Verus: Verifying Rust Programs using Linear Ghost Types (extended version)

The Rust programming language provides a powerful type system that checks linearity and borrowing, allowing code to safely manipulate memory without garbage collection and making Rust ideal for developing low-level, high-assurance systems. For such systems, formal verification can be useful to prove functional correctness properties beyond type safety. This paper presents Verus, an SMT-based tool for formally verifying Rust programs. With Verus, programmers express proofs and specifications using the Rust language, allowing proofs to take advantage of Rust's linear types and borrow checking. We show how this allows proofs to manipulate linearly typed permissions that let Rust code safely manipulate memory, pointers, and concurrent resources. Verus organizes proofs and specifications using a novel mode system that distinguishes specifications, which are not checked for linearity and borrowing, from executable code and proofs, which are checked for linearity and borrowing. We formalize Verus' linearity, borrowing, and modes in a small lambda calculus, for which we prove type safety and termination of specifications and proofs. We demonstrate Verus on a series of examples, including pointer-manipulating code (an xor-based doubly linked list), code with interior mutability, and concurrent code

Suppression of lung cancer progression by biocompatible glycerol triacrylate–spermine-mediated delivery of shAkt1

Background: Polyethylenimine (PEI)-based nonviral gene-delivery systems are commonly employed because of their high transfection efficiency. However, the toxic nature of PEI is a significant obstacle in clinical gene therapy. In this study, we developed biocompatible glycerol triacrylate-spermine (GT-SPE) polyspermine as a nanosized gene carrier for potential lung cancer gene therapy. Methods: The GT-SPE was synthesized using the Michael addition reaction between GT and SPE. The molecular weight was characterized using gel permeability chromatography multiangle laser light scattering and the composition of the polymer was analyzed using proton nuclear magnetic resonance. Results: The GT-SPE successfully protected the DNA from nucleases. The average particle size of the GT-SPE was 121 nm with a zeta potential of +23.45 mV. The GT-SPE was found to be less toxic than PEI for various cell lines, as well as for a murine model. Finally, our results showed that the GT-SPE/small hairpin Akt1 (shAkt1) complex suppressed lung tumorigenesis in a K-ras(LA1) lung cancer mice model by inducing apoptosis through the Akt signaling pathway and cell cycle arrest. Aerosol delivered GT-SPE/shAkt1, which reduced matrix metalloproteinase-9 activity and suppressed the expression levels of proliferating cell nuclear antigen, as well as vascular endothelial growth factors and CD31, which are known proliferation and angiogenesis markers, respectively. Conclusion: Our data suggest that GT-SPE may be a candidate for short hairpin-shaped RNA-based aerosol lung cancer gene therapy

Histone acylation marks respond to metabolic perturbations and enable cellular adaptation

Acetylation is the most studied histone acyl modification and has been recognized as a fundamental player in metabolic gene regulation, whereas other short-chain acyl modifications have only been recently identified, and little is known about their dynamics or molecular functions at the intersection of metabolism and epigenetic gene regulation. In this study, we aimed to understand the link between nonacetyl histone acyl modification, metabolic transcriptional regulation, and cellular adaptation. Using antibodies specific for butyrylated, propionylated, and crotonylated H3K23, we analyzed dynamic changes of H3K23 acylation upon various metabolic challenges. Here, we show that H3K23 modifications were highly responsive and reversibly regulated by nutrient availability. These modifications were commonly downregulated by the depletion of glucose and recovered based on glucose or fatty acid availability. Depletion of metabolic enzymes, namely, ATP citrate lyase, carnitine acetyltransferase, and acetyl-CoA synthetase, which are involved in Ac-CoA synthesis, resulted in global loss of H3K23 butyrylation, crotonylation, propionylation, and acetylation, with a profound impact on gene expression and cellular metabolic states. Our data indicate that Ac-CoA/CoA and central metabolic inputs are important for the maintenance of histone acylation. Additionally, genome-wide analysis revealed that acyl modifications are associated with gene activation. Our study shows that histone acylation acts as an immediate and reversible metabolic sensor enabling cellular adaptation to metabolic stress by reprogramming gene expression. © 2020, The Author(s).1

High inorganic phosphate intake promotes tumorigenesis at early stages in a mouse model of lung cancer

© 2015 Lee et al. Inorganic phosphate (Pi) is required by all living organisms for the development of organs such as bone, muscle, brain, and lungs, regulating the expression of several critical genes as well as signal transduction. However, little is known about the effects of prolonged dietary Pi consumption on lung cancer progression. This study investigated the effects of a highphosphate diet (HPD) in a mouse model of adenocarcinoma. K-rasLA1 mice were fed a normal diet (0.3% Pi) or an HPD (1% Pi) for 1, 2, or 4 months. Mice were then sacrificed and subjected to inductively coupled plasma mass/optical emission spectrometry and laser ablation inductively coupled plasma mass-spectrometry analyses, western blot analysis, histopathological, immunohistochemical, and immunocytochemical analyses to evaluate tumor formation and progression (including cell proliferation, angiogenesis, and apoptosis), changes in ion levels and metabolism, autophagy, epithelial-to-mesenchymal transition, and protein translation in the lungs. An HPD accelerated tumorigenesis, as evidenced by increased adenoma and adenocarcinoma rates as well as tumor size. However, after 4 months of the HPD, cell proliferation was arrested, and marked increases in liver and lung ion levels and in energy production via the tricarboxylic acid cycle in the liver were observed, which were accompanied by increased autophagy and decreased angiogenesis and apoptosis. These results indicate that an HPD initially promotes but later inhibits lung cancer progression because of metabolic adaptation leading to tumor cell quiescence. Moreover, the results suggest that carefully regulated Pi consumption are effective in lung cancer prevention

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

In situ hybridization for the detection of the apxIV gene in the lungs of pigs experimentally infected with twelve Actinobacillus pleuropneumoniae serotypes

The detection of the apxIV gene in lung tissues from pigs experimentally infected with the 12 major A. pleuropneumoniae serotype (1 to 12) reference strains was studied by in situ hybridization using a non-radioactive digoxigenin-labeled DNA probe. In situ hybridization produced a distinct positive signal in all pigs inoculated with the 12 A. pleuropneumoniae serotypes. Positive hybridization typically exhibited a dark-brown to black reaction product in intracellular and extracellular locations, without background staining. A strong hybridization signal was seen in degenerated alveolar leukocytes (“oat cells”) adjacent to the foci of coagulative necrosis and in the alveolar spaces. The in situ hybridization methodology developed for the detection of the apxIV gene is a valuable tool for the diagnosis of porcine pleuropneumonia caused by A. pleuropneumoniae when only formalin-fixed tissues are submitted for diagnosis.Détection par hybridation in situ du gène apxIV dans les poumons de porcs infectés expérimentalement par douze sérotypes de Actinobacillus pleuropneumoniae. La détection du gène apxIV dans les tissus pulmonaires de porcs infectés expérimentalement par les douze sérotypes majeurs des souches de référence (1 à 12) de Actinobacillus pleuropneumoniae a été effectuée par hybridation in situ utilisant une sonde à ADN non radioactive marquée à la digoxigénine. L'hybridation in situ a produit un signal positif distinct chez tous les porcs inoculés par les douze sérotypes de A. pleuropneumoniae. Un résultat positif d'hybridation entraînait typiquement un produit de réaction marron foncé à noir localisé en intra- et en extra-cellulaire, sans bruit de fond. Un signal fort d'hybridation a été observé dans les leucocytes alvéolaires dégénérés adjacents aux foyers de nécrose et dans les espaces alvéolaires. La méthode d'hybridation in situ développée pour la détection du gène apxIV est un outil précieux pour le diagnostic de la pleuropneumonie porcine causée par A. pleuropneumoniae lorsque seuls les tissus fixés dans le formol sont soumis pour le diagnostic

A Comparative Field Evaluation of the Effect of Growth Performance Between Porcine Circovirus Type 2a (PCV2a)- and PCV2b-Based Bivalent Vaccines Containing PCV2 and Mycoplasma hyopneumoniae

The objective of this study was to compare two different bivalent vaccines containing porcine circovirus type 2 (PCV2) and Mycoplasma hyopneumoniae. One vaccine contained PCV2a and the other contained PCV2b, and both were administered on a farm suffering from subclinical PCV2d infection and enzootic pneumonia. A total of 180 pigs were randomly divided into 3 groups (60 pigs per group; male pigs = 30 and female pigs = 30). Bivalent vaccination significantly improved growth performance in both vaccinated groups as compared to the unvaccinated (UnVac) group. Growth performance measured by body weight and average daily weight gain (ADWG) was not significantly different between the two bivalent-vaccinated groups (VacA and VacB). Both bivalent vaccines elicited high levels of neutralizing antibodies and interferon-gamma secreting cells (IFN-gamma-SC) against PCV2d, leading to a reduction in the levels of PCV2d blood viral load as compared to unvaccinated animals. Similarly, both bivalent vaccines elicited high levels of IFN-gamma-SC against M. hyopneumoniae that reduced the level of M. hyopneumoniae laryngeal viral loads as compared to unvaccinated animals. Significant differences in severity of lung and lymphoid lesions were observed in both vaccinated groups as compared to the UnVac group. These comparative field data demonstrated that both bivalent vaccines are good candidates for controlling subclinical PCV2d infection and enzootic pneumonia in swine farms suffering from an existing infection.N

Non-Inferiority Field Study Comparing the Administrations by Conventional Needle-Syringe and Needle-Free Injectors of a Trivalent Vaccine Containing Porcine Circovirus Types 2a/2b and Mycoplasma hyopneumoniae

The objective of this study was to assess the clinical, immunological, microbiological, and pathological evaluation of trivalent vaccine containing porcine circovirus types 2a/b (PCV2a/b) and Mycoplasma hyopneumoniae given by two different needle-free injection devices compared with conventional needle-syringe injection in a herd with subclinical PCV2d infection and enzootic pneumonia. A total of 240 21-day-old pigs, which weighed between 5 to 6 kg, were randomly divided into four groups (60 pigs per group, 30 = male and 30 = female per group). Injection site reactions in the pigs were minimal for the two needle-free injection devices and needle-syringe injection. Trivalent vaccination of pigs with two needle-free injection devices was not inferior to conventional needle-syringe injection for growth performance. Trivalent vaccination of pigs with two different needle-free injection devices reduced levels of PCV2d loads in serum and M. hyopneumoniae loads in the larynx equally compared to the conventional needle-syringe injection. The amount of PCV2d load in serum from the needle-free Pulse FX injection device at 49 days post vaccination showed non-inferiority to conventional needle-syringe injection. The immune response against PCV2 and M. hyopneumoniae to trivalent vaccine given with the needle-free Pulse FX injection device was non-inferior to conventional needle-syringe injection. The pigs from the two needle-free injection device and conventional needle-syringe injection had significantly (p < 0.05) lower macroscopic and microscopic lung lesion scores, and microscopic lymphoid lesions than from unvaccinated. The results of this study demonstrated that vaccination of trivalent vaccine by the two needle-free Pulse injection devices used in the study was non-inferior to that by conventional needle-syringe injection for growth performance, immune response against PCV2 and M. hyopneumoniae, and reduction of PCV2 viremia

An Android Security Extension to Protect Personal Information against Illegal Accesses and Privilege Escalation Attacks

Abstract Recently, it is widespread for malware to collect sensitive information owned by third-party applications as well as to escalate its privilege to the system level (the highest level) on the Android platform. An attack of obtaining root-level privilege in an Android environment can form a serious threat to users from the viewpoint of breaking down the whole security system. This paper proposes a new scheme that effectively prevents privilege escalation attacks and protects users' personal information in Android. Our proposed scheme can detect and respond to malware that illegally acquires rootlevel privilege using pWhitelist, a list of trusted programs with root-level permission. Moreover, the scheme does not permit even a privileged program to access users' personal information based on the principle of least privilege. As a result, it protects personal information against illegal accesses by malicious applications even though they illegally obtain root-level permissions by exploiting vulnerabilities of trusted programs

Command Recognition Using Binarized Convolutional Neural Network with Voice and Radar Sensors for Human-Vehicle Interaction

Recently, as technology has advanced, the use of in-vehicle infotainment systems has increased, providing many functions. However, if the driver’s attention is diverted to control these systems, it can cause a fatal accident, and thus human–vehicle interaction is becoming more important. Therefore, in this paper, we propose a human–vehicle interaction system to reduce driver distraction during driving. We used voice and continuous-wave radar sensors that require low complexity for application to vehicle environments as resource-constrained platforms. The proposed system applies sensor fusion techniques to improve the limit of single-sensor monitoring. In addition, we used a binarized convolutional neural network algorithm, which significantly reduces the computational workload of the convolutional neural network in command classification. As a result of performance evaluation in noisy and cluttered environments, the proposed system showed a recognition accuracy of 96.4%, an improvement of 7.6% compared to a single voice sensor-based system, and 9.0% compared to a single radar sensor-based system