on a SiC substrate is used to estimate the damping rate in graphene and to reveal the importance of phonon excitations in an insulating substrate. A signature of the hybridization between graphene's pi plasmon and the substrate's phonon is found in the stopping force. A friction coefficient that is calculated for slow charges moving above graphene on a metallic substrate shows an interplay between the low-energy single-particle excitations in both systems.Comment: 13 pages, 5 figures, submitted to Nanotechnology for a special issue related to the NGC 2009 conference (http://asdn.net/ngc2009/index.shtml

Turn-Around-Time Improvements for Positive Blood Cultures from Incorporation of Workflow Modifications

Background: Emergence of direct from positive blood culture bottle identification (ID) methods reveal opportunities for improving bacterial ID and select resistance marker detection turn-around-times. Each system has various advantages and disadvantages; each institution must select the method/s that best fit the laboratory and patient needs. Here we elucidate improvements in 24 hour workflow through incorporating multiple rapid technologies for positive blood culture ID into a 24 hour algorithm. Methods: MALDI-TOF (Bruker) analysis with sepsityper extraction (aerobic Gram-positive and anaerobic bacteria); MALDI-TOF analysis with serum separator tube concentration (Gram-negative bacteria); and a FilmArray Blood Culture Panel (Biofire) were utilized. MALDI was utilized on 1st shift for single bacterium positives. FilmArray was performed on 2nd and 3rd shift for aerobic bottles and on 1st shift for gram-positive cocci in clusters and Candida. We examined all events during our pre-modification (September-November 2013) and post-modification (late-December 2014-March 2015) time periods and defined an event as the first positive blood culture for a patient within the examined data period. The Antimicrobial Stewardship Pharmacist (ASP) was notified with identifications and also KPC carbapenemase positives, to implement a carbapenem-resistant Enterobacteriaceae (CRE) empiric treatment algorithm. For KPC positives (CRE) a custom minimum inhibitory concentration (MIC) panel was utilized, replacing a standard susceptibility panel and Etests. Finally, 2nd shift began susceptibility setup on subcultured bloods that had turned positive from 11 p.m.-6 a.m. Results: Pre- and post- workflow modification average turn-around times (TAT) and p-values are shown in the Table. Detection of either the KPC or the mecA marker significantly improved the TAT needed for phenotypic detection of carbapenem or methicillin resistance. KPC was detected in 3 Enterobactericeae. Conclusions: Improvements to patient care are to be determined, but strong collaboration with ASP is anticipated to make a significant impact on patient outcomes. Of note, while having a universal Staphylococcus species target is useful, it can lead to complications with multi-species positive bottles. With the universal Staphylococcus species target, it is not possible to differentiate between a mixed coagulase negative Staphylococcus species (CNSS) versus Staphylococcus aureus when both are present as the CNSS may harbor the mecA target, preventing adequate treatment. Furthermore, a Staphylococcus lugdunensis specific marker would be clinically useful