Closing the sea surface mixed layer temperature budget from in situ observations alone: Operation Advection during BoBBLE

Sea surface temperature (SST) is a fundamental driver of tropical weather systems such as monsoon rainfall and tropical cyclones. However, understanding of the factors that control SST variability is lacking, especially during the monsoons when in situ observations are sparse. Here we use a ground-breaking observational approach to determine the controls on the SST variability in the southern Bay of Bengal. We achieve this through the first full closure of the ocean mixed layer energy budget derived entirely from in situ observations during the Bay of Bengal Boundary Layer Experiment (BoBBLE). Locally measured horizontal advection and entrainment contribute more significantly than expected to SST evolution and thus oceanic variability during the observation period. These processes are poorly resolved by state-of-the-art climate models, which may contribute to poor representation of monsoon rainfall variability. The novel techniques presented here provide a blueprint for future observational experiments to quantify the mixed layer heat budget on longer time scales and to evaluate these processes in models

Dog Burials Associated with Human Burials in the West Indies during the Early Pre-Columbian Ceramic Age (500 BC-600 AD)

Across the Caribbean, the widespread presence of canine remains at archaeological sites from the Saladoid period raises questions about the role of “man’s best friend.” Dog (Canis familiaris) remains have been found located in both refuse middens and burials adjacent to human graves in a number of sites in the French Antilles and Barbuda, West Indies. This paper will critically examine dog remains and discuss the varied duality of the dog’s role in the Saladoid world: from food source to lifelong companion. The importance of dogs within Amerindian sites from Saint Martin, the Guadeloupe archipelago, Martinique and Barbuda will be explored from a zooarchaeological perspective, concluding with a critical discussion of changes in cultural patterns, as seen through the decline in dog remains during the Troumassoid and Suazoid period at the sites in the French Antilles. Résumé Sépultures de chiens associées à des sépultures humaines dans les Petites Antilles à l’Âge du Néoindien ancien (500 av. – 600 ap. J.-C.). Dans les Antilles, la présence généralisée de restes de chiens sur les sites de la période céramique ancienne Saladoïde soulève des questions sur le rôle de ce « meilleur ami de l’homme ». En effet, des chiens (Canis familiaris) ont été trouvés aussi bien dans des zones de rejets, qu’enterrés aux côtés de sépultures humaines dans un certain nombre de sites des Petites Antilles. Ce document examinera ces restes de chiens de façon critique et décrira les morphologies particulières des chiens des sites amérindiens de l’île de Saint-Martin, l\u27archipel de la Guadeloupe, la Martinique et de l’île de Barbuda, dans une perspective archéozoologique. Une discussion critique portera sur l\u27évolution des changements des modèles culturels, comme celui de la chute drastique des chiens enterrés pendant les périodes archéologiques plus tardives, Troumassoïde et Suazoïde, des sites des Antilles françaises. Enfin, la discussion portera sur la dualité du rôle du chien dans le monde Saladoïde, à la fois source de nourriture et compagnon de vie

Intermittency of near-bottom turbulence in tidal flow on a shallow shelf

The higher-order structure functions of vertical velocity fluctuations (transverse structure functions (TSF)) were employed to study the characteristics of turbulence intermittency in a reversing tidal flow on a 19 m deep shallow shelf of the East China Sea. Measurements from a downward-looking, bottom-mounted Acoustic Doppler Velocimeter, positioned 0.45 m above the seafloor, which spanned two semidiurnal tidal cycles, were analyzed. A classical lognormal single-parameter (mu) model for intermittency and the universal multifractal approach (specifically, the two-parameter (C-1 and alpha) log-Levy model) were employed to analyze the TSF exponent xi(q) in tidally driven turbulent boundary layer and to estimate mu, C-1, and alpha. During the energetic flooding tidal phases, the parameters of intermittency models approached the mean values of (mu) over tilde approximate to 0.24, (C) over tilde (1) approximate to 0.15, and (alpha) over tilde approximate to 1.5, which are accepted as the universal values for fully developed turbulence at high Reynolds numbers. With the decrease of advection velocity, mu and C-1 increased up to mu approximate to 0.5-0.6 and C-1 approximate to 0.25-0.35, but a decreased to about 1.4. The results explain the reported disparities between the smaller "universal" values of intermittency parameters mu and C-1 (mostly measured in laboratory and atmospheric high Reynolds number flows) and those (mu = 0.4-0.5) reported for oceanic stratified turbulence in the pycnocline, which is associated with relatively low local Reynolds numbers R-lambda w. The scaling exponents xi(2) of the second-order TSF, relative to the third-order structure function, was also found to be a decreasing function of R-lambda w, approaching the classical value of 2/3 only at very high R-lambda w. A larger departure from the universal turbulent regime at lower Reynolds numbers could be attributed to the higher anisotropy and associated intermittency of underdeveloped turbulence.U.S. Office of Naval Research [N00014-05-1-0245]; Spanish Ministry of Education and Science [FIS2008-03608]; Major State Program of China for Basic Research [2006CB400602]; Catalan Institute for Water Research (ICRA

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) a-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of “extra-target” RAS suggests the need for RAS screening in all three DAA target regions

The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives

This is the final version. Available on open access from Oxford University Press via the DOI in this recordCandida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients