A New Approach for Distributed Hypothesis Testing with Extensions to Byzantine-Resilience.
Abstract not provided.
Mitra, Aritra↗
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MassIVE MSV000085948 - Utilization of syringyl lignin-derived compounds and production of 2-pyrone-4,6-dicarboxylic acid by Pseudomonas putida KT2440: Lignin is an abundant aromatic polymer formed in plants by coupling reactions of p-coumaryl, coniferyl, and sinapyl alcohols. Pseudomonas putida KT2440 (P. putida KT2440), a robust soil bacterium, naturally catabolizes many aromatic compounds derived from lignin as carbon and energy sources and has been extensively engineered to valorize guaiacyl (G) and p-hydroxyphenyl (H) lignin-derived aromatic species to valuable chemicals. However, only a few studies report the capacity of Pseudomonads to grow on syringyl (S) lignin-derived compounds. In this work, we demonstrate that P. putida KT2440 catabolizes syringate in the presence of an auxiliary energy source. Overexpression of vanAB, encoding a native Rieske non-heme iron monooxygenase, enabled catabolism of syringate and syringaldehyde without an additional carbon and energy source. In vitro biochemical characterization of VanAB confirmed that this enzyme O-demethylates syringate to 3-O-methylgallate and, subsequently, 3-O-methylgallate to gallate, albeit 4- and 55-fold less efficiently than vanillate, respectively. Transcriptomics and proteomics experiments demonstrate that the galADBC transcripts and enzymes required for gallate catabolism are induced when vanAB is overexpressed during cultivation in syringate. Further, we show that that the endogenous protocatechuate-3,4-dioxygenase PcaHG ring-opens gallate to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a promising bio-based chemical. Constitutive overexpression of vanAB and pcaHG along with galA deletion enabled PDC production from SA at a 70% (mol/mol) yield. Furthermore, leveraging the LigAB dioxygenase from Sphingobium sp. SYK-6 and VanAB O-demethylase from Pseudomonas sp. HR199 enabled simultaneous conversion of monomers with S-, G-, and H-type functionality to PDC at 82% (mol/mol) yield. Overall, this study elucidates a native pathway for catabolism of syringyl lignin-derived compounds in P. putida KT2440 and demonstrates the potential of this robust host for biological funneling of substrates derived from all three canonical monolignols.
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Beckham, Gregg↗
MassIVE MSV000100641 - Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli: Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.
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Alexander, William G. [Oak Ridge National Laborato↗
Geometric Interpretation of a Non-Linear Extension of Quantum Mechanics
We recently introduced a particular non-linear generalization of quantum mechanics that has the property that it is exactly solvable in terms of the eigenvalues and eigenfunctions of the Hamiltonian of the usual linear quantum mechanics problem. In this paper, we suggest that the two components of the wave function represent the system described by the Hamiltonian H in two different asymptotic regions of spacetime and we show that the non-linear terms can be viewed as giving rise to gravitational effects.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
The Straightening of a River Meander Leads to Extensive Losses in Flow Complexity and Ecosystem Services
To assist river restoration efforts we need to slow the rate of river degradation. This study provides a detailed explanation of the hydraulic complexity loss when a meandering river is straightened in order to motivate the protection of river channel curvature. We used computational fluid dynamics (CFD) modeling to document the difference in flow dynamics in nine simulations with channel curvature (C) degrading from a well-established tight meander bend (C = 0.77) to a straight channel without curvature (C = 0). To control for covariates and slow the rate of loss to hydraulic complexity, each of the nine-channel realizations had equivalent bedform topography. The analyzed hydraulic variables included the flow surface elevation, streamwise and transverse unit discharge, flow velocity at streamwise, transverse, and vertical directions, bed shear stress, stream function, and the vertical hyporheic flux rates at the channel bed. The loss of hydraulic complexity occurred gradually when initially straightening the channel from C = 0.77 to C = 0.33 (i.e., the radius of the channel is three-times the channel width), and additional straightening incurred rapid losses to hydraulic complexity. Other studies have shown hydraulic complexity provides important riverine habitat and is positively correlated with biodiversity. This study demonstrates how hydraulic complexity can be gradually and then rapidly lost when unwinding a river, and hopefully will serve as a cautionary tale.
54 ENVIRONMENTAL SCIENCES↗
Extensive Genetic Diversity is Present within North American Switchgrass Germplasm
Switchgrass ( Panicum virgatum L ) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice ( Oryza sativa L.), maize ( Zea mays L.), soybean [ Glycine max (L.) Merr.], and Medicago truncatula Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.
09 BIOMASS FUELS↗
An extensive numerical survey of the correlation between outflow dynamics and accretion disk magnetization
We investigate the accretion–ejection process of jets from magnetized accretion disks. We apply a novel approach to the jet-launching problem in order to obtain correlations between the physical properties of the jet and the underlying disk. We extend and confirm the previous works of Tzeferacos et al. and Murphy et al. by scanning a large parameter range for the disk magnetization, μ{sub D}=10{sup −3.5}...10{sup −0.7}. We disentangle the disk magnetization at the foot point of the outflow as the main parameter that governs the properties of the outflow. We show how the four jet integrals known from steady-state MHD are correlated to the disk magnetization at the jet foot point. This agrees with the usual findings of the steady-state theory, however, here we obtain these correlations from time-dependent simulations that include the dynamical evolution of the disk in the treatment. In particular, we obtain robust correlations between the local disk magnetization and (i) the outflow velocity, (ii) the jet mass loading, (iii) the jet angular momentum, and (iv) the local mass accretion rate. Essentially, we find that strongly magnetized disks launch more energetic and faster jets and, due to a larger Alfvén lever arm, these jets extract more angular momentum from the underlying disk. These kinds of disk–jet systems have, however, a smaller mass loading parameter and a lower mass ejection–accretion ratio. The jets are launched at the disk surface where the magnetization is μ(r,z)≃0.1. The magnetization rapidly increases vertically providing the energy reservoir for subsequent jet acceleration. We find indications of a critical disk magnetization μ{sub D}≃0.01 that separates the regimes of magneto-centrifugally driven and magnetic pressure-driven jets.
79 ASTRONOMY AND ASTROPHYSICS↗
Star formation laws in both galactic massive clumps and external galaxies: extensive study with dust coninuum, HCN (4-3), and CS (7-6)
We observed 146 Galactic clumps in HCN (4-3) and CS (7-6) with the Atacama Submillimeter Telescope Experiment 10 m telescope. A tight linear relationship between star formation rate and gas mass traced by dust continuum emission was found for both Galactic clumps and the high redshift (z > 1) star forming galaxies (SFGs), indicating a constant gas depletion time of ∼100 Myr for molecular gas in both Galactic clumps and high z SFGs. However, low z galaxies do not follow this relation and seem to have a longer global gas depletion time. The correlations between total infrared luminosities (L {sub TIR}) and molecular line luminosities (L{sub mol}{sup ′}) of HCN (4-3) and CS (7-6) are tight and sublinear extending down to clumps with L {sub TIR} ∼ 10{sup 3} L {sub ☉}. These correlations become linear when extended to external galaxies. A bimodal behavior in the L {sub TIR}–L{sub mol}{sup ′} correlations was found for clumps with different dust temperature, luminosity-to-mass ratio, and σ {sub line}/σ {sub vir}. Such bimodal behavior may be due to evolutionary effects. The slopes of L {sub TIR}–L′{sub mol} correlations become more shallow as clumps evolve. We compared our results with lower J transition lines in Wu et al. (2010). The correlations between clump masses and line luminosities are close to linear for low effective excitation density tracers but become sublinear for high effective excitation density tracers for clumps with L {sub TIR} larger than L {sub TIR} ∼ 10{sup 4.5} L {sub ☉}. High effective excitation density tracers cannot linearly trace the total clump masses, leading to a sublinear correlations for both M {sub clump}–L′{sub mol} and L {sub TIR}–L′{sub mol} relations.
79 ASTRONOMY AND ASTROPHYSICS↗
AN EXTENSION OF THE ATHENA++ CODE FRAMEWORK FOR GRMHD BASED ON ADVANCED RIEMANN SOLVERS AND STAGGERED-MESH CONSTRAINED TRANSPORT
We present a new general relativistic magnetohydrodynamics (GRMHD) code integrated into the Athena++ framework. Improving upon the techniques used in most GRMHD codes, ours allows the use of advanced, less diffusive Riemann solvers, in particular HLLC and HLLD. We also employ a staggered-mesh constrained transport algorithm suited for curvilinear coordinate systems in order to maintain the divergence-free constraint of the magnetic field. Our code is designed to work with arbitrary stationary spacetimes in one, two, or three dimensions, and we demonstrate its reliability through a number of tests. We also report on its promising performance and scalability.
79 ASTRONOMY AND ASTROPHYSICS↗
EXTENSION OF THE MURAM RADIATIVE MHD CODE FOR CORONAL SIMULATIONS
We present a new version of the MURaM radiative magnetohydrodynamics (MHD) code that allows for simulations spanning from the upper convection zone into the solar corona. We implement the relevant coronal physics in terms of optically thin radiative loss, field aligned heat conduction, and an equilibrium ionization equation of state. We artificially limit the coronal Alfvén and heat conduction speeds to computationally manageable values using an approximation to semi-relativistic MHD with an artificially reduced speed of light (Boris correction). We present example solutions ranging from quiet to active Sun in order to verify the validity of our approach. We quantify the role of numerical diffusivity for the effective coronal heating. We find that the (numerical) magnetic Prandtl number determines the ratio of resistive to viscous heating and that owing to the very large magnetic Prandtl number of the solar corona, heating is expected to happen predominantly through viscous dissipation. We find that reasonable solutions can be obtained with values of the reduced speed of light just marginally larger than the maximum sound speed. Overall this leads to a fully explicit code that can compute the time evolution of the solar corona in response to photospheric driving using numerical time steps not much smaller than 0.1 s. Numerical simulations of the coronal response to flux emergence covering a time span of a few days are well within reach using this approach.
79 ASTRONOMY AND ASTROPHYSICS↗
An Improved Analytical Model of the Local Interstellar Magnetic Field: The Extension to Compressibility
A previously published analytical magnetohydrodynamic model for the local interstellar magnetic field in the vicinity of the heliopause (Röken et al. 2015) is extended from incompressible to compressible, yet predominantly subsonic flow, considering both isothermal and adiabatic equations of state. Exact expressions and suitable approximations for the density and the flow velocity are derived and discussed. In addition to the stationary induction equation, these expressions also satisfy the momentum balance equation along stream lines. The practical usefulness of the corresponding, still exact, analytical magnetic field solution is assessed by comparing it quantitatively to results from a fully self-consistent magnetohydrodynamic simulation of the interstellar magnetic field draping around the heliopause.
79 ASTRONOMY AND ASTROPHYSICS↗
An Extension of the Athena++ Code Framework for Radiation-magnetohydrodynamics in General Relativity Using a Finite-solid-angle Discretization
We extend the general-relativistic magnetohydrodynamics (GRMHD) capabilities of Athena++ to incorporate radiation. The intensity field in each finite-volume cell is discretized in angle, with explicit transport in both space and angle properly accounting for the effects of gravity on null geodesics, and with matter and radiation coupled in a locally implicit fashion. Here we describe the numerical procedure in detail, verifying its correctness with a suite of tests. Motivated in particular by black hole accretion in the high-accretion-rate, thin-disk regime, we demonstrate the application of the method to this problem. With excellent scaling on flagship computing clusters, the port of the algorithm to the GPU-enabled AthenaK code now allows the simulation of many previously intractable radiation-GRMHD systems.
79 ASTRONOMY AND ASTROPHYSICS↗
Extensive Globular Cluster Systems Associated with Ultra Diffuse Galaxies in the Coma Cluster
We present Hubble Space Telescope (HST) imaging of two ultra diffuse galaxies (UDGs) with measured stellar velocity dispersions in the Coma cluster. The galaxies, Dragonfly 44 and DFX1, have effective radii of 4.7 kpc and 3.5 kpc and velocity dispersions of 47{sub −6}{sup +8} km s{sup −1} and 30{sub −7}{sup +7} km s{sup −1}, respectively. Both galaxies are associated with a striking number of compact objects, tentatively identified as globular clusters: N{sub gc}=74±18 for Dragonfly 44 and N{sub gc}=62±17 for DFX1. The number of globular clusters is much higher than expected from the luminosities of the galaxies but is consistent with expectations from the empirical relation between dynamical mass and globular cluster count defined by other galaxies. Combining our data with previous HST observations of Coma UDGs we find that UDGs have a factor of 6.9{sub −2.4}{sup +1.0} more globular clusters than other galaxies of the same luminosity, in contrast to a recent study of a similar sample by Amorisco et al., but consistent with earlier results for individual galaxies. The Harris et al. relation between globular cluster count and dark matter halo mass implies a median halo mass of M{sub halo}∼1.5×10{sup 11} M{sub ⊙} for the sixteen Coma UDGs that have been observed with HST so far, with the largest and brightest having M{sub halo}∼5×10{sup 11} M{sub ⊙}.
79 ASTRONOMY AND ASTROPHYSICS↗
Load Limit Extension in Pre-Mixed Compression Ignition Using the 2-zone Combustion System
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Bergin, Mike↗
Data from: Extensive genetic diversity is present within North American switchgrass germplasm
Switchgrass (Panicum virgatum L.) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice (Oryza sativa L.), maize (Zea mays L.), soybean [Glycine max (L.) Merr.], and Medicago truncatula Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.
09 BIOMASS FUELS↗
Predicting biomass of hyperdiverse and structurally complex central Amazonian forests - a virtual approach using extensive field data
Notice on corrigendum: This paper has a corresponding corrigendum published. Please read the corrigendum first. Old-growth forests are subject to substantial changes in structure and species composition due to the intensification of human activities, gradual climate change and extreme weather events. Trees store ca. 90 % of the total aboveground biomass (AGB) in tropical forests and precise tree biomass estimation models are crucial for management and conservation. In the central Amazon, predicting AGB at large spatial scales is a challenging task due to the heterogeneity of successional stages, high tree species diversity and inherent variations in tree allometry and architecture. We parameterized generic AGB estimation models applicable across species and a wide range of structural and compositional variation related to species sorting into height layers as well as frequent natural disturbances. We used 727 trees (diameter at breast height ≥ 5 cm) from 101 genera and at least 135 species harvested in a contiguous forest near Manaus, Brazil. Sampling from this data set we assembled six scenarios designed to span existing gradients in floristic composition and size distribution in order to select models that best predict AGB at the landscape level across successional gradients. We found that good individual tree model fits do not necessarily translate into reliable predictions of AGB at the landscape level. When predicting AGB (dry mass) over scenarios using our different models and an available pantropical model, we observed systematic biases ranging from -31 % (pantropical) to +39 %, with root-mean-square error (RMSE) values of up to 130 Mg ha -1 (pantropical). Our first and second best models had both low mean biases (0.8 and 3.9 %, respectively) and RMSE (9.4 and 18.6 Mg ha -1 ) when applied over scenarios. Predicting biomass correctly at the landscape level in hyperdiverse and structurally complex tropical forests, especially allowing good performance at the margins of data availability for model construction/calibration, requires the inclusion of predictors that express inherent variations in species architecture. The model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases. Reliable biomass assessments for the Amazon basin (i.e., secondary forests) still depend on the collection of allometric data at the local/regional scale and forest inventories including species-specific attributes, which are often unavailable or estimated imprecisely in most regions.
54 ENVIRONMENTAL SCIENCES↗
Corrigendum to "Predicting biomass of hyperdiverse and structurally complex central Amazonian forests — a virtual approach using extensive field data" Published in Biogeosciences, 13, 1553-1570, 2016
Old-growth forests are subject to substantial changes in structure and species composition due to the intensification of human activities, gradual climate change and extreme weather events. Trees store ca. 90% of the total aboveground biomass (AGB) in tropical forests and precise tree biomass estimation models are crucial for management and conservation. In the central Amazon, predicting AGB at large spatial scales is a challenging task due to the heterogeneity of successional stages, high tree species diversity and inherent variations in tree allometry and architecture. We parameterized generic AGB estimation models applicable across species and a wide range of structural and compositional variation related to species sorting into height layers as well as frequent natural disturbances. We used 727 trees (diameter at breast height ≥5 cm) from 101 genera and at least 135 species harvested in a contiguous forest near Manaus, Brazil. Sampling from this data set we assembled six scenarios designed to span existing gradients in floristic composition and size distribution in order to select models that best predict AGB at the landscape level across successional gradients. We found that good individual tree model fits do not necessarily translate into reliable predictions of AGB at the landscape level. We observed systematic biases ranging from -31% (pantropical) to +39 %, with root-mean-square error (RMSE) values of up to 130-Mg ha -1 (pantropical), when predicting AGB (dry mass) over scenarios using our different models and an available pantropical model. Our first and second best models had both low mean biases (0.8 and 3.9 %, respectively) and RMSE (9.4 and 18.6 Mg ha -1 ) when applied over scenarios. Predicting biomass correctly at the landscape level in hyperdiverse and structurally complex tropical forests, especially allowing good performance at the margins of data availability for model construction/calibration, requires the inclusion of predictors that express inherent variations in species architecture. Furthermore, the model of interest should comprise the floristic composition and size-distribution variability of the target forest, implying that even generic global or pantropical biomass estimation models can lead to strong biases. Reliable biomass assessments for the Amazon basin (i.e., secondary forests) still depend on the collection of allometric data at the local/regional scale and forest inventories including species-specific attributes, which are often unavailable or estimated imprecisely in most regions.
54 ENVIRONMENTAL SCIENCES↗
A production-tagged aerosol module for Earth system models, OsloAero5.3 – extensions and updates for CAM5.3-Oslo
Abstract. We document model updates and present and discuss modeling and validation results from a further developed production-tagged aerosol module, OsloAero5.3, for use in Earth system models. The aerosol module has in this study been implemented and applied in CAM5.3-Oslo. This model is based on CAM5.3–CESM1.2 and its own predecessor model version CAM4-Oslo. OsloAero5.3 has improved treatment of emissions, aerosol chemistry, particle life cycle, and aerosol–cloud interactions compared to its predecessor OsloAero4.0 in CAM4-Oslo. The main new features consist of improved aerosol sources; the module now explicitly accounts for aerosol particle nucleation and secondary organic aerosol production, with new emissions schemes also for sea salt, dimethyl sulfide (DMS), and marine primary organics. Mineral dust emissions are updated as well, adopting the formulation of CESM1.2. The improved model representation of aerosol–cloud interactions now resolves heterogeneous ice nucleation based on black carbon (BC) and mineral dust calculated by the model and treats the activation of cloud condensation nuclei (CCN) as in CAM5.3. Compared to OsloAero4.0 in CAM4-Oslo, the black carbon (BC) mass concentrations are less excessive aloft, with a better fit to observations. Near-surface mass concentrations of BC and sea salt aerosols are also less biased, while sulfate and mineral dust are slightly more biased. Although appearing quite similar for CAM5.3-Oslo and CAM4-Oslo, the validation results for organic matter (OM) are inconclusive, since both of the respective versions of OsloAero are equipped with a limited number of OM tracers for the sake of computational efficiency. Any information about the assumed mass ratios of OM to organic carbon (OC) for different types of OM sources is lost in the transport module. Assuming that observed OC concentrations scaled by 1.4 are representative for the modeled OM concentrations, CAM5.3-Oslo with OsloAero5.3 is slightly inferior for the very sparsely available observation data. Comparing clear-sky column-integrated optical properties with data from ground-based remote sensing, we find a negative bias in optical depth globally; however, it is not as strong as in CAM4-Oslo, but has positive biases in some areas typically dominated by mineral dust emissions. Aerosol absorption has a larger negative bias than the optical depth globally. This is reflected in a lower positive bias in areas where mineral dust is the main contributor to absorption. Globally, the low bias in absorption is smaller than in CAM4-Oslo. The Ångström parameter exhibits small biases both globally and regionally, suggesting that the aerosol particle sizes are reasonably well represented. Cloud-top droplet number concentrations over oceans are generally underestimated compared to satellite retrievals, but seem to be overestimated downwind of major emissions of dust and biomass burning sources. Finally, we find small changes in direct radiative forcing at the top of the atmosphere, while the cloud radiative forcing due to anthropogenic aerosols is now more negative than in CAM4-Oslo, being on the strong side compared to the multi-model estimate in IPCC AR5. Although not all validation results in this study show improvement for the present CAM5.3-Oslo version, the extended and updated aerosol module OsloAero5.3 is more advanced and applicable than its predecessor OsloAero4.0, as it includes new parameterizations that more readily facilitate sensitivity and process studies and use in climate and Earth system model studies in general.
54 ENVIRONMENTAL SCIENCES↗