Modelling the reliability of search operations within the UK through Bayesian belief networks

This paper uses a Bayesian belief networks (BBN) methodology to assess the reliability of search and rescue (SAR) operations within the UK coastguard (maritime rescue) coordination centers. This is an extension of earlier work, which investigated the rationale of the government's decision to close a number of coordination centers. The previous study made use of secondary data sources and employed a binary logistic regression methodology to support the analysis. This study focused on the collection of primary data through a structured elicitation process, which resulted in the construction of a BBN. The main findings of the study are that approaches such as logistic regression are complementary to BBN's. The former provided a more objective assessment of associations between variables but was restricted in the level of detail that could be explicitly expressed within the model due to lack of available data. The latter method provided a much more detailed model but the validity of the numeric assessments was more questionable. Each method can be used to inform and defend the development of the other. The paper describes in detail the elicitation process employed to construct the BBN and reflects on the potential for bias

Motion of the MMS Spacecraft Relative to the Magnetic Reconnection Structure Observed on 16 Oct 2015 at 1307 UT

We analyze a magnetopause crossing by the Magnetospheric Multiscale (MMS) spacecraft at 1307 UT on 16 Oct 2016 that showed features of electron scale reconnection. For this event, we find orthonormal LMN coordinates from the magnetic field, with N and L varying respectively along the maximum gradient and maximum variance directions. We find the motion along N from the Spatio-Temporal Difference analysis and motion along L from measured particle velocities. We locate the position of the magnetic X point, finding that MMS-4 passed within about 1.4 km from the X point and that MMS-3 and MMS-2 passed within about 1.7 km and 2.4 km, respectively, from the position of maximum out of plane current

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Atlantic salmon return rate increases with smolt length

Recent declines in Atlantic salmon Salmo salar populations are generally attributed to factors in their marine life-phase. However, it is postulated that factors affecting their freshwater life-phase might impact their marine survival, such as the influence of body size. While larger smolts are widely hypothesized to have higher marine survival rates, empirical support remains scant, in part due to inadequate data and ambiguous statistical analyses. Here, we test the influence of smolt body size on marine return rates, a proxy for marine survival, using a 12-year dataset of 3688 smolts tagged with passive integrated transponders in the River Frome, Southern England. State-space models describe the probability of smolts surviving their marine phase to return as 1 sea-winter (1SW) or multi-sea-winter adults as a function of their length, while accounting for imperfect detection and missing data. Models predicted that larger smolts had higher return rates; the most parsimonious model included the effect of length on 1SW return rate. This prediction is concerning, as freshwater juvenile salmon are decreasing in size on the River Frome, and elsewhere. Thus, to maximize adult returns, restoration efforts should focus on freshwater life-stages, and maximize both the number and the size of emigrating smolts

A distance for partially labeled trees

In a number of practical situations, data have structure and the relations among its component parts need to be coded with suitable data models. Trees are usually utilized for representing data for which hierarchical relations can be defined. This is the case in a number of fields like image analysis, natural language processing, protein structure, or music retrieval, to name a few. In those cases, procedures for comparing trees are very relevant. An approximate tree edit distance algorithm has been introduced for working with trees labeled only at the leaves. In this paper, it has been applied to handwritten character recognition, providing accuracies comparable to those by the most comprehensive search method, being as efficient as the fastest.This work is supported by the Spanish Ministry projects DRIMS (TIN2009-14247-C02), and Consolider Ingenio 2010 (MIPRCV, CSD2007-00018), partially supported by EU ERDF and the Pascal Network of Excellence

Intrinsic Redshifts and the Tully-Fisher Distance Scale

The Tully-Fisher relationship (TFR) has been shown to have a relatively small observed scatter of ~ +/-0.35 mag implying an intrinsic scatter < +/-0.30 mag. However, when the TFR is calibrated from distances derived from the Hubble relation for field galaxies scatter is consistently found to be +/-0.64 to +/-0.84 mag. This significantly larger scatter requires that intrinsic TFR scatter is actually much larger than +/-0.30 mag, that field galaxies have an intrinsic TFR scatter much larger than cluster spirals, or that field galaxies have a velocity dispersion relative to the Hubble flow in excess of 1000 km s-1. Each of these potential explanations faces difficulties contradicted by available data and the results of previous studies. An alternative explanation is that the measured redshifts of galaxies are composed of a cosmological redshift component predicted from the value of the Hubble Constant and a superimposed intrinsic redshift component previously identified in other studies. This intrinsic redshift component may exceed 5000 km s-1 in individual galaxies. In this alternative scenario a possible value for the Hubble Constant is 55-60 km s-1 Mpc-1.Comment: 15 pages, Astrophysics&Space Science - Accepted for publicatio

Confronting standard models of proto-planetary disks with new mid-infrared sizes from the Keck Interferometer

This is the author accepted manuscript. The final version is available from American Astronomical Society/IOP Publishing via the DOI in this record.The published version is in ORE at http://hdl.handle.net/10871/30943We present near and mid–infrared interferometric observations made with the Keck Interferometer Nuller and near–contemporaneous spectro–photometry from the IRTF of 11 well known young stellar objects, several observed for the first time in these spectral and spatial resolution regimes. With AU–level spatial resolution, we first establish characteristic sizes of the infrared emission using a simple geometrical model consisting of a hot inner rim and mid–infrared disk emission. We find a high degree of correlation between the stellar luminosity and the mid–infrared disk sizes after using near–infrared data to remove the contribution from the inner rim. We then use a semi–analytical physical model to also find that the very widely used “star + inner dust rim+ flared disk” class of models strongly fails to reproduce the SED and spatially–resolved mid–infrared data simultaneously; specifically a more compact source of mid–infrared emission is required than results from the standard flared disk model. We explore the viability of a modification to the model whereby a second dust rim containing smaller dust grains is added, and find that the two–rim model leads to significantly improved fits in most cases. This complexity is largely missed when carrying out SED modelling alone, although detailed silicate feature fitting by McClure et al. (2013) recently came to a similar conclusion. As has been suggested recently by Menu et al. (2015), the difficulty in predicting mid–infrared sizes from the SED alone might hint at “transition disk”–like gaps in the inner AU; however, the relatively high correlation found in our mid–infrared disk size vs. stellar luminosity relation favors layered disk morphologies and points to missing disk model ingredients instead.The authors wish to acknowledge fruitful discussions with Nuria Calvet and Melissa McClure. Part of this work was performed while X. C. was a Visiting Graduate Student Research Fellow at the Infrared Processing and Analysis Center (IPAC), California Institute of Technology. The Keck Interferometer was funded by the National Aeronautics and Space Administration as part of its Exoplanet Exploration Program. Data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Mauna Kea has always had within the indigenous Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. Data presented in this paper were obtained at the Infrared Telescope Facility, which is operated by the University of Hawaii under contract NNH14CK55B with the National Aeronautics and Space Administration. We gratefully acknowledge support and participation in the IRTF/BASS observing runs by Daryl Kim, The Aerospace Corporation. This work has made use of services produced by the NASA Exoplanet Science Institute at the California Institute of Technology. M. S. was supported by NASA ADAP grant NNX09AC73G. R. W. R. was supported by the IR&D program of The Aerospace Corporatio

Migration of the Antarctic Polar Front through the mid-Pleistocene transition: evidence and climatic implications

The Antarctic Polar Front is an important biogeochemical divider in the Southern Ocean. Laminated diatom mat deposits record episodes of massive flux of the diatom Thalassiothrix antarctica beneath the Antarctic Polar Front and provide a marker for tracking the migration of the Front through time. Ocean Drilling Program Sites 1091, 1093 and 1094 are the only deep piston cored record hitherto sampled from the sediments of the circumpolar biogenic opal belt. Mapping of diatom mat deposits between these sites indicates a glacial-interglacial front migration of up to 6 degrees of latitude in the early / mid Pleistocene. The mid Pleistocene transition marks a stepwise minimum 7 degree northward migration of the locus of the Polar Front sustained for about 450 kyr until an abrupt southward return to a locus similar to its modern position and further south than any mid-Pleistocene locus. This interval from a “900 ka event” that saw major cooling of the oceans and a ?13C minimum through to the 424 ka Mid-Brunhes Event at Termination V is also seemingly characterised by 1) sustained decreased carbonate in the subtropical south Atlantic, 2) reduced strength of Antarctic deep meridional circulation, 3) lower interglacial temperatures and lower interglacial atmospheric CO2 levels (by some 30 per mil) than those of the last 400 kyr, evidencing less complete deglaciation. This evidence is consistent with a prolonged period lasting 450 kyr of only partial ventilation of the deep ocean during interglacials and suggests that the mechanisms highlighted by recent hypotheses linking mid-latitude atmospheric conditions to the extent of deep ocean ventilation and carbon sequestration over glacial-interglacial cycles are likely in operation during the longer time scale characteristic of the Mid-Pleistocene Transition. The cooling that initiated the “900 ka event” may have been driven by minima in insolation amplitude related to eccentricity modulation of precession that also affected low latitude climates as marked by threshold changes in the African monsoon system. The major thresholds in earth system behaviour through the Mid-Pleistocene Transition were likely governed by an interplay of the 100 kyr and 400 kyr eccentricity modulation of precession

Academic freedom: in justification of a universal ideal

This paper examines the justification for, and benefits of, academic freedom to academics, students, universities and the world at large. The paper surveys the development of the concept of academic freedom within Europe, more especially the impact of the reforms at the University of Berlin instigated by Wilhelm von Humboldt. Following from this, the paper examines the reasons why the various facets of academic freedom are important and why the principle should continue to be supported

Clostridium difficile sortase recognizes a (S/P)PXTG sequence motif and can accommodate diaminopimelic acid as a substrate for transpeptidation

AbstractCovalent attachment of surface proteins to the cell wall of Gram-positive bacteria requires a sortase-mediated transpeptidation reaction. In almost all Gram-positive bacteria, the housekeeping sortase, sortase A, recognizes the canonical recognition sequence LPXTG (X=any amino acid). The human pathogen Clostridium difficile carries a single putative sortase gene (cd2718) but neither transpeptidation activity nor specificity of CD2718 has been investigated. We produced recombinant CD2718 and examined its transpeptidation activity in vitro using synthetic peptides and MALDI-ToF(-ToF) MS analysis. We demonstrate that CD2718 has sortase activity with specificity for a (S/P)PXTG motif and can accommodate diaminopimelic acid as a substrate for transpeptidation