Electromagnetic reflection, transmission and energy density at boundaries of nonlocal media

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.We consider a semi-infinite spatially dispersive dielectric with unequal transverse and longitudinal susceptibilities. The effect of the boundary is characterized by arbitrary reflection coefficients for polarization waves in the material that propagate to the surface. Specific values of these coefficients correspond to various additional boundary conditions (ABC) for Maxwell's equations. We derive the electromagnetic reflection and transmission coefficients at the boundary and investigate their dependence on material parameters and ABC. We also investigate the electromagnetic zero-point and thermal spectral energy density outside the dielectric. The nonlocal response removes the boundary divergence of the spectral energy density that is present in a local model. The spectral energy density shows a large dependence on the difference between the transverse and longitudinal susceptibilities, even at distances up to 10nm from the boundary

Reflection and transmission in nonlocal susceptibility models with multiple resonances

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.We consider a semi-infinite dielectric with multiple spatially dispersive resonances in the susceptibility. The effect of the boundary is described by an arbitrary reflection coefficient for polarization waves in the material at the surface, with specific values corresponding to various additional boundary conditions (ABCs) for Maxwell's equations. We derive exact expressions for the electromagnetic reflection and transmission coefficients and present the results for a variety of materials with multiple exciton bands. We find an improved single-band approximation for heavy/light exciton bands and extend our model to exciton dispersion relations with linear $k$ terms which occur in uniaxial crystals. Finally, we calculate the spectral energy density of thermal and zero-point radiation for a variety of multi-resonance models and ABCs

Assessing and selecting gene expression signals based upon the quality of the measured dynamics

<p>Abstract</p> <p>Background</p> <p>One of the challenges with modeling the temporal progression of biological signals is dealing with the effect of noise and the limited number of replicates at each time point. Given the rising interest in utilizing predictive mathematical models to describe the biological response of an organism or analysis such as clustering and gene ontology enrichment, it is important to determine whether the dynamic progression of the data has been accurately captured despite the limited number of replicates, such that one can have confidence that the results of the analysis are capturing important salient dynamic features.</p> <p>Results</p> <p>By pre-selecting genes based upon quality before the identification of differential expression via algorithm such as EDGE, it was found that the percentage of statistically enriched ontologies (p < .05) was improved. Furthermore, it was found that a majority of the genes found via the proposed technique were also selected via an EDGE selection though the reverse was not necessarily true. It was also found that improvements offered by the proposed algorithm are anti-correlated with improvements in the various microarray platforms and the number of replicates. This is illustrated by the fact that newer arrays and experiments with more replicates show less improvement when the filtering for quality is first run before the selection of differentially expressed genes. This suggests that the increase in the number of replicates as well as improvements in array technologies are increase the confidence one has in the dynamics obtained from the experiment.</p> <p>Conclusion</p> <p>We have developed an algorithm that quantifies the quality of temporal biological signal rather than whether the signal illustrates a significant change over the experimental time course. Because the use of these temporal signals, whether it is in mathematical modeling or clustering, focuses upon the entire time series, it is necessary to develop a method to quantify and select for signals which conform to this ideal. By doing this, we have demonstrated a marked and consistent improvement in the results of a clustering exercise over multiple experiments, microarray platforms, and experimental designs.</p

Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat 3 wild emmer wheat RIL population

Mineral nutrient malnutrition, and particularly deficiency in zinc and iron, afflicts over 3 billion people worldwide. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, genepool harbors a rich allelic repertoire for mineral nutrients in the grain. The genetic and physiological basis of grain protein, micronutrients (zinc, iron, copper and manganese) and macronutrients (calcium, magnesium, potassium, phosphorus and sulfur) concentration was studied in tetraploid wheat population of 152 recombinant inbred lines (RILs), derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16). Wide genetic variation was found among the RILs for all grain minerals, with considerable transgressive effect. A total of 82 QTLs were mapped for 10 minerals with LOD score range of 3.2–16.7. Most QTLs were in favor of the wild allele (50 QTLs). Fourteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. Significant positive correlation was found between grain protein concentration (GPC), Zn, Fe and Cu, which was supported by significant overlap between the respective QTLs, suggesting common physiological and/or genetic factors controlling the concentrations of these mineral nutrients. Few genomic regions (chromosomes 2A, 5A, 6B and 7A) were found to harbor clusters of QTLs for GPC and other nutrients. These identified QTLs may facilitate the use of wild alleles for improving grain nutritional quality of elite wheat cultivars, especially in terms of protein, Zn and Fe

Optimum allocation of resources for QTL detection using a nested association mapping strategy in maize

In quantitative trait locus (QTL) mapping studies, it is mandatory that the available financial resources are spent in such a way that the power for detection of QTL is maximized. The objective of this study was to optimize for three different fixed budgets the power of QTL detection 1 − β* in recombinant inbred line (RIL) populations derived from a nested design by varying (1) the genetic complexity of the trait, (2) the costs for developing, genotyping, and phenotyping RILs, (3) the total number of RILs, and (4) the number of environments and replications per environment used for phenotyping. Our computer simulations were based on empirical data of 653 single nucleotide polymorphism markers of 26 diverse maize inbred lines which were selected on the basis of 100 simple sequence repeat markers out of a worldwide sample of 260 maize inbreds to capture the maximum genetic diversity. For the standard scenario of costs, the optimum number of test environments (Eopt) ranged across the examined total budgets from 7 to 19 in the scenarios with 25 QTL. In comparison, the Eopt values observed for the scenarios with 50 and 100 QTL were slightly higher. Our finding of differences in 1 − β* estimates between experiments with optimally and sub-optimally allocated resources illustrated the potential to improve the power for QTL detection without increasing the total resources necessary for a QTL mapping experiment. Furthermore, the results of our study indicated that also in studies using the latest genomics tools to dissect quantitative traits, it is required to evaluate the individuals of the mapping population in a high number of environments with a high number of replications per environment

Cadaveric and three-dimensional computed tomography study of the morphology of the scapula with reference to reversed shoulder prosthesis

<p>Abstract</p> <p>Purpose</p> <p>The purpose of this study is to analyze the morphology of the scapula with reference to the glenoid component implantation in reversed shoulder prosthesis, in order to improve primary fixation of the component.</p> <p>Methods</p> <p>Seventy-three 3-dimensional computed tomography of the scapula and 108 scapular dry specimens were analyzed to determine the anterior and posterior length of the glenoid neck, the angle between the glenoid surface and the upper posterior column of the scapula and the angle between the major craneo-caudal glenoid axis and the base of the coracoid process and the upper posterior column.</p> <p>Results</p> <p>The anterior and posterior length of glenoid neck was classified into two groups named "short-neck" and "long-neck" with significant differences between them. The angle between the glenoid surface and the upper posterior column of the scapula was also classified into two different types: type I (mean 50°–52°) and type II (mean 62,50°–64°), with significant differences between them (p < 0,001). The angle between the major craneo-caudal glenoid axis and the base of the coracoid process averaged 18,25° while the angle with the upper posterior column of the scapula averaged 8°.</p> <p>Conclusion</p> <p>Scapular morphological variability advices for individual adjustments of glenoid component implantation in reversed total shoulder prosthesis. Three-dimensional computed tomography of the scapula constitutes an important tool when planning reversed prostheses implantation.</p

QTL mapping in autotetraploids using SNP dosage information

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F1 population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F1 individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs

Small-Bodied Humans from Palau, Micronesia

UNLABELLED: Newly discovered fossil assemblages of small bodied Homo sapiens from Palau, Micronesia possess characters thought to be taxonomically primitive for the genus Homo. BACKGROUND: Recent surface collection and test excavation in limestone caves in the rock islands of Palau, Micronesia, has produced a sizeable sample of human skeletal remains dating roughly between 940-2890 cal ybp. PRINCIPLE FINDINGS: Preliminary analysis indicates that this material is important for two reasons. First, individuals from the older time horizons are small in body size even relative to "pygmoid" populations from Southeast Asia and Indonesia, and thus may represent a marked case of human insular dwarfism. Second, while possessing a number of derived features that align them with Homo sapiens, the human remains from Palau also exhibit several skeletal traits that are considered to be primitive for the genus Homo. SIGNIFICANCE: These features may be previously unrecognized developmental correlates of small body size and, if so, they may have important implications for interpreting the taxonomic affinities of fossil specimens of Homo

Scalable quantum register based on coupled electron spins in a room temperature solid

Realization of devices based on quantum laws might lead to building processors that outperform their classical analogues and establishing unconditionally secure communication protocols. Solids do usually present a serious challenge to quantum coherence. However, owing to their spin-free lattice and low spin orbit coupling, carbon materials and particularly diamond are suitable for hosting robust solid state quantum registers. We show that scalable quantum logic elements can be realized by exploring long range magnetic dipolar coupling between individually addressable single electron spins associated with separate color centers in diamond. Strong distance dependence of coupling was used to characterize the separation of single qubits 98 A with unprecedented accuracy (3 A) close to a crystal lattice spacing. Our demonstration of coherent control over both electron spins, conditional dynamics, selective readout as well as switchable interaction, opens the way towards a room temperature solid state scalable quantum register. Since both electron spins are optically addressable, this solid state quantum device operating at ambient conditions provides a degree of control that is currently available only for atomic systems.Comment: original submitted version of the manuscrip