Avoiding Pandemic Fears in the Subway and Conquering the Platypus.

Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the "normal subway microbiome." In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10.1128/mSystems.00018-16) showed that microbial communities on transit surfaces in the Boston subway system are maintained from a metapopulation of human skin commensals and environmental generalists and that reanalysis of the New York subway data with appropriate methods did not detect the pathogens. We note that commonly used software pipelines can produce results that lack prima facie validity (e.g., reporting widespread distribution of notorious endemic species such as the platypus or the presence of pathogens) but that appropriate use of inclusion and exclusion sets can avoid this issue

Morphology, sedimentary infill and depositional environments of the Early Quaternary North Sea Basin (56°-62°N)

The North Sea Basin has been subsiding during the Quaternary and contains hundreds of metres of fill. Seismic surveys (170 000 km2) provide new evidence on Early Quaternary sedimentation, from about 2.75 Ma to around the Brunhes-Matuyama boundary (0.78 Ma). We present an informal seismic stratigraphy for the Early Quaternary of the North Sea, and calculate sediment volumes for major units. Early Quaternary sediment thickness is > 1000 m in the northern basin and >700 m in the central basin (total about 40 000 km3). Northern North Sea basin-fill comprises several clinoform units, prograding westward over 60 000 km2. Architecture of the central basin also comprises clinoforms, building from the southeast. To the west, an acoustically layered and mounded unit (Unit Z) was deposited. Remaining accommodation space was filled with fine-grained sediments of two Central Basin units. Above these units, an Upper Regional Unconformity-equivalent (URU) records a conformable surface with flat-lying units that indicate stronger direct glacial influence than on the sediments below. On the North Sea Plateau north of 59°N, the Upper Regional Unconformity (URU) is defined by a shift from westward to eastward dipping seismic reflectors, recording a major change in sedimentation, with the Shetland Platform becoming a significant source. A model of Early Quaternary sediment delivery to the North Sea shows sources from the Scandinavian ice sheet and major European rivers. Clinoforms prograding west in the northern North Sea Basin, representing glacigenic debris flows, indicate an ice sheet on the western Scandinavian margin. In the central basin, sediments are generally fine-grained, suggesting a distal fluvial or glacifluvial origin from European rivers. Ploughmarks also demonstrate that icebergs, derived from an ice sheet to the north, drifted into the central North Sea Basin. By contrast, sediments and glacial landforms above the URU provide evidence for the later presence of a grounded ice sheet.We thank Det norske oljeselskap for financial support and permission to publish this work. We also thank Petroleum Geoservices and TGS for permission to publish seismic lines and seismic amplitude maps and Exploro AS for their support of the project.This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S0264817214001342

Boundedness properties of fermionic operators

The fermionic second quantization operator $d\Gamma(B)$ is shown to be bounded by a power $N^{s/2}$ of the number operator $N$ given that the operator $B$ belongs to the $r$-th von Neumann-Schatten class, $s=2(r-1)/r$. Conversely, number operator estimates for $d\Gamma(B)$ imply von Neumann-Schatten conditions on $B$. Quadratic creation and annihilation operators are treated as well.Comment: 15 page

Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR

Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments

Applications of Canonical Transformations

Canonical transformations are defined and discussed along with the exponential, the coherent and the ultracoherent vectors. It is shown that the single-mode and the $n$-mode squeezing operators are elements of the group of canonical transformations. An application of canonical transformations is made, in the context of open quantum systems, by studying the effect of squeezing of the bath on the decoherence properties of the system. Two cases are analyzed. In the first case the bath consists of a massless bosonic field with the bath reference states being the squeezed vacuum states and squeezed thermal states while in the second case a system consisting of a harmonic oscillator interacting with a bath of harmonic oscillators is analyzed with the bath being initially in a squeezed thermal state.Comment: 14 page

Prolyl 4-hydroxlase activity is essential for development and cuticle formation in the human infective parasitic nematode Brugia malayi

Collagen prolyl 4-hydroxylases (C-P4H) are required for formation of extracellular matrices in higher eukaryotes. These enzymes convert proline residues within the repeat regions of collagen polypeptides to 4-hydroxyproline, a modification essential for the stability of the triple helix. C-P4Hs are most often oligomeric complexes, with enzymatic activity contributed by the α subunits, and the β subunits formed by protein disulfide isomerase (PDI). Here we characterise this enzyme class in the important human parasitic nematode Brugia malayi. All potential C-P4H subunits were identified by detailed bioinformatic analysis of sequence databases, function was investigated both by RNAi in the parasite and heterologous expression in Caenorhabditis elegans, while biochemical activity and complex formation were examined via co-expression in insect cells. Simultaneous RNAi of two B. malayi C-P4H α subunit-like genes resulted in a striking, highly penetrant body morphology phenotype in parasite larvae. This was replicated by single RNAi of a B. malayi C-P4H β subunit-like PDI. Surprisingly however, the B. malayi proteins were not capable of rescuing a C. elegans α subunit mutant, whereas the human enzymes could. In contrast, the B. malayi PDI did functionally complement the lethal phenotype of a C. elegans β subunit mutant. Comparison of recombinant and parasite derived material indicates that enzymatic activity may be dependent on a non-reducible, inter-subunit cross-link, present only in the parasite. We therefore demonstrate that C-P4H activity is essential for development of B. malayi and uncover a novel parasite-specific feature of these collagen biosynthetic enzymes that may be exploited in future parasite control

Flow and retreat of the Late Quaternary Pine Island-Thwaites palaeo-ice stream, West Antarctica

Multibeam swath bathymetry and sub-bottom profiler data are used to establish constraints on the flow and retreat history of a major palaeo-ice stream that carried the combined discharge from the parts of the West Antarctic Ice Sheet now occupied by the Pine Island and Thwaites glacier basins. Sets of highly elongated bedforms show that, at the last glacial maximum, the route of the Pine Island-Thwaites palaeo-ice stream arced north-northeast following a prominent cross-shelf trough. In this area, the grounding line advanced to within similar to 68 km of, and probably reached, the shelf edge. Minimum ice thickness is estimated at 715 m on the outer shelf, and we estimate a minimum ice discharge of similar to 108 km(3) yr(-1) assuming velocities similar to today's Pine Island glacier (similar to 2.5 km yr(-1)). Additional bed forms observed in a trough northwest of Pine Island Bay likely formed via diachronous ice flows across the outer shelf and demonstrate switching ice stream behavior. The "style" of ice retreat is also evident in five grounding zone wedges, which suggest episodic deglaciation characterized by halts in grounding line migration up-trough. Stillstands occurred in association with changes in ice bed gradient, and phases of inferred rapid retreat correlate to higher bed slopes, supporting theoretical studies that show bed geometry as a control on ice margin recession. However, estimates that individual wedges could have formed within several centuries still imply a relatively rapid overall retreat. Our findings show that the ice stream channeled a substantial fraction of West Antarctica's discharge in the past, just as the Pine Island and Thwaites glaciers do today

Eskers formed at the beds of modern surge-type tidewater glaciers in Spitsbergen

This is the author accepted manuscript. The final version is available from the Geological Society of London via https://doi.org/doi.org/10.1144/M46.7

3D seismic imagery of deeply buried iceberg ploughmarks in North Sea sediments

This is the author accepted manuscript. The final version is available from the Geological Society of London via https://doi.org//10.1144/M46.9

Current-modified recessional-moraine ridges on the NW Spitsbergen shelf

Terminal and recessional moraine ridges are built up on high-latitude continental shelves and in fjords during glacial maxima and still-stands punctuating deglaciation. Such ridges are often found in association with relatively shallow banks and are seldom located in major crossshelf troughs where past ice streams tend to have produced subglacial landforms streamlined in the direction of former ice flow (e.g. Dahlgren et al. 2002; Dowdeswell & Elverhøi 2002; Ottesen & Dowdeswell 2009). Many of these ridges are relatively large, at tens of metres in height above the general level of the seafloor, and have been modified little during the Holocene (e.g. Ottesen et al. 2005). The preservation of these prominent submarine glacial landforms is often linked to relatively low interglacial sedimentation rates and to the lowenergy process environment that is typical of many polar shelves after deglaciation. An exception, however, is where moraine ridges are present at relatively shallow water depths, a situation sometimes enhanced by isostatic rebound during the Holocene. In these circumstances, current and wave action can result in significant modification of moraine ridges.This is the author accepted manuscript. The final version is available from the Geological Society of London via https://doi.org/10.1144/M46.6