Models of helically symmetric binary systems

Results from helically symmetric scalar field models and first results from a convergent helically symmetric binary neutron star code are reported here; these are models stationary in the rotating frame of a source with constant angular velocity omega. In the scalar field models and the neutron star code, helical symmetry leads to a system of mixed elliptic-hyperbolic character. The scalar field models involve nonlinear terms that mimic nonlinear terms of the Einstein equation. Convergence is strikingly different for different signs of each nonlinear term; it is typically insensitive to the iterative method used; and it improves with an outer boundary in the near zone. In the neutron star code, one has no control on the sign of the source, and convergence has been achieved only for an outer boundary less than approximately 1 wavelength from the source or for a code that imposes helical symmetry only inside a near zone of that size. The inaccuracy of helically symmetric solutions with appropriate boundary conditions should be comparable to the inaccuracy of a waveless formalism that neglects gravitational waves; and the (near zone) solutions we obtain for waveless and helically symmetric BNS codes with the same boundary conditions nearly coincide.Comment: 19 pages, 7 figures. Expanded version of article to be published in Class. Quantum Grav. special issue on Numerical Relativit

Centaurus A at Ultra-High Energies

We review the importance of Centaurus A in high energy astrophysics as a nearby object with many of the properties expected of a major source of very high energy cosmic rays and gamma-rays. We examine observational techniques and the results so far obtained in the energy range from 200 GeV to above 100 EeV and attempt to fit those data with expectations of Centaurus A as an astrophysical source from VHE to UHE energies.Comment: 11 pages, 4 figures, accepted for publication in PAS

Dietary intake of inulin-type fructans in active and inactive Crohn’s disease and healthy controls: a case-control study

Background and Aims: Prebiotic inulin-type fructans are widely consumed in the diet and may have contrasting effects in Crohn’s disease by stimulating gut microbiota and/or by generating functional gastrointestinal symptoms. The aim of this study was to measure fructan and oligofructose intakes in patients with active and inactive Crohn’s disease compared with healthy controls. Methods: Patients with active Crohn’s disease (n=98), inactive Crohn’s (n=99) and healthy controls (n=106) were recruited to a case-control study. Dietary intake of inulin-type fructans was measured using a specific food frequency questionnaire and was compared between the three groups and between patients with different disease phenotypes (Montreal classification). Associations between intakes and disease activity (Harvey Bradshaw Index, HBI) were also undertaken. Results: Patients with active Crohn’s disease had lower fructan intakes (median 2.9 g/d, IQR 1.8) than those with inactive Crohn’s (3.6 g/d, 2.1, P=0.036) or controls (3.9 g/d, 2.1, P=0.003) and lower oligofructose intakes (2.8 g/d, 1.8) than inactive Crohn’s (3.5 g/d, 2.2, P=0.048) or controls (3.8 g/d, 2.1, P=0.003). There were no differences in intakes related to disease site or behaviour. There were negative correlations between HBI wellbeing score and fructan intake (ρ=-0.154, P=0.03) and oligofructose intake (ρ=-0.156, P=0.028) and for the HBI abdominal pain score and fructan (ρ=-0.164, P=0.021) and oligofructose intake (ρ=-0.157, P=0.027). Conclusions: Patients with active Crohn’s disease consume lower quantities of fructans and oligofructose than their inactive counterparts and healthy controls. The impact of lower intakes of prebiotic fructans on gut microbiota are unknown and warrant further research

Oligomerization of the vesicular stomatitis virus phosphoprotein is dispensable for mRNA synthesis but facilitates RNA replication

Nonsegmented negative-strand (NNS) RNA viruses possess a ribonucleoprotein template in which the genomic RNA is sequestered within a homopolymer of nucleocapsid protein (N). The viral RNA-dependent RNA polymerase (RdRP) resides within an approximately 250-kDa large protein (L), along with unconventional mRNA capping enzymes: a GDP:polyribonucleotidyltransferase (PRNT) and a dual-specificity mRNA cap methylase (MT). To gain access to the N-RNA template and orchestrate the

WHOI Hawaii Ocean Timeseries Station (WHOTS) : WHOTS-10 2013 mooring turnaround cruise report

The Woods Hole Oceanographic Institution (WHOI) Hawaii Ocean Timeseries Site (WHOTS), 100 km north of Oahu, Hawaii, is intended to provide long-term, high-quality air-sea fluxes as a part of the NOAA Climate Observation Program. The WHOTS mooring also serves as a coordinated part of the Hawaii Ocean Timeseries (HOT) program, contributing to the goals of observing heat, fresh water and chemical fluxes at a site representative of the oligotrophic North Pacific Ocean. The approach is to maintain a surface mooring outfitted for meteorological and oceanographic measurements at a site near 22.75°N, 158°W by successive mooring turnarounds. These observations will be used to investigate air–sea interaction processes related to climate variability. This report documents recovery of the ninth WHOTS mooring (WHOTS-9) and deployment of the tenth mooring (WHOTS-10). Both moorings used Surlyn foam buoys as the surface element and were outfitted with two Air–Sea Interaction Meteorology (ASIMET) systems. Each ASIMET system measures, records, and transmits via Argos satellite the surface meteorological variables necessary to compute air–sea fluxes of heat, moisture and momentum. The upper 155 m of the moorings were outfitted with oceanographic sensors for the measurement of temperature, conductivity and velocity in a cooperative effort with R. Lukas of the University of Hawaii. A pCO2 system and ancillary sensors were installed on the buoys in cooperation with Chris Sabine at the Pacific Marine Environmental Laboratory. A set of radiometers were installed in cooperation with Sam Laney at WHOI. The WHOTS mooring turnaround was done on the NOAA ship Hi’ialakai by the Upper Ocean Processes Group of the Woods Hole Oceanographic Institution. The cruise took place between 9 and 16 July 2013. Operations began with deployment of the WHOTS-10 mooring on 10 July. This was followed by meteorological intercomparisons and CTDs. Recovery of the WHOTS-9 mooring took place on 14 July. This report describes these cruise operations, as well as some of the in-port operations and pre-cruise buoy preparations.Funding was provided by the National Oceanic and Atmospheric Administration under Grant. No. NA090AR4320129 and the Cooperative Institute for the North Atlantic Region (CINAR

No Massive Companion to the Coherent Radio-Emitting M Dwarf GJ 1151

The recent detection of circularly polarized, long-duration (>8 hr) low-frequency (~150 MHz) radio emission from the M4.5 dwarf GJ 1151 has been interpreted as arising from a star-planet interaction via the electron cyclotron maser instability. The existence or parameters of the proposed planets have not been determined. Using 20 new HARPS-N observations, we put 99th-percentile upper limits on the mass of any close companion to GJ 1151 at Msini < 5.6 M earth. With no stellar, brown dwarf, or giant planet companion likely in a close orbit, our data are consistent with detected radio emission emerging from a magnetic interaction between a short-period terrestrial-mass planet and GJ 1151

WHOI Hawaii Ocean Timeseries Station (WHOTS): WHOTS-11 2014 mooring Turnaround Cruise Report

The Woods Hole Oceanographic Institution (WHOI) Hawaii Ocean Timeseries Site (WHOTS), 100 km north of Oahu, Hawaii, is intended to provide long-term, high-quality air-sea fluxes as a part of the NOAA Climate Observation Program. The WHOTS mooring also serves as a coordinated part of the Hawaii Ocean Timeseries (HOT) program, contributing to the goals of observing heat, fresh water and chemical fluxes at a site representative of the oligotrophic North Pacific Ocean. The approach is to maintain a surface mooring outfitted for meteorological and oceanographic measurements at a site near 22.75°N, 158°W by successive mooring turnarounds. These observations will be used to investigate air–sea interaction processes related to climate variability. This report documents recovery of the tenth WHOTS mooring (WHOTS-10) and deployment of the eleventh mooring (WHOTS-11). Both moorings used Surlyn foam buoys as the surface element and were outfitted with two Air–Sea Interaction Meteorology (ASIMET) systems. Each ASIMET system measures, records, and transmits via Argos satellite the surface meteorological variables necessary to compute air–sea fluxes of heat, moisture and momentum. The upper 155 m of the moorings were outfitted with oceanographic sensors for the measurement of temperature, conductivity and velocity in a cooperative effort with R. Lukas of the University of Hawaii. A pCO2 system and ancillary sensors were installed on the buoys in cooperation with Chris Sabine at the Pacific Marine Environmental Laboratory. A set of radiometers were installed in cooperation with Sam Laney at WHOI. The WHOTS mooring turnaround was done on the NOAA ship Hi’ialakai by the Upper Ocean Processes Group of the Woods Hole Oceanographic Institution. The cruise took place between 15 and 23 July 2014. Operations began with deployment of the WHOTS-11 mooring on 16 July. This was followed by meteorological intercomparisons and CTDs. Recovery of the WHOTS-10 mooring took place on 20 July. This report describes these cruise operations, as well as some of the in-port operations and pre-cruise buoy preparations.Funding was provided by the National Oceanic and Atmospheric Administration under Grant No. NA140AR4320158 and the Cooperative Institute for the North Atlantic Region (CINAR

WHOI Hawaii Ocean Timeseries Station (WHOTS) : WHOTS-8 2011 mooring turnaround cruise report

Note: author "Ludovic Bariteau" is incorrectly listed as "Bariteau Ludovic" on the Cover and Title Page.The Woods Hole Oceanographic Institution (WHOI) Hawaii Ocean Timeseries (HOT) Site (WHOTS), 100 km north of Oahu, Hawaii, is intended to provide long-term, high-quality air-sea fluxes as a part of the NOAA Climate Observation Program. The WHOTS mooring also serves as a coordinated part of the HOT program, contributing to the goals of observing heat, fresh water and chemical fluxes at a site representative of the oligotrophic North Pacific Ocean. The approach is to maintain a surface mooring outfitted for meteorological and oceanographic measurements at a site near 22.75°N, 158°W by successive mooring turnarounds. These observations will be used to investigate air–sea interaction processes related to climate variability. This report documents recovery of the seventh WHOTS mooring (WHOTS-7) and deployment of the eighth mooring (WHOTS-8). Both moorings used Surlyn foam buoys as the surface element and were outfitted with two Air–Sea Interaction Meteorology (ASIMET) systems. Each ASIMET system measures, records, and transmits via Argos satellite the surface meteorological variables necessary to compute air–sea fluxes of heat, moisture and momentum. The upper 155 m of the moorings were outfitted with oceanographic sensors for the measurement of temperature, conductivity and velocity in a cooperative effort with R. Lukas of the University of Hawaii. A pCO2 system was installed on the WHOTS-8 buoy in a cooperative effort with Chris Sabine at the Pacific Marine Environmental Laboratory. A set of radiometers were installed in cooperation with Sam Laney at WHOI. The WHOTS mooring turnaround was done on the NOAA ship Hi’ialakai by the Upper Ocean Processes Group of the Woods Hole Oceanographic Institution. The cruise took place between 5 July and 13 July 2011. Operations began with deployment of the WHOTS-8 mooring on 6 July. This was followed by meteorological intercomparisons and CTDs. Recovery of WHOTS-7 took place on 11 July 2011. This report describes these cruise operations, as well as some of the in-port operations and pre-cruise buoy preparations.Funding was provided by the National Oceanic and Atmospheric Administration under Grant No. NA090AR4320129 and the Cooperative Institute for the North Atlantic Region (CINAR)

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : baryon acoustic oscillations in the Data Releases 10 and 11 Galaxy samples

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations (BAO) in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 (DR11) sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released DR9 and DR10 samples. Assuming a concordance Λ cold dark matter (ΛCDM) cosmological model, the DR11 sample covers a volume of 13 Gpc3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7σ in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, rd, which has a value of rd,fid = 149.28 Mpc in our fiducial cosmology. We find DV = (1264 ± 25 Mpc)(rd/rd,fid) at z = 0.32 and DV = (2056 ± 20 Mpc)(rd/rd,fid) at z = 0.57. At 1.0 per cent, this latter measure is the most precise distance constraint ever obtained from a galaxy survey. Separating the clustering along and transverse to the line of sight yields measurements at z = 0.57 of DA = (1421 ± 20 Mpc)(rd/rd,fid) and H = (96.8 ± 3.4 km s−1 Mpc−1)(rd,fid/rd). Our measurements of the distance scale are in good agreement with previous BAO measurements and with the predictions from cosmic microwave background data for a spatially flat CDM model with a cosmological constant.Publisher PDFPeer reviewe