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

Towards a Coulomb gas of instantons in the SO(4)xU(1) Higgs model on R_4

The $SO(4)\times U(1)$ Higgs model on $\R_4$ is extended by a $F^3$ term so that the action receives a nonvanishing contribution from the interactions of 2-instantons and 3-instantons, and can be expressed as the inverse of the Laplacian on $\R_4$ in terms of the mutual distances of the instantons. The one-instanton solutions of both the basic and the extended models have been studied in detail numerically.Comment: 29 pages LaTeX, 4 Figures available from authors on reques

Towards predicting post-editing productivity

Machine translation (MT) quality is generally measured via automatic metrics, producing scores that have no meaning for translators who are required to post-edit MT output or for project managers who have to plan and budget for transla- tion projects. This paper investigates correlations between two such automatic metrics (general text matcher and translation edit rate) and post-editing productivity. For the purposes of this paper, productivity is measured via processing speed and cognitive measures of effort using eye tracking as a tool. Processing speed, average fixation time and count are found to correlate well with the scores for groups of segments. Segments with high GTM and TER scores require substantially less time and cognitive effort than medium or low-scoring segments. Future research involving score thresholds and confidence estimation is suggested

All-optical memory based on the injection locking bistability of a two-color laser diode

We study the injection locking bistability of a specially engineered two-color semiconductor Fabry-Perot laser. Oscillation in the uninjected primary mode leads to a bistability of single mode and two-color equilibria. With pulsed modulation of the injected power we demonstrate an all-optical memory element based on this bistability, where the uninjected primary mode is switched with 35 dB intensity contrast. Using experimental and theoretical analysis, we describe the associated bifurcation structure, which is not found in single mode systems with optical injection.Comment: 5 pages, 5 figure

Changing social contracts in climate-change adaptation

Risks from extreme weather events are mediated through state, civil society and individual action 1 , 2 . We propose evolving social contracts as a primary mechanism by which adaptation to climate change proceeds. We use a natural experiment of policy and social contexts of the UK and Ireland affected by the same meteorological event and resultant flooding in November 2009. We analyse data from policy documents and from household surveys of 356 residents in western Ireland and northwest England. We find significant differences between perceptions of individual responsibility for protection across the jurisdictions and between perceptions of future risk from populations directly affected by flooding events. These explain differences in stated willingness to take individual adaptive actions when state support retrenches. We therefore show that expectations for state protection are critical in mediating impacts and promoting longer-term adaptation. We argue that making social contracts explicit may smooth pathways to effective and legitimate adaptation

The Governance of Globalization: The Political Economy of Anglo-American Hegemony, 1793-2003

Modern globalization (which includes free flows of trade and factors of production across frontiers, stable rates of exchange, the containment of warfare and mercantilism, the preservation of the environment and latterly the protection of cities against rogue states and terrorism) are among the public goods provided for the world economy as a whole are represented as a beginning outcome of 6 decades of "hegemony" exercised by governments in Washington from l941 to 2003. The view promulgated largely by Anglo-American social scientists that the United Kingdom (and before that other powers) also supplied significant public goods for the international order has been degraded in this paper into theory without history. In short the assertion that American Hegemony can be perceived as a succession to the Pax Britannica from l793-l914 is virtually a myth.

Observation of quantum interference as a function of Berry's phase in a complex Hadamard optical network

Emerging models of quantum computation driven by multi-photon quantum interference, while not universal, may offer an exponential advantage over classical computers for certain problems. Implementing these circuits via geometric phase gates could mitigate requirements for error correction to achieve fault tolerance while retaining their relative physical simplicity. We report an experiment in which a geometric phase is embedded in an optical network with no closed-loops, enabling quantum interference between two photons as a function of the phase.Comment: Comments welcom

Take a stand on your decisions, or take a sit: posture does not affect risk preferences in an economic task

Physiological and emotional states can affect our decision-making processes, even when these states are seemingly insignificant to the decision at hand. We examined whether posture and postural threat affect decisions in a non-related economic domain. Healthy young adults made a series of choices between economic lotteries in various conditions, including changes in body posture (sitting vs. standing) and changes in elevation (ground level vs. atop a 0.8-meter-high platform). We compared three metrics between conditions to assess changes in risk-sensitivity: frequency of risky choices, and parameter fits of both utility and probability weighting parameters using cumulative prospect theory. We also measured skin conductance level to evaluate physiological response to the postural threat. Our results demonstrate that body posture does not significantly affect decision making. Secondly, despite increased skin conductance level, economic risk-sensitivity was unaffected by increased threat. Our findings indicate that economic choices are fairly robust to the physiological and emotional changes that result from posture or postural threat

Case reports of new-onset eating disorders in older adult cancer survivors

Background: It is unusual for a de novo eating disorder to emerge in late adulthood. Across a number of years, a number of patients were identified who experienced severe and unexpected weight loss post curative management of an upper abdominal cancer (i.e., cancer survivors). Each of the patients was readmitted to the tertiary surgical hospital due to complications of severe malnutrition. Each presentation was initially considered to have a major physical health problem (such as cancer recurrence). Each required extensive investigations and multidisciplinary team involvement and were later conceptualised as a new-onset (in later adulthood) eating disorder that emerged post curative cancer treatment. The team wished to better understand this group and/or characterise and/or inform the scientific community of this phenomena if not already well described. Literature review: The review identified that the re-emergence of pre-existing eating disorders at the time of cancer treatment was described; however, there was no identification of similar new-onset in later adulthood cases of eating disorders in cancer survivors in the medical literature. Review of the cases: Once ethics and consent was obtained, then the clinical course of four complex individuals were reviewed, including the use of a multidisciplinary Delphi review process, to understand commonalities and then plot a common care pathway with potential intervention points. Case presentations: Common factors identified among the four patients included the lack of a physical health (organic) cause to the weight loss and ongoing weight loss despite intense multidisciplinary care. All had abnormal attitudes and behaviours relating to food, nutritional rehabilitation and/or recovery. None returned to a healthy weight and/or healthy eating despite extensive team input. The presentations were ultimately conceptualised as having severe disordered eating behaviours and in at least three cases met criteria for a formal eating disorder. The cohort had similar psychosocial characteristics including low socioeconomic status and complex family dynamics. None had prior formal psychiatric care. The outcomes were poor; one patient died, another required admission to a specialist eating disorder admission with a subsequent relapsing remitting course, and the remaining two had complicated chronic courses. Conclusion: Similar cases may be underreported. If identified earlier, there may be a role for intervention to prevent high morbidity and mortality and to support clinical teams managing similar complex patients

Antiphase dynamics in a multimode semiconductor laser with optical injection

A detailed experimental study of antiphase dynamics in a two-mode semiconductor laser with optical injection is presented. The device is a specially designed Fabry-Perot laser that supports two primary modes with a THz frequency spacing. Injection in one of the primary modes of the device leads to a rich variety of single and two-mode dynamical scenarios, which are reproduced with remarkable accuracy by a four dimensional rate equation model. Numerical bifurcation analysis reveals the importance of torus bifurcations in mediating transitions to antiphase dynamics and of saddle-node of limit cycle bifurcations in switching of the dynamics between single and two-mode regimes.Comment: 7 pages, 9 figure