Specificity Between Lactobacilli And Hymenopteran Hosts Is The Exception Rather Than The Rule

Lactobacilli (Lactobacillales: Lactobacillaceae) are well known for their roles in food fermentation, as probiotics, and in human health, but they can also be dominant members of the microbiota of some species of Hymenoptera (ants, bees, and wasps). Honey bees and bumble bees associate with host-specific lactobacilli, and some evidence suggests that these lactobacilli are important for bee health. Social transmission helps maintain associations between these bees and their respective microbiota. To determine whether lactobacilli associated with social hymenopteran hosts are generally host specific, we gathered publicly available Lactobacillus 16S rRNA gene sequences, along with Lactobacillus sequences from 454 pyrosequencing surveys of six other hymenopteran species (three sweat bees and three ants). We determined the comparative secondary structural models of 16S rRNA, which allowed us to accurately align the entire 16S rRNA gene, including fast-evolving regions. BLAST searches and maximum-likelihood phylogenetic reconstructions confirmed that honey and bumble bees have host-specific Lactobacillus associates. Regardless of colony size or within-colony oral sharing of food (trophallaxis), sweat bees and ants associate with lactobacilli that are closely related to those found in vertebrate hosts or in diverse environments. Why honey and bumble bees associate with host-specific lactobacilli while other social Hymenoptera do not remains an open question. Lactobacilli are known to inhibit the growth of other microbes and can be beneficial whether they are coevolved with their host or are recruited by the host from environmental sources through mechanisms of partner choice.National Science Foundation PRFB-1003133, DEB-0919519Texas Higher Education Coordinating Board 01923, National Institutes of Health GM067317Integrative BiologyCellular and Molecular BiologyCenter for Computational Biology and BioinformaticsBrackenridge Field Laborator

Willingness to participate in a randomized trial comparing catheters to fistulas for vascular access in incident hemodialysis patients: an international survey of nephrologists

BACKGROUND: Current guidelines favor fistulas over catheters as vascular access. Yet, the observational literature comparing fistulas to catheters has important limitations and biases that may be difficult to overcome in the absence of randomization. However, it is not clear if physicians would be willing to participate in a clinical trial comparing fistulas to catheters. OBJECTIVES: We also sought to elicit participants' opinions on willingness to participate in a future trial regarding catheters and fistulas. DESIGN: We created a three-part survey consisting of 19 questions. We collected demographic information, respondents' knowledge of the vascular access literature, appropriateness of current guideline recommendations, and their willingness to participate in a future trial. SETTING: Participants were recruited from Canada, Europe, Australia, and New Zealand. PARTICIPANTS: Participants include physicians and trainees who are involved in the care of end-stage renal disease patients requiring vascular access. MEASUREMENTS: Descriptive statistics were used to describe baseline characteristics of respondents according to geographic location. We used logistic regression to model willingness to participate in a future trial. METHODS: We surveyed nephrologists from Canada, Europe, Australia, and New Zealand to assess their willingness to participate in a randomized trial comparing fistulas to catheters in incident hemodialysis patients. RESULTS: Our results show that in Canada, 86 % of respondents were willing to participate in a trial (32 % in all patients; 54 % only in patients at high risk of primary failure). In Europe and Australia/New Zealand, the willingness to participate in a trial that included all patients was lower (28 % in Europe; 25 % in Australia/New Zealand), as was a trial that included patients at high risk of primary failure (38 % in Europe; 39 % in Australia/New Zealand). Nephrologists who have been in practice for a few years, saw a larger volume of patients, or self-identified as experts in vascular access literature were more likely to participate in a trial. LIMITATIONS: Survey distribution was limited to vascular access experts in participating European countries and ultimately led to a discrepancy in numbers of European to non-European respondents overall. Canadian views are likely over-represented in the overall outcomes. CONCLUSIONS: Our survey results suggest that nephrologists believe there is equipoise surrounding the optimal vascular access strategy and that a randomized controlled study should be undertaken, but restricted to those individuals with a high risk of primary fistula failure

Orbits for the Impatient: A Bayesian Rejection Sampling Method for Quickly Fitting the Orbits of Long-Period Exoplanets

We describe a Bayesian rejection sampling algorithm designed to efficiently compute posterior distributions of orbital elements for data covering short fractions of long-period exoplanet orbits. Our implementation of this method, Orbits for the Impatient (OFTI), converges up to several orders of magnitude faster than two implementations of MCMC in this regime. We illustrate the efficiency of our approach by showing that OFTI calculates accurate posteriors for all existing astrometry of the exoplanet 51 Eri b up to 100 times faster than a Metropolis-Hastings MCMC. We demonstrate the accuracy of OFTI by comparing our results for several orbiting systems with those of various MCMC implementations, finding the output posteriors to be identical within shot noise. We also describe how our algorithm was used to successfully predict the location of 51 Eri b six months in the future based on less than three months of astrometry. Finally, we apply OFTI to ten long-period exoplanets and brown dwarfs, all but one of which have been monitored over less than 3% of their orbits, producing fits to their orbits from astrometric records in the literature.Comment: 32 pages, 28 figures, Accepted to A

A Strategy for Finding Near Earth Objects with the SDSS Telescope

We present a detailed observational strategy for finding Near Earth Objects (NEOs) with the Sloan Digital Sky Survey (SDSS) telescope. We investigate strategies in normal, unbinned mode as well as binning the CCDs 2x2 or 3x3, which affects the sky coverage rate and the limiting apparent magnitude. We present results from 1 month, 3 year and 10 year simulations of such surveys. For each cadence and binning mode, we evaluate the possibility of achieving the Spaceguard goal of detecting 90% of 1 km NEOs (absolute magnitude H <= 18 for an albedo of 0.1). We find that an unbinned survey is most effective at detecting H <= 20 NEOs in our sample. However, a 3x3 binned survey reaches the Spaceguard Goal after only seven years of operation. As the proposed large survey telescopes (PanStarss; LSST) are at least 5-10 years from operation, an SDSS NEO survey could make a significant contribution to the detection and photometric characterization of the NEO population.Comment: Accepted by AJ -- 12 pages, 11 figure

Dataparallel C : a SIMD programming language for multicomputers

Dataparallel C is a SIMD extension to the standard C programming language. It is derived from the original C* language developed by Thinking Machines Corporation.. We have nearly completed a third-generation Dataparallel C compiler, which transforms Dataparallel C programs into SPMD-style C code suitable for compilation and execution on NCUBE multicomputers. In this paper we elaborate on the characteristics and strengths of data­parallel programming languages. We summarize the syntax and semantics of Dataparallel C, present six benchmark programs, and document the performance of these programs executing on the NCUBE 3200 multicomputer. Our work demonstrates that SIMD source programs can achieve reasonable speedup when compiled and executed on MIMD computers.Key Words : compiler, data parallel, hypercube, MIMD, multicomputer, programming language, SIM

A production-quality C* compiler for a hypercube multicomputer

We describe our third generation C* compiler for a hypercube multicomputer. This production­ quality compiler features a full implementation of the language, including general pointer-based communication and support for separate compilation. The compiler incorporates new optimiza­tions and utilizes an improved set of communication primitives. It supports a variety of standard domain decomposition primitives, and it also allows the programmer to specify a custom map­ping of data to the distributed memories of the hypercube. The performance of this compiler on benchmark programs demonstrates that high efficiency can be achieved executing SIMD code on multicomputer architectures

An axiomatic approach to electromagnetic and gravitational radiation reaction of particles in curved spacetime

The problem of determining the electromagnetic and gravitational ``self-force'' on a particle in a curved spacetime is investigated using an axiomatic approach. In the electromagnetic case, our key postulate is a ``comparison axiom'', which states that whenever two particles of the same charge $e$ have the same magnitude of acceleration, the difference in their self-force is given by the ordinary Lorentz force of the difference in their (suitably compared) electromagnetic fields. We thereby derive an expression for the electromagnetic self-force which agrees with that of DeWitt and Brehme as corrected by Hobbs. Despite several important differences, our analysis of the gravitational self-force proceeds in close parallel with the electromagnetic case. In the gravitational case, our final expression for the (reduced order) equations of motion shows that the deviation from geodesic motion arises entirely from a ``tail term'', in agreement with recent results of Mino et al. Throughout the paper, we take the view that ``point particles'' do not make sense as fundamental objects, but that ``point particle equations of motion'' do make sense as means of encoding information about the motion of an extended body in the limit where not only the size but also the charge and mass of the body go to zero at a suitable rate. Plausibility arguments for the validity of our comparison axiom are given by considering the limiting behavior of the self-force on extended bodies.Comment: 37 pages, LaTeX with style package RevTeX 3.

Gemini Planet Imager Observational Calibrations VI: Photometric and Spectroscopic Calibration for the Integral Field Spectrograph

The Gemini Planet Imager (GPI) is a new facility instrument for the Gemini Observatory designed to provide direct detection and characterization of planets and debris disks around stars in the solar neighborhood. In addition to its extreme adaptive optics and corona graphic systems which give access to high angular resolution and high-contrast imaging capabilities, GPI contains an integral field spectrograph providing low resolution spectroscopy across five bands between 0.95 and 2.5 $\mu$m. This paper describes the sequence of processing steps required for the spectro-photometric calibration of GPI science data, and the necessary calibration files. Based on calibration observations of the white dwarf HD 8049B we estimate that the systematic error in spectra extracted from GPI observations is less than 5%. The flux ratio of the occulted star and fiducial satellite spots within coronagraphic GPI observations, required to estimate the magnitude difference between a target and any resolved companions, was measured in the $H$-band to be $\Delta m = 9.23\pm0.06$ in laboratory measurements and $\Delta m = 9.39\pm 0.11$ using on-sky observations. Laboratory measurements for the $Y$, $J$, $K1$ and $K2$ filters are also presented. The total throughput of GPI, Gemini South and the atmosphere of the Earth was also measured in each photometric passband, with a typical throughput in $H$-band of 18% in the non-coronagraphic mode, with some variation observed over the six-month period for which observations were available. We also report ongoing development and improvement of the data cube extraction algorithm.Comment: 15 pages, 6 figures. Proceedings of the SPIE, 9147-30

Data-parallel programming on MIMD computers

We are convinced that the combination of data-parallel languages and MIMD hardware can make an important contribution to high speed computing. The data-parallel paradigm is a natural way to solve a large number of problems arising in science and engineering. Data-parallel programs are easier to design, implement, and debug than programs written in a MIMD language. For their part, the existence of multiple control units on MIMD computers can allow loosely-synchronous programs to execute more efficiently than they would on a SIMD architecture. In this paper we provide empirical evidence to support these assertions. We describe the implementation of two compilers for the data-parallel programming language C*. One compiler generates code for the NCUBE 3200 hypercube multicomputer, the other generates code for the Sequent Balance 21000 multiprocessor. We have compiled and executed a suite of C* programs on these two systems, and we present the execution times and speedups achieved by these programs

Airborne sampling of aerosol particles: Comparison between surface sampling at Christmas Island and P-3 sampling during PEM-Tropics B

Bulk aerosol sampling of soluble ionic compounds from the NASA Wallops Island P-3 aircraft and a tower on Christmas Island during PEM-Tropics B provides an opportunity to assess the magnitude of particle losses in the University of New Hampshire airborne bulk aerosol sampling system. We find that most aerosol-associated ions decrease strongly with height above the sea surface, making direct comparisons between mixing ratios at 30 m on the tower and the lowest flight level of the P-3 (150 m) open to interpretation. Theoretical considerations suggest that vertical gradients of sea-salt aerosol particles should show exponential decreases with height. Observed gradients of Na+ and Mg2+, combining the tower observations with P-3 samples collected below 1 km, are well described by exponential decreases (r values of 0.88 and 0.87, respectively), though the curve fit underestimates average mixing ratios at the surface by 25%. Cascade impactor samples collected on the tower show that \u3e99% of the Na+ and Mg2+mass is on supermicron particles, 65% is in the 1–6 micron range, and just 20% resides on particles with diameters larger than 9 microns. These results indicate that our airborne aerosol sampling probes must be passing particles up to at least 6 microns with high efficiency. We also observed that nss SO42− and NH4+, which are dominantly on accumulation mode particles, tended to decrease between 150 and 1000 m, but they were often considerably higher at the lowest P-3 sampling altitudes than at the tower. This finding is presently not well understood