From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly's NG50 is 1.94 million bp, an eightfold increase

Optimal Prandtl number for heat transfer in rotating Rayleigh-Benard convection

Numerical data for the heat transfer as a function of the Prandtl (Pr) and Rossby (Ro) numbers in turbulent rotating Rayleigh-Benard convection are presented for Rayleigh number Ra = 10^8. When Ro is fixed the heat transfer enhancement with respect to the non-rotating value shows a maximum as function of Pr. This maximum is due to the reduced efficiency of Ekman pumping when Pr becomes too small or too large. When Pr becomes small, i.e. for large thermal diffusivity, the heat that is carried by the vertical vortices spreads out in the middle of the cell, and Ekman pumping thus becomes less efficient. For higher Pr the thermal boundary layers (BLs) are thinner than the kinetic BLs and therefore the Ekman vortices do not reach the thermal BL. This means that the fluid that is sucked into the vertical vortices is colder than for lower Pr which limits the efficiency of the upwards heat transfer.Comment: 5 pages, 6 figure

Differences in both prevalence and titre of specific immunoglobulin E among children with asthma in affluent and poor communities within a large town in Ghana.

Background Reports from several African countries have noted an increasing prevalence of asthma in areas of extensive urbanization. Objective To investigate the relevance of allergen-specific sensitization and body mass index (BMI) to asthma/wheezing and exercise-induced bronchospasm (EIB) among children from affluent and poorer communities within a large town in Ghana. Methods Children with physician-diagnosed asthma and/or current wheezing aged 9-16 years (n=99; cases) from three schools with differing socio-economic backgrounds [urban affluent (UA), urban poor (UP) or suburban/rural (SR)] were recruited from a cross-sectional study (n=1848) in Kumasi, Ghana, and matched according to age, sex and area of residence with non-asthmatic/non-wheezy controls. We assayed sera for IgE antibodies to mite, cat, dog, cockroach, Ascaris and galactose-α-1,3-galactose. Results Children from the UA school had the lowest total serum IgE. However, cases from the UA school had a higher prevalence and mean titre of sIgE to mite (71.4%, 21.2IU/mL) when compared with controls (14.3%, 0.8IU/mL) or cases from UP (30%, 0.8IU/mL) and SR community (47.8%, 1.6IU/mL). While similar findings were observed with EIB in the whole population, among cases there was no difference in IgE antibody prevalence or titre between children with or without EIB. BMI was higher among UA children with and without asthma; in UP and SR communities, children with EIB (n=14) had a significantly higher BMI compared with children with asthma/wheezing without EIB (n=38) (18.2 vs. 16.4, respectively, P<0.01). Conclusions and Clinical Relevance In the relatively affluent school, asthma/wheezing and EIB were associated with high titre IgE antibodies to mite, decreased total IgE, and increased BMI. This contrasted with children in the urban poor school and suggests that changes relevant to a Western model of childhood asthma can occur within a short geographical distance within a large city in Africa. © 2011 Blackwell Publishing Ltd

Variability of the Centimeter-Submillimeter Spectrum and Polarization of 3C 273 during Outburst

Original article can be found at: http://www.journals.uchicago.edu/ApJ/--Copyright University of Chicago Press/ AASCentimeter to submillimeter total flux and polarization monitoring data are used to investigate the nature of a prominent flare in the quasar 3C 273 during 1995/6. After removal of the quiescent level, the resulting “flare spectra" are well fitted by a simple homogeneous synchrotron source model, which in turn allows the movement of the self-absorption turnover to be tracked during the flare. Both the flare amplitude/time delay relationship and the overall spectral evolution are qualitatively consistent with existing models. The early evolution of the spectrum is best determined and is shown to be in excellent agreement with the Compton stage of the Marscher & Gear shock model. However, the polarization behavior during the flare is different at millimeter and centimeter wavelengths and the observations are difficult to reconcile with a simple transverse shock. They are, however, consistent with a conical shock for which the observed polarization properties vary with distance along the jet. Such variations may be caused, for example, by a change in cone angle owing to disruption caused by the growing component of the magnetic field parallel to the jet axis or by a moderate change in viewing angle.Peer reviewe

Boundary layer structure in turbulent thermal convection and its consequences for the required numerical resolution

Results on the Prandtl-Blasius type kinetic and thermal boundary layer thicknesses in turbulent Rayleigh-B\'enard convection in a broad range of Prandtl numbers are presented. By solving the laminar Prandtl-Blasius boundary layer equations, we calculate the ratio of the thermal and kinetic boundary layer thicknesses, which depends on the Prandtl number Pr only. It is approximated as $0.588Pr^{-1/2}$ for $Pr\ll Pr^*$ and as $0.982 Pr^{-1/3}$ for $Pr^*\ll\Pr$, with $Pr^*= 0.046$. Comparison of the Prandtl--Blasius velocity boundary layer thickness with that evaluated in the direct numerical simulations by Stevens, Verzicco, and Lohse (J. Fluid Mech. 643, 495 (2010)) gives very good agreement. Based on the Prandtl--Blasius type considerations, we derive a lower-bound estimate for the minimum number of the computational mesh nodes, required to conduct accurate numerical simulations of moderately high (boundary layer dominated) turbulent Rayleigh-B\'enard convection, in the thermal and kinetic boundary layers close to bottom and top plates. It is shown that the number of required nodes within each boundary layer depends on Nu and Pr and grows with the Rayleigh number Ra not slower than \sim\Ra^{0.15}. This estimate agrees excellently with empirical results, which were based on the convergence of the Nusselt number in numerical simulations

The supercuspidal representations of p-adic classical groups

Let G be a unitary, symplectic or special orthogonal group over a locally compact non-archimedean local field of odd residual characteristic. We construct many new supercuspidal representations of G, and Bushnell-Kutzko types for these representations. Moreover, we prove that every irreducible supercuspidal representation of G arises from our constructions.Comment: 55 pages -- minor changes from 1st version (mostly in sections 2.2, 4.2 and 6.2). To appear in Inventiones mathematicae, 2008 (DOI is not yet active as at 12 Nov 2007

Trace gas transport in the subsurface of Mars

The ExoMars Trace Gas Orbiter (TGO) will have the capability of detecting and characterizing a broad suite of trace gases in the atmosphere of Mars. Interpreting the results of this mission will require an understanding of how these trace gases are transported from their sources, which may be deep underground, to the atmosphere. Here we present results of modeling designed to measure the timescales of release from putative subsurface methane sources. These transport timescales are far longer than mixing times in the atmosphere and could be up to 10 million years

Design guidelines for assessing and controlling spacecraft charging effects

The need for uniform criteria, or guidelines, to be used in all phases of spacecraft design is discussed. Guidelines were developed for the control of absolute and differential charging of spacecraft surfaces by the lower energy space charged particle environment. Interior charging due to higher energy particles is not considered. A guide to good design practices for assessing and controlling charging effects is presented. Uniform design practices for all space vehicles are outlined

Nd:YAG development for spaceborne laser ranging system

The results of the development of a unique modelocked laser device to be utilized in future NASA space-based, ultraprecision laser ranger systems are summarized. The engineering breadboard constructed proved the feasibility of the pump-pulsed, actively modelocked, PTM Q-switched Nd:YAG laser concept for the generation of subnanosecond pulses suitable for ultra-precision ranging. The laser breadboard also included a double-pass Nd:YAG amplifier and provision for a Type II KD*P frequency doubler. The specific technical accomplishment was the generation of single 150 psec, 20-mJ pulses at 10 pps at a wavelength of 1.064 micrometers with 25 dB suppression of pre-and post-pulses