Effective Non-Hermitian Hamiltonians for Studying Resonance Statistics in Open Disordered Systems

We briefly discuss construction of energy-dependent effective non-hermitian hamiltonians for studying resonances in open disordered systemsComment: Latex, 20 pages, 1 fig. Expanded version of a talk at the Workshop on Pseudo-Hermitian Hamiltonians in Quantum Physics IX, June 21-24 2010, Zhejiang University, Hangzhou, China. Accepted for publication in the Internationa Journal of Theoretical Physics (Springer Verlag

"Hey Model!" -- Natural User Interactions and Agency in Accessible Interactive 3D Models

While developments in 3D printing have opened up opportunities for improved access to graphical information for people who are blind or have low vision (BLV), they can provide only limited detailed and contextual information. Interactive 3D printed models (I3Ms) that provide audio labels and/or a conversational agent interface potentially overcome this limitation. We conducted a Wizard-of-Oz exploratory study to uncover the multi-modal interaction techniques that BLV people would like to use when exploring I3Ms, and investigated their attitudes towards different levels of model agency. These findings informed the creation of an I3M prototype of the solar system. A second user study with this model revealed a hierarchy of interaction, with BLV users preferring tactile exploration, followed by touch gestures to trigger audio labels, and then natural language to fill in knowledge gaps and confirm understanding.Comment: Paper presented at ACM CHI 2020: Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems, ACM, New York, April 2020; Replacement: typos correcte

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

Gene disruption by structural mutations drives selection in US rice breeding over the last century.

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection

Two mini-Neptunes Transiting the Adolescent K-star HIP 113103 Confirmed with TESS and CHEOPS

We report the discovery of two mini-Neptunes in near 2:1 resonance orbits ($P=7.610303$ d for HIP 113103 b and $P=14.245651$ d for HIP 113103 c) around the adolescent K-star HIP 113103 (TIC 121490076). The planet system was first identified from the TESS mission, and was confirmed via additional photometric and spectroscopic observations, including a $\sim$17.5 hour observation for the transits of both planets using ESA CHEOPS. We place $\leq4.5$ min and $\leq2.5$ min limits on the absence of transit timing variations over the three year photometric baseline, allowing further constraints on the orbital eccentricities of the system beyond that available from the photometric transit duration alone. With a planetary radius of $R_{p}=1.829^{+0.096}_{-0.067}\,R_{\oplus}$, HIP 113103 b resides within the radius gap, and this might provide invaluable information on the formation disparities between super-Earths and mini-Neptunes. Given the larger radius $R_{p}=2.40^{+0.10}_{-0.08}\,R_{\oplus}$ for HIP 113103 c, and close proximity of both planets to HIP 113103, it is likely that HIP 113103 b might have lost (or is still losing) its primordial atmosphere. We therefore present simulated atmospheric transmission spectra of both planets using JWST, HST, and Twinkle. It demonstrates a potential metallicity difference (due to differences in their evolution) would be a challenge to detect if the atmospheres are in chemical equilibrium. As one of the brightest multi sub-Neptune planet systems suitable for atmosphere follow up, HIP 113103 b and HIP 113103 c could provide insight on planetary evolution for the sub-Neptune K-star population.Comment: 18 pages, 12 figures, accepted for publication in the Monthly Notices of the Royal Astronomical Societ

Growth Hormone Secretagogues Protect Mouse Cardiomyocytes from in vitro Ischemia/Reperfusion Injury through Regulation of Intracellular Calcium

Background: Ischemic heart disease is a leading cause of mortality. To study this disease, ischemia/reperfusion (I/R) models are widely used to mimic the process of transient blockage and subsequent recovery of cardiac coronary blood supply. We aimed to determine whether the presence of the growth hormone secretagogues, ghrelin and hexarelin, would protect/improve the function of heart from I/R injury and to examine the underlying mechanisms. Methodology/Principal Findings: Isolated hearts from adult male mice underwent 20 min global ischemia and 30 min reperfusion using a Langendorff apparatus. Ghrelin (10 nM) or hexarelin (1 nM) was introduced into the perfusion system either 10 min before or after ischemia, termed pre- and post-treatments. In freshly isolated cardiomyocytes from these hearts, single cell shortening, intracellular calcium ([Ca ] ) transients and caffeine-releasable sarcoplasmic reticulum (SR) Ca were measured. In addition, RT-PCR and Western blots were used to examine the expression level of GHS receptor type 1a (GHS-R1a), and phosphorylated phospholamban (p-PLB), respectively. Ghrelin and hexarelin pre- or post-treatments prevented the significant reduction in the cell shortening, [Ca ] transient amplitude and caffeine-releasable SR Ca content after I/R through recovery of p-PLB. GHS-R1a antagonists, [D-Lys3]-GHRP-6 (200 nM) and BIM28163 (100 nM), completely blocked the effects of GHS on both cell shortening and [Ca ] transients. Conclusion/Significance: Through activation of GHS-R1a, ghrelin and hexarelin produced a positive inotropic effect on ischemic cardiomyocytes and protected them from I/R injury probably by protecting or recovering p-PLB (and therefore SR Ca content) to allow the maintenance or recovery of normal cardiac contractility. These observations provide supporting evidence for the potential therapeutic application of ghrelin and hexarelin in patients with cardiac I/R injury

The Rapid ASKAP Continuum Survey I: Design and First Results

The Rapid ASKAP Continuum Survey (RACS) is the first large-area survey to be conducted with the full 36-antenna Australian Square Kilometre Array Pathfinder (ASKAP) telescope. RACS will provide a shallow model of the ASKAP sky that will aid the calibration of future deep ASKAP surveys. RACS will cover the whole sky visible from the ASKAP site in Western Australia, and will cover the full ASKAP band of $700-1800$ MHz. The RACS images are generally deeper than the existing NRAO VLA Sky Survey (NVSS) and Sydney University Molonglo Sky Survey (SUMSS) radio surveys and have better spatial resolution. All RACS survey products will be public, including radio images (with $\sim 15$ arcsecond resolution) and catalogues of about three million source components with spectral index and polarisation information. In this paper, we present a description of the RACS survey and the first data release of 903 images covering the sky south of declination $+41^\circ$ made over a 288 MHz band centred at 887.5 MHz.Comment: 24 pages, 17 figures, 4 tables. For associated data see https://data.csiro.au/collections/domain/casdaObservation/results/PRAS110%20-%20The%20Rapid%20ASKAP%20Continuu