Parameter Inference in the Pulmonary Circulation of Mice

This study focuses on parameter inference in a pulmonary blood cir- culation model for mice. It utilises a fluid dynamics network model that takes selected parameter values and aims to mimic features of the pulmonary haemody- namics under normal physiological and pathological conditions. This is of medical relevance as it allows monitoring of the progression of pulmonary hypertension. Constraint nonlinear optimization is successfully used to learn the parameter values

Crack fronts and damage in glass at the nanometer scale

We have studied the low speed fracture regime for different glassy materials with variable but controlled length scales of heterogeneity in a carefully mastered surrounding atmosphere. By using optical and atomic force microscopy (AFM) techniques we tracked in real-time the crack tip propagation at the nanometer scale on a wide velocity range (mm/s - pm/s and below). The influence of the heterogeneities on this velocity is presented and discussed. Our experiments reveal also -for the first time- that the crack progresses through nucleation, growth and coalescence of nanometric damage cavities within the amorphous phase. This may explain the large fluctuations observed in the crack tip velocities for the smallest values. This behaviour is very similar to what is involved, at the micrometric scale, in ductile fracture. The only difference is very likely due to the related length scales (nanometric instead of micrometric). Consequences of such a nano-ductile fracture mode observed at a temperature far below the glass transition temperature in glass is finally discussed.Comment: 12 pages, 8 figures, submitted to Journal of Physics: Condensed Matter; Invited talk at Glass and Optical Materials Division Fall 2002 Meeting, Pittsburgh, Pa, US

The Critical Exponent is Computable for Automatic Sequences

The critical exponent of an infinite word is defined to be the supremum of the exponent of each of its factors. For k-automatic sequences, we show that this critical exponent is always either a rational number or infinite, and its value is computable. Our results also apply to variants of the critical exponent, such as the initial critical exponent of Berthe, Holton, and Zamboni and the Diophantine exponent of Adamczewski and Bugeaud. Our work generalizes or recovers previous results of Krieger and others, and is applicable to other situations; e.g., the computation of the optimal recurrence constant for a linearly recurrent k-automatic sequence.Comment: In Proceedings WORDS 2011, arXiv:1108.341

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells

An integrated model checking toolset for kernel P systems

P systems are the computational models introduced in the context of membrane computing, a computational paradigm within the more general area of unconventional computing. Kernel P (kP) systems are defined to unify the specification of different variants of P systems, motivated by challenging theoretical aspects and the need to model different problems. kP systems are supported by a software framework, called kPWORKBENCH, which integrates a set of related simulation and verification methodologies and tools. In this paper, we present an extension to kPWORKBENCH with a new model checking framework supporting the formal verification of kP system models. This framework supports both LTL and CTL properties. To make the property specification an easier task, we propose a property language, composed of natural language statements. We demonstrate our proposed methodology with an example

Section Extension from Hyperbolic Geometry of Punctured Disk and Holomorphic Family of Flat Bundles

The construction of sections of bundles with prescribed jet values plays a fundamental role in problems of algebraic and complex geometry. When the jet values are prescribed on a positive dimensional subvariety, it is handled by theorems of Ohsawa-Takegoshi type which give extension of line bundle valued square-integrable top-degree holomorphic forms from the fiber at the origin of a family of complex manifolds over the open unit 1-disk when the curvature of the metric of line bundle is semipositive. We prove here an extension result when the curvature of the line bundle is only semipositive on each fiber with negativity on the total space assumed bounded from below and the connection of the metric locally bounded, if a square-integrable extension is known to be possible over a double point at the origin. It is a Hensel-lemma-type result analogous to Artin's application of the generalized implicit function theorem to the theory of obstruction in deformation theory. The motivation is the need in the abundance conjecture to construct pluricanonical sections from flatly twisted pluricanonical sections. We also give here a new approach to the original theorem of Ohsawa-Takegoshi by using the hyperbolic geometry of the punctured open unit 1-disk to reduce the original theorem of Ohsawa-Takegoshi to a simple application of the standard method of constructing holomorphic functions by solving the d-bar equation with cut-off functions and additional blowup weight functions

Fatal progression of experimental visceral leishmaniasis is associated with intestinal parasitism and secondary infection by commensal bacteria, and is delayed by antibiotic prophylaxis.

Leishmania donovani causes visceral leishmaniasis (VL), which is typically fatal without treatment. There is substantial variation between individuals in rates of disease progression, response to treatment and incidence of post-treatment sequelae, specifically post-kala-azar dermal leishmaniasis (PKDL). Nevertheless, the majority of infected people are asymptomatic carriers. Hamsters and mice are commonly used as models of fatal and non-fatal VL, respectively. Host and parasite genetics are likely to be important factors, but in general the reasons for heterogeneous disease presentation in humans and animal models are poorly understood. Host microbiota has become established as a factor in cutaneous forms of leishmaniasis but this has not been studied in VL. We induced intestinal dysbiosis in mice and hamsters by long-term treatment with broad-spectrum antibiotics in their drinking water. There were no significant differences in disease presentation in dysbiotic mice. In contrast, dysbiotic hamsters infected with L. donovani had delayed onset and progression of weight loss. Half of control hamsters had a rapid progression phenotype compared with none of the ABX-treated animals and the nine-month survival rate was significantly improved compared to untreated controls (40% vs. 10%). Antibiotic-treated hamsters also had significantly less severe hepatosplenomegaly, which was accompanied by a distinct cytokine gene expression profile. The protective effect was not explained by differences in parasite loads or haematological profiles. We further found evidence that the gut-liver axis is a key aspect of fatal VL progression in hamsters, including intestinal parasitism, bacterial translocation to the liver, malakoplakia and iron sequestration, none of which occurred in non-progressing murine VL. Diverse bacterial genera were cultured from VL affected livers, of which Rodentibacter was specifically absent from ABX-treated hamsters, indicating this pathobiont may play a role in promoting disease progression. The results provide experimental support for antibiotic prophylaxis against secondary bacterial infections as an adjunct therapy in human VL patients

Comparison of Tissue Injury from Focused Ultrasonic Propulsion of Kidney Stones Versus Extracorporeal Shock Wave Lithotripsy

Purpose Focused ultrasonic propulsion is a new non-invasive technique designed to move kidney stones and stone fragments out of the urinary collecting system. However, the extent of tissue injury associated with this technique is not known. As such, we quantitated the amount of tissue injury produced by focused ultrasonic propulsion under simulated clinical treatment conditions, and under conditions of higher power or continuous duty cycles, and compared those results to SWL injury. Materials and Methods A human calcium oxalate monohydrate stone and/or nickel beads were implanted (with ureteroscopy) into 3 kidneys of live pigs (45–55 kg) and repositioned using focused ultrasonic propulsion. Additional pig kidneys were exposed to SWL level pulse intensities or continuous ultrasound exposure of 10 minutes duration (ultrasound probe either transcutaneous or on the kidney). These kidneys were compared to 6 kidneys treated with an unmodified Dornier HM3 Lithotripter (2400 shocks, 120 SWs/min and 24 kV). Histological analysis was performed to assess the volume of hemorrhagic tissue injury created by each technique (% functional renal volume, FRV). Results SWL produced a lesion of 1.56±0.45% FRV. Ultrasonic propulsion produced no detectable lesion with the simulated clinical treatment. A lesion of 0.46±0.37% FRV or 1.15±0.49% FRV could be produced if excessive treatment parameters were used while the ultrasound probe was placed on the kidney. Conclusions Focused ultrasonic propulsion produced no detectable morphological injury to the renal parenchyma when using clinical treatment parameters and produced injury comparable in size to SWL when using excessive treatment parameters