ALBERT

Description: A three-dimensional (3-D) time-dependent, numerical magnetohydrodynamic (MHD) model with asynchronous and parallel time-marching method is used to investigate the propagation of coronal mass ejections (CMEs) in the nonhomogenous background solar wind flow. The background solar wind is constructed based on the self-consistent source surface with observed line-of-sight of magnetic field and density from the source surface of 2.5 Rs to the Earth's orbit (215 Rs) and beyond. The CMEs are simulated by means of a very simple flux rope model: a high-density, high-velocity, and high-temperature magnetized plasma blob is superimposed on a steady state background solar wind with an initial launch direction. The dynamical interaction of a CME with the background solar wind flow between 2.5 and 220 Rs is investigated. The evolution of the physical parameters at the cobpoint, which is located at the shock front region magnetically connected to ACE spacecraft, is also investigated. We have chosen the well-defined halo-CME event of 4–6 April 2000 as a test case. In this validation study we find that this 3-D MHD model, with the asynchronous and parallel time-marching method, the self-consistent source surface as initial boundary conditions, and the simple flux rope as CME model, provide a relatively satisfactory comparison with the ACE spacecraft observations at the L1 point.

Description: We present the time-dependent propagation of a Sun-Earth connection event that occurred on 4 November 1997 using a three-dimensional (3-D) numerical magnetohydrodynamics (MHD) simulation. A global steady state solar wind for this event is obtained by a 3-D SIP-CESE MHD model with Parker's 1-D solar wind solution and measured photospheric magnetic fields as the initial values. Then, superposed on the quiet background solar wind, a spherical plasmoid is used to mimic the 4 November 1997 coronal mass ejection (CME) event. The CME is assumed to arise from the evolution of a spheromak magnetic structure with high-speed, high-pressure, and high-plasma-density plasmoid near the Sun. Moreover, the axis of the initial simulated CME is put at S14W34 to conform to the observed location of this flare/CME event. The result has provided us with a relatively satisfactory comparison with the Wind spacecraft observations, such as southward interplanetary magnetic field and large-scale smooth rotation of the magnetic field associated with the CME.

Description: The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic differences at various levels from genotypes to species. The design is based on two reciprocal crosses between two individuals each chosen from a hermaphrodite or monoecious species. A multinomial distribution likelihood is constructed by combining marker information from two crosses. The EM algorithm is implemented to estimate the rate of apomixis and test its difference between two plant populations or species as the parents. The design is validated by computer simulation. A real data analysis of two reciprocal crosses between hickory ( Carya cathayensis ) and pecan ( C. illinoensis ) demonstrates the utilization and usefulness of the design in practice. The design provides a tool to address fundamental and applied questions related to the evolution and breeding of apomixis.

Description: Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

Description: Aims Nitrogen (N) fertilization and lime addition may affect soil microbial and nematode communities and ecosystem functions through changing environmental conditions, such as soil pH and soil organic carbon. The objectives of this experiment were to examine the impact of N input and liming on soil microbial and nematode communities and to identify the key environmental determinant of community composition in a century-old fertilization and crop rotation experiment. Methods The field experiment consisting of a 3-year crop rotation regime was established in 1911 in southeastern USA. Four treatments, (i) no-input control, (ii) NPK with winter legume, (iii) PK with legume and lime and (iv) NPK with legume and lime, were included in this study. Soil samples collected at the 0–5cm depth were used to determine the bacterial growth rate by the 3 H-thymidine incorporation technique. Incorporation of 13 C into neutral lipids, glycolipids and phospholipid fatty acids (PLFAs) was measured after incubation of soil with 13 C-labeled acetate for 24h. Free-living nematodes in fresh soil were extracted using a density sucrose centrifugal flotation method and identified to trophic group level. Important Findings Liming resulted in a 10-fold increase in bacterial growth rates compared with the no-input control, whereas N fertilization had no significant effect. Multivariate analysis of PLFA profiles showed that soil microbial community composition was different among the four treatments; the difference was primarily driven by soil pH. PLFAs indicative of Gram-negative bacteria covaried with soil pH, but not those of fungi and actinobacteria. Liming enhanced 13 C incorporation into neutral lipids, glycolipids and phospholipids by 2–15 times. In addition, 13 C incorporation into 16:0, 16:19, 18:19, 18:17 and 18:26 were greater than other PLFAs, suggesting that Gram-negative bacteria and fungi were more active and sensitive to simple C input. Bacterivorous nematodes were the dominant trophic group in the soil, but no significant differences in nematode communities were found among the treatments. Our results suggest that soil pH had a greater impact than N fertilization on soil microbial community composition and activity in a crop rotation system including legumes.

Description: Abstract The South Central United States is a hot spot for anthropogenic methane (CH4) emissions, with contributions from the oil/gas (O&G) and animal agriculture sectors. During frontal weather events, airflow combines enhancements from these emissions into a large plume. In this study, we take CH4 and ethane (C2H6) observations from the Atmospheric Carbon and Transport‐America campaign and adjust O&G and animal agriculture emissions such that modeled CH4 and C2H6 enhancements match the observed plume. Results from the joint CH4‐C2H6 optimization indicate that emissions from the O&G sector are 1.8 ± 0.7 (2σ) times larger than EPA inventory estimates. These results match synthesis work from recent literature and reject the possibility that this increase compared to inventories is due to a potential bias in daytime‐only measurements of these facilities. Successful modeling from this study raises the possibility of using trace gas measurements along frontal crossings to solve for emissions in other regions of the United States.

Description: The BL Lacertae object 1ES 1440+122 was observed in the energy range from 85 GeV to 30 TeV by the VERITAS array of imaging atmospheric Cherenkov telescopes. The observations, taken between 2008 May and 2010 June and totalling 53 h, resulted in the discovery of -ray emission from the blazar, which has a redshift z = 0.163. 1ES 1440+122 is detected at a statistical significance of 5.5 standard deviations above the background with an integral flux of (2.8 ± 0.7 stat ± 0.8 sys ) x 10 –12  cm –2  s –1 (1.2 per cent of the Crab Nebula's flux) above 200 GeV. The measured spectrum is described well by a power law from 0.2 to 1.3 TeV with a photon index of 3.1 ± 0.4 stat ± 0.2 sys . Quasi-simultaneous multiwavelength data from the Fermi Large Area Telescope (0.3–300 GeV) and the Swift X-ray Telescope (0.2–10 keV) are additionally used to model the properties of the emission region. A synchrotron self-Compton model produces a good representation of the multiwavelength data. Adding an external-Compton or a hadronic component also adequately describes the data.

Description: We investigate the properties of haloes, galaxies and black holes to z  = 0 in the high-resolution hydrodynamical simulation MassiveBlack-II (MBII) which evolves a cold dark matter cosmology in a comoving volume V box  = (100 Mpc h –1 ) 3 . MBII is the highest resolution simulation of this size which includes a self-consistent model for star formation, black hole accretion and associated feedback. We provide a simulation browser web application which enables interactive search and tagging of the MBII data set and publicly release our galaxy catalogues. We find that baryons affect strongly the halo mass function (MF), with 20–33 per cent change in the halo abundance below the knee of the MF ( M halo  〈 10 13.2 M h –1 at z  = 0) when compared to dark-matter-only simulations. We provide a fitting function for the halo MF out to redshift z  = 11 and discuss its limitations. We study the halo occupation distribution and clustering of galaxies, in particular the evolution and scale dependence of stochasticity and bias finding reasonable agreement with observational data. The shape of the cosmic spectral energy distribution of galaxies in MBII is consistent with observations, but lower in amplitude. The Galaxy stellar mass function (GSMF) function is broadly consistent with observations at z  ≥ 2. At z  〈 2, the population of passive low-mass ( M *  〈 10 9 M ) galaxies in MBII makes the GSMF too steep compared to observations whereas at the high-mass end ( M *  〉 10 11 M ) galaxies hosting bright AGNs make significant contributions to the GSMF. The quasar bolometric luminosity function is also largely consistent with observations. We note however that more efficient AGN feedback is necessary for the largest, rarest objects/clusters at low redshifts.

Description: Aims Drought affected by atmosphere–ocean cycle is a dominant factor influencing tree radial growth of sandy Mongolian pine ( Pinus sylvestris var. mongolica ) and regional vegetation dynamics in Hulunbuir, China. However, historical droughts and its correlations with tree radial growth and atmosphere–ocean cycle in this area have been little tested. Methods We developed tree-ring chronologies of Mongolian pine from Hulunbuir, Inner Mongolia, China and analyzed the correlations between tree-ring width index, the normalized difference vegetation index and Palmer drought severity index (PDSI), then developed a linear model to reconstruct the drought variability from 1829 to 2009. Long-term trends and its linkages with atmosphere–ocean cycle were performed by the power spectral, wavelet and teleconnection analysis. Important Findings The local moisture variations affected largely the regional vegetation dynamics and tree-ring growth of Mongolia pine in the forest–grassland transition. Using tree-ring width chronology of Mongolian pine, the reconstruction explains 49.2% of PDSI variance during their common data period (1951–2005). The reconstruction gives a broad-scale regional representation of PDSI in the Hulunbuir area, with drought occurrences in the 1850s, 1900s, 1920s, mid-1930s and at the turn of the 21st century. Comparisons with other tree-ring drought reconstructions and historical records reveal some common drought periods and drying trends in recent decades at the northern margin zones of the East Asian summer monsoon (EASM). The drying trends in these zones occurred earlier than weakening of the EASM. A REDFIT spectral analysis shows significant peaks at 7.2, 3.9, 2.7–2.8, 2.4 and 2.2 years with a 0.05 significance level, and 36.9, 18.1 and 5.0 years with 0.1 significance level. Wavelet analysis also shows similar cycles. Drought variations in the study area significantly correlated with sea surface temperatures in the western tropical Pacific Ocean and middle and northern Indian Ocean, and the Pacific Decadal Oscillation and North Atlantic Oscillation. This suggests a possible linkage with the El Niño-Southern Oscillation, the EASM and the Westerlies.

Description: In this paper, we develop a time-dependent MHD model driven by the daily-updated synoptic magnetograms (MHD-DUSM) to study the dynamic evolution of the global corona with the help of the 3D Solar-Interplanetary (SIP) adaptive mesh refinement (AMR) space-time conservation element and solution element (CESE) MHD model (SIP-AMR-CESE MHD Model). To accommodate the observations, the tangential component of the electric field at the lower boundary is specified to allow the flux evolution to match the observed changes of magnetic field. Meanwhile, the time-dependent solar surface boundary conditions derived from the method of characteristics and the mass flux limit are incorporated to couple the observation and the 3D MHD model. The simulated evolution of the global coronal structure during 2007 is compared with solar observations and solar wind measurements from both Ulysses and spacecrafts near the Earth. The MHD-DUSM model is also validated by comparisons with the standard potential field source surface (PFSS) model, the newly improved Wang-Sheeley-Arge (WSA) empirical formula, and the MHD simulation with a monthly synoptic magnetogram (MHD-MSM). Comparisons show that the MHD-DUSM results have good overall agreement with coronal and interplanetary structures, including the sizes and distributions of coronal holes, the positions and shapes of the streamer belts, and the transitions of the solar wind speeds and magnetic field polarities. The MHD-DUSM results also display many features different from those of the PFSS, the WSA, and the MHD-MSM models.