Order-of-magnitude speedup for steady states and traveling waves via Stokes preconditioning in Channelflow and Openpipeflow

Steady states and traveling waves play a fundamental role in understanding hydrodynamic problems. Even when unstable, these states provide the bifurcation-theoretic explanation for the origin of the observed states. In turbulent wall-bounded shear flows, these states have been hypothesized to be saddle points organizing the trajectories within a chaotic attractor. These states must be computed with Newton's method or one of its generalizations, since time-integration cannot converge to unstable equilibria. The bottleneck is the solution of linear systems involving the Jacobian of the Navier-Stokes or Boussinesq equations. Originally such computations were carried out by constructing and directly inverting the Jacobian, but this is unfeasible for the matrices arising from three-dimensional hydrodynamic configurations in large domains. A popular method is to seek states that are invariant under numerical time integration. Surprisingly, equilibria may also be found by seeking flows that are invariant under a single very large Backwards-Euler Forwards-Euler timestep. We show that this method, called Stokes preconditioning, is 10 to 50 times faster at computing steady states in plane Couette flow and traveling waves in pipe flow. Moreover, it can be carried out using Channelflow (by Gibson) and Openpipeflow (by Willis) without any changes to these popular spectral codes. We explain the convergence rate as a function of the integration period and Reynolds number by computing the full spectra of the operators corresponding to the Jacobians of both methods.Comment: in Computational Modelling of Bifurcations and Instabilities in Fluid Dynamics, ed. Alexander Gelfgat (Springer, 2018

An integration of enhanced social force and crowd control models for high-density crowd simulation

Social force model is one of the well-known approaches that can successfully simulate pedestrians’ movements realistically. However, it is not suitable to simulate high-density crowd movement realistically due to the model having only three basic crowd characteristics which are goal, attraction, and repulsion. Therefore, it does not satisfy the high-density crowd condition which is complex yet unique, due to its capacity, density, and various demographic backgrounds of the agents. Thus, this research proposes a model that improves the social force model by introducing four new characteristics which are gender, walking speed, intention outlook, and grouping to make simulations more realistic. Besides, the high-density crowd introduces irregular behaviours in the crowd flow, which is stopping motion within the crowd. To handle these scenarios, another model has been proposed that controls each agent with two different states: walking and stopping. Furthermore, the stopping behaviour was categorized into a slow stop and sudden stop. Both of these proposed models were integrated to form a high-density crowd simulation framework. The framework has been validated by using the comparison method and fundamental diagram method. Based on the simulation of 45,000 agents, it shows that the proposed framework has a more accurate average walking speed (0.36 m/s) compared to the conventional social force model (0.61 m/s). Both of these results are compared to the real-world data which is 0.3267 m/s. The findings of this research will contribute to the simulation activities of pedestrians in a highly dense population

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Systolic time intervals combined with Valsalva maneuver for the diagnosis of left ventricular dysfunction in COPD exacerbations

Hamdi Boubaker,1,2 Mohamed Habib Grissa,1,2 Kaouther Beltaief,1,2 Zohra Dridi,3 Mohamed Fadhel Najjar,4 Wahid Bouida,1,2 Riadh Boukef,5 Soudani Marghli,6 Semir Nouira1,2 1Department of Emergency, Fattouma Bourguiba University Hospital, 2Research Laboratory (LR12SP18), University of Monastir, 3Department of Cardiology, 4Department of Biochemistry, Fattouma Bourguiba University Hospital, Monastir, 5Department of Emergency, Sahloul University Hospital, Sousse, 6Department of Emergency, Tahar Sfar University Hospital, Mahdia, Tunisia Background: The goal of this study was to determine the value of systolic time intervals and their change during Valsalva maneuver (VM) in the diagnosis of left ventricular dysfunction (LVD) in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD).Methods: We included 166 patients admitted to the emergency department for AECOPD. Measurement of systolic time intervals included electromechanical activation time (EMAT), left ventricular ejection time (LVET), and EMAT/LVET ratio. These were performed at baseline and during the first strain phase of the VM using a computerized phonoelectrocardiographic method. The diagnosis of LVD was determined on the basis of clinical examination, echocardiography, and brain natriuretic peptide. The values of systolic time intervals were compared between patients with and without LVD; their diagnostic performance was assessed using the area under receiver operating characteristic (ROC) curve.Results: Patients with LVD (n=95) had a significantly higher EMAT and lower LVET and EMAT/LVET ratio compared to patients without LVD (n=71); the area under ROC curve was 0.79, 0.88, and 0.90, respectively, for EMAT, LVET, and EMAT/LVET ratio. All baseline systolic time intervals changed significantly during VM in patients without LVD but they did not change in patients with LVD. The area under ROC curve increased to 0.84 and 0.93, ­respectively, for EMAT and EMAT/LVET ratio but did not change for LVET.Conclusion: Simple and noninvasive measurements of systolic time intervals combined with VM could be helpful to detect or rule out LVD in patients admitted to the emergency room for COPD excacerbation. The EMAT/LVET ratio seems to have the best diagnostic value. Keywords: chronic obstructive pulmonary disease, exacerbation, systolic time intervals, Valsalva maneuver&nbsp

The emergence of Clostridium difficile PCR-ribotype 001 in Slovakia

Molecular basis of bacterial pathogenesis, virulence factors and antibiotic resistanc