Automated test sequence generation for finite state machines using genetic algorithms

Testing software implementations, formally specified using finite state automata (FSA) has been of interest. Such systems include communication protocols and control sections of safety critical systems. There is extensive literature regarding how to formally validate an FSM based specification, but testing that an implementation conforms to the specification is still an open problem. Two aspects of FSA based testing, both NP-hard problems, are discussed in this thesis and then combined. These are the generation of state verification sequences (UIOs) and the generation of sequences of conditional transitions that are easy to trigger. In order to facilitate test sequence generation a novel representation of the transition conditions and a number of fitness function algorithms are defined. An empirical study of the effectiveness on real FSA based systems and example FSAs provides some interesting positive results. The use of genetic algorithms (GAs) makes these problems scalable for large FSAs. The experiments used a software tool that was developed in Java.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

On Some Classes of mKdV Periodic Solutions

We obtain exact periodic solutions of the positive and negative modified Kortweg-de Vries (mKdV) equations. We examine the dynamical stability of these solitary wave lattices through direct numerical simulations. While the positive mKdV breather lattice solutions are found to be unstable, the two-soliton lattice solution of the same equation is found to be stable. Similarly, a negative mKdV lattice solution is found to be stable. We also touch upon the implications of these results for the KdV equation.Comment: 8 pages, 3 figures, to appear in J. Phys.

Biogenesis of the inner membrane complex is dependent on vesicular transport by the alveolate specific GTPase Rab11B

Apicomplexan parasites belong to a recently recognised group of protozoa referred to as Alveolata. These protists contain membranous sacs (alveoli) beneath the plasma membrane, termed the Inner Membrane Complex (IMC) in the case of Apicomplexa. During parasite replication the IMC is formed de novo within the mother cell in a process described as internal budding. We hypothesized that an alveolate specific factor is involved in the specific transport of vesicles from the Golgi to the IMC and identified the small GTPase Rab11B as an alveolate specific Rab-GTPase that localises to the growing end of the IMC during replication of Toxoplasma gondii. Conditional interference with Rab11B function leads to a profound defect in IMC biogenesis, indicating that Rab11B is required for the transport of Golgi derived vesicles to the nascent IMC of the daughter cell. Curiously, a block in IMC biogenesis did not affect formation of sub-pellicular microtubules, indicating that IMC biogenesis and formation of sub-pellicular microtubules is not mechanistically linked. We propose a model where Rab11B specifically transports vesicles derived from the Golgi to the immature IMC of the growing daughter parasites

Breather lattice and its stabilization for the modified Korteweg-de Vries equation

We obtain an exact solution for the breather lattice solution of the modified Korteweg-de Vries (MKdV) equation. Numerical simulation of the breather lattice demonstrates its instability due to the breather-breather interaction. However, such multi-breather structures can be stabilized through the concurrent application of ac driving and viscous damping terms.Comment: 6 pages, 3 figures, Phys. Rev. E (in press

A Gravitational Aharonov-Bohm Effect, and its Connection to Parametric Oscillators and Gravitational Radiation

A thought experiment is proposed to demonstrate the existence of a gravitational, vector Aharonov-Bohm effect. A connection is made between the gravitational, vector Aharonov-Bohm effect and the principle of local gauge invariance for nonrelativistic quantum matter interacting with weak gravitational fields. The compensating vector fields that are necessitated by this local gauge principle are shown to be incorporated by the DeWitt minimal coupling rule. The nonrelativistic Hamiltonian for weak, time-independent fields interacting with quantum matter is then extended to time-dependent fields, and applied to problem of the interaction of radiation with macroscopically coherent quantum systems, including the problem of gravitational radiation interacting with superconductors. But first we examine the interaction of EM radiation with superconductors in a parametric oscillator consisting of a superconducting wire placed at the center of a high Q superconducting cavity driven by pump microwaves. We find that the threshold for parametric oscillation for EM microwave generation is much lower for the separated configuration than the unseparated one, which then leads to an observable dynamical Casimir effect. We speculate that a separated parametric oscillator for generating coherent GR microwaves could also be built.Comment: 25 pages, 5 figures, YA80 conference (Chapman University, 2012

The role of clathrin in post-golgi trafficking in toxoplasma gondii

Apicomplexan parasites are single eukaryotic cells with a highly polarised secretory system that contains unique secretory organelles (micronemes and rhoptries) that are required for host cell invasion. In contrast, the role of the endosomal system is poorly understood in these parasites. With many typical endocytic factors missing, we speculated that endocytosis depends exclusively on a clathrin-mediated mechanism. Intriguingly, in Toxoplasma gondii we were only able to observe the endogenous clathrin heavy chain 1 (CHC1) at the Golgi, but not at the parasite surface. For the functional characterisation of Toxoplasma gondii CHC1 we generated parasite mutants conditionally expressing the dominant negative clathrin Hub fragment and demonstrate that CHC1 is essential for vesicle formation at the trans-Golgi network. Consequently, the functional ablation of CHC1 results in Golgi aberrations, a block in the biogenesis of the unique secretory microneme and rhoptry organelles, and of the pellicle. However, we found no morphological evidence for clathrin mediating endocytosis in these parasites and speculate that they remodelled their vesicular trafficking system to adapt to an intracellular lifestyle

A randomized phase II study of SM-88 plus methoxsalen, phenytoin, and sirolimus in patients with metastatic pancreatic cancer treated in the second line and beyond

BACKGROUND: This trial explores SM-88 used with methoxsalen, phenytoin, and sirolimus (MPS) in pretreated metastatic pancreatic ductal adenocarcinoma (mPDAC) METHODS: Forty-nine patients were randomized to daily 460 or 920 mg oral SM-88 with MPS (SM-88 Regimen). The primary endpoint was objective response rate (RECIST 1.1). RESULTS: Thirty-seven patients completed ≥ one cycle of SM-88 Regimen (response evaluable population). Disease control rate (DCR), overall survival (OS), and progression-free survival (PFS) did not differ significantly between dose levels. Stable disease was achieved in 9/37 patients (DCR, 24.3%); there were no complete or partial responses. Quality-of-life (QOL) was maintained and trended in favor of 920 mg. SM-88 Regimen was well tolerated; a single patient (1/49) had related grade 3 and 4 adverse events, which later resolved. In the intention-to-treat population of 49 patients, the median overall survival (mOS) was 3.4 months (95% CI: 2.7-4.9 months). Those treated in the second line had an mOS of 8.1 months and a median PFS of 3.8 months. Survival was higher for patients with stable versus progressive disease (any line; mOS: 10.6 months vs. 3.9 months; p = 0.01). CONCLUSIONS: SM-88 Regimen has a favorable safety profile with encouraging QOL effects, disease control, and survival trends. This regimen should be explored in the second-line treatment of patients with mPDAC. CLINICALTRIALS: gov Identifier: NCT03512756

Erratum: Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies.

The Abstract is incorrect in PubMed. The corrected Abstract is provided here