Source regions of infragravity waves recorded at the bottom of the equatorial Atlantic Ocean, using OBS of the PI‐LAB experiment

Infragravity waves are generated along coasts, and some small fraction of their energy escapes to the open oceans and propagates with little attenuation. Due to the scarcity of deep‐ocean observations of these waves, the mechanism and the extent of the infragravity waves energy leakage from the coasts remains poorly understood. Understanding the generation and pathways of infragravity wave energy is important among others for understanding the breakup of ice‐shelves and the contamination of high‐resolution satellite radar altimetry measurements of sea level. We examine data from 37 differential pressure gauges of Ocean Bottom Seismometers (OBS) near the equatorial mid‐Atlantic ridge, deployed during the Passive Imaging of the Lithosphere‐Asthenosphere Boundary (PI‐LAB) experiment. We use the beamforming technique to investigate the incoming directions of infragravity waves. Next, we develop a graph‐theory‐based global back‐projection method of noise cross‐correlation function envelopes, which minimizes the effects of array geometry using an adaptive weighting scheme. This approach allows us to locate the sources of the infragravity energy. We assess our observations by comparing to a global model of infragravity wave heights. Our results reveal strong coherent energy from sources and/or reflected phases at the west coast of Africa and some sources from South America. These energy sources are in good agreement with the global infragravity wave model. In addition, we also observe infragravity waves arriving from North America during specific events that mostly occur during October–February 2016. Finally, we find indications of waves that propagate with little attenuation, long distances through sea ice, reflecting off Antarctica

Imaging slab-transported fluids and their deep dehydration from seismic velocity tomography in the Lesser Antilles subduction zone

Volatiles play a pivotal role in subduction zone evolution, yet their pathways remain poorly constrained. Studying the Lesser Antilles subduction zone can yield new constraints, where old oceanic lithosphere formed by slow-spreading subducts slowly. Here we use local earthquakes recorded by the temporary VoiLA (Volatile recycling in the Lesser Antilles) deployment of ocean-bottom seismometers in the fore- and back-arc to characterize the 3-D seismic structure of the north-central Lesser Antilles subduction zone. Along the slab top, mapped based on seismicity, we find low Vp extending to 130–150 km depth, deeper than expected for magmatic oceanic crust. The slab\u27s most prominent, elevated Vp/Vs anomalies are beneath the fore- and back-arc offshore Guadeloupe and Dominica, where two subducted fracture zones lie with the obliquely subducting boundary between Proto-Caribbean and Equatorial Atlantic lithosphere. These structures, therefore, enhance hydration of the oceanic lithosphere as it forms and evolves and the subsequent dehydration of mantle serpentinite when subducted. Above the slab, we image the asthenosphere wedge as a high Vp/Vs and moderate Vp feature, indicating slab-dehydrated fluids rising through the overlying cold boundary layer that might induce melting further to the west. Our results provide new evidence for the impact of spatially-variable oceanic plate formation processes on slab dehydration and mantle wedge volatile transfer that ultimately impact volcanic processes at the surface, such as the relatively high magmatic output observed on the north-central islands in the Lesser Antilles

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories

Wide-Angle Seismic Imaging of Two Modes of Crustal Accretion in Mature Atlantic Ocean Crust

We present a high‐resolution 2‐D P‐wave velocity model from a 225‐km‐long active seismic profile, collected over ~60–75 Ma central Atlantic crust. The profile crosses five ridge segments separated by a transform and three nontransform offsets. All ridge discontinuities share similar primary characteristics, independent of the offset. We identify two types of crustal segment. The first displays a classic two‐layer velocity structure with a high gradient Layer 2 (~0.9 s$^{−1}$) above a lower gradient Layer 3 (0.2 s$^{−1}$). Here, PmP coincides with the 7.5 km s$^{−1}$ contour, and velocity increases to >7.8 km s$^{−1}$ within 1 km below. We interpret these segments as magmatically robust, with PmP representing a petrological boundary between crust and mantle. The second has a reduced contrast in velocity gradient between the upper and lower crust and PmP shallower than the 7.5 km s$^{−1}$ contour. We interpret these segments as tectonically dominated, with PmP representing a serpentinized (alteration) front. While velocity‐depth profiles fit within previous envelopes for slow‐spreading crust, our results suggest that such generalizations give a misleading impression of uniformity. We estimate that the two crustal styles are present in equal proportions on the floor of the Atlantic. Within two tectonically dominated segments, we make the first wide‐angle seismic identifications of buried oceanic core complexes in mature (>20 Ma) Atlantic Ocean crust. They have a ~20‐km‐wide “domal” morphology with shallow basement and increased upper crustal velocities. We interpret their midcrustal seismic velocity inversions as alteration and rock‐type assemblage contrasts across crustal‐scale detachment faults

Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production

© 2014 Pandit et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Surfactant Protein SP-D, a member of the collectin family, is a pattern recognition protein, secreted by mucosal epithelial cells and has an important role in innate immunity against various pathogens. In this study, we confirm that native human SP-D and a recombinant fragment of human SP-D (rhSP-D) bind to gp120 of HIV-1 and significantly inhibit viral replication in vitro in a calcium and dose-dependent manner. We show, for the first time, that SP-D and rhSP-D act as potent inhibitors of HIV-1 entry in to target cells and block the interaction between CD4 and gp120 in a dose-dependent manner. The rhSP-D-mediated inhibition of viral replication was examined using three clinical isolates of HIV-1 and three target cells: Jurkat T cells, U937 monocytic cells and PBMCs. HIV-1 induced cytokine storm in the three target cells was significantly suppressed by rhSP-D. Phosphorylation of key kinases p38, Erk1/2 and AKT, which contribute to HIV-1 induced immune activation, was significantly reduced in vitro in the presence of rhSP-D. Notably, anti-HIV-1 activity of rhSP-D was retained in the presence of biological fluids such as cervico-vaginal lavage and seminal plasma. Our study illustrates the multi-faceted role of human SPD against HIV-1 and potential of rhSP-D for immunotherapy to inhibit viral entry and immune activation in acute HIV infection. © 2014 Pandit et al.The work (Project no. 2011-16850) was supported by Medical Innovation Fund of Indian Council of Medical Research, New Delhi, India (www.icmr.nic.in/)

Multicenter evaluation of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of gram-positive aerobic bacteria

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting

Stochastic Inversion of P-to-S Converted Waves for Mantle Composition and Thermal Structure: Methodology and Application

We present a new methodology for inverting P‐to‐S receiver function (RF) waveforms directly for mantle temperature and composition. This is achieved by interfacing the geophysical inversion with self‐consistent mineral phase equilibria calculations from which rock mineralogy and its elastic properties are predicted as a function of pressure, temperature, and bulk composition. This approach anchors temperatures, composition, seismic properties, and discontinuities that are in mineral physics data, while permitting the simultaneous use of geophysical inverse methods to optimize models of seismic properties to match RF waveforms. Resultant estimates of transition zone (TZ) topography and volumetric seismic velocities are independent of tomographic models usually required for correcting for upper mantle structure. We considered two end‐member compositional models: the equilibrated equilibrium assemblage (EA) and the disequilibrated mechanical mixture (MM) models. Thermal variations were found to influence arrival times of computed RF waveforms, whereas compositional variations affected amplitudes of waves converted at the TZ discontinuities. The robustness of the inversion strategy was tested by performing a set of synthetic inversions in which crustal structure was assumed both fixed and variable. These tests indicate that unaccounted‐for crustal structure strongly affects the retrieval of mantle properties, calling for a two‐step strategy presented herein to simultaneously recover both crustal and mantle parameters. As a proof of concept, the methodology is applied to data from two stations located in the Siberian and East European continental platforms.This work was supported by a grant from the Swiss National Science Foundation (SNF project 200021_159907). B. T. was funded by a Délégation CNRS and Congé pour Recherches et Conversion Thématique from the Université de Lyon to visit the Research School of Earth Sciences (RSES), The Australian National University (ANU). B. T. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 79382

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia

Altered Immune Responses in Rhesus Macaques Co-Infected with SIV and Plasmodium cynomolgi: An Animal Model for Coincident AIDS and Relapsing Malaria

BACKGROUND:Dual epidemics of the malaria parasite Plasmodium and HIV-1 in sub-Saharan Africa and Asia present a significant risk for co-infection in these overlapping endemic regions. Recent studies of HIV/Plasmodium falciparum co-infection have reported significant interactions of these pathogens, including more rapid CD4+ T cell loss, increased viral load, increased immunosuppression, and increased episodes of clinical malaria. Here, we describe a novel rhesus macaque model for co-infection that supports and expands upon findings in human co-infection studies and can be used to identify interactions between these two pathogens. METHODOLOGY/PRINCIPAL FINDINGS:Five rhesus macaques were infected with P. cynomolgi and, following three parasite relapses, with SIV. Compared to macaques infected with SIV alone, co-infected animals had, as a group, decreased survival time and more rapid declines in markers for SIV progression, including peripheral CD4+ T cells and CD4+/CD8+ T cell ratios. The naïve CD4+ T cell pool of the co-infected animals was depleted more rapidly than animals infected with SIV alone. The co-infected animals also failed to generate proliferative responses to parasitemia by CD4+ and CD8+ T cells as well as B cells while also having a less robust anti-parasite and altered anti-SIV antibody response. CONCLUSIONS/SIGNIFICANCE:These data suggest that infection with both SIV and Plasmodium enhances SIV-induced disease progression and impairs the anti-Plasmodium immune response. These data support findings in HIV/Plasmodium co-infection studies. This animal model can be used to further define impacts of lentivirus and Plasmodium co-infection and guide public health and therapeutic interventions