Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

peer-reviewedThe generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome

Automated clinical system for chromosome analysis

An automatic chromosome analysis system is provided wherein a suitably prepared slide with chromosome spreads thereon is placed on the stage of an automated microscope. The automated microscope stage is computer operated to move the slide to enable detection of chromosome spreads on the slide. The X and Y location of each chromosome spread that is detected is stored. The computer measures the chromosomes in a spread, classifies them by group or by type and also prepares a digital karyotype image. The computer system can also prepare a patient report summarizing the result of the analysis and listing suspected abnormalities

Delocalization of Wannier-Stark ladders by phonons: tunneling and stretched polarons

We study the coherent dynamics of a Holstein polaron in strong electric fields. A detailed analytical and numerical analysis shows that even for small hopping constant and weak electron-phonon interaction, polaron states can become delocalized if a resonance condition develops between the original Wannier-Stark states and the phonon modes, yielding both tunneling and `stretched' polarons. The unusual stretched polarons are characterized by a phonon cloud that {\em trails} the electron, instead of accompanying it. In general, our novel approach allows us to show that the polaron spectrum has a complex nearly-fractal structure, due to the coherent coupling between states in the Cayley tree which describes the relevant Hilbert space. The eigenstates of a finite ladder are analyzed in terms of the observable tunneling and optical properties of the system.Comment: 7 pages, 4 figure

Nonadiabatic transitions in a Stark decelerator

In a Stark decelerator, polar molecules are slowed down and focussed by an inhomogeneous electric field which switches between two configurations. For the decelerator to work, it is essential that the molecules follow the changing electric field adiabatically. When the decelerator switches from one configuration to the other, the electric field changes in magnitude and direction, and this can cause molecules to change state. In places where the field is weak, the rotation of the electric field vector during the switch may be too rapid for the molecules to maintain their orientation relative to the field. Molecules that are at these places when the field switches may be lost from the decelerator as they are transferred into states that are not focussed. We calculate the probability of nonadiabatic transitions as a function of position in the periodic decelerator structure and find that for the decelerated group of molecules the loss is typically small, while for the un-decelerated group of molecules the loss can be very high. This loss can be eliminated using a bias field to ensure that the electric field magnitude is always large enough. We demonstrate our findings by comparing the results of experiments and simulations for the Stark deceleration of LiH and CaF molecules. We present a simple method for calculating the transition probabilities which can easily be applied to other molecules of interest.Comment: 12 pages, 9 figures, minor revisions following referee suggestion

Advanced flight control system study

A fly by wire flight control system architecture designed for high reliability includes spare sensor and computer elements to permit safe dispatch with failed elements, thereby reducing unscheduled maintenance. A methodology capable of demonstrating that the architecture does achieve the predicted performance characteristics consists of a hierarchy of activities ranging from analytical calculations of system reliability and formal methods of software verification to iron bird testing followed by flight evaluation. Interfacing this architecture to the Lockheed S-3A aircraft for flight test is discussed. This testbed vehicle can be expanded to support flight experiments in advanced aerodynamics, electromechanical actuators, secondary power systems, flight management, new displays, and air traffic control concepts

A review of the potential for rare earth element resources from European red muds: examples from Seydişehir, Turkey and Parnassus-Giona, Greece

ArticleRare earth elements (REE) are viewed as ‘critical metals’ due to a complex array of production and political issues, most notably a near monopoly in supply from China. Red mud, the waste product of the Bayer process that produces alumina from bauxite, represents a potential secondary resource of REE. Karst-bauxite deposits represent the ideal source material for REE-enriched red mud as the conditions during formation of the bauxite allow for the retention of REE. The REE pass through the Bayer Process and are concentrated in the waste material. Millions of tonnes of red mud are currently stockpiled in onshore storage facilities across Europe, representing a potential REE resource. Red mud from two case study sites, one in Greece and the other in Turkey, has been found to contain an average of approximately 1 000 ppm total REE, with an enrichment of light over heavy REE. Although this is relatively low grade when compared with typical primary REE deposits (Mountain Pass and Mount Weld up to 80 000 ppm), it is of interest because of the large volumes available, the cost benefits of reprocessing waste, and the low proportion of contained radioactive elements. This work shows that around 12 000 tonnes of REE exist in red mud at the two case study areas alone, with much larger resources existing across Europe as a whole.The research leading to these results has received funding from the European 669 Community’s Seventh Framework Programme ([FP7/2007-2013]) under Grant 670 Agreement no. 309373

Relationships of attitudes toward homework and time spent on homework to course outcomes: The case of foreign language learning

In previous studies of homework in core academic subjects, positive student attitudes toward homework were linked to higher achievement, whereas time spent on homework showed an inconsistent relationship with achievement. This study examined the generalizability of these findings to foreign language learning by analyzing 2,342 adult students' attitudes toward assigned homework, time spent on assigned homework, and achievement outcomes in a variety of foreign language courses. Student ratings of the relevance of homework, the usefulness of feedback provided on homework, and the fairness of homework grading were positively correlated with teacher-assigned grades and standardized proficiency test scores in listening, reading, and speaking. Reported time spent on homework, however, was negatively correlated with these measures. In hierarchical regression analyses, all homework-related variables emerged as significant predictors of outcomes after controlling for potential covariates such as language learning aptitude, demographic variables, and affective factors. Thus, these results provide evidence that language course outcomes are positively associated with attitudes toward homework but negatively associated with time spent on homework. Possible interpretations of these findings are discussed. We suggest that the negative association follows in part from the opportunity cost of time spent on assigned homework, which decreases time spent on individualized study that may be more beneficial for improving language course outcomes

[OII] Emission, Eigenvector 1 and Orientation in Radio-quiet Quasars

We present supportive evidence that the Boroson and Green eigenvector 1 is not driven by source orientation. Until recently it was generally accepted that eigenvector 1 does not depend on orientation as it strongly correlates with [OIII]5007 emission, thought to be an isotropic property. However, recent studies of radio-loud AGN have questioned the isotropy of [OIII] emission and concluded that [OII]3727 emission is isotropic. In this paper we investigate the relation between eigenvector 1 and [OII] emission in radio-quiet BQS (Bright Quasar Survey) quasars, and readdress the issue of orientation as the driver of eigenvector 1. We find significant correlations between eigenvector 1 and orientation independent [OII] emission, which implies that orientation does not drive eigenvector 1. The luminosities and equivalent widths of [OIII] and [OII] correlate with one another, and the range in luminosities and equivalent widths is similar. This suggests that the radio-quiet BQS quasars are largely free of orientation dependent dust effects and ionization dependent effects in the narrow-line region. We also conclude that neither the [OIII] emission nor the [OII]/[OIII] ratio are dependent on orientation in our radio-quiet BQS quasar sample, contrary to recent results found for radio-loud quasars.Comment: 24 pages, 12 figures, accepted for publication in Ap