Predicting equilibrium states with Reynolds stress closures in channel flow and homogeneous shear flow

Turbulent channel flow and homogeneous shear flow have served as basic building block flows for the testing and calibration of Reynolds stress models. A direct theoretical connection is made between homogeneous shear flow in equilibrium and the log-layer of fully-developed turbulent channel flow. It is shown that if a second-order closure model is calibrated to yield good equilibrium values for homogeneous shear flow it will also yield good results for the log-layer of channel flow provided that the Rotta coefficient is not too far removed from one. Most of the commonly used second-order closure models introduce an ad hoc wall reflection term in order to mask deficient predictions for the log-layer of channel flow that arise either from an inaccurate calibration of homogeneous shear flow or from the use of a Rotta coefficient that is too large. Illustrative model calculations are presented to demonstrate this point which has important implications for turbulence modeling

Application of a new K-tau model to near wall turbulent flows

A recently developed K-tau model for near wall turbulent flows is applied to two severe test cases. The turbulent flows considered include the incompressible flat plate boundary layer with the adverse pressure gradients and incompressible flow past a backward facing step. Calculations are performed for this two-equation model using an anisotropic as well as isotropic eddy-viscosity. The model predictions are shown to compare quite favorably with experimental data

To Duckweeds (\u3cem\u3eLandoltia punctata\u3c/em\u3e), Nanoparticulate Copper Oxide is More Inhibitory than the Soluble Copper in the Bulk Solution

CuO nanoparticles (CuO-NP) were synthesized in a hydrogen diffusion flame. Particle size and morphology were characterized using scanning mobility particle sizing, Brunauer–Emmett–Teller analysis, dynamic light scattering, and transmission electron microscopy. The solubility of CuO-NP varied with both pH and presence of other ions. CuO-NP and comparable doses of soluble Cu were applied to duckweeds, Landoltia punctata. Growth was inhibited 50% by either 0.6 mg L−1 soluble copper or by 1.0 mg L−1 CuO-NP that released only 0.16 mg L−1 soluble Cu into growth medium. A significant decrease of chlorophyll was observed in plants stressed by 1.0 mg L−1 CuO-NP, but not in the comparable 0.2 mg L−1 soluble Cu treatment. The Cu content of fronds exposed to CuO-NP is four times higher than in fronds exposed to an equivalent dose of soluble copper, and this is enough to explain the inhibitory effects on growth and chlorophyll content

NetProphet 3: A machine learning framework for transcription factor network mapping and multi-omics integration

MOTIVATION: Many methods have been proposed for mapping the targets of transcription factors (TFs) from gene expression data. It is known that combining outputs from multiple methods can improve performance. To date, outputs have been combined by using either simplistic formulae, such as geometric mean, or carefully hand-tuned formulae that may not generalize well to new inputs. Finally, the evaluation of accuracy has been challenging due to the lack of genome-scale, ground-truth networks. RESULTS: We developed NetProphet3, which combines scores from multiple analyses automatically, using a tree boosting algorithm trained on TF binding location data. We also developed three independent, genome-scale evaluation metrics. By these metrics, NetProphet3 is more accurate than other commonly used packages, including NetProphet 2.0, when gene expression data from direct TF perturbations are available. Furthermore, its integration mode can forge a consensus network from gene expression data and TF binding location data. AVAILABILITY AND IMPLEMENTATION: All data and code are available at https://zenodo.org/record/7504131#.Y7Wu3i-B2x8. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

The prion strain phenomenon: molecular basis and unprecedented features.

Prions are unconventional infectious agents responsible for transmissible spongiform encephalopathies. Compelling evidences indicate that prions are composed exclusively by a misfolded form of the prion protein (PrP(Sc)) that replicates in the absence of nucleic acids. One of the most challenging problems for the prion hypothesis is the existence of different strains of the infectious agent. Prion strains have been characterized in most of the species. Biochemical characteristics of PrP(Sc) used to identify each strain include glycosylation profile, electrophoretic mobility, protease resistance, and sedimentation. In vivo, prion strains can be differentiated by the clinical signs, incubation period after inoculation and the lesion profiles in the brain of affected animals. Sources of prion strain diversity are the inherent conformational flexibility of the prion protein, the presence of PrP polymorphisms and inter-species transmissibility. The existence of the strain phenomenon is not only a scientific challenge, but it also represents a serious risk for public health. The dynamic nature and inter-relations between strains and the potential for the generation of a large number of new prion strains is the perfect recipe for the emergence of extremely dangerous new infectious agents

L’endocardite à Bartonella en Tunisie: Particularités lésionnelles et évolutives

L'endocardite à Bartonalla est une infection ubiquitaire, son diagnostic est difficile vu qu'il s'agit souvent d'endocardite à hémoculture négative. Lebut de cette étude est d'analyser les particularités lésionnelles et  évolutives de cette entité dans un pays du nord d'Afrique, la Tunisie et dedémontrer la gravité de cette infection. Nous avons étudié  rétrospectivement les dossiers médicaux de 20 patients atteints  d'endocardite à Bartonella, confirmée selon les critères de Dukes modifiés. L'âge moyen de nos patients était 37 ans avec une prédominance  masculine (SR=3). Tous nos malades avaient un niveau socio-économique bas. Le motif essentiel de consultation était la dyspnée, 6 patients étaient admis dans un tableau d'insuffisance cardiaque congestive. Une  prédilection des lésions au niveau de la valve aortique a été notée (14 cas). Quatorze patients avaient des végétations endocarditiques avec une taille qui dépasse 10 mm chez 8 malades. La majorité des patients (18 patients) présentaient une régurgitation valvulaire massive en rapport principalement avec des mutilations importantes (6 cas de ruptures de cordages mitraux, 2 cas de déchirures des sigmoïdes aortiques, un cas de perforation valvulaire aortique, un cas de désinsertion de prothèse  mitrale). Quinze malades (3/4) avaient nécessité une chirurgie à la phase active de la maladie, l'indication majeure était l'insuffisance cardiaque. Une complication neurologique était notée chez 2 malades et une  complication rénale chez 3 malades. Treize patients étaient guéris, 5 malades étaient décédés et 2 malades opérés ont présenté une  réinfection à staphylococcus aureus et à candida albicans en  postopératoire. L'endocardite à Bartonella est une infection grave. Cette Bactérie possède un potentiel destructif important. Le recours à la chirurgie est quasi constant. La morbi-mortalité est élevée. La recherche de cette bactérie devrait être alors systématique chez nos malades suspects d'endocardite d'autant plus que la bartonellose est endémique sur nos terres

The mechanistic and prognostic implications of heart rate variability analysis in patients with cirrhosis

Chronic liver damage leads to scarring of the liver tissue and ultimately a systemic illness known as cirrhosis. Patients with cirrhosis exhibit multi-organ dysfunction and high mortality. Reduced heart rate variability (HRV) is a hallmark of cirrhosis, reflecting a state of defective cardiovascular control and physiological network disruption. Several lines of evidence have revealed that decreased HRV holds prognostic information and can predict survival of patients independent of the severity of liver disease. Thus, the aim of this review is to shed light on the mechanistic and prognostic implications of HRV analysis in patients with cirrhosis. Notably, several studies have extensively highlighted the critical role systemic inflammation elicits in conferring the reduction in patients’ HRV. It appears that IL-6 is likely to play a central mechanistic role, whereby its levels also correlate with manifestations, such as autonomic neuropathy and hence the partial uncoupling of the cardiac pacemaker from autonomic control. Reduced HRV has also been reported to be highly correlated with the severity of hepatic encephalopathy, potentially through systemic inflammation affecting specific brain regions, involved in both cognitive function and autonomic regulation. In general, the prognostic ability of HRV analysis holds immense potential in improving survival rates for patients with cirrhosis, as it may indeed be added to current prognostic indicators, to ultimately increase the accuracy of selecting the recipient most in need of liver transplantation. However, a network physiology approach in the future is critical to delineate the exact mechanistic basis by which decreased HRV confers poor prognosis

Magnetisation studies in Co-Tb / Pt multilayers

We have studied the magnetization in Co86Tb14/Pt multilayers under fields up to 1.8 T and as at room temperature. As the do-Tb layer thickness (tCoTb) decreases below 200 Å the saturation magnetization magnetization (M) increases, the rectangularity of the M-H loops and the coercivity (Hc ) decrease. The effective anisotropy Keff of the multilayers was determined by a torque magnetometer. The product Keff×tCoTb shows a linear dependence with tCoTb as normally found for the superlatices yielding the bulk and surface anisotropies of 106 erg/cm3 and –0.2 erg/cm2 , respectively. These results are explained in terms of an interfacial Co-Pt layer. Keff and Hc are related by the equation Hc = α Keffn/M with the fitting parameters α and n.We have studied the magnetization in Co86Tb14/Pt multilayers under fields up to 1.8 T and as at room temperature. As the do-Tb layer thickness (tCoTb) decreases below 200 Å the saturation magnetization magnetization (M) increases, the rectangularity of the M-H loops and the coercivity (Hc ) decrease. The effective anisotropy Keff of the multilayers was determined by a torque magnetometer. The product Keff×tCoTb shows a linear dependence with tCoTb as normally found for the superlatices yielding the bulk and surface anisotropies of 106 erg/cm3 and –0.2 erg/cm2 , respectively. These results are explained in terms of an interfacial Co-Pt layer. Keff and Hc are related by the equation Hc = α Keffn/M with the fitting parameters α and n

1,3,6-Trimethyl­pyrano[4,3-b]pyrrol-4(1H)-one

All the non-H atoms of the title compound, C10H11NO2, are almost coplanar [maximum deviation = 0.040 (3) Å]. The crystal structure is stabilized by C—H⋯O hydrogen bonds