TRX: A Formally Verified Parser Interpreter

Parsing is an important problem in computer science and yet surprisingly little attention has been devoted to its formal verification. In this paper, we present TRX: a parser interpreter formally developed in the proof assistant Coq, capable of producing formally correct parsers. We are using parsing expression grammars (PEGs), a formalism essentially representing recursive descent parsing, which we consider an attractive alternative to context-free grammars (CFGs). From this formalization we can extract a parser for an arbitrary PEG grammar with the warranty of total correctness, i.e., the resulting parser is terminating and correct with respect to its grammar and the semantics of PEGs; both properties formally proven in Coq.Comment: 26 pages, LMC

Trichloroethylene Exposure during Cardiac Valvuloseptal Morphogenesis Alters Cushion Formation and Cardiac Hemodynamics in the Avian Embryo

It is controversial whether trichloroethylene (TCE) is a cardiac teratogen. We exposed chick embryos to 0, 0.4, 8, or 400 ppb TCE/egg during the period of cardiac valvuloseptal morphogenesis (2–3.3 days’ incubation). Embryo survival, valvuloseptal cellularity, and cardiac hemodynamics were evaluated at times thereafter. TCE at 8 and 400 ppb/egg reduced embryo survival to day 6.25 incubation by 40–50%. At day 4.25, increased proliferation and hypercellularity were observed within the atrioventricular and outflow tract primordia after 8 and 400 ppb TCE. Doppler ultrasound revealed that the dorsal aortic and atrioventricular blood flows were reduced by 23% and 30%, respectively, after exposure to 8 ppb TCE. Equimolar trichloroacetic acid (TCA) was more potent than TCE with respect to increasing mortality and causing valvuloseptal hypercellularity. These results independently confirm that TCE disrupts cardiac development of the chick embryo and identifies valvuloseptal development as a period of sensitivity. The hypercellular valvuloseptal profile is consistent with valvuloseptal heart defects associated with TCE exposure. This is the first report that TCA is a cardioteratogen for the chick and the first report that TCE exposure depresses cardiac function. Valvuloseptal hypercellularity may narrow the cardiac orifices, which reduces blood flow through the heart, thereby compromising cardiac output and contributing to increased mortality. The altered valvuloseptal formation and reduced hemodynamics seen here are consistent with such an outcome. Notably, these effects were observed at a TCE exposure (8 ppb) that is only slightly higher than the U.S. Environmental Protection Agency maximum containment level for drinking water (5 ppb)

Timing of Resource Availability Drives Divergent Social Systems and Home Range Dynamics in Ecologically Similar Tree Squirrels

Intraspecific variation in home range size has important implications for the distribution of animals across landscapes and the spatial structuring of population, community, and ecosystem processes. Among species of similar trophic guild and body mass, differences in home range size can reflect extrinsic variables that exert divergent selective forces upon spacing behavior and social organization. We tested predictions about how resource availability and timing influence social system, home range size, and territoriality in two tree squirrel species of similar size and ecological niches but that differ in foraging strategy and social organization. We estimated home range size and intraspecific home range core overlap in the Mt. Graham red squirrel (Tamiasciurus fremonti grahamensis; Arizona USA; MGRS) and the Eurasian red squirrel (Sciurus vulgaris; Alps, Italy; ERS) as functions of species, sex, season, and individual's body mass. However, body mass did not explain differences found between the two species. We found MGRS home ranges being three times smaller with higher core area exclusivity compared to ERS in all seasons. In fact, territorial MGRS evolved in a system of brief resource pulses and are larder hoarders, whereas ERS experience prolonged resource availability and are non-territorial. Only male MGRSs increased their home range during the breeding season, reflecting interspecific differences in social organization and mating behavior. Male ERS home ranges always overlap with several females to enhance mating success although male and female MGRS maintain nearly exclusive territories throughout the year. Only during spring and summer do males temporarily leave their food-based territory to increase mating opportunities with neighboring estrus females. Home range comparisons between ecologically similar species emphasize the importance of divergent extrinsic factors in shaping variability in body size–home range size scaling relationships. Timing in resource availability influenced the social structure and space use in tree squirrels of similar body size, highlighting how the coevolution of arboreal squirrels with conifer tree species has shaped their natural history

The even darker side of the eastern gray squirrel (Sciurus carolinensis): a review of global introductions, invasion biology, and pest management strategies

Huynh, H.M., Bertolino, S., Lurz, P.W.W., Koprowski, J.L., Williams, G.R., Thompson, C.W., McAlpine, D.F

Serum CA19-9 response as a surrogate for clinical outcome in patients receiving fixed-dose rate gemcitabine for advanced pancreatic cancer

The use of serial serum measurements of the carbohydrate antigen 19-9 (CA19-9) to guide treatment decisions and serve as a surrogate end point in clinical trial design requires further validation. We investigated whether CA19-9 decline represents an accurate surrogate for survival and time to treatment failure (TTF) in a cohort of 76 patients with advanced pancreatic cancer receiving fixed-dose rate gemcitabine in three separate studies. Statistically significant correlations between percentage CA19-9 decline and both overall survival and TTF were found, with median survival ranging from 12.0 months for patients with the greatest degree of biomarker decline (>75%) compared with 4.3 months in those whose CA19-9 did not decline during therapy (P<0.001). Using specific thresholds, patients with ⩾25% decline in CA19-9 during treatment had significantly better outcomes than those who did not (median survival and TTF of 9.6 and 4.6 months vs 4.4 and 1.5 months; P<0.001). Similar results were seen using both 50 and 75% as cutoff points. We conclude that serial CA19-9 measurements correlate well with clinical outcomes in this patient population, and that decline in this biomarker should be entertained for possible use as a surrogate end point in clinical trials for the selection of new treatments in this disease

Experimental removals reveal dietary niche partitioning facilitates coexistence between native and introduced species

Niche overlap between native species and ecologically similar invaders can lead to competitive exclusion of threatened native species, but if two such species also co-occur naturally elsewhere, interactions between native and introduced populations may mirror coevolved niche partitioning that reduces competition and promotes coexistence.A single, insular population of Fremont's squirrel (Tamiasciurus fremonti) the Mount Graham red squirrel (MGRS; T. f. grahamensis) in the Pinaleño Mountains, Arizona, USA, is critically endangered and resource competition with introduced Abert's squirrels (Sciurus aberti) may threaten its long-term persistence. The species are naturally synoptic in other mountain sites, and both consume diets comprised primarily of conifer seeds and fungi.We conducted experimental removals of introduced Abert's squirrels and used stable isotope analysis of diets before and after removals, and of diets in naturally syntopic populations to test the hypothesis that dietary niche partitioning can facilitate coexistence between native and introduced species. We also developed a novel approach to determine the influence of fluctuating food availability on carbon enrichment in consumers.Mount Graham red squirrels and introduced Abert's squirrels partitioned the dietary niche similarly to naturally syntopic populations. Removals had no apparent effect. Diet of MGRS was more closely linked to availability of resources than to presence of Abert's squirrels.Flexible dietary niche of introduced Abert's squirrels may have allowed them to exploit a resource opportunity in syntopy with MGRS. Variable food production of MGRS habitat may intensify competition in poor years, and territorial defense against non-native Abert's squirrels likely imposes fitness costs on individual MGRS. Similarity in our model species' diets may make MGRS more vulnerable to competition if climate change eliminates the advantages of larder-hoarding. Where introduced populations of ecologically similar species are better adapted to changing conditions, they may ultimately replace southern peripheral populations of native species.USDA Forest Service; American Society of Mammalogists Grant in Aid of Research; T&E Inc. Grants for Conservation Biology; University of Arizona; Arizona Game and Fish DepartmentOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Relativistic supernova 2009bb exploded close to an atomic gas cloud

Context. The host galaxies of gamma-ray bursts (GRBs) have been claimed to have experienced a recent inflow of gas from the intergalactic medium. This is because their atomic gas distribution is not centred on their optical emission and because they are deficient in molecular gas given their high star formation rates (SFRs). Similar studies have not been conducted for host galaxies of relativistic supernovae (SNe), which may have similar progenitors. Aims. The potential similarity of the powering mechanisms of relativistic SNe and GRBs allowed us to make a prediction that relativistic SNe are born in environments similar to those of GRBs, that is, ones which are rich in atomic gas. Here we embark on testing this hypothesis by analysing the properties of the host galaxy NGC 3278 of the relativistic SN 2009bb. This is the first time the atomic gas properties of a relativistic SN host are provided and the first time resolved 21 cm-hydrogen-line (HâI) information is provided for a host of an SN of any type in the context of the SN position. Methods. We obtained radio observations with the Australia Telescope Compact Array (ATCA) covering the Hâ I line, and optical integral field unit spectroscopy observations with the Multi Unit Spectroscopic Explorer (MUSE) at the Very Large Telescope (VLT). Moreover, we analysed archival carbon monoxide (CO) and multi-wavelength data for this galaxy. Results. The atomic gas distribution of NGC 3278 is not centred on the optical galaxy centre, but instead around a third of atomic gas resides in the region close to the SN position. This galaxy has a few times lower atomic and molecular gas masses than predicted from its SFR. Its specific SFR (sSFR â SFR/M) is approximately two to three times higher than the main-sequence value, placing it at the higher end of the main sequence, towards starburst galaxies. SN 2009bb exploded close to the region with the highest SFR density and the lowest age, as evident from high Hα EW, corresponding to the age of the stellar population of ~5.5 Myr. Assuming this timescale was the lifetime of the progenitor star, its initial mass would have been close to ~36 M. Conclusions. As for GRB hosts, the gas properties of NGC 3278 are consistent with a recent inflow of gas from the intergalactic medium, which explains the concentration of atomic gas close to the SN position and the enhanced SFR. Super-solar metallicity at the position of the SN (unlike for most GRBs) may mean that relativistic explosions signal a recent inflow of gas (and subsequent star formation), and their type (GRBs or SNe) is determined either (i) by the metallicity of the inflowing gas, so that metal-poor gas results in a GRB explosion and metal-rich gas (for example a minor merger with an evolved galaxy or re-Accretion of expelled gas) results in a relativistic SN explosion without an accompanying GRB, or (ii) by the efficiency of gas mixing (efficient mixing for SN hosts leading to a quick disappearance of metal-poor regions), or (iii) by the type of the galaxy (more metal-rich galaxies would result in only a small fraction of star formation being fuelled by metal-poor gas).© ESO 2018.We thank Joanna Baradziej for help to improve this paper, and Giuliano Pignata, Carlos Contreras, and Maximilian Stritzinger for sharing the H-band image. M.J.M. acknowledges the support of the National Science Centre, Poland, through the POLONEZ grant 2015/19/P/ST9/04010; and the UK Science and Technology Facilities Council; this project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 665778. J.H. was supported by a VILLUM FONDEN Investigator grant (project number 16599). L.G. was supported in part by the US National Science Foundation under Grant AST-1311862. L.K.H. acknowledges funding from the INAF PRIN-SKA program 1.05.01.88.04. A.d.U.P. acknowledges support from the European Commission (FP7-PEOPLE-2012-CIG 322307) and from the Spanish project AYA2012-39362-C02-02. S.D.V. is supported by the French National Research Agency (ANR) under contract ANR-16-CE31-0003 BEaPro. The Australia Telescope Compact Array is part of the Australia Telescope National Facility, which is funded by the Commonwealth of Australia for operation as a National Facility managed by CSIRO. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programme(s) 095.D-0172(A). This publication makes use of data products from the Wide-field Infrared Survey Explorer, which is a joint project of the University of California, Los Angeles, and the Jet Propulsion Laboratory/California Institute of Technology, funded by the National Aeronautics and Space Administration. We acknowledge the usage of the Hyper-Leda database (http://leda.univ-lyon1.fr). This research has made use of the GHostS database (http://www.grbhosts.org), which is partly funded by Spitzer/NASA grant RSA Agreement No. 1287913; the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration; SAOImage DS9, developed by Smithsonian Astrophysical Observatory (Joye & Mandel 2003); and NASA's Astrophysics Data System Bibliographic Services.Peer reviewe

A Submillimeter Galaxy Illuminating its Circumgalactic Medium:Lyα Scattering in a Cold, Clumpy Outflow

We report the detection at 850 μm of the central source in SSA22-LAB1, the archetypal "Lyman-α Blob" (LAB), a 100 kpc scale radio-quiet emission-line nebula at z = 3.1. The flux density of the source, S 850 = 4.6 ± 1.1 mJy, implies the presence of a galaxy or group of galaxies with a total luminosity of L IR ≈ 1012 L ⊙. The position of an active source at the center of a ~50 kpc radius ring of linearly polarized Lyα emission detected by Hayes et al. suggests that the central source is leaking Lyα photons preferentially in the plane of the sky, which undergo scattering in H I clouds at a large galactocentric radius. The Lyα morphology around the submillimeter detection is reminiscent of a biconical outflow, and the average Lyα line profiles of the two "lobes" are dominated by a red peak, which is expected for a resonant line emerging from a medium with a bulk velocity gradient that is outflowing relative to the line center. Taken together, these observations provide compelling evidence that the central active galaxy (or galaxies) is responsible for a large fraction of the extended Lyα emission and morphology. Less clear is the history of the cold gas in the circumgalactic medium being traced by Lyα: is it mainly pristine material accreting into the halo that has not yet been processed through an interstellar medium (ISM), now being blown back as it encounters an outflow, or does it mainly comprise gas that has been swept-up within the ISM and expelled from the galaxy

A resolved map of the infrared excess in a Lyman Break Galaxy at z=3

The version of record, © 2016 The American Astronomical Society, M. P. Koprowski, K. E. K. Coppin, J. E. Geach, N. K. Hine, M. Bremer, S. Chapman, L. J. M. Davies, T. Hayashino, K. K. Knudsen, M. Kubo, B. D. Lehmer, Y. Matsuda, D. J. B. Smith, P. P. van der Werf, G. Violino, and T. Yamada, ‘A RESOLVED MAP OF THE INFRARED EXCESS IN A LYMAN BREAK GALAXY AT z = 3’, The Astrophysical Journal Letters, Vol 828(2), is available via doi: 10.3847/2041-8205/828/2/L21We have observed the dust continuum of ten z=3.1 Lyman Break Galaxies with the Atacama Large Millimeter/Submillimeter Array at ~450 mas resolution in Band 7. We detect and resolve the 870um emission in one of the targets with an integrated flux density of S(870)=(192+/-57) uJy, and measure a stacked 3-sigma signal of S(870)=(67+/-23) uJy for the remaining nine. The total infrared luminosities estimated from full spectral energy distribution fits are L(8-1000um)=(8.4+/-2.3)x10^10 Lsun for the detection and L(8-1000um)=(2.9+/-0.9)x10^10 Lsun for the stack. With HST ACS I-band imaging we map the rest-frame UV emission on the same scale as the dust, effectively resolving the 'infrared excess' (IRX=L_FIR/L_UV) in a normal galaxy at z=3. Integrated over the galaxy we measure IRX=0.56+/-0.15, and the galaxy-averaged UV slope is beta=-1.25+/-0.03. This puts the galaxy a factor of ~10 below the IRX-beta relation for local starburst nuclei of Meurer et al. (1999). However, IRX varies by more than a factor of 3 across the galaxy, and we conclude that the complex relative morphology of the dust relative to UV emission is largely responsible for the scatter in the IRX-beta relation at high-z. A naive application of a Meurer-like dust correction based on the UV slope would dramatically over-estimate the total star formation rate, and our results support growing evidence that when integrated over the galaxy, the typical conditions in high-z star-forming galaxies are not analogous to those in the local starburst nuclei used to establish the Meurer relation.Peer reviewe