Ferrite: A Judgmental Embedding of Session Types in Rust

This paper introduces Ferrite, a shallow embedding of session types in Rust. In contrast to existing session type libraries and embeddings for mainstream languages, Ferrite not only supports linear session types but also shared session types. Shared session types allow sharing (aliasing) of channels while preserving session fidelity (preservation) using type modalities for acquiring and releasing sessions. Ferrite adopts a propositions as types approach and encodes typing derivations as Rust functions, with the proof of successful type-checking manifesting as a Rust program. We provide an evaluation of Ferrite using Servo as a practical example, and demonstrate how safe communication can be achieved in the canvas component using Ferrite

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans

<p>Abstract</p> <p>Background</p> <p><it>Drosophila albomicans </it>is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.</p> <p>Methods</p> <p>We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.</p> <p>Results</p> <p>We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 <it>Drosophila genomes</it>. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.</p> <p>Conclusions</p> <p>Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in <it>D. albomicans</it>.</p

Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma

Hepatitis B virus (HBV) can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis. Here by conducting high-throughput viral integration detection and RNA sequencing, we identify 4,225 HBV integration events in tumour and adjacent non-tumour samples from 426 patients with HCC. We show that HBV is prone to integrate into rare fragile sites and functional genomic regions including CpG islands. We observe a distinct pattern in the preferential sites of HBV integration between tumour and non-tumour tissues. HBV insertional sites are significantly enriched in the proximity of telomeres in tumours. Recurrent HBV target genes are identified with few that overlap. The overall HBV integration frequency is much higher in tumour genomes of males than in females, with a significant enrichment of integration into chromosome 17. Furthermore, a cirrhosis-dependent HBV integration pattern is observed, affecting distinct targeted genes. Our data suggest that HBV integration has a high potential to drive oncogenic transformation

Skin infectome of patients with a tick bite history

IntroductionTicks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people.MethodsA total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings.ResultsFour bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins.DiscussionAdvances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients’ skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness

Ferrite: A Judgmental Embedding of Session Types in Rust (Artifact)

This artifact provides a VirtualBox image containing the snapshots of source code for Ferrite and Servo at the time the main paper was published

Ferrite: A Judgmental Embedding of Session Types in Rust

Funding Information: Funding Stephanie Balzer: National Science Foundation Award No. CCF-1718267. Bernardo Toninho: FCT/MCTES grant NOVALINCS/BASE UIDB/04516/2020. Publisher Copyright: © Ruo Fei Chen, Stephanie Balzer, and Bernardo Toninho; licensed under Creative Commons License CC-BY 4.0Session types have proved viable in expressing and verifying the protocols of message-passing systems. While message passing is a dominant concurrency paradigm in practice, real world software is written without session types. A limitation of existing session type libraries in mainstream languages is their restriction to linear session types, precluding application scenarios that demand sharing and thus aliasing of channel references. This paper introduces Ferrite, a shallow embedding of session types in Rust that supports both linear and shared sessions. The formal foundation of Ferrite constitutes the shared session type calculus SILLS, which Ferrite encodes via a novel judgmental embedding technique. The fulcrum of the embedding is the notion of a typing judgment that allows reasoning about shared and linear resources to type a session. Typing rules are then encoded as functions over judgments, with a valid typing derivation manifesting as a well-typed Rust program. This Rust program generated by Ferrite serves as a certificate, ensuring that the application will proceed according to the protocol defined by the session type. The paper details the features and implementation of Ferrite and includes a case study on implementing Servo's canvas component in Ferrite.publishersversionpublishe

Analysis of Shear Bond Strength and Morphology of Er:YAG Laser-Recycled Ceramic Orthodontic Brackets

Objective. The aim of this study was to compare the recycling of deboned ceramic brackets via an Er:YAG laser or via the traditional chairside processing methods of flaming and sandblasting; shear bond strength and morphological changes were evaluated in recycled brackets versus new brackets. Materials and Methods. 3M Clarity Self-Ligating Ceramic Brackets with a microcrystalline base were divided into groups subjected to flaming, sandblasting, or exposure to an Er:YAG laser. New ceramic brackets served as a control group. Shear bond strengths were determined with an Electroforce test machine and tested for statistical significance through analysis of variance. Morphological examinations of the recycled ceramic bracket bases were conducted with scanning electron microscopy and confocal laser scanning microscopy. Residue on the bracket base was analyzed with Raman spectroscopy. Results. Faded, dark adhesive was left on recycled bracket bases processed via flaming. Adhesive was thoroughly removed by both sandblasting and exposure to an Er:YAG laser. Compared with new brackets, shear bond strength was lower after sandblasting (p<0.05), but not after exposure to an Er:YAG laser. The Er:YAG laser caused no damage to the bracket. Conclusion. Er:YAG lasers effectively remove adhesive from the bases of ceramic brackets without damaging them; thus, this method may be preferred over other recycling methods