Particle size segregation in granular flow in silos

Segregation and layering of alumina in storage silos are investigated, with a view to predicting output quality versus time, given known variations in input quality on emplacement. A variety of experiments were conducted, existing relevant publications were reviewed, and the basis for an algorithm for predicting the effect of withdrawing from a central flowing region, in combination with variations in quality due to geometric, layering and segregation effects, is described in this report

Reduced micro-deformation attenuation in large-mode area photonic crystal fibers for visible applications

We consider large-mode area photonic crystal fibers for visible applications where micro-deformation induced attenuation becomes a potential problem when the effective area A_eff is sufficiently large compared to lambda^2. We argue how a slight increase in fiber diameter D can be used in screening the high-frequency components of the micro-deformation spectrum mechanically and we confirm this experimentally for both 15 and 20 micron core fibers. For typical bending-radii (R~16 cm) the operating band-width increases by ~3-400 nm to the low-wavelength side.Comment: Accepted for Optics Letter

Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

<p>Abstract</p> <p>Background</p> <p>Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an <it>in silico </it>approach to anchor molecular markers onto the soybean physical map.</p> <p>Results</p> <p>A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 <it>Bst</it>Y I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1× genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform <it>in silico </it>mapping on 80,700 Williams 82 BAC end sequences (BES). This <it>in silico </it>analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource.</p> <p>Conclusion</p> <p>We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions in the genome, as well as for extending physical map contigs.</p

Stimulated emission of polarization-entangled photons

Entangled photon pairs -- discrete light quanta that exhibit non-classical correlations -- play a crucial role in quantum information science (for example in demonstrations of quantum non-locality and quantum cryptography). At the macroscopic optical field level non-classical correlations can also be important, as in the case of squeezed light, entangled light beams and teleportation of continuous quantum variables. Here we use stimulated parametric down-conversion to study entangled states of light that bridge the gap between discrete and macroscopic optical quantum correlations. We demonstrate experimentally the onset of laser-like action for entangled photons. This entanglement structure holds great promise in quantum information science where there is a strong demand for entangled states of increasing complexity.Comment: 5 pages, 4 figures, RevTeX

Phytophthora Root Rot Resistance in Soybean E00003

Phytophthora root rot (PRR) is a devastating disease in soybean [Glycine max (L.) Merr.] production. Michigan elite soybean E00003 is resistant to Phytophthora sojae and has been used as a resistance source in breeding. Genetic control of PRR resistance in this source is unknown. To facilitate marker-assisted selection (MAS), the PRR resistance loci in E00003 and their map locations need to be determined. In this study, a genetic mapping approach was used to identify major PRR -resistant loci in E00003. The mapping population consists of 240 F4–derived lines developed by crossing E00003 with the P. sojae susceptible line PI 567543C. In 2009 and 2010, the mapping population was evaluated in the greenhouse for PRR resistance against P. sojae races 1, 4, and 7, using modified rice (Oryza sativa L.) grain inoculation method. The population was genotyped with seven simple sequence repeat (SSR) and three single nucleotide polymorphism (SNP) markers derived from bulk segregant analysis. The heritability of resistance in the population ranged from 83 to 94%. A major locus, contributing 50 to 76% of the phenotypic variation, was mapped within a 3 cM interval in the Rps1 region. The interval was further saturated with more BARCSOY SSRs and SNPs with TaqMan assays. Two SSRs and three SNPs within the Rps1k gene were highly associated with PRR resistance in the mapping population. The major resistance gene in E00003 is either allelic or tightly linked to Rps1k.The molecular markers located in the Rps1k gene can be used to improve MAS for PRR resistance

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

Background: The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% of the soybean whole genome sequence developed by the Joint Genome Institute, Department of Energy, but its marker density was only sufficient to properly orient 66% of the sequence scaffolds. The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence. To that end, next generation sequencing and high-throughput genotyping were combined to obtain a much higher resolution genetic map that could be used to anchor and orient most of the remaining sequence and to help validate the integrity of the existing scaffold builds. Results: A total of 7,108 to 25,047 predicted SNPs were discovered using a reduced representation library that was subsequently sequenced by the Illumina sequence-by-synthesis method on the clonal single molecule array platform. Using multiple SNP prediction methods, the validation rate of these SNPs ranged from 79% to 92.5%. A high resolution genetic map using 444 recombinant inbred lines was created with 1,790 SNP markers. Of the 1,790 mapped SNP markers, 1,240 markers had been selectively chosen to target existing un-anchored or un-oriented sequence scaffolds, thereby increasing the amount of anchored sequence to 97%. Conclusion: We have demonstrated how next generation sequencing was combined with high-throughput SNP detection assays to quickly discover large numbers of SNPs. Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8× whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism

Quantum sticking, scattering and transmission of 4He atoms from superfluid 4He surfaces

We develop a microscopic theory of the scattering, transmission, and sticking of 4He atoms impinging on a superfluid 4He slab at near normal incidence, and inelastic neutron scattering from the slab. The theory includes coupling between different modes and allows for inelastic processes. We find a number of essential aspects that must be observed in a physically meaningful and reliable theory of atom transmission and scattering; all are connected with multiparticle scattering, particularly the possibility of energy loss. These processes are (a) the coupling to low-lying (surface) excitations (ripplons/third sound) which is manifested in a finite imaginary part of the self energy, and (b) the reduction of the strength of the excitation in the maxon/roton region

QTL for seed protein and amino acids in the Benning × Danbaekkong soybean population

Soybean, rather than nitrogen-containing forages, is the primary source of quality protein in feed formulations for domestic swine, poultry, and dairy industries. As a sole dietary source of protein, soybean is deficient in the amino acids lysine (Lys), threonine (Thr), methionine (Met), and cysteine (Cys). Increasing these amino acids would benefit the feed industry. The objective of the present study was to identify quantitative trait loci (QTL) associated with crude protein (cp) and amino acids in the ‘Benning’ × ‘Danbaekkong’ population. The population was grown in five southern USA environments. Amino acid concentrations as a fraction of cp (Lys/cp, Thr/cp, Met/cp, Cys/cp, and Met + Cys/cp) were determined by near-infrared reflectance spectroscopy. Four QTL associated with the variation in crude protein were detected on chromosomes (Chr) 14, 15, 17, and 20, of which, a QTL on Chr 20 explained 55 % of the phenotypic variation. In the same chromosomal region, QTL for Lys/cp, Thr/cp, Met/cp, Cys/cp and Met + Cys/cp were detected. At these QTL, the Danbaekkong allele resulted in reduced levels of these amino acids and increased protein concentration. Two additional QTL for Lys/cp were detected on Chr 08 and 20, and three QTL for Thr/cp on Chr 01, 09, and 17. Three QTL were identified on Chr 06, 09 and 10 for Met/cp, and one QTL was found for Cys/cp on Chr 10. The study provides information concerning the relationship between crude protein and levels of essential amino acids and may allow for the improvement of these traits in soybean using marker-assisted selection

Parametric localized modes in quadratic nonlinear photonic structures

We analyze two-color spatially localized modes formed by parametrically coupled fundamental and second-harmonic fields excited at quadratic (or chi-2) nonlinear interfaces embedded into a linear layered structure --- a quasi-one-dimensional quadratic nonlinear photonic crystal. For a periodic lattice of nonlinear interfaces, we derive an effective discrete model for the amplitudes of the fundamental and second-harmonic waves at the interfaces (the so-called discrete chi-2 equations), and find, numerically and analytically, the spatially localized solutions --- discrete gap solitons. For a single nonlinear interface in a linear superlattice, we study the properties of two-color localized modes, and describe both similarities and differences with quadratic solitons in homogeneous media.Comment: 9 pages, 8 figure

Genetic Characterization of the Soybean Nested Association Mapping Population

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [Glycine max (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on recombinant inbred lines (RILs) across the families and identified and annotated 525,772 high confidence SNPs that were used to impute the SNP alleles in the RILs. The segregation distortion in most families significantly favored the alleles from the female parent, and there was no significant difference of residual heterozygosity in the euchromatic vs. heterochromatic regions. The genotypic datasets for the RILs and parents are publicly available and are anticipated to be useful to map quantitative trait loci (QTL) controlling important traits in soybean