Bidirectionally Tolerating Inconsistency: Partial Transformations

Abstract. A foundational property of bidirectional transformations is that they should be correct: that is, the transformation should succeed in restoring consistency between any models it is given. In practice, how-ever, transformation engines sometimes fail to restore consistency, e.g. because there is no consistent model to return, or because the tool is unable to select a best model to return from among equally good candi-dates. In this paper, we formalise properties that may nevertheless hold in such circumstances and discuss relationships and implications.

Faithful Modeling of Product Lines with Kripke Structures and Modal Logic

Software product lines are now an established framework for software design. They are specified by special diagrams called feature models. For formal analysis, the latter are usually encoded by Boolean propositional theories. We discuss a major deficiency of this semantics, and show that it can be fixed by considering a product to be an instantiation process rather than its final result. We call intermediate states of this process partial products, and argue that what a feature model really defines is a poset of its partial products. We argue that such structures can be viewed as special Kripke structure that we call partial product Kripke structures, ppKS. To specify these Kripke structures, we propose a CTL-based logic, called partial product CTL, ppCTL. We show how to represent a feature model M by a ppCTL theory ML(M) (ML stands for modal logic) such that any ppKS satisfying the theory is equal to the partial product line determined by M. Hence, ML(M) can be considered a sound and complete representation of M. We also discuss several applications of the modal logic view in feature modeling, including refactoring of feature models

Brown carbon aerosol in the North American continental troposphere: sources, abundance, and radiative forcing

Chemical components of organic aerosol (OA) selectively absorb light at short wavelengths. In this study, the prevalence, sources, and optical importance of this so called brown carbon (BrC) aerosol component are investigated throughout the North American continental tropospheric column during a summer of extensive biomass burning. Spectrophotometric absorption measurements on extracts of bulk aerosol samples collected from an aircraft over the central USA were analyzed to directly quantify BrC abundance. BrC was found to be prevalent throughout the 1 to 12 km altitude measurement range, with dramatic enhancements in biomass-burning plumes. BrC to black carbon (BC) ratios, under background tropospheric conditions, increased with altitude, consistent with a corresponding increase in the absorption Ångström exponent (AAE) determined from a three-wavelength particle soot absorption photometer (PSAP). The sum of inferred BC absorption and measured BrC absorption at 365 nm was within 3 % of the measured PSAP absorption for background conditions and 22 % for biomass burning. A radiative transfer model showed that BrC absorption reduced top-of atmosphere (TOA) aerosol forcing by ∼ 20 % in the background troposphere. Extensive radiative model simulations applying this study background tropospheric conditions provided a look-up chart for determining radiative forcing efficiencies of BrC as a function of a surface-measured BrC : BC ratio and single scattering albedo (SSA). The chart is a first attempt to provide a tool for better assessment of brown carbon’s forcing effect when one is limited to only surface data. These results indicate that BrC is an important contributor to direct aerosol radiative forcing

Comparison of chemical characteristics of 495 biomass burning plumes intercepted by the NASA DC-8 aircraft during the ARCTAS/CARB-2008 field campaign

This paper compares measurements of gaseous and particulate emissions from a wide range of biomass-burning plumes intercepted by the NASA DC-8 research aircraft during the three phases of the ARCTAS-2008 experiment: ARCTAS-A, based out of Fairbanks, Alaska, USA (3 April to 19 April 2008); ARCTAS-B based out of Cold Lake, Alberta, Canada (29 June to 13 July 2008); and ARCTAS-CARB, based out of Palmdale, California, USA (18 June to 24 June 2008). Approximately 500 smoke plumes from biomass burning emissions that varied in age from minutes to days were segregated by fire source region and urban emission influences. The normalized excess mixing ratios (NEMR) of gaseous (carbon dioxide, acetonitrile, hydrogen cyanide, toluene, benzene, methane, oxides of nitrogen and ozone) and fine aerosol particulate components (nitrate, sulfate, ammonium, chloride, organic aerosols and water soluble organic carbon) of these plumes were compared. A detailed statistical analysis of the different plume categories for different gaseous and aerosol species is presented in this paper. The comparison of NEMR values showed that CH4 concentrations were higher in air-masses that were influenced by urban emissions. Fresh biomass burning plumes mixed with urban emissions showed a higher degree of oxidative processing in comparison with fresh biomass burning only plumes. This was evident in higher concentrations of inorganic aerosol components such as sulfate, nitrate and ammonium, but not reflected in the organic components. Lower NOx NEMRs combined with high sulfate, nitrate and ammonium NEMRs in aerosols of plumes subject to long-range transport, when comparing all plume categories, provided evidence of advanced processing of these plumes

A method for isolating and culturing placental cells from failed early equine pregnancies

Early pregnancy loss occurs in 6–10% of equine pregnancies making it the main cause of reproductive wastage. Despite this, reasons for the losses are known in only 16% of cases. Lack of viable conceptus material has inhibited investigations of many potential genetic and pathological causes. We present a method for isolating and culturing placental cells from failed early equine pregnancies. Trophoblast cells from 18/30 (60%) failed equine pregnancies of gestational ages 14–65 days were successfully cultured in three different media, with the greatest growth achieved for cells cultured in AmnioChrome™ Plus. Genomic DNA of a suitable quality for molecular assays was also isolated from 29/30 of these cases. This method will enable future investigations determining pathologies causing EPL

Therapeutic Efficacy of Potent Neutralizing HIV-1-Specific Monoclonal Antibodies in SHIV-Infected Rhesus Monkeys

HIV-1-specific monoclonal antibodies (mAbs) with extraordinary potency and breadth have recently been described. In humanized mice, combinations of mAbs have been shown to suppress viremia, but the therapeutic potential of these mAbs has not yet been evaluated in primates with an intact immune system. Here we show that administration of a cocktail of HIV-1-specific mAbs, as well as the single glycan-dependent mAb PGT121, resulted in a rapid and precipitous decline of plasma viremia to undetectable levels in rhesus monkeys chronically infected with the pathogenic virus SHIV-SF162P3. A single mAb infusion afforded up to a 3.1 log decline of plasma viral RNA in 7 days and also reduced proviral DNA in peripheral blood, gastrointestinal mucosa, and lymph nodes without the development of viral resistance. Moreover, following mAb administration, host Gag-specific T lymphocyte responses exhibited improved functionality. Virus rebounded in the majority of animals after a median of 56 days when serum mAb titers had declined to undetectable levels, although a subset of animals maintained long-term virologic control in the absence of further mAb infusions. These data demonstrate a profound therapeutic effect of potent neutralizing HIV-1-specific mAbs in SHIV-infected rhesus monkeys as well as an impact on host immune responses. Our findings strongly encourage the investigation of mAb therapy for HIV-1 in humans

In situ measurements of water uptake by black carbon-containing aerosol in wildfire plumes

Water uptake by black carbon (BC)-containing aerosol was quantified in North American wildfire plumes of varying age (1 to ~40 h old) sampled during the SEAC4RS mission (2013). A Humidified Dual SP2 (HD-SP2) is used to optically size BC-containing particles under dry and humid conditions from which we extract the hygroscopicity parameter, κ, of materials internally mixed with BC. Instrumental variability and the uncertainty of the technique are briefly discussed. An ensemble average κ of 0.04 is found for the set of plumes sampled, consistent with previous estimates of bulk aerosol hygroscopicity from biomass burning sources. The temporal evolution of κ in the Yosemite Rim Fire plume is explored to constrain the rate of conversion of BC-containing aerosol from hydrophobic to more hydrophilic modes in these emissions. A BC-specific κ increase of ~0.06 over 40 h is found, fit well with an exponential curve corresponding to a transition from a κ of 0 to a κ of ~0.09 with an e-folding time of 29 h. Although only a few percent of wildfire particles contain BC, a similar κ increase is estimated for bulk aerosol and the measured aerosol composition is used to infer that the observed κ change is driven by a combination of incorporation of ammonium sulfate and oxidation of existing organic materials. Finally, a substantial fraction of wildfire-generated BC-containing aerosol is calculated to be active as cloud condensation nuclei shortly after emission likely indicating efficient wet removal. These results can constrain model treatment of BC from wildfire sources

Notions of Bidirectional Computation and Entangled State Monads

Bidirectional transformations (bx) support principled consistency maintenance between data sources. Each data source corresponds to one perspective on a composite system, manifested by operations to ‘get’ and ‘set’ a view of the whole from that particular perspective. Bx are important in a wide range of settings, including databases, interactive applications, and model-driven development. We show that bx are naturally modelled in terms of mutable state; in particular, the ‘set’ operations are stateful functions. This leads naturally to considering bx that exploit other computational effects too, such as I/O, nondeterminism, and failure, all largely ignored in the bx literature to date. We present a semantic foundation for symmetric bidirectional transformations with effects. We build on the mature theory of monadic encapsulation of effects in functional programming, develop the equational theory and important combinators for effectful bx, and provide a prototype implementation in Haskell along with several illustrative examples