Deuterium adsorption on (and desorption from) SiC(0001)-(3×3), (√3×√3)R30°, (6√3×6√3)R30° and quasi-free standing graphene obtained by hydrogen intercalation

International audienceWe present a comparative high-resolution electron energy-loss spectroscopy study on the interaction of atomic hydrogen and deuterium with various reconstructions of SiC(0 0 0 1). We first show that on both the (3 × 3) and reconstructions, deuterium atoms only bind to silicon atoms, thereby confirming the silicon-rich appellation of these reconstructions. Deuterium passivation of the (3 × 3) is only reversible when exposed to atomic deuterium at a surface temperature of 700 K since tri- and dideuterides, necessary precursors for silicon etching, are not stable. On the other hand, we show that the deuteration of the is always reversible because precursors to silicon etching are scarce on the surface. Then, we demonstrate that hydrogen (deuterium) adsorption at 300 K on both the (buffer-layer) and the quasi-free-standing graphene occurs on carbon atoms justifying their carbon-rich appellation. Comparison of the deuterium binding in the intercalation layer of quasi-free-standing graphene with the deuterated surface provides some indication on the bonding structure at the substrate intercalation layer. Finally, by measuring C-H (C-D) vibrational frequencies and hydrogen (deuterium) desorption temperatures we suggest that partial sp2-to-sp3 rehybridization occurs for the carbon atoms of the buffer-layer because of the corrugation related to covalent bonding to the SiC substrate. In contrast, on quasi-free-standing graphene hydrogen (deuterium) atoms adsorb similarly to what is observed on graphite, i.e. without preferential sticking related to the underlying SiC substrate

Production of negative ions on graphite surface in H₂/D₂ plasmas: experiments and SRIM calculations

In previous works, surface-produced negative-ion distribution-functions have been measured in H2 and D2 plasmas using graphite surfaces (highly oriented pyrolitic graphite). In the present paper, we use the srim software to interpret the measured negative-ion distribution-functions. For this purpose, the distribution-functions of backscattered and sputtered atoms arising due to the impact of hydrogen ions on a-CH and a-CD surfaces are calculated. The srim calculations confirm the experimental deduction that backscattering and sputtering are the mechanisms of the origin of the creation of negative ions at the surface. It is shown that the srim calculations compare well with the experiments regarding the maximum energy of the negative ions and reproduce the experimentally observed isotopic effect. A discrepancy between calculations and measurements is found concerning the yields for backscattering and sputtering. An explanation is proposed based on a study of the emitted-particle angular-distributions as calculated by srim

Dynamic fuel retention in tokamak wall materials: An in situ laboratory study of deuterium release from polycrystalline tungsten at room temperature

International audienceRetention of deuterium ion implanted in polycrystalline tungsten samples is studied in situ in an ultra-high vacuum apparatus equipped with a low-flux ion source and a high sensitivity thermo-desorption setup. Retention as a function of ion fluence was measured in the 10^17 -10^21 D+/m^2 range. By combining this new fluence range with the literature in situ experimental data, we evidence the existence of a retention = fluence^ 0.645±0.025 relationship which describes deuterium retention behavior on polycrystalline tungsten on 8 orders of magnitude of fluence. Evolution of deuterium retention as a function of the sample storage time in vacuum at room temperature was followed. A loss of 50% of the retained deuterium is observed when the storage time is increased from 2 h to 135 h. The role of the surface and of natural bulk defects on the deuterium retention/release in polycrystalline tungsten is discussed in light of the behavior of the single desorption peak obtained with Temperature Programmed Desorption

First-Principles Studies of Hydrogenated Si(111)--7×\times7

The relaxed geometries and electronic properties of the hydrogenated phases of the Si(111)-7$\times$7 surface are studied using first-principles molecular dynamics. A monohydride phase, with one H per dangling bond adsorbed on the bare surface is found to be energetically favorable. Another phase where 43 hydrogens saturate the dangling bonds created by the removal of the adatoms from the clean surface is found to be nearly equivalent energetically. Experimental STM and differential reflectance characteristics of the hydrogenated surfaces agree well with the calculated features.Comment: REVTEX manuscript with 3 postscript figures, all included in uu file. Also available at http://www.phy.ohiou.edu/~ulloa/ulloa.htm

De novo TBR1 variants cause a neurocognitive phenotype with ID and autistic traits:report of 25 new individuals and review of the literature

TBR1, a T-box transcription factor expressed in the cerebral cortex, regulates the expression of several candidate genes for autism spectrum disorders (ASD). Although TBR1 has been reported as a high-confidence risk gene for ASD and intellectual disability (ID) in functional and clinical reports since 2011, TBR1 has only recently been recorded as a human disease gene in the OMIM database. Currently, the neurodevelopmental disorders and structural brain anomalies associated with TBR1 variants are not well characterized. Through international data sharing, we collected data from 25 unreported individuals and compared them with data from the literature. We evaluated structural brain anomalies in seven individuals by analysis of MRI images, and compared these with anomalies observed in TBR1 mutant mice. The phenotype included ID in all individuals, associated to autistic traits in 76% of them. No recognizable facial phenotype could be identified. MRI analysis revealed a reduction of the anterior commissure and suggested new features including dysplastic hippocampus and subtle neocortical dysgenesis. This report supports the role of TBR1 in ID associated with autistic traits and suggests new structural brain malformations in humans. We hope this work will help geneticists to interpret TBR1 variants and diagnose ASD probands

Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.Molecular Psychiatry advance online publication, 31 May 2016; doi:10.1038/mp.2016.84

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Reversible hydrogenation of deuterium-intercalated quasi-free-standing graphene on SiC(0001)

Hydrogenation of deuterium-intercalated quasi-free-standing monolayer graphene on SiC(0001) is obtained and studied with low-energy electron diffraction and high-resolution electron energy loss spectroscopy. While the carbon honeycomb structure remains intact, it is shown that a significant band gap opens in the hydrogenated material. Vibrational spectroscopy evidences for hydrogen chemisorption on the quasi-free-standing graphene is provided and its thermal stability is studied