Parallel Recursive State Compression for Free

This paper focuses on reducing memory usage in enumerative model checking, while maintaining the multi-core scalability obtained in earlier work. We present a tree-based multi-core compression method, which works by leveraging sharing among sub-vectors of state vectors. An algorithmic analysis of both worst-case and optimal compression ratios shows the potential to compress even large states to a small constant on average (8 bytes). Our experiments demonstrate that this holds up in practice: the median compression ratio of 279 measured experiments is within 17% of the optimum for tree compression, and five times better than the median compression ratio of SPIN's COLLAPSE compression. Our algorithms are implemented in the LTSmin tool, and our experiments show that for model checking, multi-core tree compression pays its own way: it comes virtually without overhead compared to the fastest hash table-based methods.Comment: 19 page

Monitoring of Cell Layer Integrity with a Current-Driven Organic Electrochemical Transistor

The integrity of CaCo-2 cell barriers is investigated by organic electrochemical transistors (OECTs) in a current-driven configuration. Ion transport through cellular barriers via the paracellular pathway is modulated by tight junctions between adjacent cells. Rupturing its integrity by H2O2 is monitored by the change of the output voltage in the transfer characteristics. It is demonstrated that by operating the OECT in a current-driven configuration, the sensitive and temporal resolution for monitoring the cell barrier integrity is strongly enhanced as compared to the OECT transient response measurement. As a result, current-driven OECTs are useful tools to assess dynamic and critical changes in tight junctions, relevant for clinical applications as drug targeting and screening

The influence of an externally applied electric field on residual microparticle charge in a spatio-temporal afterglow plasma

The residual charge of dust particles in spatial and temporal afterglow plasmas is relevant in many fundamental research fields and technological applications. It has been shown in both spatial and temporal afterglow plasmas that the presence of an externally applied electric field can greatly influence the residual dust particle charge. However, this has not yet been explored in a combined spatiotemporal afterglow plasma. In this work, the influence of an externally applied electric field on the residual microparticle charge is, therefore, investigated in a spatiotemporal afterglow plasma. It is found that the measured charge is predominantly affected by changes to the spatial component of the spatiotemporal afterglow when an electric field is applied, while the influence on the temporal component seems to be significantly less relevant. Our results contribute to an improved understanding of particle (de-)charging in afterglow plasmas and are highly relevant to the design of applications in which afterglow plasmas are present and where the charge of dust particles needs to be controlled for the sake of (nano)contamination control.</p

IGR J22517+2218=MG3 J225155+2217: a new gamma-ray lighthouse in the distant Universe

We report on the identification of a new soft gamma ray source, namely IGR J22517+2218, detected with IBIS/INTEGRAL. The source, which has an observed 20-100 keV flux of ~4 x10^-11 erg cm-2 s-1, is spatially coincident with MG3 J225155+2217, a quasar at z=3.668. The Swift/XRT 0.5-10 keV continuum is flat (Gamma=1.5) with evidence for a spectral curvature below 1-2 keV either due to intrinsic absorption (NH=3 +/- 2 x 10^22 cm-2) or to a change in slope (Delta Gamma= 0.5). X-ray observations indicate flux variability over a 6 days period which is further supported by a flux mismatch between Swift and INTEGRAL spectra. IGR J22517+2218 is radio loud and has a flat radio spectrum; optically it is a broad line emitting quasar with the atypical property of hosting a narrow line absorption system. The Source Spectral Energy Distribution is unusual compared to blazars of similar type: either it has the synchrotron peak in the X/gamma-ray band (i.e. much higher than generally observed) or the Compton peak in the MeV range (i.e. lower than typically measured). IGR J22517+2218=MG3 J225155+2217 is the second most distant blazar detected above 20 keV and a gamma-ray lighthouse shining from the edge of our Universe.Comment: 4 pages, 4 figures, Accepted for publication in Astrophysical Journal Letter

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Exact solution of the Zeeman effect in single-electron systems

Contrary to popular belief, the Zeeman effect can be treated exactly in single-electron systems, for arbitrary magnetic field strengths, as long as the term quadratic in the magnetic field can be ignored. These formulas were actually derived already around 1927 by Darwin, using the classical picture of angular momentum, and presented in their proper quantum-mechanical form in 1933 by Bethe, although without any proof. The expressions have since been more or less lost from the literature; instead, the conventional treatment nowadays is to present only the approximations for weak and strong fields, respectively. However, in fusion research and other plasma physics applications, the magnetic fields applied to control the shape and position of the plasma span the entire region from weak to strong fields, and there is a need for a unified treatment. In this paper we present the detailed quantum-mechanical derivation of the exact eigenenergies and eigenstates of hydrogen-like atoms and ions in a static magnetic field. Notably, these formulas are not much more complicated than the better-known approximations. Moreover, the derivation allows the value of the electron spin gyromagnetic ratio $g_s$ to be different from 2. For completeness, we then review the details of dipole transitions between two hydrogenic levels, and calculate the corresponding Zeeman spectrum. The various approximations made in the derivation are also discussed in details.Comment: 18 pages, 4 figures. Submitted to Physica Script

Dysbetalipoproteinaemia-clinical and pathophysiological features

Objectives. Dysbetalipoproteinaemia (type III hyperlipidaemia, broad-beta disease) is a highly atherogenic genetic disorder of lipoprotein metabolism. It presents with a severe mixed hyperlipidaemia in which the ratio of total cholesterol to triglycerides is typically 2:1. There is a high incidence of atherosclerotic complications and severe hypertriglyceridaemia may cause pancreatitis. Highly effective therapy is available and affected families also benefit from genetic counselling.We present a review of our experience with dysbetalipoproteinaemia at the lipid clinic of Groote Schuur Hospital to enhance awareness of this serious condition, for which the index of suspicion should be raised.Design. Retrospective review of case records, 1969- 2001.Setting. Lipid clinic of Groote Schuur Hospital, Cape Town.Subjects. Patients with dysbetalipoproteinaemia diagnosed by the presence of cholesterol-enriched very-low-density lipoproteins (VLDL) and/or dyslipidaemia associated with homozygosity for apolipoprotein E2 or carriers of the apoE2 (Arg 145 →Cys) mutation.Results. One hundred and five patients were identified, 55 of whom were male and 50 female. The age at presentation was 48.8 ± 11.1 years (mean, standard deviation). Total cholesterol was 12.0 ± 5.5 mmol/l and plasma triglycerides 8.3 ± 9.8 mmol/1. The ratio (by mass) of cholesterol to triglycerides within VLDL was 0.52 ± 0.17, while VLDL cholesterol to plasma triglycerides was 0.33 ± 0.09. Fifty patients were E2 homozygotes while 22 carried the apoE2(Arg→ 145 Cys) mutation. Palmar crease xanthomas occurred in 20% of patients, cutaneous xanthomas in 18%, and tendon xanthomas in 13%. Coronary artery disease was found in 47% of patients and peripheral vascular disease in 20%. Fibrates were the most commonly used hypolipidaemic agents (48%), while 31% of patients received combination therapy with a fibrate and statin. Statin monotherapy was used in 11% of patients and a few patients were treated with niacin or required no drug therapy. The treated cholesterol was 5.7 ± 2.4 mmol/1, with plasma triglycerides of 2.7 ± 1.9 mmol/1. Conclusions. Dysbetalipoproteinaemia is a highly atherogenic disorder and is extremely responsive to therapy. A significant proportion of dysbetalipoproteinaemia locally is caused by the apoE2(Arg→ 145 Cys) mutation and is therefore dominantly inherited. This mutation is particularly prevalent in the black community where dysbetalipoproteinaemia may be undiagnosed in many patients. Patients with severe mixed hyperlipidaemia or clinical stigmata of dyslipidaemia should be assessed at a lipid clinic for a specific diagnosis and initiation of therapy.

Effect of the proprotein convertase subtilisin/kexin type 9 inhibitor evolocumab on glycemia, body weight, and new-onset diabetes mellitus

Statin therapy modestly increases new-onset diabetes risk. The effect of proprotein convertase subtilisin/kexin type 9 inhibition on new-onset diabetes, glycemia, and weight remains unclear. We studied the effects of the proprotein convertase subtilisin/kexin type 9 inhibitor evolocumab on fasting plasma glucose, glycated hemoglobin, weight, and new-onset diabetes mellitus. We pooled 1-year (48-week) data for participants who had completed an evolocumab parent study before entering an open-label extension (OLE) trial. Data were available for 4,802 participants (1,602 on standard of care [SOC]; 3,200 on evolocumab plus SOC) in 2 OLE trials. Evolocumab lowered low-density lipoprotein cholesterol by approximately 60% compared with SOC alone. Over the first year of the OLE trials, there was no difference in median (Q1, Q3) change in glycated hemoglobin (0.1% [-0.1, 0.2] for both SOC and evolocumab plus SOC) and fasting plasma glucose (0.06 mmol/L [-0.28, 0.38 mmol/L] for SOC and 0.06 mmol/L [-0.28, 0.44 mmol/L] for evolocumab plus SOC). Mean weight change (standard error) at 1 year was -0.1 kg (0.2) on SOC compared with 0.3 kg (0.1) on evolocumab plus SOC. The exposure-adjusted incidence rate (95% confidence intervals) for new-onset diabetes per 100 patient years was 3.7 (2.9 to 4.7) on control/SOC alone and 3.9 (3.2 to 4.6) on evolocumab/evolocumab plus SOC treatment. Glycemic changes observed in 6,430 participants at week 12 in the parent studies were comparable with OLE trial findings. In conclusion, evolocumab therapy has no effect on glucose homeostasis over 1 year of open-label treatment

Program Correctness by Transformation

Deductive program verification can be used effectively to verify high-level programs, but can be challenging for low-level, high-performance code. In this paper, we argue that compilation and program transformations should be made annotation-aware, i.e. during compilation and program transformation, not only the code should be changed, but also the corresponding annotations. As a result, if the original high-level program could be verified, also the resulting low-level program can be verified. We illustrate this approach on a concrete case, where loop annotations that capture possible loop parallelisations are translated into specifications of an OpenCL kernel that corresponds to the parallel loop. We also sketch how several commonly used OpenCL kernel transformations can be adapted to also transform the corresponding program annotations. Finally, we conclude the paper with a list of research challenges that need to be addressed to further develop this approach