CNV analysis in a large schizophrenia sample implicates deletions at 16p12.1 and SLC1A1 and duplications at 1p36.33 and CGNL1

Large and rare copy number variants (CNVs) at several loci have been shown to increase risk for schizophrenia. Aiming to discover novel susceptibility CNV loci, we analysed 6,882 cases and 11,255 controls genotyped on Illumina arrays, most of which have not been used for this purpose before. We identified genes enriched for rare exonic CNVs among cases, and then attempted to replicate the findings in an additional 14,568 cases and 15,274 controls. In a combined analysis of all samples, 12 distinct loci were enriched among cases with nominal levels of significance (P500kb), rare CNVs showed a 1.2% excess in cases after excluding known schizophrenia-associated loci, suggesting that additional susceptibility loci exist. However, even larger samples are required for their discovery.

Support for the Multidimensional Adolescent Stress Questionnaire in a Sample of Adolescents in the United Kingdom

Adolescence is a time of physical, social and emotional development, and this development can be accompanied by feelings of stress. The Adolescent Stress Questionnaire is a 56-item scale measuring stress in 10 domains. Developed in Australia, the scale has been translated, and its reliability and validity have been tested in a number of countries across Europe, where the 10-factor, 56-item version of the scale has received little support. The present study tested the factor structure, construct validity and reliability in a sample (n=610) of adolescents in the United Kingdom. Support was found for the 10-factor, 56-item version of the scale, and correlations with self-concept measures, sex scores on stress factors and Cronbach's α-values, suggesting that the scale may be a viable assessment tool for adolescent stress. Results for alcohol-specific analyses support the domain-specific nature of the scale. Future work may seek to investigate the stability of age-specific stress domains (e.g. the stress of Emerging Adult Responsibility) in samples that include younger adolescents. 

What happens in court?:The development of understanding of the legal system in a sample of Irish children and adults

A total sample of three hundred and sixty (N=360) Irish children and adults, drawn from nine age groups, were administered the specially designed Legal Knowledge and Perception of Court Interview Schedule. Analyses of variance revealed a main effect for age of participant. Participants demonstrated increasing knowledge of the legal system with increasing age. The findings of the present study suggest inter alia that Irish children, particularly those under nine years of age, do not possess sufficient understanding of the legal system to enable them to participate as effectively as they might as witnesses. The potential for developing a systematic programme of preparing child witnesses for their involvement in the legal process is discussed.

The influence of parents, older siblings, and non-parental care on infant development at nine months of age

Background: The majority of research examining the influence of social environment on early child development suggests benefits to two-parent households, but contradictory evidence for the effects of siblings. The aims of the present study were to examine the influence of the child's proximal social environment, and the effects of interactions between socioeconomic status and social environment on developmental outcomes.

Methods: Primary caregivers of a representative sample of 10,748 nine-month-old infants in Ireland completed the Ages and Stages Questionnaire and provided information on social environment. Adjustment was made for infant and maternal characteristics, household income, and area where the child was living at the time of the study. Further analyses tested for interactions between social environment and household income.

Results: Binary logistic regressions indicated no effects for number of parents in the household. However, the presence of siblings in the household was a consistent predictor of failing to reach milestones in communication, gross motor, problem-solving, and personal-social development. Furthermore, there was a gradient of increasing likelihood of failing in gross motor, problem-solving, and personal-social development with increasing numbers of siblings. Care by a grandparent decreased the likelihood of failing in communication and personal-social development.

Conclusions:These findings do not support the majority of research that finds positive benefits for two-parent households. Similarly, the findings suggest limited effects for non-parental care. However, the observed negative effects of siblings support both the confluence and resource dilution models of sibling effect. Examination of follow-up data may elucidate current findings.

Impact of sample preparation on mineralogical analysis of zero-valent iron reactive barrier materials

Permeable reactive barriers (PRBs) of zero-valent iron (Fe⁰) are increasingly being used to remediate contaminated ground water. Corrosion of Fe⁰ filings and tbe formation of precipitates can occur when the PRB material comes in contact with ground water and may reduce the lifespan and effectiveness of the barrier. At present, there are no routine procedures for preparing and analyzing the mineral precipitates from Fe⁰ PRB material. These procedures are needed because mineralogical composition of corrosion products used to interpret the barrier processes can change with iron oxidation and sample preparation. The objectives of this study were (i) to investigate a method of preparing Fe⁰ reactive barrier material for mineralogical analysis by X-ray diffraction (XRD), and (ii) to identify Fe mineral phases and rates of transformations induced by different mineralogical preparation techniques. Materials from an in situ Fe⁰ PRB were collected by undisturbed coring and processed for XRD analysis after different times since sampling for three size fractions and by various drying treatments. We found that whole-sample preparation for analysis was necessary because mineral precipitates occurred within the PRB material in different size fractions of the samples. Green rusts quickly disappeared from acetone-dried samples and were not present in air-dried and oven-dried samples Maghemite/magnetite content increased over time and in oven-dried samples, especially after heating to 105°C. We conclude that care must be taken during sample preparation of Fe⁰ PRB material, especially for detection of green rusts, to ensure accurate identification of minerals present within the barrier system.

Toward Characterization Of The Type IIP Supernova Progenitor Population: A Statistical Sample Of Light Curves From Pan-STARRS1

In recent years, wide-field sky surveys providing deep multi-band imaging have presented a new path for indirectly characterizing the progenitor populations of core-collapse supernovae (SN): systematic light curve studies. We assemble a set of 76 grizy-band Type IIP SN light curves from Pan-STARRS1, obtained over a constant survey program of 4 years and classified using both spectroscopy and machine learning-based photometric techniques. We develop and apply a new Bayesian model for the full multi-band evolution of each light curve in the sample. We find no evidence of a sub-population of fast-declining explosions (historically referred to as "Type IIL" SNe). However, we identify a highly significant relation between the plateau phase decay rate and peak luminosity among our SNe IIP. These results argue in favor of a single parameter, likely determined by initial stellar mass, predominantly controlling the explosions of red supergiants. This relation could also be applied for supernova cosmology, offering a standardizable candle good to an intrinsic scatter of 0.2 mag. We compare each light curve to physical models from hydrodynamic simulations to estimate progenitor initial masses and other properties of the Pan-STARRS1 Type IIP SN sample. We show that correction of systematic discrepancies between modeled and observed SN IIP light curve properties and an expanded grid of progenitor properties, are needed to enable robust progenitor inferences from multi-band light curve samples of this kind. This work will serve as a pathfinder for photometric studies of core-collapse SNe to be conducted through future wide field transient searches.

MarcoPolo-R near earth asteroid sample return mission

MarcoPolo-R is a sample return mission to a primitive Near-Earth Asteroid (NEA) proposed in collaboration with NASA. It will rendezvous with a primitive NEA, scientifically characterize it at multiple scales,and return a unique sample to Earth unaltered by the atmospheric entry process or terrestrial weathering. MarcoPolo-R will return bulk samples (up to 2 kg) from an organic-rich binary asteroid to Earth for laboratory analyses, allowing us to: explore the origin of planetary materials and initial stages of habitable planet formation; identify and characterize the organics and volatiles in a primitive asteroid; understand the unique geomorphology, dynamics and evolution of a binaryNEA. This project is based on the previous Marco Polo mission study,which was selected for the Assessment Phase of the first round of Cosmic Vision. Its scientific rationale was highly ranked by ESA committees andit was not selected only because the estimated cost was higher than theallotted amount for an M class mission. The cost of Marco Polo-R will be reduced to within the ESA medium mission budget by collaboration withAPL (John Hopkins University) and JPL in the NASA program for coordination with ESA's Cosmic Vision Call. The baseline target is a binary asteroid (175706) 1996 FG3, which offers a very efficient operational and technical mission profile. A binary target also providesenhanced science return. The choice of this target will allow newinvestigations to be performed more easily than at a single object, andalso enables investigations of the fascinating geology and geophysics ofasteroids that are impossible at a single object. Several launch windows have been identified in the time-span 2020-2024. A number of otherpossible primitive single targets of high scientific interest have beenidentified covering a wide range of possible launch dates. The baselinemission scenario of Marco Polo-R to 1996 FG3 is as follows: a singleprimary spacecraft provided by ESA, carrying the Earth Re-entry Capsule, sample acquisition and transfer system provided by NASA, will be launched by a Soyuz-Fregat rocket from Kourou into GTO and using two space segment stages. Two similar missions with two launch windows, in 2021 and 2022 and for both sample return in 2029 (with mission durationof 7 and 8 years), have been defined. Earlier or later launches, in 2020 or 2024, also offer good opportunities. All manoeuvres are carried out by a chemical propulsion system. MarcoPolo-R takes advantage of three industrial studies completed as part of the previous Marco Polo mission (see ESA/SRE (2009)3, Marco Polo Yellow Book) and of the expertise of the consortium led by Dr. A.F. Cheng (PI of the NASA NEAR Shoemaker mission) of the JHU-APL, including JPL, NASA ARC, NASA LaRC, and MIT.

Measurement method and apparatus for analysing the metal or metal ion conten of a sample

2. K. Gow, P.K.J Robertson, P.M. Pollard, and K. Christidis

Design characteristic of randomised controlled trials for geographic atrophy in age-related macular degeneration: selection of outcomes and sample size calculation

PurposeThe selection of suitable outcomes and sample size calculation are critical factors in the design of a randomised controlled trial (RCT). The goal of this study was to identify the range of outcomes and information on sample size calculation in RCTs on geographic atrophy (GA).MethodsWe carried out a systematic review of age-related macular degeneration (AMD) RCTs. We searched MEDLINE, EMBASE, Scopus, Cochrane Library, www.controlled-trials.com, and www.ClinicalTrials.gov. Two independent reviewers screened records. One reviewer collected data and the second reviewer appraised 10% of collected data. We scanned references lists of selected papers to include other relevant RCTs.ResultsLiterature and registry search identified 3816 abstracts of journal articles and 493 records from trial registries. From a total of 177 RCTs on all types of AMD, 23 RCTs on GA were included. Eighty-one clinical outcomes were identified. Visual acuity (VA) was the most frequently used outcome, presented in 18 out of 23 RCTs and followed by the measures of lesion area. For sample size analysis, 8 GA RCTs were included. None of them provided sufficient Information on sample size calculations.ConclusionsThis systematic review illustrates a lack of standardisation in terms of outcome reporting in GA trials and issues regarding sample size calculation. These limitations significantly hamper attempts to compare outcomes across studies and also perform meta-analyses.

Systematic Uncertainties Associated with the Cosmological Analysis of the First PAN-STARRS1 Type Ia Supernova Sample

We probe the systematic uncertainties from the 113 Type Ia supernovae (SN Ia) in the Pan-STARRS1 (PS1) sample along with 197 SN Ia from a combination of low-redshift surveys. The companion paper by Rest et al. describes the photometric measurements and cosmological inferences from the PS1 sample. The largest systematic uncertainty stems from the photometric calibration of the PS1 and low-z samples. We increase the sample of observed Calspec standards from 7 to 10 used to define the PS1 calibration system. The PS1 and SDSS-II calibration systems are compared and discrepancies up to ∼0.02 mag are recovered. We find uncertainties in the proper way to treat intrinsic colors and reddening produce differences in the recovered value of w up to 3%. We estimate masses of host galaxies of PS1 supernovae and detect an insignificant difference in distance residuals of the full sample of 0.037 ± 0.031 mag for host galaxies with high and low masses. Assuming flatness and including systematic uncertainties in our analysis of only SNe measurements, we find w = -1.120^+0.360_-0.206(Stat)^+0.269_-0.291(Sys). With additional constraints from Baryon acoustic oscillation, cosmic microwave background (CMB) (Planck) and H₀ measurements, we find w = -1.166^+0.072_-0.069 and Ω_m = 0.280^+0.013_-0.012 (statistical and systematic errors added in quadrature). The significance of the inconsistency with w = -1 depends on whether we use Planck or Wilkinson Microwave Anisotropy Probe measurements of the CMB: w_{BAO+H0+SN+WMAP} = -1.124^+0.083_-0.065.

RMA with quantile normalization mixes biological signals between different sample groups in microarray data analysis

Quantile normalization (QN) is a technique for microarray data processing and is the default normalization method in the Robust Multi-array Average (RMA) procedure, which was primarily designed for analysing gene expression data from Affymetrix arrays. Given the abundance of Affymetrix microarrays and the popularity of the RMA method, it is crucially important that the normalization procedure is applied appropriately. In this study we carried out simulation experiments and also analysed real microarray data to investigate the suitability of RMA when it is applied to dataset with different groups of biological samples. From our experiments, we showed that RMA with QN does not preserve the biological signal included in each group, but rather it would mix the signals between the groups. We also showed that the Median Polish method in the summarization step of RMA has similar mixing effect. RMA is one of the most widely used methods in microarray data processing and has been applied to a vast volume of data in biomedical research. The problematic behaviour of this method suggests that previous studies employing RMA could have been misadvised or adversely affected. Therefore we think it is crucially important that the research community recognizes the issue and starts to address it. The two core elements of the RMA method, quantile normalization and Median Polish, both have the undesirable effects of mixing biological signals between different sample groups, which can be detrimental to drawing valid biological conclusions and to any subsequent analyses. Based on the evidence presented here and that in the literature, we recommend exercising caution when using RMA as a method of processing microarray gene expression data, particularly in situations where there are likely to be unknown subgroups of samples.