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At least 1,549 records · Page 86

Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase

Significance NOV1 is a stilbene cleavage oxygenase (SCO). SCOs cleave the central double bond of stilbenes, forming two phenolic aldehydes. Many stilbenes, such as resveratrol, are produced by plants as secondary metabolites. They are also formed from lignin during kraft pulping. SCOs are related to carotenoid cleavage oxygenases (CCOs), which cleave β-carotene or apocarotenoids. Carotenoids play important roles in photosynthesis and light perception in the eye. We present the structure of an SCO and the structure of a CCO-related enzyme in ternary complex with oxygen and substrate. This structure allows us to propose a mechanism relevant to both SCOs and CCOs, where the substrate is activated for reaction with a ferric-superoxo electrophile by active site base-catalyzed deprotonation of a phenol group.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity

Shroom-mediated remodeling of the actomyosin cytoskeleton is a critical driver of cellular shape and tissue morphology that underlies the development of many tissues including the neural tube, eye, intestines, and vasculature. Shroom uses a conserved SD2 domain to direct the subcellular localization of Rho-associated kinase (Rock), which in turn drives changes in the cytoskeleton and cellular morphology through its ability to phosphorylate and activate non-muscle myosin II. Here in this paper, we present the structure of the human Shroom-Rock binding module, revealing an unexpected stoichiometry for Shroom in which two Shroom SD2 domains bind independent surfaces on Rock. Mutation of interfacial residues impaired Shroom-Rock binding in vitro and resulted in altered remodeling of the cytoskeleton and loss of Shroom-mediated changes in cellular morphology. In addition, we provide the first direct evidence that Shroom can function as a Rock activator. These data provide molecular insight into the Shroom-Rock interface and demonstrate that Shroom directly participates in regulating cytoskeletal dynamics, adding to its known role in Rock localization.

59 BASIC BIOLOGICAL SCIENCES↗

Reproductive Behavior and Success of Captive-Reared Chinook Salmon Spawning under Natural Conditions

Abstract In response to declining returns of Pacific salmon Oncorhynchus spp., captive-rearing programs have emerged as one approach to maintain natural-origin stocks while mechanisms responsible for their decline are addressed. However, it remains unclear if observed differences in reproductive behavior between captive-origin (captive) and natural-origin (natural) Chinook Salmon O. tshawytscha in laboratory experiments accurately predict reproductive success of captive salmon in the natural environment. Over a 4-year period, 859 natural Chinook Salmon juveniles were collected for full-term rearing in captivity. From these, we returned 247 maturing adults to their natal stream over 2 years, assessed trends in habitat use, monitored their courtship and spawning behaviors, and sampled their redds to determine if fertilized eggs were present. Habitat use followed a logical trend toward spawning areas as the season progressed. Captive fish were smaller and spawned later than did natural fish, but their size did not prevent females from constructing redds or prevent males from courting and fertilizing eggs. Captive fish were observed participating in 16 spawning events over two seasons. Captive and natural males displayed the same courtship behaviors, but natural males were more aggressive. Captive females selected redd sites similar to those of natural females and displayed digging behavior consistent with published observations. Eggs were collected from 22 of the 26 redds sampled, and survival to organogenesis was 68.3% in 2001 and 34.6% in 2002. The decline in 2002 was at least partially due to an apparent failure of females from brood year 1997 to produce viable eggs. We estimated captive fish contributed 19,000 eyed eggs to the population. If the 859 juveniles reared in captivity had been left in the stream, fewer than one adult would be expected to have returned. Growth, timing of spawning, and egg survival issues remain in captive fish, which illustrates a need to focus future research on improved culture techniques. Received July 21, 2011; accepted October 26, 2012

Venditti, David A.↗

Rejoinder

We would like to thank all of the discussants for their thoughtful and insightful comments. We heartily agree with Willis Jensen’s remark that the collection of views from multiple different perspectives possible with a discussion paper has added greatly to the overall contribution. Roger Hoerl compactly and eloquently summarized our thoughts about the role of statisticians on teams: “to objectively lead a team of subject matter experts through the minefield of problem resolution.” We agree with Benjamin Slade that this leadership role can be achieved either through formally leading the team or by being an active, engaged member of the team with an eye on the overall goals of the team and impacting the structure of the decision-making process. Hoerl also highlights what solutions interdisciplinary teams should be seeking – namely those that are “the best business … or scientific solution[s], rather than the best statistical solutions.” If this is how we define the objective of the team’s problem-solving or decision-making efforts, then establishing ourselves as fully-included team members or even working towards leading the team efforts should become easier.

97 MATHEMATICS AND COMPUTING↗

Evaluation of Digital Nautical Chart data for confirmation and expansion of GeoNames data

Here, this work examines how Digital Nautical Chart (DNC) data may contribute to the evolution and refinement of GeoNames data for near-shore features. GeoNames features are point data with one or more possible place names. DNC Earth Cover Text (ECRText) objects are map labels positioned nearby their real word counterpart. ECRText feature map position strikes a compromise between association with real features and cartographic readability. This work explores whether ECRText features can confirm (or expand names for) existing locations or contribute new locations through data conflation. Due to name variations and spatial position, conflating these data are nontrivial. Previous work engaged in a brief examination using the trigram string matching algorithm under coarse proximity constraints, indicating that ECRText could provide additional value to GeoNames. This work builds on that study, by engaging in a deeper examination of spatial proximity and exploring conflation agreement across an ensemble of string matching approaches. The result finds strong ensemble agreement about ECRText features which already exist in GeoNames but mixed results about which features contribute new information, as well as exploring why some of these matching techniques fail. With an eye toward automation, computational efficiency was found not to be a constraint in sustaining updates.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

MONSTER IN THE DARK: THE ULTRALUMINOUS GRB 080607 AND ITS DUSTY ENVIRONMENT

We present early-time optical through infrared photometry of the bright Swift gamma-ray burst (GRB) 080607, starting only 6 s following the initial trigger in the rest frame. Complemented by our previously published spectroscopy, this high-quality photometric data set allows us to solve for the extinction properties of the redshift 3.036 sightline, giving perhaps the most detailed information to date on the ultraviolet continuum absorption properties of any sightline outside our Local Group. The extinction properties are not adequately modeled by any ordinary extinction template (including the average Milky Way, Large Magellanic Cloud, and Small Magellanic Cloud curves), partially because the 2175 A feature (while present) is weaker by about a factor of two than when seen under similar circumstances locally. However, the spectral energy distribution is exquisitely fitted by the more general Fitzpatrick and Massa parameterization of Local-Group extinction, putting it in the same family as some peculiar Milky Way extinction curves. After correcting for this (considerable, A{sub V} = 3.3 {+-} 0.4 mag) extinction, GRB 080607 is revealed to have been among the most optically luminous events ever observed, comparable to the naked-eye burst GRB 080319B. Its early peak time (t{sub rest} < 6 s) indicates a high initial Lorentz factor ({Gamma}>600), while the extreme luminosity may be explained in part by a large circumburst density. Only because of its early high luminosity could the afterglow of GRB 080607 be studied in such detail in spite of the large attenuation and great distance, making this burst an excellent prototype for the understanding of other highly obscured extragalactic objects, and of the class of 'dark' GRBs in particular.

79 ASTRONOMY AND ASTROPHYSICS↗

SEARCHING FOR EXTRATERRESTRIAL INTELLIGENCE SIGNALS IN ASTRONOMICAL SPECTRA, INCLUDING EXISTING DATA

The main purpose of this article is to make astronomers aware that Searches for Extraterrestrial Intelligence (SETIs) can be carried out by analyzing standard astronomical spectra, including those they have already taken. Simplicity is the outstanding advantage of a search in spectra. The spectra can be analyzed by simple eye inspection or a few lines of code that uses Fourier transform software. Theory, confirmed by published experiments, shows that periodic signals in spectra can be easily generated by sending light pulses separated by constant time intervals. While part of this article, like all articles on SETIs, is highly speculative the basic physics is sound. In particular, technology now available on Earth could be used to send signals having the required energy to be detected at a target located 1000 lt-yr away. Extraterrestrial Intelligence (ETI) could use these signals to make us aware of their existence. For an ETI, the technique would also have the advantage that the signals could be detected both in spectra and searches for intensity pulses like those currently carried out on Earth.

79 ASTRONOMY AND ASTROPHYSICS↗

The EB factory project. II. Validation with the Kepler field in preparation for K2 and TESS

Large repositories of high precision light curve data, such as the Kepler data set, provide the opportunity to identify astrophysically important eclipsing binary (EB) systems in large quantities. However, the rate of classical “by eye” human analysis restricts complete and efficient mining of EBs from these data using classical techniques. To prepare for mining EBs from the upcoming K2 mission as well as other current missions, we developed an automated end-to-end computational pipeline—the Eclipsing Binary Factory (EBF)—that automatically identifies EBs and classifies them into morphological types. The EBF has been previously tested on ground-based light curves. To assess the performance of the EBF in the context of space-based data, we apply the EBF to the full set of light curves in the Kepler “Q3” Data Release. We compare the EBs identified from this automated approach against the human generated Kepler EB Catalog of ∼2600 EBs. When we require EB classification with ⩾90% confidence, we find that the EBF correctly identifies and classifies eclipsing contact (EC), eclipsing semi-detached (ESD), and eclipsing detached (ED) systems with a false positive rate of only 4%, 4%, and 8%, while complete to 64%, 46%, and 32%, respectively. When classification confidence is relaxed, the EBF identifies and classifies ECs, ESDs, and EDs with a slightly higher false positive rate of 6%, 16%, and 8%, while much more complete to 86%, 74%, and 62%, respectively. Through our processing of the entire Kepler “Q3” data set, we also identify 68 new candidate EBs that may have been missed by the human generated Kepler EB Catalog. We discuss the EBF's potential application to light curve classification for periodic variable stars more generally for current and upcoming surveys like K2 and the Transiting Exoplanet Survey Satellite.

79 ASTRONOMY AND ASTROPHYSICS↗

Astrometry of Pluto from 1930-1951 observations: The Lampland plate collection

We present a new analysis of 843 photographic plates of Pluto taken by Carl Lampland at Lowell Observatory from 1930–1951. This large collection of plates contains useful astrometric information that improves our knowledge of Pluto's orbit. This improvement provides critical support to the impending flyby of Pluto by New Horizons. New Horizons can do inbound navigation of the system to improve its targeting. This navigation is capable of nearly eliminating the sky-plane errors but can do little to constrain the time of closest approach. Thus the focus on this work was to better determine Pluto's heliocentric distance and to determine the uncertainty on that distance with a particular eye to eliminating systematic errors that might have been previously unrecognized. This work adds 596 new astrometric measurements based on the USNO CCD Astrograph Catalog 4. With the addition of these data the uncertainty of the estimated heliocentric position of Pluto in Developmental Ephemerides 432 (DE432) is at the level of 1000 km. This new analysis gives us more confidence that these estimations are accurate and are sufficient to support a successful flyby of Pluto by New Horizons.

79 ASTRONOMY AND ASTROPHYSICS↗

LATE-TIME OBSERVATIONS OF GRB 080319B: JET BREAK, HOST GALAXY, AND ACCOMPANYING SUPERNOVA

The Swift-discovered GRB 080319B was by far the most distant source ever observed at naked-eye brightness, reaching a peak apparent magnitude of 5.3 at a redshift of z = 0.937. We present our late-time optical (Hubble Space Telescope, Gemini, and Very Large Telescope) and X-ray (Chandra) observations, which confirm that an achromatic break occurred in the power-law afterglow light curve at {approx}11 days post-burst. This most likely indicates that the gamma-ray burst (GRB) outflow was collimated, which for a uniform jet would imply a total energy in the jet E{sub jet} {approx}> 10{sup 52} erg. Our observations also show a late-time excess of red light, which is well explained if the GRB was accompanied by a supernova (SN), similar to those seen in some other long-duration GRBs. The latest observations are dominated by light from the host and show that the GRB took place in a faint dwarf galaxy (r(AB) {approx} 27.0, rest frame M{sub B} {approx} -17.2). This galaxy is small even by the standards of other GRB hosts, which is suggestive of a low-metallicity environment. Intriguingly, the properties of this extreme event-a small host and bright SN-are entirely typical of the very low luminosity bursts such as GRB 980425 and GRB 060218.

79 ASTRONOMY AND ASTROPHYSICS↗

THE LATE PEAKING AFTERGLOW OF GRB 100418A

GRB 100418A is a long gamma-ray burst (GRB) at redshift z = 0.6235 discovered with the Swift Gamma-ray Burst Explorer with unusual optical and X-ray light curves. After an initial short-lived, rapid decline in X-rays, the optical and X-ray light curves observed with Swift are approximately flat or rising slightly out to at least {approx}7 x 10{sup 3} s after the trigger, peak at {approx}5 x 10{sup 4} s, and then follow an approximately power-law decay. Such a long optical plateau and late peaking is rarely seen in GRB afterglows. Observations with Rapid Eye Mount during a gap in the Swift coverage indicate a bright optical flare at {approx}2.5 x 10{sup 4} s. The long plateau phase of the afterglow is interpreted using either a model with continuous injection of energy into the forward shock of the burst or a model in which the jet of the burst is viewed off-axis. In both models the isotropic kinetic energy in the late afterglow after the plateau phase is {>=}10{sup 2} times the 10{sup 51} erg of the prompt isotropic gamma-ray energy release. The energy injection model is favored because the off-axis jet model would require the intrinsic T{sub 90} for the GRB jet viewed on-axis to be very short, {approx}10 ms, and the intrinsic isotropic gamma-ray energy release and the true jet energy to be much higher than the typical values of known short GRBs. The non-detection of a jet break up to t {approx} 2 x 10{sup 6} s indicates a jet half-opening angle of at least {approx}14{sup 0}, and a relatively high-collimation-corrected jet energy of E{sub jet} {>=} 10{sup 52} erg.

79 ASTRONOMY AND ASTROPHYSICS↗

PAndAS' PROGENY: EXTENDING THE M31 DWARF GALAXY CABAL

We present the discovery of five new dwarf galaxies, Andromeda XXIII-XXVII, located in the outer halo of M31. These galaxies were discovered during the second year of data from the Pan-Andromeda Archaeological Survey (PAndAS), a photometric survey of the M31/M33 subgroup conducted with the MegaPrime/MegaCam wide-field camera on the Canada-France-Hawaii Telescope. The current PAndAS survey now provides an almost complete panoramic view of the M31 halo out to an average projected radius of {approx}150 kpc. Here we present for the first time the metal-poor stellar density map for this whole region, not only as an illustration of the discovery space for satellite galaxies, but also as a birds-eye view of the ongoing assembly process of an L{sub *} disk galaxy. Four of the newly discovered satellites appear as well-defined spatial overdensities of stars lying on the expected locus of metal-poor (-2.5 < [Fe/H] < -1.3) red giant branch stars at the distance of M31. The fifth overdensity, And XXVII, is embedded in an extensive stream of such stars and is possibly the remnant of a strong tidal disruption event. Based on distance estimates from horizontal branch magnitudes, all five have metallicities typical of dwarf spheroidal galaxies ranging from [Fe/H] =-1.7 {+-} 0.2 to [Fe/H] =-1.9 {+-} 0.2 and absolute magnitudes ranging from M{sub V} = -7.1 {+-} 0.5 to M{sub V} = -10.2 {+-} 0.5. These five additional satellites bring the number of dwarf spheroidal galaxies in this region to 25 and continue the trend whereby the brighter dwarf spheroidal satellites of M31 generally have much larger half-light radii than their Milky Way counterparts. With an extended sample of M31 satellite galaxies, we also revisit the spatial distribution of this population and in particular we find that, within the current projected limits of the PAndAS survey, the surface density of satellites is essentially constant out to 150 kpc. This corresponds to a radial density distribution of satellites varying as r{sup -1}, a result seemingly in conflict with the predictions of cosmological simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

CLASSIFYING STRUCTURES IN THE INTERSTELLAR MEDIUM WITH SUPPORT VECTOR MACHINES: THE G16.05-0.57 SUPERNOVA REMNANT

We apply Support Vector Machines (SVMs)-a machine learning algorithm-to the task of classifying structures in the interstellar medium (ISM). As a case study, we present a position-position-velocity (PPV) data cube of {sup 12}CO J = 3-2 emission toward G16.05-0.57, a supernova remnant that lies behind the M17 molecular cloud. Despite the fact that these two objects partially overlap in PPV space, the two structures can easily be distinguished by eye based on their distinct morphologies. The SVM algorithm is able to infer these morphological distinctions, and associate individual pixels with each object at >90% accuracy. This case study suggests that similar techniques may be applicable to classifying other structures in the ISM-a task that has thus far proven difficult to automate.

79 ASTRONOMY AND ASTROPHYSICS↗

COMPARISON OF RADIO-FREQUENCY INTERFERENCE MITIGATION STRATEGIES FOR DISPERSED PULSE DETECTION

Impulsive radio-frequency signals from astronomical sources are dispersed by the frequency-dependent index of refraction of the interstellar media and so appear as chirped signals when they reach Earth. Searches for dispersed impulses have been limited by false detections due to radio-frequency interference (RFI) and, in some cases, artifacts of the instrumentation. Many authors have discussed techniques to excise or mitigate RFI in searches for fast transients, but comparisons between different approaches are lacking. This work develops RFI mitigation techniques for use in searches for dispersed pulses, employing data recorded in a 'Fly's Eye' mode of the Allen Telescope Array as a test case. We gauge the performance of several RFI mitigation techniques by adding dispersed signals to data containing RFI and comparing false alarm rates at the observed signal-to-noise ratios of the added signals. We find that Huber filtering is most effective at removing broadband interferers, while frequency centering is most effective at removing narrow frequency interferers. Neither of these methods is effective over a broad range of interferers. A method that combines Huber filtering and adaptive interference cancelation provides the lowest number of false positives over the interferers considered here. The methods developed here have application to other searches for dispersed pulses in incoherent spectra, especially those involving multiple beam systems.

79 ASTRONOMY AND ASTROPHYSICS↗

THE RED SUPERGIANT PROGENITOR OF SUPERNOVA 2012aw (PTF12bvh) IN MESSIER 95

We report on the direct detection and characterization of the probable red supergiant (RSG) progenitor of the intermediate-luminosity Type II-Plateau (II-P) supernova (SN) 2012aw in the nearby (10.0 Mpc) spiral galaxy Messier 95 (M95; NGC 3351). We have identified the star in both Hubble Space Telescope images of the host galaxy, obtained 17-18 yr prior to the explosion, and near-infrared ground-based images, obtained 6-12 yr prior to the SN. The luminous supergiant showed evidence for substantial circumstellar dust, manifested as excess line-of-sight extinction. The effective total-to-selective ratio of extinction to the star was R'{sub V} Almost-Equal-To 4.35, which is significantly different from that of diffuse interstellar dust (i.e., R{sub V} = 3.1), and the total extinction to the star was therefore, on average, A{sub V} Almost-Equal-To 3.1 mag. We find that the observed spectral energy distribution for the progenitor star is consistent with an effective temperature of 3600 K (spectral type M3), and that the star therefore had a bolometric magnitude of -8.29. Through comparison with recent theoretical massive-star evolutionary tracks we can infer that the RSG progenitor had an initial mass 15 {approx}< M{sub ini}(M{sub Sun }) < 20. Interpolating by eye between the available tracks, we surmise that the star had initial mass {approx}17-18 M{sub Sun }. The circumstellar dust around the progenitor must have been destroyed in the explosion, as the visual extinction to the SN is found to be low (A{sub V} = 0.24 mag with R{sub V} = 3.1).

79 ASTRONOMY AND ASTROPHYSICS↗

A MULTI-SPACECRAFT VIEW OF A GIANT FILAMENT ERUPTION DURING 2009 SEPTEMBER 26/27

We analyze multi-spacecraft observations of a giant filament eruption that occurred during 2009 September 26 and 27. The filament eruption was associated with a relatively slow coronal mass ejection. The filament consisted of a large and a small part, and both parts erupted nearly simultaneously. Here we focus on the eruption associated with the larger part of the filament. The STEREO satellites were separated by about 117 Degree-Sign during this event, so we additionally used SoHO/EIT and CORONAS/TESIS observations as a third eye (Earth view) to aid our measurements. We measure the plane-of-sky trajectory of the filament as seen from STEREO-A and TESIS viewpoints. Using a simple trigonometric relation, we then use these measurements to estimate the true direction of propagation of the filament which allows us to derive the true R/R{sub Sun }-time profile of the filament apex. Furthermore, we develop a new tomographic method that can potentially provide a more robust three-dimensional (3D) reconstruction by exploiting multiple simultaneous views. We apply this method also to investigate the 3D evolution of the top part of filament. We expect this method to be useful when SDO and STEREO observations are combined. We then analyze the kinematics of the eruptive filament during its rapid acceleration phase by fitting different functional forms to the height-time data derived from the two methods. We find that for both methods an exponential function fits the rise profile of the filament slightly better than parabolic or cubic functions. Finally, we confront these results with the predictions of theoretical eruption models.

79 ASTRONOMY AND ASTROPHYSICS↗

A FRAMEWORK FOR INTERPRETING FAST RADIO TRANSIENTS SEARCH EXPERIMENTS: APPLICATION TO THE V-FASTR EXPERIMENT

We define a framework for determining constraints on the detection rate of fast transient events from a population of underlying sources, with a view to incorporate beam shape, frequency effects, scattering effects, and detection efficiency into the metric. We then demonstrate a method for combining independent data sets into a single event rate constraint diagram, using a probabilistic approach to the limits on parameter space. We apply this new framework to present the latest results from the V-FASTR experiment, a commensal fast transients search using the Very Long Baseline Array (VLBA). In the 20 cm band, V-FASTR now has the ability to probe the regions of parameter space of importance for the observed Lorimer and Keane fast radio transient candidates by combining the information from observations with differing bandwidths, and properly accounting for the source dispersion measure, VLBA antenna beam shape, experiment time sampling, and stochastic nature of events. We then apply the framework to combine the results of the V-FASTR and Allen Telescope Array Fly's Eye experiments, demonstrating their complementarity. Expectations for fast transients experiments for the SKA Phase I dish array are then computed, and the impact of large differential bandwidths is discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

On the relaxation behaviors of slow and classical glitches: Observational biases and their opposite recovery trends

We study the pulsar timing properties and the data analysis methods of glitch recoveries. In some cases one first fits the times of arrival (TOAs) to obtain the 'time-averaged' frequency ν and its first derivative ν-dot , and then fits models to them. However, our simulations show that ν and ν-dot obtained in this way are systematically biased unless the time intervals between the nearby data points of TOAs are smaller than about 10{sup 4} s, which is much shorter than typical observation intervals. Alternatively, glitch parameters can be obtained by fitting the phases directly with relatively smaller biases, but the initial recovery time scale is usually chosen by eye, which may introduce a strong bias. We also construct a phenomenological model by assuming a pulsar spin-down law of ν-dot ν{sup −3}=−H{sub 0}G(t) with G(t) = 1 + κe {sup –t/τ} for a glitch recovery, where H {sub 0} is a constant and κ and τ are the glitch parameters to be found. This model can reproduce the observed data of slow glitches from B1822–09 and the giant classical glitch of B2334+61, with κ < 0 or κ > 0, respectively. We then use this model to simulate TOA data and test several fitting procedures for a glitch recovery. The best procedure is (1) to use a very high order polynomial (e.g., to 50th order) to precisely describe the phase, (2) obtain ν(t) and ν-dot (t) from the polynomial, then (3) obtain the glitch parameters from ν(t) or ν-dot (t). Finally, the uncertainty in the starting time t {sub 0} of a classical glitch causes uncertainties in some glitch parameters, but less so for a slow glitch, t {sub 0}, of which can be determined from data.

79 ASTRONOMY AND ASTROPHYSICS↗