Simulating Charged Defects in Silicon Dangling Bond Logic Systems to Evaluate Logic Robustness

Recent research interest in emerging logic systems based on quantum dots has been sparked by the experimental demonstration of nanometer-scale logic devices composed of atomically sized quantum dots made of silicon dangling bonds (SiDBs), along with the availability of SiQAD, a computer-aided design tool designed for this technology. Latest design automation frameworks have enabled the synthesis of SiDB circuits that reach the size of $32\times10^3\,\text{nm}^{2}$ -- orders of magnitude more complex than their hand-designed counterparts. However, current SiDB simulation engines do not take defects into account, which is important to consider for these sizable systems. This work proposes a formulation for incorporating fixed-charge simulation into established ground state models to cover an important class of defects that has a non-negligible effect on nearby SiDBs at the $10\,\text{nm}$ scale and beyond. The formulation is validated by implementing it into SiQAD's simulation engine and computationally reproducing experiments on multiple defect types, revealing a high level of accuracy. The new capability is applied towards studying the tolerance of several established logic gates against the introduction of a single nearby defect to establish the corresponding minimum required clearance. These findings are compared against existing metrics to form a foundation for logic robustness studies.Comment: 7 pages, 5 figures, 2 table

Knockdown of interferon-induced transmembrane protein 1 (IFITM1) inhibits proliferation, migration, and invasion of glioma cells

Interferon-induced transmembrane protein 1 (IFITM1) has recently been identified as a new molecular marker in human colorectal cancer. However, its role in glioma carcinogenesis is not known. In this study, we demonstrated that suppression of IFITM1 expression significantly inhibited proliferation of glioma cells in a time-dependent manner. The growth inhibitory effect was mediated by cell cycle arrest. Furthermore, IFITM1 knockdown significantly inhibited migration and invasion of glioma cells, which could be attributed to decreased expression and enzymatic activity of matrix metalloproteinase 9. Taken together, these results suggest that IFITM1 is a potential therapeutic target for gliomas

Inhibition of neuroinflammation in BV2 microglia by the biflavonoid kolaviron is dependent on the Nrf2/ARE antioxidant protective mechanism

Kolaviron is a mixture of bioflavonoids found in the nut of the West African edible seed Garcinia kola, and it has been reported to exhibit a wide range of pharmacological activities. In this study, we investigated the effects of kolaviron in neuroinflammation. The effects of kolaviron on the expression of nitric oxide/inducible nitric oxide synthase (iNOS), prostaglandin E2 (PGE2)/cyclooxygenase-2, cellular reactive oxygen species (ROS) and the pro-inflammatory cytokines were examined in lipopolysaccharide (LPS)-stimulated BV2 microglial cells. Molecular mechanisms of the effects of kolaviron on NF-B and Nrf2/ARE signalling pathways were analysed by immunoblotting, binding assay, and reporter assay. RNA interference was used to investigate the role of Nrf2 in the anti-inflammatory effect of kolaviron. Neuroprotective effect of kolaviron was assessed in a BV2 microglia/HT22 hippocampal neuron co-culture. Kolaviron inhibited the protein levels of NO/iNOS, PGE2/COX-2, cellular ROS and the proinflammatory cytokines (TNFα and IL-6) in LPS-stimulated microglia. Further mechanistic studies showed that kolaviron inhibited neuroinflammation by inhibiting IB/NF-B signalling pathway in LPS-activated BV2 microglia. Kolaviron produced antioxidant effect in BV2 microglia by increasing HO-1 via the Nrf2/ antioxidant response element (ARE) pathway. RNAi experiments revealed that Nrf2 is need for the anti-inflammatory effect of kolaviron. Kolaviron protected HT22 neurons from neuroinflammation-induced toxicity. Kolaviron inhibits neuroinflammation through Nrf2-dependent mechanisms. This compound may therefore be beneficial in neuroinflammation-related neurodegenerative disorders

Genomic organisation analysis of novel immunoglobulin-like transcripts in Atlantic salmon (Salmo salar) reveals a tightly clustered and multigene family

Copyright 2011 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

The Characterization of Twenty Sequenced Human Genomes

We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways

Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections

Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5′UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers

The 3′ UTR Variants in the GRP78 Are Not Associated with Overall Survival in Resectable Hepatocellular Carcinoma

Background: Elevated glucose-regulated protein 78 (GRP78) levels in tissues have been known to be related with poor prognosis in hepatocellular carcinoma (HCC) patients. Though the variants in the 3′ untranslated region (UTR) of GRP78 gene were not associated with HCC risk, we wonder whether these polymorphisms affect survival of HCC patients. Methodology/Principal Findings: Blood samples of HCC patients were maintained in our specimen bank between 1996 to 2003. DNA from 576 unrelated and resectable patients with HCC was typed for rs16927997 (T>C), rs1140763 (T>C) and rs12009 (T>C) by TaqMan assays. The Kaplan-Meier method and log-rank test were used to estimate overall survival. Linkage disequilibrium (LD) analysis identified a total of 3 haplotypes and 6 diplotypes in this region. The distribution of haplotype was not related to the clinical characteristics. Univariate analysis showed that the allele, genotype, haplotype and diplotype did not effect the survival. None of the clinical features show a significant association (P correced>0.05) with overall patient outcome in multiple comparisons. Conclusions/Significance: There is no noteworthy influence of 3′ UTR variants in the GRP78 on prognosis of resectable HCC in the Chinese population. © 2011 Zhu et al.published_or_final_versio