Runs of homozygosity implicate autozygosity as a schizophrenia risk factor

Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Here, we use runs of homozygosity in genome-wide SNP data to estimate the proportion of the autosome that exists in autozygous tracts in 9,388 cases with schizophrenia and 12,456 controls. We estimate that the odds of schizophrenia increase by ~17% for every 1% increase in genome-wide autozygosity. This association is not due to one or a few regions, but results from many autozygous segments spread throughout the genome, and is consistent with a role for multiple recessive or partially recessive alleles in the etiology of schizophrenia. Such a bias towards recessivity suggests that alleles that increase the risk of schizophrenia have been selected against over evolutionary time

Digital LED Pixels: Instructions for use and a characterization of their properties

This article details how to control light emitting diodes (LEDs) using an ordinary desktop computer. By combining digitally addressable LEDs with an off-the-shelf microcontroller (Arduino), multiple LEDs can be controlled independently and with a high degree of temporal, chromatic, and luminance precision. The proposed solution is safe (can be powered by a 5-V battery), tested (has been used in published research), inexpensive (∼ $60 +$2 per LED), highly interoperable (can be controlled by any type of computer/operating system via a USB or Bluetooth connection), requires no prior knowledge of electrical engineering (components simply require plugging together), and uses widely available components for which established help forums already exist. Matlab code is provided, including a ‘minimal working example’ of use suitable for use by beginners. Properties of the recommended LEDs are also characterized, including their response time, luminance profile, and color gamut. Based on these, it is shown that the LEDs are highly stable in terms of both luminance and chromaticity, and do not suffer from issues of warm-up, chromatic shift, and slow response times associated with traditional CRT and LCD monitor technology

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

<p>Abstract</p> <p>Background</p> <p>The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation.</p> <p>Results</p> <p>A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place.</p> <p>Conclusion</p> <p>The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions.</p

Magnetic interactions in iron superconductors: A review

High temperature superconductivity in iron pnictides and chalcogenides emerges when a magnetic phase is suppressed. The multi-orbital character and the strength of correlations underlie this complex phenomenology, involving magnetic softness and anisotropies, with Hund's coupling playing an important role. We review here the different theoretical approaches used to describe the magnetic interactions in these systems. We show that taking into account the orbital degree of freedom allows us to unify in a single phase diagram the main mechanisms proposed to explain the (\pi,0) order in iron pnictides: the nesting-driven, the exchange between localized spins, and the Hund induced magnetic state with orbital differentiation. Comparison of theoretical estimates and experimental results helps locate the Fe superconductors in the phase diagram. In addition, orbital physics is crucial to address the magnetic softness, the doping dependent properties, and the anisotropies.Comment: Invited review article for a focus issue of Comptes Rendus Physique: 26 pages, 10 figures. Revised version, as accepted. Small changes throughout the text plus new subsection (Sec. IIIE

In Vitro Reassortment between Endemic H1N2 and 2009 H1N1 Pandemic Swine Influenza Viruses Generates Attenuated Viruses

The pandemic H1N1 (pH1N1) influenza virus was first reported in humans in the spring of 2009 and soon thereafter was identified in numerous species, including swine. Reassortant viruses, presumably arising from the co-infection of pH1N1 and endemic swine influenza virus (SIV), were subsequently identified from diagnostic samples collected from swine. In this study, co-infection of swine testicle (ST) cells with swine-derived endemic H1N2 (MN745) and pH1N1 (MN432) yielded two reassortant H1N2 viruses (R1 and R2), both possessing a matrix gene derived from pH1N1. In ST cells, the reassortant viruses had growth kinetics similar to the parental H1N2 virus and reached titers approximately 2 log10 TCID50/mL higher than the pH1N1 virus, while in A549 cells these viruses had similar growth kinetics. Intranasal challenge of pigs with H1N2, pH1N1, R1 or R2 found that all viruses were capable of infecting and transmitting between direct contact pigs as measured by real time reverse transcription PCR of nasal swabs. Lung samples were also PCR-positive for all challenge groups and influenza-associated microscopic lesions were detected by histology. Interestingly, infectious virus was detected in lung samples for pigs challenged with the parental H1N2 and pH1N1 at levels significantly higher than either reassortant virus despite similar levels of viral RNA. Results of our experiment suggested that the reassortant viruses generated through in vitro cell culture system were attenuated without gaining any selective growth advantage in pigs over the parental lineages. Thus, reassortant influenza viruses described in this study may provide a good system to study genetic basis of the attenuation and its mechanism

Rapid characterisation of vegetation structure to predict refugia and climate change impacts across a global biodiversity hotspot

Identification of refugia is an increasingly important adaptation strategy in conservation planning under rapid anthropogenic climate change. Granite outcrops (GOs) provide extraordinary diversity, including a wide range of taxa, vegetation types and habitats in the Southwest Australian Floristic Region (SWAFR). However, poor characterization of GOs limits the capacity of conservation planning for refugia under climate change. A novel means for the rapid identification of potential refugia is presented, based on the assessment of local-scale environment and vegetation structure in a wider region. This approach was tested on GOs across the SWAFR. Airborne discrete return Light Detection And Ranging (LiDAR) data and Red Green and Blue (RGB) imagery were acquired. Vertical vegetation profiles were used to derive 54 structural classes. Structural vegetation types were described in three areas for supervised classification of a further 13 GOs across the region.Habitat descriptions based on 494 vegetation plots on and around these GOs were used to quantify relationships between environmental variables, ground cover and canopy height. The vegetation surrounding GOs is strongly related to structural vegetation types (Kappa = 0.8) and to its spatial context. Water gaining sites around GOs are characterized by taller and denser vegetation in all areas. The strong relationship between rainfall, soil-depth, and vegetation structure (R2 of 0.8–0.9) allowed comparisons of vegetation structure between current and future climate. Significant shifts in vegetation structural types were predicted and mapped for future climates. Water gaining areas below granite outcrops were identified as important putative refugia. A reduction in rainfall may be offset by the occurrence of deeper soil elsewhere on the outcrop. However, climate change interactions with fire and water table declines may render our conclusions conservative. The LiDAR-based mapping approach presented enables the integration of site-based biotic assessment with structural vegetation types for the rapid delineation and prioritization of key refugia

Population level determinants of acute mountain sickness among young men: a retrospective study

<p>Abstract</p> <p>Background</p> <p>Many visitors, including military troops, who enter highland regions from low altitude areas may suffer from acute mountain sickness (AMS), which negatively impacts workable man-hours and increases healthcare costs. The aim of this study was to evaluate the population level risk factors and build a multivariate model, which might be applicable to reduce the effects of AMS on Chinese young men traveling to this region.</p> <p>Methods</p> <p>Chinese highland military medical records were used to obtain data of young men (n = 3727) who entered the Tibet plateau between the years of 2006-2009. The relationship between AMS and travel profile, demographic characteristics, and health behaviors were evaluated by logistic regression. Univariate logistic models estimated the crude odds ratio. The variables that showed significance in the univariate model were included in a multivariate model to derive adjusted odds ratios and build the final model. Data corresponding to odd and even years (2 subsets) were analyzed separately and used in a simple cross-validation.</p> <p>Results</p> <p>Univariate analysis indicated that travel profile, prophylactic use, ethnicity, and province of birth were all associated with AMS in both subsets. In multivariate analysis, young men who traveled from lower altitude (600-800 m <it>vs</it>. 1300-1500 m, adjusted odds ratio (AOR) = 1.32-1.44) to higher altitudes (4100-4300 m <it>vs</it>. 2900-3100 m, AOR = 3.94-4.12; 3600-3700 m <it>vs</it>. 2900-3100 m, AOR = 2.71-2.74) by air or rapid land transport for emergency mission deployment (emergency land deployment <it>vs</it>. normal land deployment, AOR = 2.08-2.11; normal air deployment <it>vs</it>. normal land deployment, AOR = 2.00-2.20; emergency air deployment <it>vs</it>. normal land deployment, AOR = 2.40-3.34) during the cold season (cold <it>vs</it>. warm, AOR = 1.25-1.28) are at great risk for developing AMS. Non-Tibetan male soldiers (Tibetan <it>vs</it>. Han, AOR = 0.03-0.08), born and raised in lower provinces (eastern <it>vs</it>. northwestern, AOR = 1.32-1.39), and deployed without prophylaxis (prophylactic drug <it>vs</it>. none, AOR = 0.75-0.76), also represented a population at significantly increased risk for AMS. The predicted model was built; the area under receiver operating characteristic curve was 0.703.</p> <p>Conclusion</p> <p>Before a group of young men first enter a high altitude area, it is important that a health service plan should be made referring to the group's travel profile and with respect to young men's ethnicity and province of birth. Low-cost Chinese traditional prophylactic drugs might have some effect on decreasing the risk of AMS, although this needs further verification.</p

Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

<p>Abstract</p> <p>Background</p> <p>A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identical by descent) on phenotypes. However, it is unknown which current ROH detection program, and which set of parameters within a given program, is optimal for differentiating ROHs that are truly autozygous from ROHs that are homozygous at the marker level but vary at unmeasured variants between the markers.</p> <p>Method</p> <p>We simulated 120 Mb of sequence data in order to know the true state of autozygosity. We then extracted common variants from this sequence to mimic the properties of SNP platforms and performed ROH analyses using three popular ROH detection programs, PLINK, GERMLINE, and BEAGLE. We varied detection thresholds for each program (e.g., prior probabilities, lengths of ROHs) to understand their effects on detecting known autozygosity.</p> <p>Results</p> <p>Within the optimal thresholds for each program, PLINK outperformed GERMLINE and BEAGLE in detecting autozygosity from distant common ancestors. PLINK's sliding window algorithm worked best when using SNP data pruned for linkage disequilibrium (LD).</p> <p>Conclusion</p> <p>Our results provide both general and specific recommendations for maximizing autozygosity detection in genome-wide SNP data, and should apply equally well to research on whole-genome autozygosity burden or to research on whether specific autozygous regions are predictive using association mapping methods.</p