Fully Composable and Adequate Verified Compilation with Direct Refinements between Open Modules (Technical Report)

Verified compilation of open modules (i.e., modules whose functionality depends on other modules) provides a foundation for end-to-end verification of modular programs ubiquitous in contemporary software. However, despite intensive investigation in this topic for decades, the proposed approaches are still difficult to use in practice as they rely on assumptions about the internal working of compilers which make it difficult for external users to apply the verification results. We propose an approach to verified compositional compilation without such assumptions in the setting of verifying compilation of heterogeneous modules written in first-order languages supporting global memory and pointers. Our approach is based on the memory model of CompCert and a new discovery that a Kripke relation with a notion of memory protection can serve as a uniform and composable semantic interface for the compiler passes. By absorbing the rely-guarantee conditions on memory evolution for all compiler passes into this Kripke Memory Relation and by piggybacking requirements on compiler optimizations onto it, we get compositional correctness theorems for realistic optimizing compilers as refinements that directly relate native semantics of open modules and that are ignorant of intermediate compilation processes. Such direct refinements support all the compositionality and adequacy properties essential for verified compilation of open modules. We have applied this approach to the full compilation chain of CompCert with its Clight source language and demonstrated that our compiler correctness theorem is open to composition and intuitive to use with reduced verification complexity through end-to-end verification of non-trivial heterogeneous modules that may freely invoke each other (e.g., mutually recursively)

Cryopreservation in Ophthalmology

Amniotic membranes (AMs) and corneas are critical materials in ocular surface reconstruction. AM has specific structures (e.g., basement and two types of cells with stemness characteristics: amniotic epithelial cells and amniotic mesenchymal cells), which contribute to its attractive physical and biological properties that make it fundamental to clinical application. The corneal endothelial cell is a vital part of the cornea, which can influence postoperative vision directly. However, widespread use of fresh AM and cornea has been limited due to their short use span and safety concerns. To overcome these concerns, different preservation methods have been introduced. Cryopreservation is distinguished from many preservation methods for its attractive advantages of prolonged use span, optimally retained tissue structure, and minimized infection risk. This review will focus on recent advances of cryopreserved AM and cornea, including different cryopreservation methods and their indications in ophthalmology

CRISPR/Cas9‐mediated somatic correction of a novel coagulator factor IX gene mutation ameliorates hemophilia in mouse

The X‐linked genetic bleeding disorder caused by deficiency of coagulator factor IX, hemophilia B, is a disease ideally suited for gene therapy with genome editing technology. Here, we identify a family with hemophilia B carrying a novel mutation, Y371D, in the human F9 gene. The CRISPR/Cas9 system was used to generate distinct genetically modified mouse models and confirmed that the novel Y371D mutation resulted in a more severe hemophilia B phenotype than the previously identified Y371S mutation. To develop therapeutic strategies targeting this mutation, we subsequently compared naked DNA constructs versus adenoviral vectors to deliver Cas9 components targeting the F9 Y371D mutation in adult mice. After treatment, hemophilia B mice receiving naked DNA constructs exhibited correction of over 0.56% of F9 alleles in hepatocytes, which was sufficient to restore hemostasis. In contrast, the adenoviral delivery system resulted in a higher corrective efficiency but no therapeutic effects due to severe hepatic toxicity. Our studies suggest that CRISPR/Cas‐mediated in situ genome editing could be a feasible therapeutic strategy for human hereditary diseases, although an efficient and clinically relevant delivery system is required for further clinical studies

Effects of Melanocortin 3 and 4 Receptor Deficiency on Energy Homeostasis in Rats

Melanocortin-3 and 4 receptors (MC3R and MC4R) can regulate energy homeostasis, but their respective roles especially the functions of MC3R need more exploration. Here Mc3r and Mc4r single and double knockout (DKO) rats were generated using CRISPR-Cas9 system. Metabolic phenotypes were examined and data were compared systematically. Mc3r KO rats displayed hypophagia and decreased body weight, while Mc4r KO and DKO exhibited hyperphagia and increased body weight. All three mutants showed increased white adipose tissue mass and adipocyte size. Interestingly, although Mc3r KO did not show a significant elevation in lipids as seen in Mc4r KO, DKO displayed even higher lipid levels than Mc4r KO. DKO also showed more severe glucose intolerance and hyperglycaemia than Mc4r KO. These data demonstrated MC3R deficiency caused a reduction of food intake and body weight, whereas at the same time exhibited additive effects on top of MC4R deficiency on lipid and glucose metabolism. This is the first phenotypic analysis and systematic comparison of Mc3r KO, Mc4r KO and DKO rats on a homogenous genetic background. These mutant rats will be important in defining the complicated signalling pathways of MC3R and MC4R. Both Mc4r KO and DKO are good models for obesity and diabetes research

Cryogenic in-memory computing using tunable chiral edge states

Energy-efficient hardware implementation of machine learning algorithms for quantum computation requires nonvolatile and electrically-programmable devices, memristors, working at cryogenic temperatures that enable in-memory computing. Magnetic topological insulators are promising candidates due to their tunable magnetic order by electrical currents with high energy efficiency. Here, we utilize magnetic topological insulators as memristors (termed magnetic topological memristors) and introduce a chiral edge state-based cryogenic in-memory computing scheme. On the one hand, the chiral edge state can be tuned from left-handed to right-handed chirality through spin-momentum locked topological surface current injection. On the other hand, the chiral edge state exhibits giant and bipolar anomalous Hall resistance, which facilitates the electrical readout. The memristive switching and reading of the chiral edge state exhibit high energy efficiency, high stability, and low stochasticity. We achieve high accuracy in a proof-of-concept classification task using four magnetic topological memristors. Furthermore, our algorithm-level and circuit-level simulations of large-scale neural networks based on magnetic topological memristors demonstrate a software-level accuracy and lower energy consumption for image recognition and quantum state preparation compared with existing memristor technologies. Our results may inspire further topological quantum physics-based novel computing schemes.Comment: 33 pages, 12 figure

Implications for Cation Selectivity and Evolution by a Novel Cation Diffusion Facilitator Family Member From the Moderate Halophile Planococcus dechangensis

In the cation diffusion facilitator (CDF) family, the transported substrates are confined to divalent metal ions, such as Zn2+, Fe2+, and Mn2+. However, this study identifies a novel CDF member designated MceT from the moderate halophile Planococcus dechangensis. MceT functions as a Na+(Li+, K+)/H+ antiporter, together with its capability of facilitated Zn2+ diffusion into cells, which have not been reported in any identified CDF transporters as yet. MceT is proposed to represent a novel CDF group, Na-CDF, which shares significantly distant phylogenetic relationship with three known CDF groups including Mn-CDF, Fe/Zn-CDF, and Zn-CDF. Variation of key function-related residues to “Y44-S48-Q150” in two structural motifs explains a significant discrimination in cation selectivity between Na-CDF group and three major known CDF groups. Functional analysis via site-directed mutagenesis confirms that MceT employs Q150, S158, and D184 for the function of MceT as a Na+(Li+, K+)/H+ antiporter, and retains D41, D154, and D184 for its facilitated Zn2+ diffusion into cells. These presented findings imply that MceT has evolved from its native CDF family function to a Na+/H+ antiporter in an evolutionary strategy of the substitution of key conserved residues to “Q150-S158-D184” motif. More importantly, the discovery of MceT contributes to a typical transporter model of CDF family with the unique structural motifs, which will be utilized to explore the cation-selective mechanisms of secondary transporters

Generation of obese rat model by transcription activator-like effector nucleases targeting the leptin receptor gene

Abstract The laboratory rat is a valuable mammalian model organism for basic research and drug discovery. Here we demonstrate an efficient methodology by applying transcription activator-like effector nucleases (TALENs) technology to generate Leptin receptor (Lepr) knockout rats on the Sprague Dawley (SD) genetic background. Through direct injection of in vitro transcribed mRNA of TALEN pairs into SD rat zygotes, somatic mutations were induced in two of three resulting pups. One of the founders carrying bi-allelic mutation exhibited early onset of obesity and infertility. The other founder carried a chimeric mutation which was efficiently transmitted to the progenies. Through phenotyping of the resulting three lines of rats bearing distinct mutations in the Lepr locus, we found that the strains with a frame-shifted or premature stop codon mutation led to obesity and metabolic disorders. However, no obvious defect was observed in a strain with an in-frame 57 bp deletion in the extracellular domain of Lepr. This suggests the deleted amino acids do not significantly affect Lepr structure and function. This is the first report of generating the Lepr mutant obese rat model in SD strain through a reverse genetic approach. This suggests that TALEN is an efficient and powerful gene editing technology for the generation of disease models.</jats:p