Observation of a Self-Limiting, Shear-Induced Turbulent Inversion Layer Above Marine Stratocumulus

High-resolution measurements of thermodynamic, microphysical, and turbulence properties inside a turbulent inversion layer above a marine stratocumulus cloud layer are presented. The measurements are performed with the helicopter-towed measurement payload Airborne Cloud Turbulence Observation System (ACTOS), which allows for sampling with low true air speeds and steep profiles through cloud top. Vertical profiles show that the turbulent inversion layer consists of clear air above the cloud top, with nearly linear profiles of potential temperature, horizontal wind speed, absolute humidity, and concentration of interstitial aerosol. The layer is turbulent, with an energy dissipation rate nearly the same as that in the lower cloud, suggesting that the two are actively coupled, but with significant anisotropic turbulence at the large scales within the turbulent inversion layer. The turbulent inversion layer is traversed six times and the layer thickness is observed to vary between 37 and 85 m, whereas the potential temperature and horizontal wind speed differences at the top and bottom of the layer remain essentially constant. The Richardson number therefore increases with increasing layer thickness, from approximately 0. 2 to 0. 7, suggesting that the layer develops to the point where shear production of turbulence is sufficiently weak to be balanced by buoyancy suppression. This picture is consistent with prior numerical simulations of the evolution of turbulence in localized stratified shear layers. It is observed that the large eddy scale is suppressed by buoyancy and is on the order of the Ozmidov scale, much less than the thickness of the turbulent inversion layer, such that direct mixing between the cloud top and the free troposphere is inhibited, and the entrainment velocity tends to decrease with increasing turbulent inversion-layer thickness. Qualitatively, the turbulent inversion layer likely grows through nibbling rather than engulfment

Genome Wide Transcriptome Analysis of Dendritic Cells Identifies Genes with Altered Expression in Psoriasis

Activation of dendritic cells by different pathogens induces the secretion of proinflammatory mediators resulting in local inflammation. Importantly, innate immunity must be properly controlled, as its continuous activation leads to the development of chronic inflammatory diseases such as psoriasis. Lipopolysaccharide (LPS) or peptidoglycan (PGN) induced tolerance, a phenomenon of transient unresponsiveness of cells to repeated or prolonged stimulation, proved valuable model for the study of chronic inflammation. Thus, the aim of this study was the identification of the transcriptional diversity of primary human immature dendritic cells (iDCs) upon PGN induced tolerance. Using SAGESeq approach, a tag-based transcriptome sequencing method, we investigated gene expression changes of primary human iDCs upon stimulation or restimulation with Staphylococcus aureus derived PGN, a widely used TLR2 ligand. Based on the expression pattern of the altered genes, we identified non-tolerizeable and tolerizeable genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (Kegg) analysis showed marked enrichment of immune-, cell cycle- and apoptosis related genes. In parallel to the marked induction of proinflammatory mediators, negative feedback regulators of innate immunity, such as TNFAIP3, TNFAIP8, Tyro3 and Mer are markedly downregulated in tolerant cells. We also demonstrate, that the expression pattern of TNFAIP3 and TNFAIP8 is altered in both lesional, and non-lesional skin of psoriatic patients. Finally, we show that pretreatment of immature dendritic cells with anti-TNF-α inhibits the expression of IL-6 and CCL1 in tolerant iDCs and partially releases the suppression of TNFAIP8. Our findings suggest that after PGN stimulation/restimulation the host cell utilizes different mechanisms in order to maintain critical balance between inflammation and tolerance. Importantly, the transcriptome sequencing of stimulated/restimulated iDCs identified numerous genes with altered expression to date not associated with role in chronic inflammation, underlying the relevance of our in vitro model for further characterization of IFNprimed iDCs

Vinegar production from fruit concentrates: effect on volatile composition and antioxidant activity

Vinegar stands as a highly appreciated fermented food product due to several functional properties and multiple applications. This work focuses on vinegar production from fruit wines derived from fruit concentrates, to attain a food product with nutritional added value. Four fruit vinegars (orange, mango, cherry and banana), were produced and characterized, with total acidities of 5.3 ± 0.3% for orange, 5.6 ± 0.2% for mango, 4.9 ± 0.4% for cherry and 5.4 ± 0.4% for banana. Acetification showed impact on aroma volatiles, mainly related to oxidative reactions. Minor volatiles associated with varietal aroma were identified, monoterpenic alcohols in orange vinegar, esters in banana vinegar, C13-norisoprenoids in cherry vinegar and lactones in mango vinegar, indicating fruit vinegars differentiated sensory quality. Total antioxidant activity analysis by FRAP, revealed fruit vinegars potential to preserve and deliver fruit functional properties. Antioxidant activity of fruit vinegars, expressed as equivalents of Fe2SO4, was of 11.0 ± 1.67 mmol L1 for orange, 4.8 ± 0.5 mmol L1 for mango, 18.6 ± 2.33 mmol L1 for cherry and 3.7 ± 0.3 mmol L1 for banana. Therefore, fruit vinegars presented antioxidant activity close to the reported for the corresponding fruit, and between 8 and 40 folds higher than the one found in commercial cider vinegar, demonstrating the high functional potential of these novel vinegar products.Authors would like to acknowledge the financial funding of: FruitVinegarDRINK QREN Project (Ref. 23209), Project "BioInd-Biotechnology and Bioengineering for improved Industrial and Agro-Food processes, REF. NORTE-07-0124-FEDER-000028" Co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER and the FCT Strategic Project Pest OE/EQB/LA0023/2013. Authors would also like to acknowledge the participation of Mendes Goncalves S.A. and Frulact S.A. staff, for the active input, which led to the work basis and rationale.info:eu-repo/semantics/publishedVersio

Prostate-specific antigen testing in Tyrol, Austria: prostate cancer mortality reduction was supported by an update with mortality data up to 2008

Objectives: The objective of this study was to update an in-depth analysis of the time trend for prostate cancer (PCA) mortality in the population of Tyrol by 5 years, namely to 2008. In Tyrol, prostate-specific antigen (PSA) tests were introduced in 1988/89; more than three-quarters of all men in the age group 45–74 had at least one PSA test in the past decade. Methods: We applied the same model as in a previous publication, i.e., an age-period-cohort model using Poisson regression, to the mortality data covering more than three decades from 1970 to 2008. Results: For Tyrol from 2004 to 2008 in the age group 60+ period terms show a significant reduction in prostate cancer mortality with a risk ratio of 0.70 (95% confidence interval 0.57, 0.87) for Tyrol, and for Austria excluding Tyrol a moderate reduction with a risk ratio of 0.92 (95% confidence interval 0.87, 0.97), each compared to the mortality rate in the period 1989–1993. Conclusions: This update strengthens our previously published results, namely that PSA testing offered to a population at no charge can reduce prostate cancer mortality. The extent of mortality reduction is in line with that reported in the other recent publications. However, our data do not permit us to fully assess the harms associated with PCA screening, and no recommendation for PSA screening can be made without a careful evaluation of overdiagnosis and overtreatment

VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines

BACKGROUND: Vaccine development in the post-genomic era often begins with the in silico screening of genome information, with the most probable protective antigens being predicted rather than requiring causative microorganisms to be grown. Despite the obvious advantages of this approach – such as speed and cost efficiency – its success remains dependent on the accuracy of antigen prediction. Most approaches use sequence alignment to identify antigens. This is problematic for several reasons. Some proteins lack obvious sequence similarity, although they may share similar structures and biological properties. The antigenicity of a sequence may be encoded in a subtle and recondite manner not amendable to direct identification by sequence alignment. The discovery of truly novel antigens will be frustrated by their lack of similarity to antigens of known provenance. To overcome the limitations of alignment-dependent methods, we propose a new alignment-free approach for antigen prediction, which is based on auto cross covariance (ACC) transformation of protein sequences into uniform vectors of principal amino acid properties. RESULTS: Bacterial, viral and tumour protein datasets were used to derive models for prediction of whole protein antigenicity. Every set consisted of 100 known antigens and 100 non-antigens. The derived models were tested by internal leave-one-out cross-validation and external validation using test sets. An additional five training sets for each class of antigens were used to test the stability of the discrimination between antigens and non-antigens. The models performed well in both validations showing prediction accuracy of 70% to 89%. The models were implemented in a server, which we call VaxiJen. CONCLUSION: VaxiJen is the first server for alignment-independent prediction of protective antigens. It was developed to allow antigen classification solely based on the physicochemical properties of proteins without recourse to sequence alignment. The server can be used on its own or in combination with alignment-based prediction methods. It is freely-available online at the URL:

El Niño Modulations Over The Past Seven Centuries (Letter to the editor)

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Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm

Metamorphically competent larvae of the marine tubeworm Hydroides elegans can be induced to metamorphose by biofilms of the bacterium Pseudoalteromonas luteoviolacea strain HI1. Mutational analysis was used to identify four genes that are necessary for metamorphic induction and encode functions that may be related to cell adhesion and bacterial secretion systems. No major differences in biofilm characteristics, such as biofilm cell density, thickness, biomass and EPS biomass, were seen between biofilms composed of P. luteoviolacea (HI1) and mutants lacking one of the four genes. The analysis indicates that factors other than those relating to physical characteristics of biofilms are critical to the inductive capacity of P. luteoviolacea (HI1), and that essential inductive molecular components are missing in the non-inductive deletion-mutant strains

Identification of a Bacteria-produced Benzisoxazole with Antibiotic Activity against Multi-drug Resistant Acinetobacter baumannii

The emergence of multi-drug resistant pathogenic bacteria represents a serious and growing threat to national healthcare systems. Most pressing is an immediate need for the development of novel antibacterial agents to treat Gram-negative multi-drug resistant infections, including the opportunistic, hospital-derived pathogen, Acinetobacter baumannii. Herein we report a naturally occurring 1,2-benzisoxazole with minimum inhibitory concentrations as low as 6.25 μg ml−1 against clinical strains of multi-drug resistant A. baumannii and investigate its possible mechanisms of action. This molecule represents a new chemotype for antibacterial agents against A. baumannii and is easily accessed in two steps via de novo synthesis. In vitro testing of structural analogs suggest that the natural compound may already be optimized for activity against this pathogen. Our results demonstrate that supplementation of 4-hydroxybenzoate in minimal media was able to reverse 1,2-benzisoxazole’s antibacterial effects in A. baumannii. A search of metabolic pathways involving 4-hydroxybenzoate coupled with molecular modeling studies implicates two enzymes, chorismate pyruvate-lyase and 4-hydroxybenzoate octaprenyltransferase, as promising leads for the target of 3,6-dihydroxy-1,2-benzisoxazole

Nickel and helium evidence for melt above the core–mantle boundary

High ^(3)He/^(4)He ratios in some basalts have generally been interpreted as originating in an incompletely degassed lower-mantle source. This helium source may have been isolated at the core–mantle boundary region since Earth’s accretion. Alternatively, it may have taken part in whole-mantle convection and crust production over the age of the Earth; if so, it is now either a primitive refugium at the core–mantle boundary or is distributed throughout the lower mantle. Here we constrain the problem using lavas from Baffin Island, West Greenland, the Ontong Java Plateau, Isla Gorgona and Fernandina (Galapagos). Olivine phenocryst compositions show that these lavas originated from a peridotite source that was about 20 per cent higher in nickel content than in the modern mid-ocean-ridge basalt source. Where data are available, these lavas also have high ^(3)He/^(4)He. We propose that a less-degassed nickel-rich source formed by core–mantle interaction during the crystallization of a melt-rich layer or basal magma ocean, and that this source continues to be sampled by mantle plumes. The spatial distribution of this source may be constrained by nickel partitioning experiments at the pressures of the core–mantle boundary