EHAP-ORAM: Efficient Hardware-Assisted Persistent ORAM System for Non-volatile Memory

Oblivious RAM (ORAM) protected access pattern is essential for secure NVM. In the ORAM system, data and PosMap metadata are maps in pairs to perform secure access. Therefore, we focus on the problem of crash consistency in the ORAM system. Unfortunately, using traditional software-based support for ORAM system crash consistency is not only expensive, it can also lead to information leaks. At present, there is no relevant research on the specific crash consistency mechanism supporting the ORAM system. To support crash consistency without damaging ORAM system security and compromising the performance, we propose EHAP-ORAM. Firstly, we analyze the access steps of basic ORAM to obtain the basic requirements to support the ORAM system crash consistency. Secondly, improve the ORAM controller. Thirdly, for the improved hardware system, we propose several persistence protocols supporting the ORAM system crash consistency. Finally, we compared our persistent ORAM with the system without crash consistency support, non-recursive and recursive EHAP-ORAM only incurs 3.36% and 3.65% performance overhead. The results show that EHAP-ORAM not only supports effective crash consistency with minimal performance and hardware overhead but also is friendly to NVM lifetime

RDMAS: a web server for RNA deleterious mutation analysis

BACKGROUND: The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness. RESULTS: The RDMAS web server we describe here is an online tool for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. Several structure comparison methods have been integrated; sub-optimal structures predicted can be optionally involved to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate quick analysis. CONCLUSION: RDMAS can be used to explore the structure alterations which cause mutations pathogenic, and to predict deleterious mutations which may help to determine the functionally critical regions. RDMAS is freely accessed via

H-ORAM: A Cacheable ORAM Interface for Efficient I/O Accesses

Oblivious RAM (ORAM) is an effective security primitive to prevent access pattern leakage. By adding redundant memory accesses, ORAM prevents attackers from revealing the patterns in the access sequences. However, ORAM tends to introduce a huge degradation on the performance. With growing address space to be protected, ORAM has to store the majority of data in the lower level storage, which further degrades the system performance. In this paper, we propose Hybrid ORAM (H-ORAM), a novel ORAM primitive to address large performance degradation when overflowing the user data to storage. H-ORAM consists of a batch scheduling scheme for enhancing the memory bandwidth usage, and a novel ORAM interface that returns data without waiting for the I/O access each time. We evaluate H-ORAM on a real machine implementation. The experimental results show that that H-ORAM outperforms the state-of-the-art Path ORAM by 19.8x for a small data set and 22.9x for a large data set

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyze 50 complex traits and diseases using ∼7 million common single-nucleotide polymorphisms (SNPs) and 96 annotations. SBayesRC improves prediction accuracy by 14% in European ancestry and up to 34% in cross-ancestry prediction compared to the baseline method SBayesR, which does not use annotations, and outperforms other methods, including LDpred2, LDpred-funct, MegaPRS, PolyPred-S and PRS-CSx. Investigation of factors affecting prediction accuracy identifies a significant interaction between SNP density and annotation information, suggesting whole-genome sequence variants with annotations may further improve prediction. Functional partitioning analysis highlights a major contribution of evolutionary constrained regions to prediction accuracy and the largest per-SNP contribution from nonsynonymous SNPs

Multi-ancestry genome-wide association study accounting for gene-psychosocial factor interactions identifies novel loci for blood pressure traits

Psychological and social factors are known to influence blood pressure (BP) and risk of hypertension and associated cardiovascular diseases. To identify novel BP loci, we carried out genome-wide association meta-analyses of systolic, diastolic, pulse, and mean arterial BP, taking into account the interaction effects of genetic variants with three psychosocial factors: depressive symptoms, anxiety symptoms, and social support. Analyses were performed using a two-stage design in a sample of up to 128,894 adults from five ancestry groups. In the combined meta-analyses of stages 1 and 2, we identified 59 loci (p value < 5e−8), including nine novel BP loci. The novel associations were observed mostly with pulse pressure, with fewer observed with mean arterial pressure. Five novel loci were identified in African ancestry, and all but one showed patterns of interaction with at least one psychosocial factor. Functional annotation of the novel loci supports a major role for genes implicated in the immune response (PLCL2), synaptic function and neurotransmission (LIN7A and PFIA2), as well as genes previously implicated in neuropsychiatric or stress-related disorders (FSTL5 and CHODL). These findings underscore the importance of considering psychological and social factors in gene discovery for BP, especially in non-European populations

Molecular Electrocatalytic Processes in Carbon Nanopipettes

Conductive nanopipettes have been recognized as powerful multifunctional platforms for electrochemical sensing applications in confined spaces. However, the electron-transfer processes of many biological analytes (i.e., enzymes or proteins) are slow and coupled with chemical reactions, which have not been well elucidated in conductive nanopipettes. In this Letter, both experimental and simulation methods are used to study electron-transfer processes coupled to chemical reactions (EC mechanism) in carbon nanopipettes (CNPs). It is demonstrated that the electroactive species can serve as redox mediator to help oxidize and reduce the nonelectroactive analytes of interest in the solution and produce noticeable catalytic current signals. Besides, glutathione was directly measured by using ferrocenemethanol as the redox mediator in the CNPs. The elucidated EC processes in CNPs would offer a new opportunity to measure nonelectroactive analytes in biological fields

Current Advances in the Biosynthesis, Metabolism, and Transcriptional Regulation of α-Tomatine in Tomato

Steroid glycoalkaloids (SGAs) are a class of cholesterol-derived metabolites commonly found in the Solanaceae plants. α-Tomatine, a well-known bitter-tasting compound, is the major SGA in tomato, accumulating extensively in all plant tissues, particularly in the leaves and immature green fruits. α-Tomatine exhibits diverse biological activities that contribute to plant defense against pathogens and herbivores, as well as conferring certain medicinal benefits for human health. This review summarizes the current knowledge on α-tomatine, including its molecular chemical structure, physical and chemical properties, biosynthetic and metabolic pathways, and transcriptional regulatory mechanisms. Moreover, potential future research directions and applications of α-tomatine are also discussed