R package hiphop: parentage assignment using bi-allelic genetic markers. Statistical software

Can be used for paternity and maternity assignment and outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of mismatches of these individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms). It elaborates on a prior exclusion method based on the Homozygous Opposite Test (HOT; Huisman 2017 ) by introducing the additional exclusion criterion HIPHOP (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential parents are excluded if they have more mismatches than can be expected due to genotyping error and mutation, and thereby one can identify the true genetic parents and detect situations where one (or both) of the true parents is not sampled. Package 'hiphop' can deal with (a) the case where there is contextual information about parentage of the mother (i.e. a female has been seen to be involved in reproductive tasks such as nest building), but paternity is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, because there is no contextual information on which female laid eggs and which male fertilized them (e.g. polygynandrous mating system where multiple females and males deposit young in a common nest, or organisms with external fertilisation that breed in aggregations)

Costs of compliance with EU regulations and competitiveness of the EU dairy sector

The introduction of cross-compliance mechanism in the European Union with its 2003 CAPreform might affect the costs of production and thus competitiveness of the EU. Little evidence is available to asses the costs of compliance with regulations and it implication for trade. In this study a farm level competitiveness analysis of the impacts of the Nitrate Directive and the Identification & registration Directive focuses on the dairy sector in Germany, France, Italy, Netherlands and UK (within EU), and the US and New Zealand (outside EU). The findings from this study are integrated into a trade analysis which assesses the impact of compliance costs on competitiveness of the various trading nations in global trade. Representative farm studies were used as a basis for the cost increase calculations. Best-estimates of compliance are used from the existing literature and expert judgements. The negative impact of these measures (for nitrates, and animal identification and registration) on EU imports and exports are less than 3 percent. If a smaller increase in compliance takes place, these already relatively small trade impacts will be further diminished. When the standards for nitrate pollution taken by the US and New Zealand are taken into account along with full compliance assumption in all countries analysed, this would only slightly improve the EU exports. The trade impacts obtained when no changes are assumed to happen in key competitor countries can thus be argued as providing the upper bound of the likely trade impacts

Fixation locations when grasping partly occluded objects

When grasping an object, subjects tend to look at the contact positions of the digits (A. M. Brouwer, V. H. Franz, D. Kerzel, & K. R. Gegenfurtner, 2005; R. S. Johansson, G. Westling, A. Bäckström, & J. R. Flanagan, 2001). However, these contact positions are not always visible due to occlusion. Subjects might look at occluded parts to determine the location of the contact positions based on extrapolated information. On the other hand, subjects might avoid looking at occluded parts since no object information can be gathered there. To find out where subjects fixate when grasping occluded objects, we let them grasp flat shapes with the index finger and thumb at predefined contact positions. Either the contact position of the thumb or the finger or both was occluded. In a control condition, a part of the object that does not involve the contact positions was occluded. The results showed that subjects did look at occluded object parts, suggesting that they used extrapolated object information for grasping. Additionally, they preferred to look in the direction of the index finger. When the contact position of the index finger was occluded, this tendency was inhibited. Thus, an occluder does not prevent fixations on occluded object parts, but it does affect fixation locations especially in conditions where the preferred fixation location is occluded. © ARVO

Cerebrospinal Fluid Sex Steroid Hormones in Bacterial Meningitis

Unfavorable outcome in bacterial meningitis is related to excessive inflammation and higher inflammatory markers have been reported in female than in male patients. Sex steroid hormones have immunomodulatory properties and can be found in the cerebrospinal fluid (CSF); however, their actions have not been studied in bacterial meningitis. We investigated the association between CSF sex steroid hormone levels and inflammatory parameters, disease severity, and outcome in pneumococcal meningitis. We identified adults with culture-proven pneumococcal meningitis in a prospective cohort study (2006-2014). We measured estradiol and testosterone in CSF using liquid chromatography-tandem mass spectrometry and sex hormone-binding globulin (SHBG) using an enzyme-linked immunoassay. Hormone levels were compared according to outcome, which was graded using the Glasgow Outcome Scale (a score of 5 indicating favorable, 1-4 unfavorable outcome). Correlation analysis was used to measure the association between hormone levels and inflammatory cytokines, chemokines, and complement factors as well as severity of illness, as measured by the Glasgow Coma Scale and the Dutch Meningitis Risk Score. We included 60 patients: 20 men, 20 premenopausal (50 years) women. Twenty-one (35%) patients had an unfavorable outcome and 11 (18%) died. Cases with an unfavorable outcome exhibited higher estradiol (median 14.0 vs 5.0 pmol/L, P = .04) and lower SHBG (0.40 vs 1.0 nmol/L, P = .03) levels compared with those with a favorable outcome. Estradiol was positively correlated with C-reactive protein (R = 0.42, P = .001), CSF protein (R = 0.33, P = .01), and proinflammatory cytokine levels. CSF concentrations of the sex steroid hormone estradiol were associated with outcome and CSF inflammation. Understanding the dose and time-dependent interaction between sex steroid hormones and the inflammatory response in bacterial meningitis represents an important and understudied topic.info:eu-repo/semantics/publishedVersio

Quantum-Statistical Current Correlations in Multi-Lead Chaotic Cavities

Quantum mechanics requires that identical particles are treated as indistinguishable. This requirement leads to correlations in the fluctuating properties of a system. Theoretical predictions are made for an experiment on a multi-lead chaotic quantum dot which can identify exchange effects in electronic current-current correlations. Interestingly, we find that the ensemble averaged exchange effects are of the order of the channel number, and are insensitive to dephasing.Comment: 4 pages REVTEX, including two figure

The galaxy environment in GAMA G3C groups using the Kilo Degree Survey Data Release 3

We aim to investigate the galaxy environment in GAMA Galaxy Groups Catalogue (G3C) using a volume-limited galaxy sample from the Kilo Degree Survey Data Release 3. The k-Nearest Neighbour technique is adapted to take into account the probability density functions (PDFs) of photometric redshifts in our calculations. This algorithm was tested on simulated KiDS tiles, showing its capability of recovering the relation between galaxy colour, luminosity and local environment. The characterization of the galaxy environment in G3C groups shows systematically steeper density contrasts for more massive groups. The red galaxy fraction gradients in these groups is evident for most of group mass bins. The density contrast of red galaxies is systematically higher at group centers when compared to blue galaxy ones. In addition, distinct group center definitions are used to show that our results are insensitive to center definitions. These results confirm the galaxy evolution scenario which environmental mechanisms are responsible for a slow quenching process as galaxies fall into groups and clusters, resulting in a smooth observed colour gradients in galaxy systems.Comment: 14 pages, Accepted to MNRA

On hyperovals of polar spaces

We derive lower and upper bounds for the size of a hyperoval of a finite polar space of rank 3. We give a computer-free proof for the uniqueness, up to isomorphism, of the hyperoval of size 126 of H(5, 4) and prove that the near hexagon E-3 has up to isomorphism a unique full embedding into the dual polar space DH(5, 4)

Describing and measuring leadership within school teams by applying a social network perspective

Despite the growing number of studies that acknowledge a crucial role of distributed leadership within schools, limited knowledge exists on how to describe and measure this multi-faceted concept. In a social network study with 130 respondents, from 14 Dutch school teams carrying out collaborative innovation, we theoretically describe three core aspects of the social interaction process of distributed leadership: collective, dynamic, or relational. Furthermore, we empirically explore how to measure all these three aspects of distributed leadership from a social network perspective, whereas most research focuses on either collective or dynamic. Our findings indicate that three network measures (density, reciprocity, indegree centralization) form a coherent combination to measure distributed leadership in school teams in terms of collective, relational, and dynamic, respectively. Furthermore, based on the combination of measures we found differences in distributed leadership between school teams. Thus, adding the relational aspect in addition to the collective and dynamic aspects seems to be informative to measure distributed leadership. Our study motivates to take a social network perspective, instead of the mostly used aggregation approaches, to measure distributed leadership in school teams

Reflection of light from a disordered medium backed by a phase-conjugating mirror

This is a theoretical study of the interplay of optical phase-conjugation and multiple scattering. We calculate the intensity of light reflected by a phase-conjugating mirror when it is placed behind a disordered medium. We compare the results of a fully phase-coherent theory with those from the theory of radiative transfer. Both methods are equivalent if the dwell time \tau_{dwell} of a photon in the disordered medium is much larger than the inverse of the frequency shift 2\Delta\omega acquired at the phase-conjugating mirror. When \tau_{dwell} \Delta\omega < 1, in contrast, phase coherence drastically affects the reflected intensity. In particular, a minimum in the dependence of the reflectance on the disorder strength disappears when \Delta\omega is reduced below 1/\tau_{dwell}. The analogies and differences with Andreev reflection of electrons at the interface between a normal metal and a superconductor are discussed.Comment: 27 pages RevTeX with 11 figures included with psfi