Relationships between estimated autozygosity and complex traits in the UK Biobank

<div><p>Inbreeding increases the risk of certain Mendelian disorders in humans but may also reduce fitness through its effects on complex traits and diseases. Such inbreeding depression is thought to occur due to increased homozygosity at causal variants that are recessive with respect to fitness. Until recently it has been difficult to amass large enough sample sizes to investigate the effects of inbreeding depression on complex traits using genome-wide single nucleotide polymorphism (SNP) data in population-based samples. Further, it is difficult to infer causation in analyses that relate degree of inbreeding to complex traits because confounding variables (e.g., education) may influence both the likelihood for parents to outbreed and offspring trait values. The present study used runs of homozygosity in genome-wide SNP data in up to 400,000 individuals in the UK Biobank to estimate the proportion of the autosome that exists in autozygous tracts—stretches of the genome which are identical due to a shared common ancestor. After multiple testing corrections and controlling for possible sociodemographic confounders, we found significant relationships in the predicted direction between estimated autozygosity and three of the 26 traits we investigated: age at first sexual intercourse, fluid intelligence, and forced expiratory volume in 1 second. Our findings corroborate those of several published studies. These results may imply that these traits have been associated with Darwinian fitness over evolutionary time. However, some of the autozygosity-trait relationships were attenuated after controlling for background sociodemographic characteristics, suggesting that alternative explanations for these associations have not been eliminated. Care needs to be taken in the design and interpretation of ROH studies in order to glean reliable information about the genetic architecture and evolutionary history of complex traits.</p></div

Eigenfunctions for smooth expanding circle maps

We construct a real-analytic circle map for which the corresponding Perron-Frobenius operator has a real-analytic eigenfunction with an eigenvalue outside the essential spectral radius when acting upon $C^1$-functions.Comment: 10 pages, 2 figure

Tuberculosis vaccine strain _Mycobacterium bovis_ BCG Russia is a natural _recA_ mutant

The current tuberculosis vaccine is a live vaccine derived from _Mycobacterium bovis_ and attenuated by serial _in vitro_ passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Gu&#xe9;rin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains, we aimed to inactivate _recA_ by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was successful in three out of four strains. However, only illegitimate recombination was observed in BCG substrain Russia. Sequence analyses of _recA_ revealed that a single nucleotide insertion in the 5&#x27; part of _recA_ led to a translational frameshift with an early stop codon making BCG Russia a natural _recA_ mutant. At the protein level BCG Russia failed to express RecA. According to phylogenetic analyses BCG Russia is an ancient vaccine strain most closely related to the parental _M. bovis_. Our data suggest that _recA_ inactivation in BCG Russia occurred early and is in part responsible for its high degree of genomic stability, resulting in a substrain that has less genetic alterations than other vaccine substrains with respect to _M. bovis_ AF2122/97 wild type

Loadcell supports for a dynamic force plate

An apparatus was developed to accurately measure components of force along three mutually perpendicular axes, torque, and the center of pressure imposed by the foot of a subject walking over its surface. The data obtained were used to supplement high-speed motion picture and electromyographic (EMG) data for in-depth studies of normal or abnormal human gait. Significant features of the design (in particular, the mechanisms used to support the loadcell transducers) are described. Results of the development program and typical data obtained with the device are presented and discussed

SkyMapper and the Southern Sky Survey - a resource for the southern sky

SkyMapper is amongst the first of a new generation of dedicated, wide-field survey telescopes. The 1.3m SkyMapper telescope features a 5.7 square degree field-of-view Cassegrain imager and will see first light in late 2007. The primary goal of the facility is to conduct the Southern Sky Survey a six colour, six epoch survey of the southern sky. The survey will provide photometry for objects between 8th and 23rd magnitude with global photometric accuracy of 0.03 magnitudes and astrometry to 50 mas. This will represent a valuable scientific resource for the southern sky and in addition provide a basis for photometric and astrometric calibration of imaging data.Comment: 6 pages, 4 figures, proceedings of ESO Calibration Workshop 200

Constraining the Circumbinary Envelope of Z CMa via imaging polarimetry

Z CMa is a complex binary system, composed of a Herbig Be and an FU Ori star. The Herbig star is surrounded by a dust cocoon of variable geometry, and the whole system is surrounded by an infalling envelope. Previous spectropolarimetric observations have reported a preferred orientation of the polarization angle, perpendicular to the direction of a large, parsec-sized jet associated with the Herbig star. The variability in the amount of polarized light has been associated to changes in the geometry of the dust cocoon that surrounds the Herbig star. We aim to constrain the properties of Z CMa by means of imaging polarimetry at optical wavelengths. Using ExPo, a dual-beam imaging polarimeter which operates at optical wavelengths, we have obtained imaging (linear) polarimetric data of Z CMa. Our observations were secured during the return to quiescence after the 2008 outburst. We detect three polarized features over Z CMa. Two of these features are related to the two jets reported in this system: the large jet associated to the Herbig star, and the micro-jet associated to the FU Ori star. Our results suggest that the micro-jet extends to a distance ten times larger than reported in previous studies. The third feature suggests the presence of a hole in the dust cocoon that surrounds the Herbig star of this system. According to our simulations, this hole can produce a pencil beam of light that we see scattered off the low-density envelope surrounding the system.Comment: Accepted for publication in A\&

Instrumental polarisation at the Nasmyth focus of the E-ELT

The ~39-m European Extremely Large Telescope (E-ELT) will be the largest telescope ever built. This makes it particularly suitable for sensitive polarimetric observations, as polarimetry is a photon-starved technique. However, the telescope mirrors may severely limit the polarimetric accuracy of instruments on the Nasmyth platforms by creating instrumental polarisation and/or modifying the polarisation signal of the object. In this paper we characterise the polarisation effects of the two currently considered designs for the E-ELT Nasmyth ports as well as the effect of ageing of the mirrors. By means of the Mueller matrix formalism, we compute the response matrices of each mirror arrangement for a range of zenith angles and wavelengths. We then present two techniques to correct for these effects that require the addition of a modulating device at the polarisation-free intermediate focus that acts either as a switch or as a part of a two-stage modulator. We find that the values of instrumental polarisation, Stokes transmission reduction and cross- talk vary significantly with wavelength, and with pointing, for the lateral Nasmyth case, often exceeding the accuracy requirements for proposed polarimetric instruments. Realistic ageing effects of the mirrors after perfect calibration of these effects may cause polarimetric errors beyond the requirements. We show that the modulation approach with a polarimetric element located in the intermediate focus reduces the instrumental polarisation effects down to tolerable values, or even removes them altogether. The E-ELT will be suitable for sensitive and accurate polarimetry, provided frequent calibrations are carried out, or a dedicated polarimetric element is installed at the intermediate focus.Comment: Accepted for publication in A&

Crustal structure and rift flank uplift of the Adare Trough, Antarctica

The Adare Trough, located 100 km northeast of Cape Adare, Antarctica, represents the extinct third arm of a Tertiary spreading ridge between East and West Antarctica. It is characterized by pronounced asymmetric rift flanks elevated up to over 2 km above the trough's basement, accompanied by a large positive mantle Bouguer anomaly. On the basis of recently acquired seismic reflection and ship gravity data, we invert mantle Bouguer anomalies from the Adare Trough and obtain an unexpectedly large oceanic crustal thickness maximum of 9–10.5 km underneath the extinct ridge. A regional positive residual basement depth anomaly between 1 and 2.5 km in amplitude characterizes ocean crust from offshore Victoria Land to the Balleny Islands and north of Iselin Bank. The observations and models indicate that the mid/late Tertiary episode of slow spreading between East and West Antarctica was associated with a mantle thermal anomaly. The increasing crustal thickness toward the extinct ridge indicates that this thermal mantle anomaly may have increased in amplitude through time during the Adare spreading episode. This scenario is supported by a mantle convection model, which indicates the formation and strengthening of a major regional negative upper mantle density anomaly in the southwest Pacific in the last 50 million years. The total amount of post-26 Ma extension associated with Adare Trough normal faulting was about 7.5 km, in anomalously thick oceanic crust with a lithospheric effective elastic thickness (EET) between 3.5 and 5 km. This corresponds to an age between 3 and 5 million years based on a thermal boundary layer model and supports a scenario in which the Adare Trough formed soon after spreading between East and West Antarctica ceased, confined to relatively weak lithosphere with anomalously thick oceanic crust. There is little evidence for major subsequent structural activity in the Adare trough area from the available seismic data, indicating that this part of the West Antarctic Rift system became largely inactive in the early Miocene, with the exception of minor structural reactivation which is visible in the seismic data as offsets up to end of the early Pliocene

An analytical analysis of vesicle tumbling under a shear flow

Vesicles under a shear flow exhibit a tank-treading motion of their membrane, while their long axis points with an angle < 45 degrees with respect to the shear stress if the viscosity contrast between the interior and the exterior is not large enough. Above a certain viscosity contrast, the vesicle undergoes a tumbling bifurcation, a bifurcation which is known for red blood cells. We have recently presented the full numerical analysis of this transition. In this paper, we introduce an analytical model that has the advantage of being both simple enough and capturing the essential features found numerically. The model is based on general considerations and does not resort to the explicit computation of the full hydrodynamic field inside and outside the vesicle.Comment: 19 pages, 9 figures, to be published in Phys. Rev.

On Urabe's criteria of isochronicity

We give a short proof of Urabe's criteria for the isochronicity of periodical solutions of the equation $\ddot{x}+g(x)=0$. We show that apart from the harmonic oscillator there exists a large family of isochronous potentials which must all be non-polynomial and not symmetric (an even function of the coordinate x).Comment: 8 page