Comprehensibility of UML-based Formal Model – A Series of Controlled Experiments

This paper summarises two controlled experiments conducted on a model that integrates the use of semi-formal notation, the Unified Modelling Language (UML) and a formal notation, B. The experiments assessed the comprehensibility of the model, namely UML-B. The first experiment compared the comprehensibility of a UML-B model and a B model. In the second experiment, the model was compared with an Event-B model, a new generation of B. The experiments assessed the ability of the model to present information and to promote problem domain understanding. The measurement focused on the efficiency in performing the comprehension tasks. The experiments employed a cross-over design and were conducted on third-year and masters students. The results suggest that the integration of semi-formal and formal notations expedites the subjects’ comprehension tasks with accuracy even with limited hours of training

Advances in Chimeric Antigen Receptor T-Cell Therapies for Solid Tumors.

In 2017, the US Food and Drug Administration approved the first two novel cellular immunotherapies using synthetic, engineered receptors known as chimeric antigen receptors (CARs), tisagenlecleucel (Kymriah) and axicabtagene ciloleucel (Yescarta), expressed by patient-derived T cells for the treatment of hematological malignancies expressing the B-cell surface antigen CD19 in both pediatric and adult patients. This approval marked a major milestone in the use of antigen-directed living drugs for the treatment of relapsed or refractory blood cancers, and with these two approvals, there is increased impetus to expand not only the target antigens but also the tumor types that can be targeted. This state-of-the-art review will focus on the challenges, advances, and novel approaches being used to implement CAR T-cell immunotherapy for the treatment of solid tumors

Refining Nodes and Edges of State Machines

State machines are hierarchical automata that are widely used to structure complex behavioural specifications. We develop two notions of refinement of state machines, node refinement and edge refinement. We compare the two notions by means of examples and argue that, by adopting simple conventions, they can be combined into one method of refinement. In the combined method, node refinement can be used to develop architectural aspects of a model and edge refinement to develop algorithmic aspects. The two notions of refinement are grounded in previous work. Event-B is used as the foundation for our refinement theory and UML-B state machine refinement influences the style of node refinement. Hence we propose a method with direct proof of state machine refinement avoiding the detour via Event-B that is needed by UML-B

Towards a method for rigorous development of generic requirements patterns

We present work in progress on a method for the engineering, validation and verification of generic requirements using domain engineering and formal methods. The need to develop a generic requirement set for subsequent system instantiation is complicated by the addition of the high levels of verification demanded by safety-critical domains such as avionics. Our chosen application domain is the failure detection and management function for engine control systems: here generic requirements drive a software product line of target systems. A pilot formal specification and design exercise is undertaken on a small (twosensor) system element. This exercise has a number of aims: to support the domain analysis, to gain a view of appropriate design abstractions, for a B novice to gain experience in the B method and tools, and to evaluate the usability and utility of that method.We also present a prototype method for the production and verification of a generic requirement set in our UML-based formal notation, UML-B, and tooling developed in support. The formal verification both of the structural generic requirement set, and of a particular application, is achieved via translation to the formal specification language, B, using our U2B and ProB tools

Sexual selection and assortative mating : an experimental test

This work was funded by the Marie Curie Initial Training Network ‘Understanding the evolutionary origin of biological diversity’ (ITN-2008-213780 SPECIATION) and by a US National Science Foundation grant (DEB 0093149) and NERC grants (NE/B504065/1; NE/D003741/1) to RRS.Mate choice and mate competition can both influence the evolution of sexual isolation between populations. Assortative mating may arise if traits and preferences diverge in step, and, alternatively, mate competition may counteract mating preferences and decrease assortative mating. Here, we examine potential assortative mating between populations of Drosophila pseudoobscura that have experimentally evolved under either increased (‘polyandry’) or decreased (‘monogamy’) sexual selection intensity for 100 generations. These populations have evolved differences in numerous traits, including a male signal and female preference traits. We use a two males: one female design, allowing both mate choice and competition to influence mating outcomes, to test for assortative mating between our populations. Mating latency shows subtle effects of male and female interactions, with females from the monogamous populations appearing reluctant to mate with males from the polyandrous populations. However, males from the polyandrous populations have a significantly higher probability of mating regardless of the female's population. Our results suggest that if populations differ in the intensity of sexual selection, effects on mate competition may overcome mate choice.PostprintPeer reviewe

Fatty-acid uptake in prostate cancer cells using dynamic microfluidic raman technology

It is known that intake of dietary fatty acid (FA) is strongly correlated with prostate cancer progression but is highly dependent on the type of FAs. High levels of palmitic acid (PA) or arachidonic acid (AA) can stimulate the progression of cancer. In this study, a unique experimental set-up consisting of a Raman microscope, coupled with a commercial shear-flow microfluidic system is used to monitor fatty acid uptake by prostate cancer (PC-3) cells in real-time at the single cell level. Uptake of deuterated PA, deuterated AA, and the omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were monitored using this new system, while complementary flow cytometry experiments using Nile red staining, were also conducted for the validation of the cellular lipid uptake. Using this novel experimental system, we show that DHA and EPA have inhibitory effects on the uptake of PA and AA by PC-3 cells

Sperm morphology and the evolution of intracellular sperm-egg interactions

This is the final version of the article. Available from Wiley via the DOI in this record.Sperm morphology is incredibly diverse, even among closely related species, yet the coevolution between males and females of fertilization recognition systems is necessary for successful karyogamy (male and female pronuclear fusion). In most species, the entire sperm enters the egg during fertilization so sperm morphological diversity may impact the intracellular sperm–egg interactions necessary for karyogamy. We quantified morphological variation of sperm inside eggs prior to and following karyogamy in several species of Drosophila to understand whether evolution of sperm morphology could influence intracellular sperm–egg interactions (ISEIs). We measured seven parameters that describe ISEIs among species to determine whether these parameters varied both within a species across development and across species at the same developmental stage. We used heterospecific crosses to test the relative role of male origin, female origin, and interaction between the male and female in determining ISEIs. We found that sperm shape changed within a species as development proceeded and, at particular development stages, species varied in some ISEIs. Parental origin had an effect on some ISEIs, with a general trend for a stronger female effect. Overall, our findings identify conserved and variable ISEIs among species and demonstrate the potential to contribute understanding to gamete evolution and development.Leverhulme Trus

Nonequilibrium Temperature and Thermometry in Heat-Conducting Phi-4 Models

We analyze temperature and thermometry for simple nonequilibrium heat-conducting models. We show in detail, for both two- and three-dimensional systems, that the ideal gas thermometer corresponds to the concept of a local instantaneous mechanical kinetic temperature. For the Phi-4 models investigated here the mechanical temperature closely approximates the local thermodynamic equilibrium temperature. There is a significant difference between kinetic temperature and the nonlocal configurational temperature. Neither obeys the predictions of extended irreversible thermodynamics. Overall, we find that kinetic temperature, as modeled and imposed by the Nos\'e-Hoover thermostats developed in 1984, provides the simplest means for simulating, analyzing, and understanding nonequilibrium heat flows.Comment: 20 pages with six figures, revised following review at Physical Review

The genetic basis and adult reproductive consequences of developmental thermal plasticity

Increasing temperature and thermal variability generate profound selection on populations. Given the fast rate of environmental change, understanding the role of plasticity and genetic adaptation in response to increasing temperatures is critical. This may be especially true for thermal effects on reproductive traits in which thermal fertility limits at high temperatures may be lower than for survival traits. Consequences of changing environments during development on adult phenotypes may be particularly problematic for core traits such as reproduction that begin early in development. Here we examine the consequences of developmental thermal plasticity on subsequent adult reproductive traits and its genetic basis. We used a panel of Drosophila melanogaster (the Drosophila Genetic Reference Panel; DGRP) in which male fertility performance was previously defined as either showing relatively little (status = ‘high’-performing lines) or substantial (‘low’-performing lines) decline when exposed to increasing developmental temperatures. We used a thermal reaction norm approach to quantify variation in the consequences of developmental thermal plasticity on multiple adult reproductive traits, including sex-specific responses, and to identify candidate genes underlying such variation. Developmental thermal stress impacted the means and thermal reaction norms of all reproductive traits except offspring sex ratio. Mating success declined as temperature increased with no difference between high and low lines, whereas increasing temperature resulted in declines for both male and female fertility and productivity but depended on line status. Fertility and offspring number were positively correlated within and between the sexes across lines, but males were more affected than females. We identified 933 SNPs with significant evolved genetic differentiation between high and low lines. In all, 54 of these lie within genomic windows of overall high differentiation, have significant effects of genotype on the male thermal reaction norm for productivity and are associated with 16 genes enriched for phenotypes affecting reproduction, stress responses and autophagy in Drosophila and other organisms. Our results illustrate considerable plasticity in male thermal limits on several reproductive traits following development at high temperature, and we identify differentiated loci with relevant phenotypic effects that may contribute to this population variation. While our work is on a single population, phenotypic results align with an increasing number of studies demonstrating the potential for stronger selection of thermal stress on reproductive traits, particularly in males. Such large fitness costs may have both short- and long-term consequences for the evolution of populations in response to a warming world.info:eu-repo/semantics/publishedVersio

Human GUCY2C-Targeted Chimeric Antigen Receptor (CAR)-Expressing T Cells Eliminate Colorectal Cancer Metastases.

One major hurdle to the success of adoptive T-cell therapy is the identification of antigens that permit effective targeting of tumors in the absence of toxicities to essential organs. Previous work has demonstrated that T cells engineered to express chimeric antigen receptors (CAR-T cells) targeting the murine homolog of the colorectal cancer antigen GUCY2C treat established colorectal cancer metastases, without toxicity to the normal GUCY2C-expressing intestinal epithelium, reflecting structural compartmentalization of endogenous GUCY2C to apical membranes comprising the intestinal lumen. Here, we examined the utility of a human-specific, GUCY2C-directed single-chain variable fragment as the basis for a CAR construct targeting human GUCY2C-expressing metastases. Human GUCY2C-targeted murine CAR-T cells promoted antigen-dependent T-cell activation quantified by activation marker upregulation, cytokine production, and killing of GUCY2C-expressing, but not GUCY2C-deficient, cancer cells in vitro. GUCY2C CAR-T cells provided long-term protection against lung metastases of murine colorectal cancer cells engineered to express human GUCY2C in a syngeneic mouse model. GUCY2C murine CAR-T cells recognized and killed human colorectal cancer cells endogenously expressing GUCY2C, providing durable survival in a human xenograft model in immunodeficient mice. Thus, we have identified a human GUCY2C-specific CAR-T cell therapy approach that may be developed for the treatment of GUCY2C-expressing metastatic colorectal cancer