Search

Statechart notations with ‘run to completion’ semantics, are popular with engineers for designing controllers that respond to events in the environment with a sequence of state transitions. However, they lack formal refinement and rigorous verification methods. Open image in new window , on the other hand, is based on refinement from an initial abstraction and is designed to make formal verification by automatic theorem provers feasible. We introduce a notion of refinement into a ‘run to completion’ statechart modelling notation, and leverage Open image in new window tool support for theorem proving. We describe the difficulties in translating ‘run to completion’ semantics into Open image in new window refinements and suggest a solution. We outline how safety and liveness properties could be verified.

The aggregation of attractive colloids has been extensively studied from both theoretical and experimental perspectives as the fraction of solid particles is changed, and the range, type, and strength of attractive or repulsive forces between particles varies. The resulting gels, consisting of disordered assemblies of attractive colloidal particles, have also been investigated with regards to percolation, phase separation, and the mechanical characteristics of the resulting fractal networks. Despite tremendous progress in our understanding of the gelation process, and the exploration of different routes for arresting the dynamics of attractive colloids, the complex interplay between convective transport processes and many-body effects in such systems has limited our ability to drive the system toward a specific configuration. Here, we study a model attractive colloidal system over a wide range of particle characteristics and flow conditions undergoing aggregation far from equilibrium. The complex multiscale dynamics of the system can be understood using a time-rate-transformation diagram adapted from understanding of materials processing in block copolymers, supercooled liquids, and much stiffer glassy metals to direct targeted assembly of attractive colloidal particles. Keywords: Colloidal gels, Directed assembly, Rheology, Attractive colloids, Targeted-design of colloids

We present a characterization of short-term stability of Kauffman's $NK$ (random) Boolean networks under arbitrary distributions of transfer functions. Given such a Boolean network where each transfer function is drawn from the same distribution, we present a formula that determines whether short-term chaos (damage spreading) will happen. Our main technical tool which enables the formal proof of this formula is the Fourier analysis of Boolean functions, which describes such functions as multilinear polynomials over the inputs. Numerical simulations on mixtures of threshold functions and nested canalyzing functions demonstrate the formula's correctness.

A series of potent, selective platelet-derived growth factor receptor-family kinase inhibitors was optimized starting from a globally selective lead molecule 4 through structural modifications aimed at improving the physiochemical and pharmacokinetic properties, as exemplified by 18b. Further clearance reduction via per-methylation of the α-carbons of a solubilizing piperidine nitrogen resulted in advanced leads 22a and 22b. Results from a mouse tumor xenograft, a collagen-induced arthritis model, and a 7 day rat in vivo tolerability study culminated in the selection of compound 22b (AC710) as a preclinical development candidate.

We present a rigorous mathematical framework for analyzing dynamics of a broad class of Boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in Boolean network analysis, and offer analogous characterizations for novel classes of random Boolean networks. We precisely connect the short-run dynamic behavior of a Boolean network to the average influence of the transfer functions. We show that some of the assumptions traditionally made in the more common mean-field analysis of Boolean networks do not hold in general. For example, we offer some evidence that imbalance, or expected internal inhomogeneity, of transfer functions is a crucial feature that tends to drive quiescent behavior far more strongly than previously observed., To appear as a Letter in Physical Review Letters 8 pages, 4 figures

A demyelinating disease induced in C57B1/6N mice by intracranial injection of a coronavirus (murine hepatitis virus strain A59) is followed by functional recovery and efficient CNS myelin repair. To study the biological properties of the cells involved in this repair process, glial cells were isolated and cultured from spinal cords of these young adult mice during demyelination and remyelination. Using three-color immunofluorescence combined with [3H]thymidine autoradiography, we have analyzed the antigenic phenotype and mitotic potential of individual glial cells. We identified oligodendrocytes with an antibody to galactocerebroside, astrocytes with an antibody to glial fibrillary acidic protein, and oligodendrocyte-type 2 astrocyte (O-2A) progenitor cells with the O4 antibody. Cultures from demyelinated tissue differed in several ways from those of age-matched controls: first, the total number of O-2A lineage cells was strikingly increased; second, the O-2A population consisted of a higher proportion of O4-positive astrocytes and cells of mixed oligodendrocyte-astrocyte phenotype; and third, all the cell types within the O-2A lineage showed enhanced proliferation. This proliferation was not further enhanced by adding PDGF, basic fibroblast growth factor (bFGF), or insulin-like growth factor I (IGF-I) to the defined medium. However, bFGF and IGF-I seemed to influence the fate of O-2A lineage cells in cultures of demyelinated tissue. Basic FGF decreased the percentage of cells expressing galactocerebroside. In contrast, IGF-I increased the relative proportion of oligodendrocytes. Thus, O-2A lineage cells from adult mice display greater phenotypic plasticity and enhanced mitotic potential in response to an episode of demyelination. These properties may be linked to the efficient remyelination achieved in this demyelinating disease.

A crystallization model appropriate for application in continuum modeling of complex processes is presented. As an extension to the previously developed Schneider equations [ W. Schneider, A. Köppel, and J. Berger, "Non-isothermal crystallization of polymers," Int. Polym. Proc. 2, 151 (1988) ], the model presented here allows one to account for the growth of crystals of various shapes and to distinguish between one-, two-, and three-dimensional growth, e.g., between rod-like, plate-like, and sphere-like growth. It is explained how a priori knowledge of the shape and growth processes is to be built into the model in a compact form and how experimental data can be used in conjunction with the dynamic model to determine its growth parameters. The model is capable of treating transient processing conditions and permits their straightforward implementation. By using thermodynamic methods, the intimate relation between the crystal shape and the driving forces for phase change is highlighted. All these capabilities and the versatility of the method are made possible by the consistent use of four structural variables to describe the crystal shape and number density, irrespective of the growth dimensionality.

The Rad51 gene of Saccharomyces cerevisiae is required for genetic recombination and recombinational repair of DNA strand breaks. In higher eukaryotes Rad51 is essential for embryonic development, and is involved in cell proliferation and DNA repair. Here we show that human Rad51 (HsRad51) is proteolytically cleaved during apoptosis in two T-lymphocyte cell lines, Jurkat and PFI-285. Apoptosis was induced by camptothecin or anti-Fas monoclonal antibody (anti-Fas mAb). HsRad51 was cleaved with similar kinetics as human poly(ADP-ribose) polymerase (HsPARP) after treatment with either agent. The time course of cleavage coincided with internucleosomal DNA fragmentation. The HsRad51 fragments observed in apoptotic cells were identical to those generated from in vitro translated (IVT) HsRad51 exposed to activated Jurkat S-100 extract in a cell-free system. In each case, cleavage of HsRad51 was abolished by acetyl-Asp-Glu-Val-Asp-aldehyde (Ac-DEVD-CHO). However, cleavage of IVT HsRad51 could not be demonstrated using purified caspase-2, -3 or -6 to -10, and the identity of the responsible protease thus remains to be determined. In summary, we have shown that HsRad51 belongs to a group of repair proteins, including PARP and DNA-dependent protein kinase, which are specifically cleaved during the execution phase of apoptosis.

ObjectiveMyocyte death occurs by necrosis and caspase-mediated apoptosis in the setting of myocardial infarction. In vitro studies suggest that caspase activation within myocytes causes contractile protein degradation without inducing cell death. Thus, caspase activation may evoke left ventricular remodeling through 2 independent processes post-myocardial infarction. However, the effects of caspase activation on left ventricular geometry post-myocardial infarction remain unclear. This project applied broad-spectrum caspase inhibition to a chronic porcine model of myocardial infarction.MethodsCoronary snares and sonomicrometry crystals in remote and area-at-risk regions were placed in pigs (n = 22, 34 kg). Geometric measurements at end diastole and end systole, including left ventricular area by echocardiography and interregional distance by sonomicrometry, were obtained at baseline. Coronary occlusion was instituted for 60 minutes, followed by reperfusion and repeated geometric measurements at 7 days, including left ventriculography. At reperfusion, pigs were randomized to saline (n = 12) or caspase inhibition (n = 10, IDN6734, 2 mg/kg intravenously, then 2 mg · kg · h for 24 hours) at a dose that achieved desired plasma concentrations (790 ± 142 ng/mL) as predicted by prior pharmacokinetic studies.ResultsInfarct size and 24-hour troponin-I values were not significantly different between the saline and caspase inhibition groups (51% ± 8% vs 42% ± 6% and 189 ± 20 ng/mL vs 152 ± 26 ng/mL, respectively, P > .10). At 7 days, end-diastole volume was increased in both groups compared with reference control values (47 ± 1 mL, P < .05), but it was decreased with caspase inhibition (72 ± 4 mL) compared with saline (84 ± 4 mL, P < .05). Similarly, end-diastole and end-systole areas increased by 32% ± 3% and 81% ± 16% in the saline group but were attenuated with caspase inhibition (19% ± 3% and 31% ± 10%, respectively, P < .05). End-diastole interregional distance increased by 30% ± 7% in the saline group but was attenuated with caspase inhibition (12% ± 5%, P < .05).ConclusionDespite equivalent degrees of myocardial injury, caspase inhibition reduced post-myocardial infarction left ventricular remodeling as evidenced by multiple, independent assessments of left ventricular dilation. Thus, caspase activation alters left ventricular geometry in the absence of significant effects on myocardial injury.