A genome-wide linkage and association scan reveals novel loci for autism

Member of the Autism Genome Project Consortium: Astrid M. VicenteAlthough autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success. Genome-wide association studies using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits. Consequently, we initiated a linkage and association mapping study using half a million genome-wide single nucleotide polymorphisms (SNPs) in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed an SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 x 10(-7)). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening whereas the discovery of a single novel association demonstrates the action of common variants

Pre-hospital body surface potential mapping improves early diagnosis of acute coronary artery occlusion in patients with ventricular fibrillation and cardiac arrest

Aims: To determine whether 80-lead body surface potential mapping (BSPM) improves detection of acute coronary artery occlusion in patients presenting with out-of-hospital cardiac arrest (OHCA) due to ventricular fibrillation (VF) and who survived to reach hospital. Methods and results: Of 645 consecutive patients with OHCA who were attended by the mobile coronary care unit, VF was the initial rhythm in 168 patients. Eighty patients survived initial resuscitation, 59 of these having had BSPM and 12-lead ECG post-return of spontaneous circulation (ROSC) and in 35 patients (age 69±13 yrs; 60% male) coronary angiography performed within 24. h post-ROSC. Of these, 26 (74%) patients had an acutely occluded coronary artery (TIMI flow grade [TFG] 0/1) at angiography. Twelve-lead ECG criteria showed ST-segment elevation (STE) myocardial infarction (STEMI) using Minnesota 9-2 criteria - sensitivity 19%, specificity 100%; ST-segment depression (STD) =0.05. mV in =2 contiguous leads - sensitivity 23%, specificity 89%; and, combination of STEMI or STD criteria - sensitivity 46%, specificity 100%. BSPM STE occurred in 23 (66%) patients. For the diagnosis of TFG 0/1 in a main coronary artery, BSPM STE had sensitivity 88% and specificity 100% (c-statistic 0.94), with STE occurring most commonly in either the posterior, right ventricular or high right anterior territories. Conclusion: Among OHCA patients presenting with VF and who survived resuscitation to reach hospital, post-resuscitation BSPM STE identifies acute coronary occlusion with sensitivity 88% and specificity 100% (c-statistic 0.94). © 2012 Elsevier Ireland Ltd

Time-dependent Stochastic Modeling of Solar Active Region Energy

A time-dependent model for the energy of a flaring solar active region is presented based on a stochastic jump-transition model (Wheatland and Glukhov 1998; Wheatland 2008; Wheatland 2009). The magnetic free energy of the model active region varies in time due to a prescribed (deterministic) rate of energy input and prescribed (random) flare jumps downwards in energy. The model has been shown to reproduce observed flare statistics, for specific time-independent choices for the energy input and flare transition rates. However, many solar active regions exhibit time variation in flare productivity, as exemplified by NOAA active region AR 11029 (Wheatland 2010). In this case a time-dependent model is needed. Time variation is incorporated for two cases: 1. a step change in the rates of flare jumps; and 2. a step change in the rate of energy supply to the system. Analytic arguments are presented describing the qualitative behavior of the system in the two cases. In each case the system adjusts by shifting to a new stationary state over a relaxation time which is estimated analytically. The new model retains flare-like event statistics. In each case the frequency-energy distribution is a power law for flare energies less than a time-dependent rollover set by the largest energy the system is likely to attain at a given time. For Case 1, the model exhibits a double exponential waiting-time distribution, corresponding to flaring at a constant mean rate during two intervals (before and after the step change), if the average energy of the system is large. For Case 2 the waiting-time distribution is a simple exponential, again provided the average energy of the system is large. Monte Carlo simulations of Case~1 are presented which confirm the analytic estimates. The simulation results provide a qualitative model for observed flare statistics in active region AR 11029.Comment: 25 pages, 9 figure

Assessing the influence of the rhizosphere on soil hydraulic properties using X-ray computed tomography and numerical modelling

© 2015 © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. Understanding the dynamics of water distribution in soil is crucial for enhancing our knowledge of managing soil and water resources. The application of X-ray computed tomography (CT) to the plant and soil sciences is now well established. However, few studies have utilized the technique for visualizing water in soil pore spaces. Here this method is utilized to visualize the water in soil in situ and in three-dimensions at successive reductive matric potentials in bulk and rhizosphere soil. The measurements are combined with numerical modelling to determine the unsaturated hydraulic conductivity, providing a complete picture of the hydraulic properties of the soil. The technique was performed on soil cores that were sampled adjacent to established roots (rhizosphere soil) and from soil that had not been influenced by roots (bulk soil). A water release curve was obtained for the different soil types using measurements of their pore geometries derived from CT imaging and verified using conventional methods, such as pressure plates. The water, soil, and air phases from the images were segmented and quantified using image analysis. The water release characteristics obtained for the contrasting soils showed clear differences in hydraulic properties between rhizosphere and bulk soil, especially in clay soil. The data suggest that soils influenced by roots (rhizosphere soil) are less porous due to increased aggregation when compared with bulk soil. The information and insights obtained on the hydraulic properties of rhizosphere and bulk soil will enhance our understanding of rhizosphere biophysics and improve current water uptake models

A framework for the detection of de novo mutations in family-based sequencing data

Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father's age at conception and the number of DNMs in female offspring's X chromosome, consistent with previous literature reports

The First Magnetic Fields

We review current ideas on the origin of galactic and extragalactic magnetic fields. We begin by summarizing observations of magnetic fields at cosmological redshifts and on cosmological scales. These observations translate into constraints on the strength and scale magnetic fields must have during the early stages of galaxy formation in order to seed the galactic dynamo. We examine mechanisms for the generation of magnetic fields that operate prior during inflation and during subsequent phase transitions such as electroweak symmetry breaking and the quark-hadron phase transition. The implications of strong primordial magnetic fields for the reionization epoch as well as the first generation of stars is discussed in detail. The exotic, early-Universe mechanisms are contrasted with astrophysical processes that generate fields after recombination. For example, a Biermann-type battery can operate in a proto-galaxy during the early stages of structure formation. Moreover, magnetic fields in either an early generation of stars or active galactic nuclei can be dispersed into the intergalactic medium.Comment: Accepted for publication in Space Science Reviews. Pdf can be also downloaded from http://canopus.cnu.ac.kr/ryu/cosmic-mag1.pd

Survivability of copper projectiles during hypervelocity impacts in porous ice: A laboratory investigation of the survivability of projectiles impacting comets or other bodies

AbstractDuring hypervelocity impact (>a few kms−1) the resulting cratering and/or disruption of the target body often outweighs interest on the outcome of the projectile material, with the majority of projectiles assumed to be vaporised. However, on Earth, fragments, often metallic, have been recovered from impact sites, meaning that metallic projectile fragments may survive a hypervelocity impact and still exist within the wall, floor and/or ejecta of the impact crater post-impact. The discovery of the remnant impactor composition within the craters of asteroids, planets and comets could provide further information regarding the impact history of a body. Accordingly, we study in the laboratory the survivability of 1 and 2mm diameter copper projectiles fired onto ice at speeds between 1.00 and 7.05kms−1. The projectile was recovered intact at speeds up to 1.50kms−1, with no ductile deformation, but some surface pitting was observed. At 2.39kms−1, the projectile showed increasing ductile deformation and broke into two parts. Above velocities of 2.60kms−1 increasing numbers of projectile fragments were identified post impact, with the mean size of the fragments decreasing with increasing impact velocity. The decrease in size also corresponds with an increase in the number of projectile fragments recovered, as with increasing shock pressure the projectile material is more intensely disrupted, producing smaller and more numerous fragments. The damage to the projectile is divided into four classes with increasing speed and shock pressure: (1) minimal damage, (2) ductile deformation, start of break up, (3) increasing fragmentation, and (4) complete fragmentation. The implications of such behaviour is considered for specific examples of impacts of metallic impactors onto Solar System bodies, including LCROSS impacting the Moon, iron meteorites onto Mars and NASA’s “Deep Impact” mission where a spacecraft impacted a comet