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1.
  • Anney, Richard, et al. (författare)
  • A genome-wide scan for common alleles affecting risk for autism.
  • 2010
  • Ingår i: Human Molecular Genetics. - 0964-6906. ; 19:20, s. 4072-4082
  • Tidskriftsartikel (refereegranskat)abstract
    • Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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2.
  • Anney, Richard, et al. (författare)
  • Individual common variants exert weak effects on the risk for autism spectrum disorders.
  • 2012
  • Ingår i: Human Molecular Genetics. - 0964-6906. ; 21:21, s. 4781-92
  • Tidskriftsartikel (refereegranskat)abstract
    • While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASD), the contribution of common variation to ASD risk is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating association of individual SNPs, we also sought evidence that common variants, en masse, might affect risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest p-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. By contrast, allele-scores derived from the transmission of common alleles to Stage 1 cases significantly predict case-status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele-score results, it is reasonable to conclude that common variants affect ASD risk but their individual effects are modest.
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3.
  • Casey, Jillian P, et al. (författare)
  • A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.
  • 2012
  • Ingår i: Human Genetics. - 0340-6717. ; 131:4, s. 565-579
  • Tidskriftsartikel (refereegranskat)abstract
    • Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
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4.
  • Pinto, Dalila, et al. (författare)
  • Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders.
  • 2014
  • Ingår i: American journal of human genetics. - 1537-6605. ; 94:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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5.
  • Pinto, Dalila, et al. (författare)
  • Functional impact of global rare copy number variation in autism spectrum disorders.
  • 2010
  • Ingår i: Nature. - 0028-0836. ; 466:7304, s. 368-372
  • Tidskriftsartikel (refereegranskat)abstract
    • The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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6.
  • Aho-Mantila, L., et al. (författare)
  • Assessment of SOLPS5.0 divertor solutions with drifts and currents against L-mode experiments in ASDEX Upgrade and JET
  • 2017
  • Ingår i: Plasma Physics and Controlled Fusion. - : IOP PUBLISHING LTD. - 0741-3335 .- 1361-6587. ; 59:3
  • Tidskriftsartikel (refereegranskat)abstract
    • The divertor solutions obtained with the plasma edge modelling tool SOLPS5.0 are discussed. The code results are benchmarked against carefully analysed L-mode discharges at various density levels with and without impurity seeding in the full-metal tokamaks ASDEX Upgrade and JET. The role of the cross-field drifts and currents in the solutions is analysed in detail, and the improvements achieved by fully activating the drift and current terms in view of matching the experimental signals are addressed. The persisting discrepancies are also discussed.
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7.
  • Aiba, N., et al. (författare)
  • Analysis of ELM stability with extended MHD models in JET, JT-60U and future JT-60SA tokamak plasmas
  • 2018
  • Ingår i: Plasma Physics and Controlled Fusion. - : Institute of Physics (IOP). - 0741-3335 .- 1361-6587. ; 60:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The stability with respect to a peeling-ballooning mode (PBM) was investigated numerically with extended MHD simulation codes in JET, JT-60U and future JT-60SA plasmas. The MINERVA-DI code was used to analyze the linear stability, including the effects of rotation and ion diamagnetic drift (omega(*i)), in JET-ILW and JT-60SA plasmas, and the JOREK code was used to simulate nonlinear dynamics with rotation, viscosity and resistivity in JT-60U plasmas. It was validated quantitatively that the ELM trigger condition in JET-ILW plasmas can be reasonably explained by taking into account both the rotation and omega(*i) effects in the numerical analysis. When deuterium poloidal rotation is evaluated based on neoclassical theory, an increase in the effective charge of plasma destabilizes the PBM because of an acceleration of rotation and a decrease in omega(*i). The difference in the amount of ELM energy loss in JT-60U plasmas rotating in opposite directions was reproduced qualitatively with JOREK. By comparing the ELM affected areas with linear eigenfunctions, it was confirmed that the difference in the linear stability property, due not to the rotation direction but to the plasma density profile, is thought to be responsible for changing the ELM energy loss just after the ELM crash. A predictive study to determine the pedestal profiles in JT-60SA was performed by updating the EPED1 model to include the rotation and w*i effects in the PBM stability analysis. It was shown that the plasma rotation predicted with the neoclassical toroidal viscosity degrades the pedestal performance by about 10% by destabilizing the PBM, but the pressure pedestal height will be high enough to achieve the target parameters required for the ITER-like shape inductive scenario in JT-60SA.
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8.
  • Aiba, N., et al. (författare)
  • Numerical analysis of ELM stability with rotation and ion diamagnetic drift effects in JET
  • 2017
  • Ingår i: Nuclear Fusion. - EUROfus Consortium, JET, Culham Sci Ctr, Abingdon OX14 3DB, Oxon, England. [Aiba, N.] Natl Inst Quantum & Radiol Sci & Technol, Rokkasho, Aomori 0393212, Japan. [Giroud, C.; Saarelma, S.; Lupelli, I.; Casson, F. J.; Pamela, S.; Maggi, C. F.] Culham Ctr Fus Energy, Culham Sci Ctr, Abingdon OX14 3DB, Oxon, England. [Honda, M.; Urano, H.] Natl Inst Quantum & Radiol Sci & Technol, Naka, Ibaraki 3110193, Japan. [Delabie, E.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Frassinetti, L.] KTH, Div Fus Plasma Phys, SE-10041 Stockholm, Sweden. : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 57:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Stability to the type-I edge localized mode (ELM) in JET plasmas was investigated numerically by analyzing the stability to a peeling-ballooning mode with the effects of plasma rotation and ion diamagnetic drift. The numerical analysis was performed by solving the extended Frieman-Rotenberg equation with the MINERVA-DI code. To take into account these effects in the stability analysis self-consistently, the procedure of JET equilibrium reconstruction was updated to include the profiles of ion temperature and toroidal rotation, which are determined based on the measurement data in experiments. With the new procedure and MINERVA-DI, it was identified that the stability analysis including the rotation effect can explain the ELM trigger condition in JET with ITER like wall (JET-ILW), though the stability in JET with carbon wall (JET-C) is hardly affected by rotation. The key difference is that the rotation shear in JET-ILW plasmas analyzed in this study is larger than that in JET-C ones, the shear which enhances the dynamic pressure destabilizing a peeling-ballooning mode. In addition, the increase of the toroidal mode number of the unstable MHD mode determining the ELM trigger condition is also important when the plasma density is high in JET-ILW. Though such modes with high toroidal mode number are strongly stabilized by the ion diamagnetic drift effect, it was found that plasma rotation can sometimes overcome this stabilizing effect and destabilizes the peeling-ballooning modes in JET-ILW.
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9.
  • Akiyama, Kazunori, et al. (författare)
  • First Sagittarius A* Event Horizon Telescope Results. II. EHT and Multiwavelength Observations, Data Processing, and Calibration
  • 2022
  • Ingår i: Astrophysical Journal Letters. - 2041-8213 .- 2041-8205. ; 930:2
  • Tidskriftsartikel (refereegranskat)abstract
    • We present Event Horizon Telescope (EHT) 1.3 mm measurements of the radio source located at the position of the supermassive black hole Sagittarius A* (Sgr A*), collected during the 2017 April 5-11 campaign. The observations were carried out with eight facilities at six locations across the globe. Novel calibration methods are employed to account for Sgr A*'s flux variability. The majority of the 1.3 mm emission arises from horizon scales, where intrinsic structural source variability is detected on timescales of minutes to hours. The effects of interstellar scattering on the image and its variability are found to be subdominant to intrinsic source structure. The calibrated visibility amplitudes, particularly the locations of the visibility minima, are broadly consistent with a blurred ring with a diameter of similar to 50 mu as, as determined in later works in this series. Contemporaneous multiwavelength monitoring of Sgr A* was performed at 22, 43, and 86 GHz and at near-infrared and X-ray wavelengths. Several X-ray flares from Sgr A* are detected by Chandra, one at low significance jointly with Swift on 2017 April 7 and the other at higher significance jointly with NuSTAR on 2017 April 11. The brighter April 11 flare is not observed simultaneously by the EHT but is followed by a significant increase in millimeter flux variability immediately after the X-ray outburst, indicating a likely connection in the emission physics near the event horizon. We compare Sgr A*'s broadband flux during the EHT campaign to its historical spectral energy distribution and find that both the quiescent emission and flare emission are consistent with its long-term behavior.
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10.
  • Akiyama, Kazunori, et al. (författare)
  • First Sagittarius A* Event Horizon Telescope Results. IV. Variability, Morphology, and Black Hole Mass
  • 2022
  • Ingår i: Astrophysical Journal Letters. - 2041-8213 .- 2041-8205. ; 930:2
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper we quantify the temporal variability and image morphology of the horizon-scale emission from Sgr A*, as observed by the EHT in 2017 April at a wavelength of 1.3 mm. We find that the Sgr A* data exhibit variability that exceeds what can be explained by the uncertainties in the data or by the effects of interstellar scattering. The magnitude of this variability can be a substantial fraction of the correlated flux density, reaching similar to 100% on some baselines. Through an exploration of simple geometric source models, we demonstrate that ring-like morphologies provide better fits to the Sgr A* data than do other morphologies with comparable complexity. We develop two strategies for fitting static geometric ring models to the time-variable Sgr A* data; one strategy fits models to short segments of data over which the source is static and averages these independent fits, while the other fits models to the full data set using a parametric model for the structural variability power spectrum around the average source structure. Both geometric modeling and image-domain feature extraction techniques determine the ring diameter to be 51.8 +/- 2.3 mu as (68% credible intervals), with the ring thickness constrained to have an FWHM between similar to 30% and 50% of the ring diameter. To bring the diameter measurements to a common physical scale, we calibrate them using synthetic data generated from GRMHD simulations. This calibration constrains the angular size of the gravitational radius to be 4.8(-0.7)(+1.4) mu as, which we combine with an independent distance measurement from maser parallaxes to determine the mass of Sgr A* to be 4.0(-0.6)(+1.1) x 10(6) M-circle dot.
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