Quickstrom: property-based acceptance testing with LTL specifications

We present Quickstrom, a property-based testing system for acceptance testing of interactive applications. Using Quickstrom, programmers can specify the behaviour of web applications as properties in our testing-oriented dialect of Linear Temporal Logic (LTL) called QuickLTL, and then automatically test their application against the given specification with hundreds of automatically generated interactions. QuickLTL extends existing finite variants of LTL for the testing use-case, determining likely outcomes from partial traces whose minimum length is itself determined by the LTL formula. This temporal logic is embedded in our specification language, Specstrom, which is designed to be approachable to web programmers, expressive for writing specifications, and easy to analyse. Because Quickstrom tests only user-facing behaviour, it is agnostic to the implementation language of the system under test. We therefore formally specify and test many implementations of the popular TodoMVC benchmark, used for evaluation and comparison across various web frontend frameworks and languages. Our tests uncovered bugs in almost half of the available implementations.Comment: 13 pages, this is a technical report of a paper to appear at Programming Languages Design and Implementation (PLDI 2022

Overcoming Restraint: Composing Verification of Foreign Functions with Cogent

Cogent is a restricted functional language designed to reduce the cost of developing verified systems code. Because of its sometimes-onerous restrictions, such as the lack of support for recursion and its strict uniqueness type system, Cogent provides an escape hatch in the form of a foreign function interface (FFI) to C code. This poses a problem when verifying Cogent programs, as imported C components do not enjoy the same level of static guarantees that Cogent does. Previous verification of file systems implemented in Cogent merely assumed that their C components were correct and that they preserved the invariants of Cogent's type system. In this paper, we instead prove such obligations. We demonstrate how they smoothly compose with existing Cogent theorems, and result in a correctness theorem of the overall Cogent-C system. The Cogent FFI constraints ensure that key invariants of Cogent's type system are maintained even when calling C code. We verify reusable higher-order and polymorphic functions including a generic loop combinator and array iterators and demonstrate their application to several examples including binary search and the BilbyFs file system. We demonstrate the feasibility of verification of mixed Cogent-C systems, and provide some insight into verification of software comprised of code in multiple languages with differing levels of static guarantees

Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections

Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis protocols are needed for genotyping in epidemiological studies and drug efficacy trials of P. falciparum.; Targeted sequencing of molecular marker csp and novel marker cpmp was conducted in duplicate on mixtures of parasite culture strains and 37 field samples. A protocol allowing to multiplex up to 384 samples in a single sequencing run was applied. Software "HaplotypR" was developed for data analysis.; Cpmp was highly diverse (He = 0.96) in contrast to csp (He = 0.57). Minority clones were robustly detected if their frequency was >1%. False haplotype calls owing to sequencing errors were observed below that threshold.; To reliably detect haplotypes at very low frequencies, experiments are best performed in duplicate and should aim for coverage of >10'000 reads/amplicon. When compared to length polymorphic marker msp2, highly multiplexed amplicon sequencing displayed greater sensitivity in detecting minority clones

Cogent: uniqueness types and certifying compilation

This paper presents a framework aimed at significantly reducing the cost of proving functional correctness for low-level operating systems components. The framework is designed around a new functional programming language, Cogent. A central aspect of the language is its uniqueness type system, which eliminates the need for a trusted runtime or garbage collector while still guaranteeing memory safety, a crucial property for safety and security. Moreover, it allows us to assign two semantics to the language: The first semantics is imperative, suitable for efficient C code generation, and the second is purely functional, providing a user-friendly interface for equational reasoning and verification of higher-level correctness properties. The refinement theorem connecting the two semantics allows the compiler to produce a proof via translation validation certifying the correctness of the generated C code with respect to the semantics of the Cogent source program. We have demonstrated the effectiveness of our framework for implementation and for verification through two file system implementations

CH-01 is a hypoxia-activated prodrug that sensitizes cells to hypoxia/reoxygenation through inhibition of Chk1 and aurora A

The increased resistance of hypoxic cells to all forms of cancer therapy presents a major barrier to the successful treatment of most solid tumors. Inhibition of the essential kinase Checkpoint kinase 1 (Chk1) has been described as a promising cancer therapy for tumors with high levels of hypoxia-induced replication stress. However, as inhibition of Chk1 affects normal replication and induces DNA damage, these agents also have the potential to induce genomic instability and contribute to tumorigenesis. To overcome this problem, we have developed a bioreductive prodrug, which functions as a Chk1/Aurora A inhibitor specifically in hypoxic conditions. To achieve this activity, a key functionality on the Chk1 inhibitor (CH-01) is masked by a bioreductive group, rendering the compound inactive as a Chk1/Aurora A inhibitor. Reduction of the bioreductive group nitro moiety, under hypoxic conditions, reveals an electron-donating substituent that leads to fragmentation of the molecule, affording the active inhibitor. Most importantly, we show a significant loss of viability in cancer cell lines exposed to hypoxia in the presence of CH-01. This novel approach targets the most aggressive and therapy-resistant tumor fraction while protecting normal tissue from therapy-induced genomic instability. © 2013 American Chemical Society

Systemic inflammatory markers and disease severity in chronic obstructive pulmonary disease—the effect of acute exercise and pulmonary rehabilitation

Background: Decreased physical capacity and increased systemic inflammatory response are frequently observed in patients with chronic obstructive pulmonary disease (COPD). The relationship between the inflammatory response and disease severity and the immunological response to exercise were addressed in COPD. Objective: The first objective was to identify systemic biomarkers and their relationship with COPD severity. The second objective was to examine the effect of both acute exercise and pulmonary rehabilitation on these biomarkers. Methods: Forty subjects participated in the study. Thirty-two patients with moderate or severe COPD and 8 healthy nonsmokers completed the study. Spirometry was preformed. Physical capacity was determined by a progressive symptom-limited cycle ergo meter (incremental) test. Blood samples were analyzed for C-reactive protein (CRP), pro-inflammatory cytokines (IL-6, TNF-α), pro-fibrotic cytokines (TGF-β) and oxidative burst in circulating leukocytes before and after exercise, and before and after pulmonary rehabilitation. Results: IL-6, CRP, WCC and TGF-β were higher in COPD (p < 0.05) than eight healthy controls. WCC, IL-6, TNF-α, CRP and TGF-β were negatively related to forced expiratory volume in 1 s (FEV1) (r = 0.4054, 0.3221, 0.1528, 0.1846 and 0.1187, respectively). Acute exercise increased circulating leucocytes and oxidative stress in both groups (p = 0.000, 0.0049 respectively), while IL-6 was increased in COPD group ((p = 0.0115) and circulating TNF-α in healthy control (p = 0.0369). Pulmonary rehabilitation didn’t modify the levels of inflammatory mediators. Conclusions: Reduced lung function is associated with increased levels of systemic inflammatory markers and acute exercise can further increase this inflammatory response. However pulmonary rehabilitation is unlikely to exacerbate systemic inflammation in COPD. Keywords Systemic Inflammation, COPD, Oxidative Stress, Pulmonary Rehabilitatio

Augmented Reality Technology to Facilitate Proficiency in Emergency Medical Procedures

Background: Augmented reality (AR) conveys an experience during which the user’s real-time environment is enhanced by computer-generated perceptual information; it is being investigated as a solution to enhance medical education and clinical practice. There is little literature on its utility for teaching emergency procedures. Methods: A within-subjects trial was performed comparing traditional training to AR guidance for two emergency procedures. Lay-subjects and emergency medical technicians received video training and AR guidance for performing bag-valve-mask ventilation and needle-decompression. Subjects performed both procedures in a simulation setting after each training modality. Subject performance, acceptability and usability were analyzed. Results: There was no difference in procedural performance between lay or EMT subjects for AR training, and no difference in subject-reported usefulness between the AR and control training. Conclusion: AR mediated guidance for emergency medical procedures is feasible and efficacious. Subject performance after AR training was statistically undistinguishable from a didactic educational modality

Adapting to Climate Change: The urgency and some challenges to begin

Our response to the challenge of climate change will shape our future in many different and crucial ways. Adaptation is about realizing the impacts of climate change and acting in such a way to limit negative impacts and embrace positive outcomes in order to reduce our vulnerability from the effects of climate change