Large-Eddy Simulation of inhomogeneous canopy flows using high resolution terrestrial laser scanning data

The effect of sub-tree forest heterogeneity in the flow past a clearing is investigated by means of large-eddy simulation (LES). For this purpose, a detailed representation of the canopy has been acquired by terrestrial laser scanning for a patch of approximately 190m length in the field site “Tharandter Wald”, near the city of Dresden, Germany. The scanning data are used to produce a high resolution plant area distribution (PAD) that is averaged over approximately one tree height (30m) along the transverse direction, in order to simplify the LES study. Despite the smoothing involved with this procedure, the resulting two-dimensional PAD maintains a rich vertical and horizontal structure. For the LES study, the PAD is embedded in a larger domain covered with an idealized, horizontally homogeneous canopy. Simulations are performed for neutral conditions and compared to a LES with homogeneous PAD and recent field measurements. The results reveal a considerable influence of small-scale plant distribution on the mean velocity field as well as on turbulence data. Particularly near the edges of the clearing, where canopy structure is highly variable, usage of a realistic PAD appears to be crucial for capturing the local flow structure. Inside the forest, local variations in plant density induce a complex pattern of upward and downward motions, which remain visible in the mean flow and make it difficult to identify the “adjustment zone” behind the windward edge of the clearing

Large-Eddy Simulation Study of the Effects on Flow of a Heterogeneous Forest at Sub-tree Resolution

Abstract The effect of three-dimensional plant heterogeneity on flow past a clearing is investigated by means of large-eddy simulation. A detailed representation of the canopy has been acquired by terrestrial laser scanning for a patch of approximately 328m length and 172m width at the field site “TharandterWald”, near the city of Dresden, Germany. The scanning data are used to produce a highly resolved, three-dimensional plant area distribution representing the actual canopy. Hence, the vegetation maintains a rich horizontal and vertical structure including the three-dimensional clearing. The scanned plant area density is embedded in a larger domain, which is filled with a heterogeneous forest generated by the virtual canopy generator of Bohrer et al. (Tellus B 59:566–576, 2007). Based on forest inventory maps and airborne laser scanning, the characteristics of the actual canopy are preserved. Furthermore, the topography is extracted from a digital terrain model with some modifications to accommodate for periodic boundary conditions. A large-eddy simulation is performed for neutral atmospheric conditions and compared to simulations of a two-dimensional plant area density and an one-year-long field experiment conducted at the corresponding field site. The results reveal a considerable influence of the plant heterogeneity on the mean velocity field as well as on the turbulent quantities. The three-dimensional environment, e.g., the oblique edges combined with horizontal and vertical variations in plant area density and the topography create a sustained vertical and cross-flow velocity. Downstream of the windward forest edge an enhanced gust zone develops, whose intensity and relative position are influenced by the local canopy density and, therefore, is not constant along the edge. These results lead us to the conclusion that the usage of a three-dimensional plant area distribution is essential for capturing the flow features inside the canopy and within the mixing layer above

Von willebrand and factor VIII portosystemic circulation gradient in cirrhosi. Implications for portal vein thrombosis

OBJECTIVES: Portal vein thrombosis seems to be dependent on local hypercoagulation and venous stasis; data regarding endothelial damage are lacking. METHODS: von Willebrad factor, a marker of endothelial damage/perturbation, factor VIII, and lipopolysaccharides (LPS) were studied in the portal and systemic circulation of 20 cirrhotic patients undergoing transjugular intrahepatic portosystemic procedure. RESULTS: von Willebrad factor, factor VIII, and LPS were higher in the portal compared with systemic circulation, with a significant correlation between LPS and the other 2 variables. DISCUSSION: Endothelial damage and hypercoagulation coexist in the portal tree of patients with cirrhosis, and both could contribute to portal vein thrombosis. LPS may be a potential trigger of endothelial damage

Staphylococcus epidermidis Strategies to Avoid Killing by Human Neutrophils

Staphylococcus epidermidis is a leading nosocomial pathogen. In contrast to its more aggressive relative S. aureus, it causes chronic rather than acute infections. In highly virulent S. aureus, phenol-soluble modulins (PSMs) contribute significantly to immune evasion and aggressive virulence by their strong ability to lyse human neutrophils. Members of the PSM family are also produced by S. epidermidis, but their role in immune evasion is not known. Notably, strong cytolytic capacity of S. epidermidis PSMs would be at odds with the notion that S. epidermidis is a less aggressive pathogen than S. aureus, prompting us to examine the biological activities of S. epidermidis PSMs. Surprisingly, we found that S. epidermidis has the capacity to produce PSMδ, a potent leukocyte toxin, representing the first potent cytolysin to be identified in that pathogen. However, production of strongly cytolytic PSMs was low in S. epidermidis, explaining its low cytolytic potency. Interestingly, the different approaches of S. epidermidis and S. aureus to causing human disease are thus reflected by the adaptation of biological activities within one family of virulence determinants, the PSMs. Nevertheless, S. epidermidis has the capacity to evade neutrophil killing, a phenomenon we found is partly mediated by resistance mechanisms to antimicrobial peptides (AMPs), including the protease SepA, which degrades AMPs, and the AMP sensor/resistance regulator, Aps (GraRS). These findings establish a significant function of SepA and Aps in S. epidermidis immune evasion and explain in part why S. epidermidis may evade elimination by innate host defense despite the lack of cytolytic toxin expression. Our study shows that the strategy of S. epidermidis to evade elimination by human neutrophils is characterized by a passive defense approach and provides molecular evidence to support the notion that S. epidermidis is a less aggressive pathogen than S. aureus

TurbEFA: an interdisciplinary effort to investigate the turbulent flow across a forest clearing

the atmosphere within turbulence closure models is mainly limited by a realistic three-dimensional (3D) representation of the vegetation architecture. Within this contribution we present a method to record the 3D vegetation structure and to use this information to derive model parameters that are suitable for numerical flow models. A mixed conifer forest stand around a clearing was scanned and represented by a dense 3D point cloud applying a terrestrial laser scanner. Thus, the plant area density (PAD) with a resolution of one cubic meter was provided for analysis and for numerical simulations. Multi-level high-frequency wind velocity measurements were recorded simultaneously by 27 ultrasonic anemometers on 4 towers for a period of one year. The relationship between wind speed, Reynolds stress and PAD was investigated and a parametrization of the drag coefficient CD by the PAD is suggested. The derived 3D vegetation model and a simpler model (based on classical forest assessments of the site) were applied in a boundary layer model (BLM) and in large-eddy simulations (LES). The spatial development of the turbulent flow over the clearing is further demonstrated by the results of a wind tunnel experiment. The project showed, that the simulation results were improved significantly by the usage of realistic vegetation models. 3D simulations are necessary to depict the influence of heterogeneous canopies on the turbulent flow. Whereas we found limits for the mapping of the vegetation structure within the wind tunnel, there is a considerable potential for numerical simulations. The field measurements and the LES gave new insight into the turbulent flow in the vicinity and across the clearing. The results show that the zones of intensive turbulence development can not be restricted to the locations found in previous studies with more idealized canopies

Role of portal venous platelet activation in patients with decompensated cirrhosis and TIPS

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Mobile Genetic Element-Encoded Cytolysin Connects Virulence to Methicillin Resistance in MRSA

Bacterial virulence and antibiotic resistance have a significant influence on disease severity and treatment options during bacterial infections. Frequently, the underlying genetic determinants are encoded on mobile genetic elements (MGEs). In the leading human pathogen Staphylococcus aureus, MGEs that contain antibiotic resistance genes commonly do not contain genes for virulence determinants. The phenol-soluble modulins (PSMs) are staphylococcal cytolytic toxins with a crucial role in immune evasion. While all known PSMs are core genome-encoded, we here describe a previously unidentified psm gene, psm-mec, within the staphylococcal methicillin resistance-encoding MGE SCCmec. PSM-mec was strongly expressed in many strains and showed the physico-chemical, pro-inflammatory, and cytolytic characteristics typical of PSMs. Notably, in an S. aureus strain with low production of core genome-encoded PSMs, expression of PSM-mec had a significant impact on immune evasion and disease. In addition to providing high-level resistance to methicillin, acquisition of SCCmec elements encoding PSM-mec by horizontal gene transfer may therefore contribute to staphylococcal virulence by substituting for the lack of expression of core genome-encoded PSMs. Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs

Short-term western diet aggravates non-alcoholic fatty liver disease (NAFLD) with portal hypertension in TGR(mREN2)27 rats

Non-alcoholic fatty liver disease (NAFLD) is gaining in importance and is linked to obesity. Especially, the development of fibrosis and portal hypertension in NAFLD patients requires treatment. Transgenic TGR(mREN2)27 rats overexpressing mouse renin spontaneously develop NAFLD with portal hypertension but without obesity. This study investigated the additional role of obesity in this model on the development of portal hypertension and fibrosis. Obesity was induced in twelve-week old TGR(mREN2)27 rats after receiving Western diet (WD) for two or four weeks. Liver fibrosis was assessed using standard techniques. Hepatic expression of transforming growth factor-β1 (TGF-β1), collagen type Iα1, α-smooth muscle actin, and the macrophage markers Emr1, as well as the chemoattractant Ccl2, interleukin-1β (IL1β) and tumor necrosis factor-α (TNFα) were analyzed. Assessment of portal and systemic hemodynamics was performed using the colored microsphere technique. As expected, WD induced obesity and liver fibrosis as confirmed by Sirius Red and Oil Red O staining. The expression of the monocyte-macrophage markers, Emr1, Ccl2, IL1β and TNFα were increased during feeding of WD, indicating infiltration of macrophages into the liver, even though this increase was statistically not significant for the EGF module-containing mucin-like receptor (Emr1) mRNA expression levels. Of note, portal pressure increased with the duration of WD compared to animals that received a normal chow. Besides obesity, WD feeding increased systemic vascular resistance reflecting systemic endothelial and splanchnic vascular dysfunction. We conclude that transgenic TGR(mREN2)27 rats are a suitable model to investigate NAFLD development with liver fibrosis and portal hypertension. Tendency towards elevated expression of Emr1 is associated with macrophage activity point to a significant role of macrophages in NAFLD pathogenesis, probably due to a shift of the renin-angiotensin system towards a higher activation of the classical pathway. The hepatic injury induced by WD in TGR(mREN2)27 rats is suitable to evaluate different stages of fibrosis and portal hypertension in NAFLD with obesity

Collisional Velocities and Rates in Resonant Planetesimal Belts

We consider a belt of small bodies around a star, captured in one of the external or 1:1 mean-motion resonances with a massive perturber. The objects in the belt collide with each other. Combining methods of celestial mechanics and statistical physics, we calculate mean collisional velocities and collisional rates, averaged over the belt. The results are compared to collisional velocities and rates in a similar, but non-resonant belt, as predicted by the particle-in-a-box method. It is found that the effect of the resonant lock on the velocities is rather small, while on the rates more substantial. The collisional rates between objects in an external resonance are by about a factor of two higher than those in a similar belt of objects not locked in a resonance. For Trojans under the same conditions, the collisional rates may be enhanced by up to an order of magnitude. Our results imply, in particular, shorter collisional lifetimes of resonant Kuiper belt objects in the solar system and higher efficiency of dust production by resonant planetesimals in debris disks around other stars.Comment: 31 pages, 11 figures (some of them heavily compressed to fit into arxiv-maximum filesize), accepted for publication at "Celestial Mechanics and Dynamical Astronomy

Distribution and Regulation of the Mobile Genetic Element-Encoded Phenol-Soluble Modulin PSM-mec in Methicillin-Resistant Staphylococcus aureus

The phenol-soluble modulin PSM-mec is the only known staphylococcal toxin that is encoded on a mobile antibiotic resistance determinant, namely the staphylococcal cassette chromosome (SCC) element mec encoding resistance to methicillin. Here we show that the psm-mec gene is found frequently among methicillin-resistant Staphylococcus aureus (MRSA) strains of SCCmec types II, III, and VIII, and is a conserved part of the class A mec gene complex. Controlled expression of AgrA versus RNAIII in agr mutants of all 3 psm-mec-positive SCCmec types demonstrated that expression of psm-mec, which is highly variable, is controlled by AgrA in an RNAIII-independent manner. Furthermore, psm-mec isogenic deletion mutants showed only minor changes in PSMα peptide production and unchanged (or, as previously described, diminished) virulence compared to the corresponding wild-type strains in a mouse model of skin infection. This indicates that the recently reported regulatory impact of the psm-mec locus on MRSA virulence, which is opposite to that of the PSM-mec peptide and likely mediated by a regulatory RNA, is minor when analyzed in the original strain background. Our study gives new insight in the distribution, regulation, and role in virulence of the PSM-mec peptide and the psm-mec gene locus