Radiation-doped SiC*/Si heterostructure formation and defects evolution

The authors consider heterostructures of silicon carbide obtained during endotaxy on silicon substrates. The question is raised in connection with the description of the endotaxy process itself at the structural level. Authors focus on the technological aspects of the formation of a stable β-SiC/Si heterostructure by endotaxy in relation to the evolution of point defects of various nature and their probable association models with the participation of a radionuclide impurity at the micro-alloying level: 1) the growth of the SiC*/Si thin layer with C-14 atoms in the doping process; 2) physical properties of defects formation; 3) some interface between properties and efficiency.

Families of Generalized Quasisymmetry Models: A ϕ-Divergence Approach

The quasisymmetry (QS) model for square contingency tables is revisited, highlighting properties and features on the basis of its alternative definitions. More parsimonious QS-type models, such as the ordinal QS model for ordinal classification variables and models based on association models (AMs) with homogeneous row and column scores, are discussed. All these models are linked to the local odds ratios (LOR). QS-type models and AMs were extended in the literature for generalized odds ratios other than LOR. Furthermore, in an information-theoretic context, they are expressed as distance models from a parsimonious reference model (the complete symmetry for QS and the independence for AMs), while they satisfy closeness properties with respect to Kullback–Leibler (KL) divergence. Replacing the KL by ϕ divergence, flexible classes of QS-type models for LOR, AMs for LOR, and AMs for generalized odds ratios were generated. However, special QS-type models that are based on homogeneous AMs for LOR have not been extended to ϕ-divergence-based classes so far, or the QS-type models for generalized odds ratios. In this work, we develop these missing extensions, and discuss QS-type models and their generalizations in depth. These flexible families enrich the modeling options, leading to models of better fit and sound interpretation, as illustrated by representative examples.

Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies

Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power and therefore often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease association models. For sequencing-based genetic studies, because all variants included in the association analyses have passed sequencing-related quality control measures, this conventional approach treats every variant as equal and ignores the substantial differences still remaining in variant qualities and characteristics such as genotype quality scores, alternative allele fractions (fraction of reads supporting alternative allele at a variant position) and sequencing depths. In the Alzheimer’s Disease Sequencing Project (ADSP) exome dataset of 9,904 cases and controls, we discovered hidden variant-level differences between sample batches of three sequencing centers and two exome capture kits. Although sequencing centers were included as a covariate in our association models, we observed differences at the variant level in genotype quality and alternative allele fraction between samples processed by different exome capture kits that significantly impacted both the confidence of variant detection and the identification of disease-associated variants. Furthermore, we found that a subset of top disease-risk variants came exclusively from samples processed by one exome capture kit that was more effective at capturing the alternative alleles compared to the other kit. Our findings highlight the importance of additional variant-level quality control for large sequencing-based genetic studies. More importantly, we demonstrate that automatically filtering out variants with batch differences may lead to false negatives if the batch discordances come largely from quality differences and if the batch-specific variants have better quality.

Impact of Variant-level Batch Effects on Identification of Genetic Risk Factors in Large Sequencing Studies

Background: Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power but often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease association models. For sequencing-based genetic studies, because all variants included in the association analyses have passed quality control measures, this conventional approach treats every variant as equal and ignores the substantial differences still remaining in variant qualities and characteristics such as genotype quality scores, alternative allele fractions (fraction of reads supporting alternative allele at a variant position) and sequencing depths. Results: In the Alzheimer’s Disease Sequencing Project (ADSP) exome dataset of 9,904 cases and controls, we discovered hidden variant-level differences between sample batches of three sequencing centers and two exome capture kits. Although sequencing centers were included as a covariate in our association models, we observed differences at the variant level in genotype quality and alternative allele fraction between samples processed by different exome capture kits that significantly impacted both the confidence of variant detection and the identification of disease-associated variants. Furthermore, we found that the association signals of a subset of top disease risk variants came exclusively from samples processed by one exome capture kit that was more effective at capturing the alternative alleles compared to the other kit. Conclusions: Our findings highlight the importance of additional variant-level quality control for large sequencing-based genetic studies. More importantly, we demonstrate that automatically filtering out variants with batch differences may lead to false negatives if the batch discordance came largely from quality differences and if the variants from one batch had better quality scores.

Inference for Ordinal Log-Linear Models Based on Algebraic Statistics

Tools of algebraic statistics combined with MCMC algorithms have been used in contingency table analysis for model selection and model fit testing of log-linear models. However, this approach has not been considered so far for association models, which are special log-linear models for tables with ordinal classification variables. The simplest association model for two-way tables, the uniform (U) association model, has just one parameter more than the independence model and is applicable when both classification variables are ordinal. Less parsimonious are the row (R) and column (C) effect association models, appropriate when at least one of the classification variables is ordinal. Association models have been extended for multidimensional contingency tables as well. Here, we adjust algebraic methods for association models analysis and investigate their eligibility, focusing mainly on two-way tables. They are implemented in the statistical software R and illustrated on real data tables. Finally the algebraic model fit and selection procedure is assessed and compared to the asymptotic approach in terms of a simulation study.

On Secure Simple Pairing in Bluetooth Standard v5.0-Part I: Authenticated Link Key Security and Its Home Automation and Entertainment Applications

Bluetooth is an important technical standard for short-range and low-power wireless communication. The home automation and entertainment (HAE) systems often make use of Bluetooth technology to link different Bluetooth devices and form Bluetooth networks. The security concerns of the HAE systems are raised due to massive deployment of the Bluetooth devices. The Bluetooth standard mainly depends on the secure simple pairing (SSP) solution to protect the Bluetooth devices. Hence, we investigate the SSP solution according to the Bluetooth standard v5.0. The contributions are threefold. (1) A formal security model is proposed to evaluate SSP’s association models and authenticated link key. (2) We formally analyze two SSP protocols and present the security requirements for basic cryptographic modules in these SSP protocols. (3) We discuss the typical SSP applications in the HAE systems. Our results are useful to not only evaluating and designing the SSP protocols but also enhancing the security of the HAE systems in which the Bluetooth access is available.