Observation of Motion Dependent Nonlinear Dispersion with Narrow Linewidth Atoms in an Optical Cavity

As an alternative to state-of-the-art laser frequency stabilisation using ultra-stable cavities, it has been proposed to exploit the non-linear effects from coupling of atoms with a narrow transition to an optical cavity. Here we have constructed such a system and observed non-linear phase shifts of a narrow optical line by strong coupling of a sample of strontium-88 atoms to an optical cavity. The sample temperature of a few mK provides a domain where the Doppler energy scale is several orders of magnitude larger than the narrow linewidth of the optical transition. This makes the system sensitive to velocity dependent multi-photon scattering events (Dopplerons) that affect the cavity field transmission and phase. By varying the number of atoms and the intra-cavity power we systematically study this non-linear phase signature which displays roughly the same features as for much lower temperature samples. This demonstration in a relatively simple system opens new possibilities for alternative routes to laser stabilization at the sub 100 mHz level and superradiant laser sources involving narrow line atoms. The understanding of relevant motional effects obtained here has direct implications for other atomic clocks when used in relation with ultranarrow clock transitions.Comment: 9 pages (including 4 pages of Supplemental Information), 6 figures. Updated to correspond to the published versio

EpiGEN: an epistasis simulation pipeline

Abstract Summary Simulated data are crucial for evaluating epistasis detection tools in genome-wide association studies. Existing simulators are limited, as they do not account for linkage disequilibrium (LD), support limited interaction models of single nucleotide polymorphisms (SNPs) and only dichotomous phenotypes or depend on proprietary software. In contrast, EpiGEN supports SNP interactions of arbitrary order, produces realistic LD patterns and generates both categorical and quantitative phenotypes. Availability and implementation EpiGEN is implemented in Python 3 and is freely available at https://github.com/baumbachlab/epigen. Supplementary information Supplementary data are available at Bioinformatics online

Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections

Gut microbiota composition is associated with human and rodent Plasmodium infections, yet the mechanism by which gut microbiota affects the severity of malaria remains unknown. Humoral immunity is critical in mediating the clearance of Plasmodium blood stage infections, prompting the hypothesis that mice with gut microbiota-dependent decreases in parasite burden exhibit better germinal center (GC) responses. In support of this hypothesis, mice with a low parasite burden exhibit increases in GC B cell numbers and parasite-specific antibody titers, as well as better maintenance of GC structures and a more targeted, qualitatively different antibody response. This enhanced humoral immunity affects memory, as mice with a low parasite burden exhibit robust protection against challenge with a heterologous, lethal Plasmodium species. These results demonstrate that gut microbiota composition influences the biology of spleen GCs as well as the titer and repertoire of parasite-specific antibodies, identifying potential approaches to develop optimal treatments for malaria

The effect of a virtual reality environment on gaze behaviour and motor skill learning

Objective: Virtual reality (VR) systems hold significant potential for training skilled behaviours and are currently receiving intense interest in the sporting domain. They offer both practical and pedagogical benefits, but there are concerns about the effect that perceptual deficiencies in VR systems (e.g. reduced haptic information, and stereoscopic display distortions) may have on learning and performance. ‘Specificity of learning’ theories suggest that VR could be ineffective (or even detrimental) if important differences (e.g. perceptual deficiencies) exist between practice and real task performance conditions. Nevertheless, ‘structural learning’ theories suggest VR could be a useful training tool, despite these deficiencies, because a trainee can still learn the underlying structure of the behaviour. We explored these theoretical predictions using golf putting as an exemplar skill. Method: In Experiment 1 we used a repeated measures design to assess putting accuracy (radial error) and quiet eye duration of expert golfers (n = 18) on real putts before and after 40 VR ‘warm up’ putts. In Experiment 2, novice golfers (n = 40) were assigned to either VR or real-world putting training. Putting accuracy and quiet eye durations were then assessed on a real-world retention test. Results: Both visual guidance (quiet eye) and putting accuracy were disrupted temporarily when moving from VR to real putting (Experiment 1). However, real-world and VR practice produced comparable improvements in putting accuracy in novice golfers (Experiment 2). Conclusion: Overall, the results suggest that: (i) underlying skill structures can be learned in VR and transferred to the real-world; (ii) perceptual deficiencies will place limits on the use of VR. These findings demonstrate the challenges and opportunities for VR as a training tool, and emphasise the need to empirically test the costs and benefits of specific systems before deploying VR training

An uncharted island: searching for experimentation in Olivier Messiaen’s Île de feu 1

© 2013 David John TieriThis thesis offers a detailed examination of Olivier Messiaen’s (1908-1992) short piano work Île de feu 1 from the Quatre Études de rythme (1949-1950). Though these pieces are recognised for their radical and innovative features, their representation in the existing literature is uneven, and Île de feu 1 has been relatively neglected. Since this work is usually lumped with analytical discussions of its companion pieces, it is normally assumed to be experimental by default. This study therefore proposes to examine Île de feu 1 as a work worthy of its own analytical attention. It considers the contextual position of this piece within Messiaen’s experimental period (1949-1952) and attempts to establish a connection with the innovative quasi-serialist processes that he developed during this time. The analysis adopts the theoretical framework of Messiaen’s self-described compositional procedures, endeavouring to identify in this piece such techniques as: Greek and Indian rhythmic patterns, non-retrogradable rhythms, canonic devices, and the modes of limited transposition, in addition to the influences of theology and birdsong. The results of this technical analysis suggest that Île de feu 1 is less concerned with explicit experimentation, since it only displays an abstract association with such processes and is mainly constructed with the most fundamental features of Messiaen’s musical language. The thesis concludes that Île de feu 1 is a significant point in the evolution of Messiaen’s style, exhibiting as it does those traits that were developed in his earlier pieces, and anticipating a return to these features in the works that follow the experimental period

Open Quantum Systems with Applications to Precision Measurements

A spectrally pure coherent light source is an important component in precision measurement applications, such as an atomic clock. The more spectrally pure the coherent light source, or the narrower the linewidth of its power spectrum, the better for atomic clock experiments. A coherent light light source, such as a laser, is intrinsically an open quantum system, meaning that it gains and loses energy from an external environment. The aim of this thesis is to study various open quantum systems in an attempt to discover a scheme in which an extremely spectrally pure coherent light source might be realized. Therefore, this thesis begins by introducing the two main approaches to treating open quantum systems, the quantum master equation approach, and the quantum Langevin equation approach. In addition to deriving these from first principles, many of the solution methods to these approaches are given and then demonstrated using computer simulations. These include the quantum jump algorithm, the quantum state diffusion algorithm, the cumulant expansion method, and the method of c-number Langevin equations. Using these methods, the theory of the crossover between lasing and steady state superradiance is presented. It is shown that lasing and steady state superradiance might be demonstrated in the same physical system, but in different parameter regimes. The parameter space between these two extreme limits is explored, and the benefits and drawbacks of operating a system at a given set of parameters, i.e. to achieve the most spectrally pure light source, are discussed. We also consider the phase stability of a laser that is locked to a cavity QED system comprised of atoms with an ultra-narrow optical transition. Although the atomic motion introduces Doppler broadening, the standing wave nature of the cavity causes saturated absorption, which can be used to achieve an extremely high degree of phase stabilization. The inhomogeneity introduced by finite atomic velocities can also cause optical bistability to disappear, resulting in no regions of dynamic instability that would otherwise restrict operational parameters in the experiment to be tuned outside of the optimum region where the minimum linewidth occurs

Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics

Abstract After publication of this supplement [1], it was brought to our attention that the wrong year was used in the title of the supplement. The 16th Annual UT-KBRIN Bioinformatics Summit was held in 2017

A combined approach with gene-wise normalization improves the analysis of RNA-seq data in human breast cancer subtypes.

Breast cancer (BC) is increasing in incidence and resistance to treatment worldwide. The challenges in limited therapeutic options and poor survival outcomes in BC subtypes persist because of its molecular heterogeneity and resistance to standard endocrine therapy. Recently, high throughput RNA sequencing (RNA-seq) has been used to identify biomarkers of disease progression and signaling pathways that could be amenable to specific therapies according to the BC subtype. However, there is no single generally accepted pipeline for the analysis of RNA-seq data in biomarker discovery due, in part, to the needs of simultaneously satisfying constraints of sensitivity and specificity. We proposed a combined approach using gene-wise normalization, UQ-pgQ2, followed by a Wald test from DESeq2. Our approach improved the analysis based on within-group comparisons in terms of the specificity when applied to publicly available RNA-seq BC datasets. In terms of identifying differentially expressed genes (DEGs), we combined an optimized log2 fold change cutoff with a nominal false discovery rate of 0.05 to further minimize false positives. Using this method in the analysis of two GEO BC datasets, we identified 797 DEGs uniquely expressed in triple negative BC (TNBC) and significantly associated with T cell and immune-related signaling, contributing to the immunotherapeutic efficacy in TNBC patients. In contrast, we identified 1403 DEGs uniquely expressed in estrogen positive and HER2 negative BC (ER+HER2-BC) and significantly associated with eicosanoid, notching and FAK signaling while a common set of genes was associated with cellular growth and proliferation. Thus, our approach to control for false positives identified two distinct gene expression profiles associated with these two subtypes of BC which are distinguishable by their molecular and functional attributes