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Supplemental material, sj-pdf-1-aor-10.1177_0003489421995283 for Association of Social Determinants of Health with Time to Diagnosis and Treatment Outcomes in Idiopathic Subglottic Stenosis by Jaclyn Lee, Li-Ching Huang, Lynn D. Berry, Catherine Anderson, Milan R. Amin, Michael S. Benninger, Joel H. Blumin, Jonathan M. Bock, Paul C. Bryson, Paul F. Castellanos, Sheau-Chiann Chen, Matthew S. Clary, Seth M. Cohen, Brianna K. Crawley, Seth H. Dailey, James J. Daniero, Alessandro de. Alarcon, Donald T. Donovan, Eric S. Edell, Dale C. Ekbom, Daniel S. Fink, Ramon A. Franco, C. Gaelyn Garrett, Elizabeth A. Guardiani, Alexander T. Hillel, Henry T. Hoffman, Norman D. Hogikyan, Rebecca J. Howell, Lena K. Hussain, Michael M. Johns, Jan L. Kasperbauer, Sid M. Khosla, Cheryl Kinnard, Robbi A. Kupfer, Alexander J. Langerman, Robert J. Lentz, Robert R. Lorenz, David G. Lott, Anne S. Lowery, Samir S. Makani, Fabien Maldonado, Kyle Mannion, Laura Matrka, Andrew J. McWhorter, Albert L. Merati, Matthew Mori, James L. Netterville, Karla O’Dell, Julina Ongkasuwan, Gregory N. Postma, Lindsay S. Reder, Sarah L. Rohde, Brent E. Richardson, Otis B. Rickman, Clark A. Rosen, Michael J. Rutter, Guri S. Sandhu, Joshua S. Schindler, G. Todd Schneider, Rupali N. Shah, Andrew G. Sikora, Robert J. Sinard, Marshall E. Smith, Libby J. Smith, Ahmed M.S. Soliman, Sigríður Sveinsdóttir, Douglas J. Van Daele, David Veivers, Mepi FRACS, Sunil P. Verma, Paul M. Weinberger, Philip A. Weissbrod, Christopher T. Wootten, Yu Shyr, David O. Francis and Alexander Gelbard in Annals of Otology, Rhinology & Laryngology

Supplemental Material, TS2_TPX_10.11770192623318823150 for Trends in Liver and Skin Tumor Prevalence in Brown Bullhead (Ameiurus nebulosus) from the Anacostia River, Washington, DC, and Nearby Waters by Alfred E. Pinkney, John C. Harshbarger, Michael A. Rutter, and Peter C. Sakaris in Toxicologic Pathology

Supplemental Material, TS3_TPX_10.11770192623318823150 for Trends in Liver and Skin Tumor Prevalence in Brown Bullhead (Ameiurus nebulosus) from the Anacostia River, Washington, DC, and Nearby Waters by Alfred E. Pinkney, John C. Harshbarger, Michael A. Rutter, and Peter C. Sakaris in Toxicologic Pathology

Supplemental Material, TS1_TPX_10.11770192623318823150 for Trends in Liver and Skin Tumor Prevalence in Brown Bullhead (Ameiurus nebulosus) from the Anacostia River, Washington, DC, and Nearby Waters by Alfred E. Pinkney, John C. Harshbarger, Michael A. Rutter, and Peter C. Sakaris in Toxicologic Pathology

Supplemental Material, TS4_TPX_10.11770192623318823150 for Trends in Liver and Skin Tumor Prevalence in Brown Bullhead (Ameiurus nebulosus) from the Anacostia River, Washington, DC, and Nearby Waters by Alfred E. Pinkney, John C. Harshbarger, Michael A. Rutter, and Peter C. Sakaris in Toxicologic Pathology

To identify the broader autism phenotype (BAP), the Family History Interview subject and informant versions and an observational tool (Impression of Interviewee), were developed. This study investigated whether the instruments differentiated between parents of children with autism, and parents of children with Down syndrome (DS). The BAP scores of parents of 28 multiplex autism families were compared with parents from, 32 DS families. The BAP measures provided good group differentiation but when considered together, the subject interview did not improve group differentiation. The differentiation was better for fathers than mothers. The measures do carry an important degree of validity; whether they can differentiate the BAP from other social disorders should be tested.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD 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 the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the 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. In 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 the risk for ASD but their individual effects are modest.

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.

Plane wave density functional theory codes generally assume periodicity in all three dimensions. This causes difficulties when studying charged systems, for instance energies per unit cell become infinite, and, even after being renormalised by the introduction of a uniform neutralising background, are very slow to converge with cell size. The periodicity introduces spurious electric fields which decay slowly with cell size and which also slow the convergence of other properties relating to the ground state charge density. This paper presents a simple self-consistent technique for producing rapid convergence of both energies and charge distribution in the particular geometry of 2D periodicity, as used for studying surfaces., 14 pages, 7 figures

When a system which contains a dipole, and whose dimensionality is less than three, is studied in a code which imposes periodic boundary conditions in all three dimensions, an artificial electric field arises which keeps the potential periodic. This has an impact on the total energy of the system, and on any other attribute which would respond to an electric field. Simple corrections are known for 0D systems embedded in a cubic geometry, and 2D slab systems. This paper shows how the 0D result can be extended to tetragonal geometries, and that for a particular $c/a$ ratio the correction is zero. It also considers an exponential error term absent from the usual consideration of 2D slab geometries, and discusses an empirical form for this., 10 pages. Figure 3 corrected in this version

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used Castep electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including Castep, Onetep and Vasp, as well as the widely-used ‘Gaussian cube’ file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from Castep’s binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats usable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of Castep. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is avail- able under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read Castep’s .check files, so it will have utility in other projects., This work was supported by EPSRC grant numbers EP/J017639/1, EP/P003532/1 and EP/M011925/1.