Performance Models for Split-execution Computing Systems

Split-execution computing leverages the capabilities of multiple computational models to solve problems, but splitting program execution across different computational models incurs costs associated with the translation between domains. We analyze the performance of a split-execution computing system developed from conventional and quantum processing units (QPUs) by using behavioral models that track resource usage. We focus on asymmetric processing models built using conventional CPUs and a family of special-purpose QPUs that employ quantum computing principles. Our performance models account for the translation of a classical optimization problem into the physical representation required by the quantum processor while also accounting for hardware limitations and conventional processor speed and memory. We conclude that the bottleneck in this split-execution computing system lies at the quantum-classical interface and that the primary time cost is independent of quantum processor behavior.Comment: Presented at 18th Workshop on Advances in Parallel and Distributed Computational Models [APDCM2016] on 23 May 2016; 10 page

Grain Physics and Rosseland Mean Opacities

Tables of mean opacities are often used to compute the transfer of radiation in a variety of astrophysical simulations from stellar evolution models to proto-planetary disks. Often tables, such as Ferguson et al. (2005), are computed with a predetermined set of physical assumptions that may or may not be valid for a specific application. This paper explores the effects of several assumptions of grain physics on the Rosseland mean opacity in an oxygen rich environment. We find that changing the distribution of grain sizes, either the power-law exponent or the shape of the distribution, has a marginal effect on the total mean opacity. We also explore the difference in the mean opacity between solid homogenous grains and grains that are porous or conglomorations of several species. Changing the amount of grain opacity included in the mean by assuming a grain-to-gas ratio significantly affects the mean opacity, but in a predictable way.Comment: 19 pages, 6 figures, accepted for publication in Ap

An HST/STIS Optical Transmission Spectrum of Warm Neptune GJ 436b

GJ 436b is a prime target for understanding warm Neptune exoplanet atmospheres and a target for multiple JWST GTO programs. Here, we report the first space-based optical transmission spectrum of the planet using two HST/STIS transit observations from 0.53-1.03 microns. We find no evidence for alkali absorption features, nor evidence of a scattering slope longward of 0.53 microns. The spectrum is indicative of moderate to high metallicity (~100-1000x solar) while moderate metallicity scenarios (~100x solar) require aerosol opacity. The optical spectrum also rules out some highly scattering haze models. We find an increase in transit depth around 0.8 microns in the transmission spectra of 3 different sub-Jovian exoplanets (GJ 436b, HAT-P-26b, and GJ 1214b). While most of the data come from STIS, data from three other instruments may indicate this is not an instrumental effect. Only the transit spectrum of GJ 1214b is well fit by a model with stellar plages on the photosphere of the host star. Our photometric monitoring of the host star reveals a stellar rotation rate of 44.1 days and an activity cycle of 7.4 years. Intriguingly, GJ 436 does not become redder as it gets dimmer, which is expected if star spots were dominating the variability. These insights into the nature of the GJ 436 system help refine our expectations for future observations in the era of JWST, whose higher precision and broader wavelength coverage will shed light on the composition and structure of GJ 436b's atmosphere.Comment: 20 pages, 11 figures, 5 tables, Accepted to AJ. A full version of table 1 is included as table1_mrt.tx

Relief of branch pulmonary artery stenosis reduces pulmonary valve insufficiency in a swine model

ObjectiveWe sought to determine the impact of relieving branch pulmonary artery stenosis on pulmonary valve insufficiency and right ventricular function. Long-standing pulmonary insufficiency causes progressive right ventricular dilatation, leading to decreased right ventricular function. Adults with pulmonary insufficiency are at risk of decreased exercise tolerance, arrhythmias, and sudden cardiac death. Branch pulmonary artery stenosis frequently occurs in these patients, and the presence of branch stenosis may exacerbate valve insufficiency.MethodsNeonatal piglets (n = 7) underwent surgery to create pulmonary insufficiency and left pulmonary artery stenosis. At 3 months of age, the animals underwent baseline cardiac magnetic resonance imaging followed by stenting of the left pulmonary artery. A repeat magnetic resonance imaging scan was performed 1 week after intervention. Magnetic resonance imaging evaluation included (1) velocity mapping to assess the forward and reverse flow at the main, left and right pulmonary arteries, and aorta; and (2) volumetric assessment of the right ventricle.ResultsLeft pulmonary artery flow increased from 14.5% to 36.3% of total net flow after stenting (P < .01). Pulmonary regurgitation decreased from 38.7% to 27.4% (P < .02). Right ventricular ejection fraction improved from a median of 53.5% to 58.2% after stenting (P < .01). Cardiac index improved from a median of 2.7 to 3.5 L/min/m2 (P = .01).ConclusionRelief of branch pulmonary artery stenosis reduces insufficiency and improves right ventricular systolic function in this animal model. This supports the practice of aggressive intervention in patients with branch pulmonary artery stenosis and pulmonary insufficiency

Touchstone Stars: Highlights from the Cool Stars 18 Splinter Session

We present a summary of the splinter session on "touchstone stars" -- stars with directly measured parameters -- that was organized as part of the Cool Stars 18 conference. We discuss several methods to precisely determine cool star properties such as masses and radii from eclipsing binaries, and radii and effective temperatures from interferometry. We highlight recent results in identifying and measuring parameters for touchstone stars, and ongoing efforts to use touchstone stars to determine parameters for other stars. We conclude by comparing the results of touchstone stars with cool star models, noting some unusual patterns in the differences.Comment: Proceedings of the 18th Cambridge Workshop on Cool Stars, Stellar Systems, and the Sun, Eds G. van Belle & H. Harri

Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Peer reviewedPublisher PD

The tempo of cetacean cranial evolution

The evolution of cetaceans (whales and dolphins) represents one of the most extreme adaptive transitions known, from terrestrial mammals to a highly specialized aquatic radiation that includes the largest animals alive today. Many anatomical shifts in this transition involve the feeding, respiratory, and sensory structures of the cranium, which we quantified with a high-density, three-dimensional geometric morphometric analysis of 201 living and extinct cetacean species spanning the entirety of their ∼50-million-year evolutionary history. Our analyses demonstrate that cetacean suborders occupy distinct areas of cranial morphospace, with extinct, transitional taxa bridging the gap between archaeocetes (stem whales) and modern mysticetes (baleen whales) and odontocetes (toothed whales). This diversity was obtained through three key periods of rapid evolution: first, the initial evolution of archaeocetes in the early to mid-Eocene produced the highest evolutionary rates seen in cetaceans, concentrated in the maxilla, frontal, premaxilla, and nasal; second, the late Eocene divergence of the mysticetes and odontocetes drives a second peak in rates, with high rates and disparity sustained through the Oligocene; and third, the diversification of odontocetes, particularly sperm whales, in the Miocene (∼18-10 Mya) propels a final peak in the tempo of cetacean morphological evolution. Archaeocetes show the fastest evolutionary rates but the lowest disparity. Odontocetes exhibit the highest disparity, while mysticetes evolve at the slowest pace, particularly in the Neogene. Diet and echolocation have the strongest influence on cranial morphology, with habitat, size, dentition, and feeding method also significant factors impacting shape, disparity, and the pace of cetacean cranial evolution

Improving the Specificity of Plasmodium falciparum Malaria Diagnosis in High-Transmission Settings with a Two-Step Rapid Diagnostic Test and Microscopy Algorithm

ABSTRACT Poor specificity may negatively impact rapid diagnostic test (RDT)-based diagnostic strategies for malaria. We performed real-time PCR on a subset of subjects who had undergone diagnostic testing with a multiple-antigen (histidine-rich protein 2 and pan -lactate dehydrogenase pLDH [HRP2/pLDH]) RDT and microscopy. We determined the sensitivity and specificity of the RDT in comparison to results of PCR for the detection of Plasmodium falciparum malaria. We developed and evaluated a two-step algorithm utilizing the multiple-antigen RDT to screen patients, followed by confirmatory microscopy for those individuals with HRP2-positive (HRP2 + )/pLDH-negative (pLDH − ) results. In total, dried blood spots (DBS) were collected from 276 individuals. There were 124 (44.9%) individuals with an HRP2 + /pLDH + result, 94 (34.1%) with an HRP2 + /pLDH − result, and 58 (21%) with a negative RDT result. The sensitivity and specificity of the RDT compared to results with real-time PCR were 99.4% (95% confidence interval [CI], 95.9 to 100.0%) and 46.7% (95% CI, 37.7 to 55.9%), respectively. Of the 94 HRP2 + /pLDH − results, only 32 (34.0%) and 35 (37.2%) were positive by microscopy and PCR, respectively. The sensitivity and specificity of the two-step algorithm compared to results with real-time PCR were 95.5% (95% CI, 90.5 to 98.0%) and 91.0% (95% CI, 84.1 to 95.2), respectively. HRP2 antigen bands demonstrated poor specificity for the diagnosis of malaria compared to that of real-time PCR in a high-transmission setting. The most likely explanation for this finding is the persistence of HRP2 antigenemia following treatment of an acute infection. The two-step diagnostic algorithm utilizing microscopy as a confirmatory test for indeterminate HRP2 + /pLDH − results showed significantly improved specificity with little loss of sensitivity in a high-transmission setting

Updated Parameters and a New Transmission Spectrum of HD 97658b

Recent years have seen increasing interest in the characterization of sub-Neptune-sized planets because of their prevalence in the Galaxy, contrasted with their absence in our solar system. HD 97658 is one of the brightest stars hosting a planet of this kind, and we present the transmission spectrum of this planet by combining four Hubble Space Telescope transits, 12 Spitzer/IRAC transits, and eight MOST transits of this system. Our transmission spectrum has a higher signal-to-noise ratio than those from previous works, and the result suggests that the slight increase in transit depth from wavelength 1.1–1.7 μm reported in previous works on the transmission spectrum of this planet is likely systematic. Nonetheless, our atmospheric modeling results are inconclusive, as no model provides an excellent match to our data. Nonetheless, we find that atmospheres with high C/O ratios (C/O ≳ 0.8) and metallicities of ≳100× solar metallicity are favored. We combine the mid-transit times from all of the new Spitzer and MOST observations and obtain an updated orbital period of P = 9.489295 ± 0.000005, with a best-fit transit time center at T₀ = 2456361.80690 ± 0.00038 (BJD). No transit timing variations are found in this system. We also present new measurements of the stellar rotation period (34 ± 2 days) and stellar activity cycle (9.6 yr) of the host star HD 97658. Finally, we calculate and rank the Transmission Spectroscopy Metric of all confirmed planets cooler than 1000 K and with sizes between 1 R⊕ and 4 R⊕. We find that at least a third of small planets cooler than 1000 K can be well characterized using James Webb Space Telescope, and of those, HD 97658b is ranked fifth, meaning that it remains a high-priority target for atmospheric characterization

Ultrathin Oxide Films by Atomic Layer Deposition on Graphene

In this paper, a method is presented to create and characterize mechanically robust, free standing, ultrathin, oxide films with controlled, nanometer-scale thickness using Atomic Layer Deposition (ALD) on graphene. Aluminum oxide films were deposited onto suspended graphene membranes using ALD. Subsequent etching of the graphene left pure aluminum oxide films only a few atoms in thickness. A pressurized blister test was used to determine that these ultrathin films have a Young's modulus of 154 \pm 13 GPa. This Young's modulus is comparable to much thicker alumina ALD films. This behavior indicates that these ultrathin two-dimensional films have excellent mechanical integrity. The films are also impermeable to standard gases suggesting they are pinhole-free. These continuous ultrathin films are expected to enable new applications in fields such as thin film coatings, membranes and flexible electronics.Comment: Nano Letters (just accepted