DIRK Schemes with High Weak Stage Order

Runge-Kutta time-stepping methods in general suffer from order reduction: the observed order of convergence may be less than the formal order when applied to certain stiff problems. Order reduction can be avoided by using methods with high stage order. However, diagonally-implicit Runge-Kutta (DIRK) schemes are limited to low stage order. In this paper we explore a weak stage order criterion, which for initial boundary value problems also serves to avoid order reduction, and which is compatible with a DIRK structure. We provide specific DIRK schemes of weak stage order up to 3, and demonstrate their performance in various examples.Comment: 10 pages, 5 figure

Symmetrically processed splitting integrators for enhanced hamiltonian monte carlo sampling

We construct integrators to be used in Hamiltonian (or Hybrid) Monte Carlo sampling. The new integrators are easily implementable and, for a given computational budget, may deliver five times as many accepted proposals as standard leapfrog/Verlet without impairing in any way the quality of the samples. They are based on a suitable modification of the processing technique first introduced by Butcher. The idea of modified processing may also be useful for other purposes, like the construction of high-order splitting integrators with positive coefficients

Regulation of pancreatic cancer aggressiveness by stromal stiffening

No abstract available

EUV-driven ionospheres and electron transport on extrasolar giant planets orbiting active stars

The composition and structure of the upper atmospheres of extrasolar giant planets (EGPs) are affected by the high-energy spectrum of their host stars from soft X-rays to the extreme ultraviolet (EUV). This emission depends on the activity level of the star, which is primarily determined by its age. In this study, we focus upon EGPs orbiting K- and M-dwarf stars of different ages – ϵ Eridani, AD Leonis, AU Microscopii – and the Sun. X-ray and EUV (XUV) spectra for these stars are constructed using a coronal model. These spectra are used to drive both a thermospheric model and an ionospheric model, providing densities of neutral and ion species. Ionisation – as a result of stellar radiation deposition – is included through photo-ionisation and electron-impact processes. The former is calculated by solving the Lambert-Beer law, while the latter is calculated from a supra-thermal electron transport model. We find that EGP ionospheres at all orbital distances considered (0.1−1 AU) and around all stars selected are dominated by the long-lived H+ ion. In addition, planets with upper atmospheres where H2 is not substantially dissociated (at large orbital distances) have a layer in which H3+ is the major ion at the base of the ionosphere. For fast-rotating planets, densities of short-lived H3+ undergo significant diurnal variations, with the maximum value being driven by the stellar X-ray flux. In contrast, densities of longer-lived H+ show very little day/night variability and the magnitude is driven by the level of stellar EUV flux. The H3+ peak in EGPs with upper atmospheres where H2 is dissociated (orbiting close to their star) under strong stellar illumination is pushed to altitudes below the homopause, where this ion is likely to be destroyed through reactions with heavy species (e.g. hydrocarbons, water). The inclusion of secondary ionisation processes produces significantly enhanced ion and electron densities at altitudes below the main EUV ionisation peak, as compared to models that do not include electron-impact ionisation. We estimate infrared emissions from H3+, and while, in an H/H2/He atmosphere, these are larger from planets orbiting close to more active stars, they still appear too low to be detected with current observatories

Isolation and characterization of cytotoxic and insulin-releasing components from the venom of the black-necked spitting cobra Naja nigricollis (Elapidae)

Four peptides with cytotoxic activity against BRIN-BD11 rat clonal β-cells were purified from the venom of the black-necked spitting cobra Naja nigricollis using reversed-phase HPLC. The peptides were identified as members of the three-finger superfamily of snake toxins by ESI-MS/MS sequencing of tryptic peptides. The most potent peptide (cytotoxin-1N) showed strong cytotoxic activity against three human tumour-derived cell lines (LC50 = 0.8 ± 0. 2 µM for A549 non-small cell lung adenocarcinoma cells; LC50 = 7 ± 1 µM for MDA-MB-231 breast adenocarcinoma cells; and LC50 = 9 ± 1 µM for HT-29 colorectal adenocarcinoma cells). However, all the peptides were to varying degrees cytotoxic against HUVEC human umbilical vein endothelial cells (LC50 in the range 2-22 µM) and cytotoxin-2N was moderately hemolytic (LC50 = 45 ± 3 µM against mouse erythrocytes). The lack of differential activity against cells derived from non-neoplastic tissue limits their potential for development into anti-cancer agents. In addition, two proteins in the venom, identified as isoforms of phospholipase A2, effectively stimulated insulin release from BRIN-BD11 cells (an approximately 6-fold increase in rate compared with 5.6 mM glucose alone) at a concentration (1 µM) that was not cytotoxic to the cells suggesting possible application in therapy for Type 2 diabetes

Formulation and performance of variational integrators for rotating bodies

Variational integrators are obtained for two mechanical systems whose configuration spaces are, respectively, the rotation group and the unit sphere. In the first case, an integration algorithm is presented for Euler’s equations of the free rigid body, following the ideas of Marsden et al. (Nonlinearity 12:1647–1662, 1999). In the second example, a variational time integrator is formulated for the rigid dumbbell. Both methods are formulated directly on their nonlinear configuration spaces, without using Lagrange multipliers. They are one-step, second order methods which show exact conservation of a discrete angular momentum which is identified in each case. Numerical examples illustrate their properties and compare them with existing integrators of the literature

Mechanical Systems with Symmetry, Variational Principles, and Integration Algorithms

This paper studies variational principles for mechanical systems with symmetry and their applications to integration algorithms. We recall some general features of how to reduce variational principles in the presence of a symmetry group along with general features of integration algorithms for mechanical systems. Then we describe some integration algorithms based directly on variational principles using a discretization technique of Veselov. The general idea for these variational integrators is to directly discretize Hamilton’s principle rather than the equations of motion in a way that preserves the original systems invariants, notably the symplectic form and, via a discrete version of Noether’s theorem, the momentum map. The resulting mechanical integrators are second-order accurate, implicit, symplectic-momentum algorithms. We apply these integrators to the rigid body and the double spherical pendulum to show that the techniques are competitive with existing integrators

Tissue Localization and Extracellular Matrix Degradation by PI, PII and PIII Snake Venom Metalloproteinases: Clues on the Mechanisms of Venom-Induced Hemorrhage

20 páginas, 4 figuras, 3 tablas y 7 tablas en material suplementario.Snake venom hemorrhagic metalloproteinases (SVMPs) of the PI, PII and PIII classes were compared in terms of tissue localization and their ability to hydrolyze basement membrane components in vivo, as well as by a proteomics analysis of exudates collected in tissue injected with these enzymes. Immunohistochemical analyses of co-localization of these SVMPs with type IV collagen revealed that PII and PIII enzymes co-localized with type IV collagen in capillaries, arterioles and post-capillary venules to a higher extent than PI SVMP, which showed a more widespread distribution in the tissue. The patterns of hydrolysis by these three SVMPs of laminin, type VI collagen and nidogen in vivo greatly differ, whereas the three enzymes showed a similar pattern of degradation of type IV collagen, supporting the concept that hydrolysis of this component is critical for the destabilization of microvessel structure leading to hemorrhage. Proteomic analysis of wound exudate revealed similarities and differences between the action of the three SVMPs. Higher extent of proteolysis was observed for the PI enzyme regarding several extracellular matrix components and fibrinogen, whereas exudates from mice injected with PII and PIII SVMPs had higher amounts of some intracellular proteins. Our results provide novel clues for understanding the mechanisms by which SVMPs induce damage to the microvasculature and generate hemorrhage.This work was performed in partial fulfillment of the requirements for the PhD degree for Cristina Herrera at Universidad de Costa Rica.Peer reviewe

Increased circulating microRNAs miR-342-3p and miR-21-5p in natural sheep prion disease

Scrapie is a transmissible spongiform encephalopathy (TSE), or prion disease, of sheep and goats. As no simple diagnostic tests are yet available to detect TSEs in vivo, easily accessible biomarkers could facilitate the eradication of scrapie agents from the food chain. To this end, we analysed by quantitative reverse transcription PCR a selected set of candidate microRNAs (miRNAs) from circulating blood plasma of naturally infected, classical scrapie sheep that demonstrated clear scrapie symptoms and pathology. Significant scrapie-associated increase was repeatedly found for miR-342-3p and miR-21-5p. This is the first demonstration, to our knowledge, of circulating miRNA alterations in any animal suffering from TSE. Genome-wide expression studies are warranted to investigate the true depth of miRNA alterations in naturally occurring TSEs, especially in presymptomatic animals, as the presented study demonstrates the potential feasibility of miRNAs as circulating TSE biomarkers