• The Abacus Cosmos: A Suite of Cosmological N-body Simulations

      Garrison, Lehman H.; Eisenstein, Daniel J.; Ferrer, Douglas; Tinker, Jeremy L.; Pinto, Philip A.; Weinberg, David H.; Univ Arizona, Steward Observ (IOP PUBLISHING LTD, 2018-06)
      We present a public data release of halo catalogs from a suite of 125 cosmological N-body simulations from the ABACUS project. The simulations span 40 wCDM cosmologies centered on the Planck 2015 cosmology at two mass resolutions, 4 x 10(10) h(-1) M-circle dot and 1 x 10(10) h(-1) M-circle dot, in 1.1 h(-1) Gpc and 720 h(-1) Mpc boxes, respectively. The boxes are phase-matched to suppress sample variance and isolate cosmology dependence. Additional volume is available via 16 boxes of fixed cosmology and varied phase; a few boxes of single-parameter excursions from Planck 2015 are also provided. Catalogs spanning z = 1.5 to 0.1 are available for friends-of-friends and ROCKSTAR halo finders and include particle subsamples. All data products are available at https://lgarrison.github.io/AbacusCosmos.
    • ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes

      Wasi, Mohd; Khandelwal, Nitesh Kumar; Moorhouse, Alexander J.; Nair, Remya; Vishwakarma, Poonam; Bravo Ruiz, Gustavo; Ross, Zoe K.; Lorenz, Alexander; Rudramurthy, Shivaprakash M.; Chakrabarti, Arunaloke; et al. (FRONTIERS MEDIA SA, 2019-07-16)
      ATP-binding cassette (ABC) superfamily members have a key role as nutrient importers and exporters in bacteria. However, their role as drug exporters in eukaryotes brought this superfamily member to even greater prominence. The capacity of ABC transporters to efflux a broad spectrum of xenobiotics represents one of the major mechanisms of clinical multidrug resistance in pathogenic fungi including Candida species. Candida auris, a newly emerged multidrug-resistant fungal pathogen of humans, has been responsible for multiple outbreaks of drug-resistant infections in hospitals around the globe. Our study has analyzed the entire complement of ABC superfamily transporters to assess whether these play a major role in drug resistance mechanisms of C. auris. Our bioinformatics analyses identified 28 putative ABC proteins encoded in the genome of the C. auris type-strain CBS 10913T; 20 of which contain transmembrane domains (TMDs). Quantitative real-time PCR confirmed the expression of all 20 TMD transporters, underlining their potential in contributing to the C. auris drug-resistant phenotype. Changes in transcript levels after short-term exposure of drugs and in drug-resistant C. auris isolates suggested their importance in the drug resistance phenotype of this pathogen. CAUR_02725 orthologous to CDR1, a major multidrug exporter in other yeasts, showed consistently higher expression in multidrug-resistant strains of C. auris. Homologs of other ABC transporter genes, such as CDR4, CDR6, and SNQ2, also displayed raised expression in a sub-set of clinical isolates. Together, our analysis supports the involvement of these transporters in multidrug resistance in C. auris.
    • ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-selected pink bollworm

      Mathew, Lolita G.; Ponnuraj, Jeyakumar; Mallappa, Bheemanna; Chowdary, Lingutla R.; Zhang, Jianwei; Tay, Wee Tek; Walsh, Thomas K.; Gordon, Karl H. J.; Heckel, David G.; Downes, Sharon; et al. (NATURE PUBLISHING GROUP, 2018-09-10)
      Evolution of pest resistance threatens the benefits of genetically engineered crops that produce Bacillus thuringiensis (Bt) insecticidal proteins. Strategies intended to delay pest resistance are most effective when implemented proactively. Accordingly, researchers have selected for and analyzed resistance to Bt toxins in many laboratory strains of pests before resistance evolves in the field, but the utility of this approach depends on the largely untested assumption that laboratory-and field-selected resistance to Bt toxins are similar. Here we compared the genetic basis of resistance to Bt toxin Cry2Ab, which is widely deployed in transgenic crops, between laboratory-and field-selected populations of the pink bollworm (Pectinophora gossypiella), a global pest of cotton. We discovered that resistance to Cry2Ab is associated with mutations disrupting the same ATP-binding cassette transporter gene (PgABCA2) in a laboratory-selected strain from Arizona, USA, and in field-selected populations from India. The most common mutation, loss of exon 6 caused by alternative splicing, occurred in resistant larvae from both locations. Together with previous data, the results imply that mutations in the same gene confer Bt resistance in laboratory-and field-selected strains and suggest that focusing on ABCA2 genes may help to accelerate progress in monitoring and managing resistance to Cry2Ab.
    • ABCC2 is associated with Bacillus thuringiensis Cry1Ac toxin oligomerization and membrane insertion in diamondback moth

      Ocelotl, Josue; Sánchez, Jorge; Gómez, Isabel; Tabashnik, Bruce E.; Bravo, Alejandra; Soberón, Mario; Univ Arizona, Dept Entomol (NATURE PUBLISHING GROUP, 2017-05-24)
      Cry1A insecticidal toxins bind sequentially to different larval gut proteins facilitating oligomerization, membrane insertion and pore formation. Cry1Ac interaction with cadherin triggers oligomerization. However, a mutation in an ABC transporter gene (ABCC2) is linked to Cry1Ac resistance in Plutella xylostella. Cry1AcMod, engineered to lack helix alpha-1, was able to form oligomers without cadherinbinding and effectively countered Cry1Ac resistance linked to ABCC2. Here we analyzed Cry1Ac and Cry1AcMod binding and oligomerization by western blots using brush border membrane vesicles (BBMV) from a strain of P. xylostella susceptible to Cry1Ac (Geneva 88) and a strain with resistance to Cry1Ac (NO-QAGE) linked to an ABCC2 mutation. Resistance correlated with lack of specific binding and reduced oligomerization of Cry1Ac in BBMV from NO-QAGE. In contrast, Cry1AcMod bound specifically and still formed oligomers in BBMV from both strains. We compared association of pre-formed Cry1Ac oligomer, obtained by incubating Cry1Ac toxin with a Manduca sexta cadherin fragment, with BBMV from both strains. Our results show that pre-formed oligomers associate more efficiently with BBMV from Geneva 88 than with BBMV from NO-QAGE, indicating that the ABCC2 mutation also affects the association of Cry1Ac oligomer with the membrane. These data indicate, for the first time, that ABCC2 facilitates Cry1Ac oligomerization and oligomer membrane insertion in P. xylostella.
    • ABCG2 Overexpression Contributes to Pevonedistat Resistance

      Kathawala, Rishil J; Espitia, Claudia M; Jones, Trace M; Islam, Shariful; Gupta, Pranav; Zhang, Yun-Kai; Chen, Zhe-Sheng; Carew, Jennifer S; Nawrocki, Steffan T; Univ Arizona, Dept Med, Div Translat & Regenerat Med, Canc Ctr (MDPI, 2020-02-12)
      MLN4924 (pevonedistat) is a first-in-class NEDD8-activating enzyme (NAE) inhibitor in clinical trials for the treatment of solid tumors and hematologic malignancies. Despite the promising activity of MLN4924 observed in early trials, drug resistance has been noted in some patients. Identifying the underlying cause of treatment failure may help to better stratify patients that are most likely to benefit from this novel agent. Early preclinical studies revealed that the development of NAE mutations promotes resistance to MLN4924. However, these mutations have not been detected in patients that are relapsed/refractory to MLN4924, suggesting that other mechanisms are driving clinical resistance. To better understand the potential mechanisms of MLN4924 resistance, we generated MLN4924-resistant ovarian cancer cells. Interestingly, these cells did not develop mutations in NAE. Transcriptome analyses revealed that one of the most upregulated genes in resistant cells was ABCG2. This result was validated by quantitative real-time PCR and immunoblotting. Importantly, the sensitivity of MLN4924-resistant cells was restored by lentiviral short hairpin RNA (shRNA) targeting ABCG2. Further investigation using ABCG2-overexpressing NCI-H460/MX20 cells determined that these cells are resistant to the anticancer effects of MLN4924 and can be sensitized by co-treatment with the ABCG2 inhibitors YHO-13351 and fumitremorgin C. Finally, HEK293 models with overexpression of wild-type ABCG2 (R482) and variants (R482G and R482T) all demonstrated significant resistance to MLN4924 compared to wild-type cells. Overall, these findings define an important molecular resistance mechanism to MLN4924 and demonstrate that ABCG2 may be a useful clinical biomarker that predicts resistance to MLN4924 treatment.
    • Abdominal aortic peripheral intervention to facilitate intra-aortic balloon pump support during high risk percutaneous coronary intervention: a case report

      Low, See W; Lee, Justin Z; Lee, Kwan S; Department of Cardiovascular Diseases, University of Arizona South Campus (BMC, 2015-03-10)
      Background: The use of intra-aortic balloon pump (IABP) via the trans-femoral approach has been established for hemodynamic support in patients undergoing high-risk percutaneous coronary intervention (PCI). However, there are various challenges associated with its use, especially in patients with aortoiliac occlusive arterial disease. Case presentation: We describe a case of high-risk PCI with IABP support complicated by intra-procedural detection of severe abdominal aortic stenosis that was successfully overcome with angioplasty of the stenotic lesion. Conclusions: Our report highlights distal abdominal aortic stenosis as a potential barrier to successful PCI with IABP support, and angioplasty as an effective means to overcome it.
    • The abductive approach to synthetic autonomous reasoning

      Baker, Victor; Univ Arizona, Dept Hydrol & Atmospher Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2019-05-13)
      Abductive inference, as defined by Charles S. Peirce, involves (1) observation of a surprising fact, (2) formulating (guessing) a proposition which, if true, would explain this fact as a matter of course, (3) and provisional acceptance of the proposition as true, (4) leading to its being taken as a premise for subsequent deduction, the consequences of which will then be related to further observations via induction-surprises from which can then trigger new abductive inferences, and so forth. Peirce limited this process to human reasoning because he viewed thought as a semiosis (flow of signs) continuous between the human mind and the world, such that (1) the human subject is in thought, as opposed to thought being in the subject, and that (2) there is an intrinsic ability of human beings to "guess right" as a consequence of this continuity of mind and world. The challenge posed by this view of thinking is that, unlike a human subject, any vehicle for autonomous reasoning is a newly created object that is separate from the world. It cannot be what Martin Heidegger termed a "being-in-the-world" because of the artificial separation of its thought from the world viewed as semiosis.
    • Ability-Based Emotional Intelligence Is Associated With Greater Cardiac Vagal Control and Reactivity

      Vanuk, John R; Alkozei, Anna; Raikes, Adam C; Allen, John J B; Killgore, William D S; Univ Arizona, Dept Psychiat, Social Cognit & Affect Neurosci Lab; Univ Arizona, Dept Psychol, Psychophysiol Lab (FRONTIERS MEDIA SA, 2019-06-11)
      Several distinct models of emotional intelligence (EI) have been developed over the past two decades. The ability model conceptualizes EI as a narrow set of interconnected, objectively measured, cognitive-emotional abilities, including the ability to perceive, manage, facilitate, and understand the emotions of the self and others. By contrast, trait or mixed models focus on subjective ratings of emotional/social competencies. Theoretically, EI is associated with neurobiological processes involved in emotional regulation and reactivity. The neurovisceral integration (NVI) model proposes a positive relationship between cardiac vagal control (CVC) and cognitive-emotional abilities similar to those encompassed by EI. The current study examined the association between CVC and EI. Because ability EI is directly tied to actual performance on emotional tasks, we hypothesized that individuals with higher ability-based EI scores would show greater levels of CVC at rest, and in response to a stressful task. Because mixedmodels of EI are not linked directly to observable emotional behavior, we predicted no association with CVC. Consistent with expectations, individuals with higher levels of ability EI, but not mixed EI, had higher levels of CVC. We also found that individuals with greater levels of CVC who demonstrated reactivity to a stress induction had significantly higher EI compared to individuals that did not respond to the stress induction. Our findings support the theoretically expected overlap between constructs within the NVI model and ability EI model, however, the observed effect size was small, and the associations between EI and CVC should not be taken to indicate a causal connection. Results suggest that variance in the ability to understand emotional processes in oneself and to reason about one's visceral experience may facilitate better CVC. Future work manipulating either CVC or EI may prove informative in teasing apart the causal role driving their observed relationship.
    • Ablation of cardiac myosin binding protein-C disrupts the super-relaxed state of myosin in murine cardiomyocytes

      McNamara, James W.; Li, Amy; Smith, Nicola J.; Lal, Sean; Graham, Robert M.; Kooiker, Kristina Bezold; van Dijk, Sabine J.; Remedios, Cristobal G. dos; Harris, Samantha P.; Cooke, Roger; et al. (ELSEVIER SCI LTD, 2016-05)
      Cardiac myosin binding protein-C (cMyBP-C) is a structural and regulatory component of cardiac thick filaments. It is observed in electron micrographs as seven to nine transverse stripes in the central portion of each half of the A band. Its C-terminus binds tightly to the myosin rod and contributes to thick filament structure, while the N-terminus can bind both myosin S2 and actin, influencing their structure and function. Mutations in the MYBPC3 gene (encoding cMyBP-C) are commonly associated with hypertrophic cardiomyopathy (HCM). In cardiac cells there exists a population of myosin heads in the super-relaxed (SRX) state, which are bound to the thick filament core with a highly inhibited ATPase activity. This report examines the role cMyBP-C plays in regulating the population of the SRX state of cardiac myosin by using an assay that measures single ATP turnover of myosin. We report a significant decrease in the proportion of myosin heads in the SRX state in homozygous cMyBP-C knockout mice, however heterozygous cMyBP-C knockout mice do not significantly differ from the wild type. A smaller, non-significant decrease is observed when thoracic aortic constriction is used to induce cardiac hypertrophy in mutation negative mice. These results support the proposal that cMyBP-C stabilises the thick filament and that the loss of cMyBP-C results in an untethering of myosin heads. This results in an increased myosin ATP turnover, further consolidating the relationship between thick filament structure and the myosin ATPase. Crown Copyright (C) 2016 Published by Elsevier Ltd. All rights reserved.
    • ABM Clinical Protocol #3: Supplementary Feedings in the Healthy Term Breastfed Neonate, Revised 2017

      Kellams, Ann; Harrel, Cadey; Omage, Stephanie; Gregory, Carrie; Rosen-Carole, Casey; Department of Family & Community Medicine, University of Arizona College of Medicine and Family Medicine Residenc; Department of Pediatrics, University of Virginia, Charlottesville, Virginia.; Department of Family & Community Medicine, University of Arizona College of Medicine and Family Medicine Residency, Tucson, Arizona.; Discipline of General Practice, The University of Queensland, Brisbane, Australia.; Department of Pediatrics, University of Rochester, Rochester, New York.; et al. (MARY ANN LIEBERT, INC, 2017-05)
      A central goal of The Academy of Breastfeeding Medicine is the development of clinical protocols for managing common medical problems that may impact breastfeeding success. These protocols serve only as guidelines for the care of breastfeeding mothers and infants and do not delineate an exclusive course of treatment or serve as standards of medical care. Variations in treatment may be appropriate according to the needs of an individual patient.
    • Abnormal Capillary Vasodynamics Contribute to Ictal Neurodegeneration in Epilepsy

      Leal-Campanario, Rocio; Alarcon-Martinez, Luis; Rieiro, Hector; Martinez-Conde, Susana; Alarcon-Martinez, Tugba; Zhao, Xiuli; LaMee, Jonathan; Popp, Pamela J. Osborn; Calhoun, Michael E.; Arribas, Juan I.; et al. (NATURE PUBLISHING GROUP, 2017-02-27)
      Seizure-driven brain damage in epilepsy accumulates over time, especially in the hippocampus, which can lead to sclerosis, cognitive decline, and death. Excitotoxicity is the prevalent model to explain ictal neurodegeneration. Current labeling technologies cannot distinguish between excitotoxicity and hypoxia, however, because they share common molecular mechanisms. This leaves open the possibility that undetected ischemic hypoxia, due to ictal blood flow restriction, could contribute to neurodegeneration previously ascribed to excitotoxicity. We tested this possibility with Confocal Laser Endomicroscopy (CLE) and novel stereological analyses in several models of epileptic mice. We found a higher number and magnitude of NG2+ mural-cell mediated capillary constrictions in the hippocampus of epileptic mice than in that of normal mice, in addition to spatial coupling between capillary constrictions and oxidative stressed neurons and neurodegeneration. These results reveal a role for hypoxia driven by capillary blood flow restriction in ictal neurodegeneration.
    • Abnormal language-related oscillatory responses in primary progressive aphasia

      Kielar, A.; Deschamps, T.; Jokel, R.; Meltzer, J.A.; Univ Arizona, Dept Speech Language & Hearing Sci (ELSEVIER SCI LTD, 2018)
      Patients with Primary Progressive Aphasia (PPA) may react to linguistic stimuli differently than healthy controls, reflecting degeneration of language networks and engagement of compensatory mechanisms. We used magnetoencephalography (MEG) to evaluate oscillatory neural responses in sentence comprehension, in patients with PPA and age-matched controls. Participants viewed sentences containing semantically and syntactically anomalous words that evoke distinct oscillatory responses. For age-matched controls, semantic anomalies elicited left-lateralized 8-30 Hz power decreases distributed along ventral brain regions, whereas syntactic anomalies elicited bilateral power decreases in both ventral and dorsal regions. In comparison to controls, patients with PPA showed altered patterns of induced oscillations, characterized by delayed latencies and attenuated amplitude, which were correlated with linguistic impairment measured offline. The recruitment of right hemisphere temporo-parietal areas (also found in controls) was correlated with preserved semantic processing abilities, indicating that preserved neural activity in these regions was able to support successful semantic processing. In contrast, syntactic processing was more consistently impaired in PPA, regardless of neural activity patterns, suggesting that this domain of language is particularly vulnerable to the neuronal loss. In addition, we found that delayed peak latencies of oscillatory responses were associated with lower accuracy for detecting semantic anomalies, suggesting that language deficits observed in PPA may be linked to delayed or slowed information processing.
    • Absent fathers and sexual strategies

      Hill, Sarah E.; Leyva, Randi P. Proffitt; DelPriore, Danielle J.; Univ Arizona (BRITISH PSYCHOLOGICAL SOC, 2016-06)
    • Absolute brain size predicts dog breed differences in executive function

      Horschler, Daniel J; Hare, Brian; Call, Josep; Kaminski, Juliane; Miklósi, Ádám; MacLean, Evan L; Univ Arizona, Sch Anthropol (SPRINGER HEIDELBERG, 2019-03-01)
      Large-scale phylogenetic studies of animal cognition have revealed robust links between absolute brain volume and species differences in executive function. However, past comparative samples have been composed largely of primates, which are characterized by evolutionarily derived neural scaling rules. Therefore, it is currently unknown whether positive associations between brain volume and executive function reflect a broad-scale evolutionary phenomenon, or alternatively, a unique consequence of primate brain evolution. Domestic dogs provide a powerful opportunity for investigating this question due to their close genetic relatedness, but vast intraspecific variation. Using citizen science data on more than 7000 purebred dogs from 74 breeds, and controlling for genetic relatedness between breeds, we identify strong relationships between estimated absolute brain weight and breed differences in cognition. Specifically, larger-brained breeds performed significantly better on measures of short-term memory and self-control. However, the relationships between estimated brain weight and other cognitive measures varied widely, supporting domain-specific accounts of cognitive evolution. Our results suggest that evolutionary increases in brain size are positively associated with taxonomic differences in executive function, even in the absence of primate-like neuroanatomy. These findings also suggest that variation between dog breeds may present a powerful model for investigating correlated changes in neuroanatomy and cognition among closely related taxa.
    • Absolute Hubble Space Telescope Proper Motion (HSTPROMO) of Distant Milky Way Globular Clusters: Galactocentric Space Velocities and the Milky Way Mass

      Sohn, Sangmo Tony; Watkins, Laura L.; Fardal, Mark A.; van der Marel, Roeland P.; Deason, Alis J.; Besla, Gurtina; Bellini, Andrea; Univ Arizona, Dept Astron (IOP PUBLISHING LTD, 2018-07-20)
      We present Hubble Space Telescope (HST) absolute proper motion (PM) measurements for 20 globular clusters (GCs) in the Milky Way (MW) halo at Galactocentric distances R-GC approximate to 10-100 kpc, with a median per-coordinate PM uncertainty of 0.06 mas yr(-1). Young and old halo GCs do not show systematic differences in their 3D Galactocentric velocities, derived from combining existing line-of-sight velocities. We confirm the association of Arp 2, Pal 12, Terzan 7, and Terzan 8 with Sgr. These clusters and NGC 6101 have tangential velocity v(tan) > 290 km s(-1), whereas all other clusters have v(tan) < 200 km s(-1). NGC 2419, the most distant GC in our sample, is also likely associated with the Sgr stream, whereas NGC 4147, NGC 5024, and NGC 5053 definitely are not. We use the distribution of orbital parameters derived using the 3D velocities to separate halo GCs that either formed within the MW or were accreted. We also assess the specific formation history of, e.g., Pyxis and Terzan 8. We constrain the MW mass via an estimator that considers the full 6D phase-space information for 16 of the GCs from R-GC = 10 to 40 kpc. The velocity dispersion anisotropy parameter beta = 0.609(-0.229)(+0.130). The enclosed mass M(<39.5 kpc) = 0.61(-0.12)(+0.18) x 10(12) M-circle dot, and the virial mass M-vir 2.05(-0.79)(+0.97) 10(12) M-circle dot. These are consistent with, but on the high side among, recent mass estimates in the literature.
    • The Absolute Magnitude of the Sun in Several Filters

      Willmer, Christopher N. A.; Univ Arizona, Steward Observ (IOP PUBLISHING LTD, 2018-06)
      This paper presents a table with estimates of the absolute magnitude of the Sun and the conversions from vegamag to the AB and ST systems for several wide-band filters used in ground-based and space-based observatories. These estimates use the dustless spectral energy distribution (SED) of Vega, calibrated absolutely using the SED of Sirius, to set the vegamag zero-points and a composite spectrum of the Sun that coadds space-based observations from the ultraviolet to the near-infrared with models of the Solar atmosphere. The uncertainty of the absolute magnitudes is estimated by comparing the synthetic colors with photometric measurements of solar analogs and is found to be similar to 0.02 mag. Combined with the uncertainty of similar to 2% in the calibration of the Vega SED, the errors of these absolute magnitudes are similar to 3%-4%. Using these SEDs, for three of the most utilized filters in extragalactic work the estimated absolute magnitudes of the Sun are M-B = 5.44, M-V = 4.81, and M-K = 3.27 mag in the vegamag system and M-B = 5.31, M-V = 4.80, and M-K = 5.08 mag in AB.
    • Absolute Magnitudes and Colors of RR Lyrae Stars in DECam Passbands from Photometry of the Globular Cluster M5

      Vivas, A. Katherina; Saha, Abhijit; Olsen, Knut; Blum, Robert; Olszewski, Edward W.; Claver, Jennifer; Valdes, Francisco; Axelrod, Tim; Kaleida, Catherine; Kunder, Andrea; et al. (IOP PUBLISHING LTD, 2017-08-04)
      We characterize the absolute magnitudes and colors of RR Lyrae stars in the globular cluster M5 in the ugriz filter system of the Dark Energy Camera (DECam). We provide empirical period-luminosity (P-L) relationships in all five bands based on 47 RR Lyrae stars of the type ab and 14 stars of the type c. The P-L relationships were found to be better constrained for the fundamental-mode RR Lyrae stars in the riz passbands, with dispersions of 0.03, 0.02 and 0.02 mag, respectively. The dispersion of the color at minimum light was found to be small, supporting the use of this parameter as a means to obtain accurate interstellar extinctions along the line of sight up to the distance of the RR Lyrae star. We found a trend of color at minimum light with a pulsational period that, if taken into account, brings the dispersion in color at minimum light to <= 0.016 mag for the (r - i), (i - z), and (r - z) colors. These calibrations will be very useful for using RR Lyrae stars from DECam observations as both standard candles for distance determinations and color standards for reddening measurements.
    • An absolute sodium abundance for a cloud-free ‘hot Saturn’ exoplanet

      Nikolov, N.; Sing, D. K.; Fortney, J. J.; Goyal, J. M.; Drummond, B.; Evans, T. M.; Gibson, N. P.; De Mooij, E. J. W.; Rustamkulov, Z.; Wakeford, H. R.; et al. (NATURE PUBLISHING GROUP, 2018-05-24)
      Broad absorption signatures from alkali metals, such as the sodium (Na I) and potassium (K I) resonance doublets, have long been predicted in the optical atmospheric spectra of cloud-free irradiated gas giant exoplanets(1-3). However, observations have revealed only the narrow cores of these features rather than the full pressure-broadened profiles(4-6). Cloud and haze opacity at the day-night planetary terminator are considered to be responsible for obscuring the absorption-line wings, which hinders constraints on absolute atmospheric abundances(7-9). Here we report an optical transmission spectrum for the 'hot Saturn' exoplanet WASP-96b obtained with the Very Large Telescope, which exhibits the complete pressure-broadened profile of the sodium absorption feature. The spectrum is in excellent agreement with cloud-free, solar-abundance models assuming chemical equilibrium. We are able to measure a precise, absolute sodium abundance of log epsilon(Na) = 6.9(-0.4)(+0.6), and use it as a proxy for the planet's atmospheric metallicity relative to the solar value (Z(p)/Z(circle dot) = 2.3(-1.7)(+8.9)). This result is consistent with the mass-metallicity trend observed for Solar System planets and exoplanets(10-12).
    • Absorption and stimulated emission by a thin slab obeying the Lorentz oscillator model

      Mansuripur, Masud; Univ Arizona, Coll Opt Sci (IOP PUBLISHING LTD, 2019-09-01)
      In his celebrated 1916-17 papers in which he proposed the A and B coefficients for the spontaneous and stimulated emission of energy quanta from excited atoms, Einstein conjectured that stimulated emission involves the release of individual quanta (later dubbed "photons") along the direction of an incident photon with the same energy, momentum, phase, and polarization state as that of the incident photon. According to classical electrodynamics, of course, an oscillating dipole must radiate an azimuthally symmetric electromagnetic field around its axis of oscillation. Nevertheless, Einstein suggested that the release of stored energy from excited atoms in the form of discrete quanta (photons) must be directional, and that, in the case of stimulated emission, the direction of the emitted photon must coincide with that of the incident photon. The goal of the present paper is to show that some of the prominent features of absorption and stimulated emission emerge from Maxwellian electrodynamics in conjunction with the simple mass-and-spring model of an atom known as the Lorentz oscillator model. (C) 2019 The Japan Society of Applied Physics

      Leethochawalit, Nicha; Jones, Tucker A.; Ellis, Richard S.; Stark, Daniel P.; Zitrin, A.; Univ Arizona, Dept Astron (IOP PUBLISHING LTD, 2016-11-04)
      The fraction of ionizing photons escaping from high-redshift star-forming galaxies is a key obstacle in evaluating whether galaxies were the primary agents of cosmic reionization. We previously proposed using the covering fraction of low-ionization gas, measured via deep absorption-line spectroscopy, as a proxy. We now present a significant update, sampling seven gravitationally lensed sources at 4 < z < 5. We show that the absorbing gas in our sources is spatially inhomogeneous, with a median covering fraction of 66%. Correcting for reddening according to a dust-in-cloud model, this implies an estimated absolute escape fraction of similar or equal to 19% +/- 6%. With possible biases and uncertainties, collectively we find that the average escape fraction could be reduced to no less than 11%, excluding the effect of spatial variations. For one of our lensed sources, we have sufficient signal-tonoise ratio to demonstrate the presence of such spatial variations and scatter in its dependence on the Ly alpha equivalent width, consistent with recent simulations. If this source is typical, our lower limit to the escape fraction could be reduced by a further factor similar or equal to 2. Across our sample, we find a modest anticorrelation between the inferred escape fraction and the local star formation rate, consistent with a time delay between a burst and leaking Lyman continuum photons. Our analysis demonstrates considerable variations in the escape fraction, consistent with being governed by the small-scale behavior of star-forming regions, whose activities fluctuate over short timescales. This supports the suggestion that the escape fraction may increase toward the reionization era when star formation becomes more energetic and burst-like.