A Fast Potential and Self-Gravity Solver for Non-Axisymmetric Disks

Disk self-gravity could play an important role in the dynamic evolution of interaction between disks and embedded protoplanets. We have developed a fast and accurate solver to calculate the disk potential and disk self-gravity forces for disk systems on a uniform polar grid. Our method follows closely the method given by Chan et al. (2006), in which an FFT in the azimuthal direction is performed and a direct integral approach in the frequency domain in the radial direction is implemented on a uniform polar grid. This method can be very effective for disks with vertical structures that depend only on the disk radius, achieving the same computational efficiency as for zero-thickness disks. We describe how to parallelize the solver efficiently on distributed parallel computers. We propose a mode-cutoff procedure to reduce the parallel communication cost and achieve nearly linear scalability for a large number of processors. For comparison, we have also developed a particle-based fast tree-code to calculate the self-gravity of the disk system with vertical structure. The numerical results show that our direct integral method is at least two order of magnitudes faster than our optimized tree-code approach.Comment: 8 figures, accepted to ApJ

Creatine transporter defect diagnosed by proton NMR spectroscopy in males with intellectual disability.

Creatine deficiency syndrome due to mutations in X-linked SLC6A8 gene results in nonspecific intellectual disability (ID). Diagnosis cannot be established on clinical grounds and is often based on the assessment of brain creatine levels by magnetic resonance spectroscopy (MRS). Considering high costs of MRS and necessity of sedation, this technique cannot be used as a first level-screening test. Likewise, gene test analysis is time consuming and not easily accessible to all laboratories. In this article feasibility of urine analysis (creatine/creatinine (Cr/Crn) ratio) performed by nuclear magnetic resonance (NMR) as a first level-screening test is explored. Before running a systematic selection of cases a preliminary study for further molecular analysis is shown. NMR urine spectra (n = 1,347) of male patients with an ID without a clinically recognizable syndrome were measured. On the basis of abnormal Cr/Crn ratio, three patients with the highest values were selected for molecular analysis. A confirmatory second urine test was positive in two patients and diagnosis was further confirmed by a decreased brain creatine level and by SLC6A8 gene analysis. A de novo mutation was identified in one. Another patient inherited a novel mutation from the mother who also has a mild ID. A repeat urine test was negative in the third patient and accordingly creatine level in the brain and SLC6A8 gene analysis both gave a normal result. We conclude that Cr/Crn ratio measured by NMR for male patients represents a rapid and useful first level screening test preceding molecular analysis

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism

<p>Abstract</p> <p>Background</p> <p>Autism comprises a spectrum of behavioral and cognitive disturbances of childhood development and is known to be highly heritable. Although numerous approaches have been used to identify genes implicated in the development of autism, less than 10% of autism cases have been attributed to single gene disorders.</p> <p>Methods</p> <p>We describe the use of high-resolution genome-wide tilepath microarrays and comparative genomic hybridization to identify copy number variants within 119 probands from multiplex autism families. We next carried out DNA methylation analysis by bisulfite sequencing in a proband and his family, expanding this analysis to methylation analysis of peripheral blood and temporal cortex DNA of autism cases and matched controls from independent datasets. We also assessed oxytocin receptor (OXTR) gene expression within the temporal cortex tissue by quantitative real-time polymerase chain reaction (PCR).</p> <p>Results</p> <p>Our analysis revealed a genomic deletion containing the oxytocin receptor gene, <it>OXTR </it>(MIM accession no.: 167055), previously implicated in autism, was present in an autism proband and his mother who exhibits symptoms of obsessive-compulsive disorder. The proband's affected sibling did not harbor this deletion but instead may exhibit epigenetic misregulation of this gene through aberrant gene silencing by DNA methylation. Further DNA methylation analysis of the CpG island known to regulate <it>OXTR </it>expression identified several CpG dinucleotides that show independent statistically significant increases in the DNA methylation status in the peripheral blood cells and temporal cortex in independent datasets of individuals with autism as compared to control samples. Associated with the increase in methylation of these CpG dinucleotides is our finding that <it>OXTR </it>mRNA showed decreased expression in the temporal cortex tissue of autism cases matched for age and sex compared to controls.</p> <p>Conclusion</p> <p>Together, these data provide further evidence for the role of OXTR and the oxytocin signaling pathway in the etiology of autism and, for the first time, implicate the epigenetic regulation of <it>OXTR </it>in the development of the disorder.</p> <p>See the related commentary by Gurrieri and Neri: <url>http://www.biomedcentral.com/1741-7015/7/63</url></p

Stable LU factorization of H-matrices

AbstractResults are given concerning the LU factorization of H-matrices, and Gaussian elimination with column-diagonal-dominant pivoting is shown to be applicable to H-matrices. This algorithm, which uses a symmetric permutation to exchange the most diagonally dominant column of the unreduced submatrix into the pivotal position, is shown to be numerically stable by deriving an upper bound on the growth factor associated with the backward error analysis for Gaussian elimination