Judging Similarity among Strings Described By Hierarchical Trees

The paper compares the tree-theoretical model of similarity judgement (in which the similarity between two objects is a function of the distance between them in a conceptual tree) with an averaging model of similarity judgement that is drawn jointly from information integration theory and from current research indicating the prevalence of anchoring and adjustment mechanisms in judgement. Results of an experiment are presented that suggest that even when subjects organize conceptual material as a hierarchical tree, judgments of similarity among the objects are better accounted for by an averaging mechanism than by distances in the tree. These data are discussed in terms of the differences between the representation in which knowledge is encoded and the processes that operate on the represented information

The Mass Distribution of the Strong Lensing Cluster SDSS J1531+3414

We present the mass distribution at the core of SDSS J1531+3414, a strong-lensing cluster at z=0.335. We find that the mass distribution is well described by two cluster-scale halos with a contribution from cluster-member galaxies. New HST observations of SDSS J1531+3414 reveal a signature of ongoing star formation associated with the two central galaxies at the core of the cluster, in the form of a chain of star forming regions at the center of the cluster. Using the lens model presented here, we place upper limits on the contribution of a possible lensed image to the flux at the center region, and rule out that this emission is coming from a background source.Comment: 8 pages, 5 figures; Submitted to Ap

Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, M. D., Fox, M. D., Kelly, E. L. A., Zgliczynski, B. J., Sandin, S. A., & Smith, J. E. Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific. Plos One, 15(2), (2020): e0228448, doi:10.1371/journal.pone.0228448.Upwelling is an important source of inorganic nutrients in marine systems, yet little is known about how gradients in upwelling affect primary producers on coral reefs. The Southern Line Islands span a natural gradient of inorganic nutrient concentrations across the equatorial upwelling region in the central Pacific. We used this gradient to test the hypothesis that benthic autotroph ecophysiology is enhanced on nutrient-enriched reefs. We measured metabolism and photophysiology of common benthic taxa, including the algae Porolithon, Avrainvillea, and Halimeda, and the corals Pocillopora and Montipora. We found that temperature (27.2–28.7°C) was inversely related to dissolved inorganic nitrogen (0.46–4.63 μM) and surface chlorophyll a concentrations (0.108–0.147 mg m-3), which increased near the equator. Contrary to our prediction, ecophysiology did not consistently track these patterns in all taxa. Though metabolic rates were generally variable, Porolithon and Avrainvillea photosynthesis was highest at the most productive and equatorial island (northernmost). Porolithon photosynthetic rates also generally increased with proximity to the equator. Photophysiology (maximum quantum yield) increased near the equator and was highest at northern islands in all taxa. Photosynthetic pigments also were variable, but chlorophyll a and carotenoids in Avrainvillea and Montipora were highest at the northern islands. Phycobilin pigments of Porolithon responded most consistently across the upwelling gradient, with higher phycoerythrin concentrations closer to the equator. Our findings demonstrate that the effects of in situ nutrient enrichment on benthic autotrophs may be more complex than laboratory experiments indicate. While upwelling is an important feature in some reef ecosystems, ancillary factors may regulate the associated consequences of nutrient enrichment on benthic reef organisms.This work was supported by funding from the Moore Family Foundation, the Gordon and Betty Moore Foundation, the Scripps family, and anonymous donors. The funders had no role in study design, data collection and analysis, or preparation of the manuscript

High Resolution Linear Polarimetric Imaging for the Event Horizon Telescope

Images of the linear polarization of synchrotron radiation around Active Galactic Nuclei (AGN) identify their projected magnetic field lines and provide key data for understanding the physics of accretion and outflow from supermassive black holes. The highest resolution polarimetric images of AGN are produced with Very Long Baseline Interferometry (VLBI). Because VLBI incompletely samples the Fourier transform of the source image, any image reconstruction that fills in unmeasured spatial frequencies will not be unique and reconstruction algorithms are required. In this paper, we explore extensions of the Maximum Entropy Method (MEM) to linear polarimetric VLBI imaging. In contrast to previous work, our polarimetric MEM algorithm combines a Stokes I imager that uses only bispectrum measurements that are immune to atmospheric phase corruption with a joint Stokes Q and U imager that operates on robust polarimetric ratios. We demonstrate the effectiveness of our technique on 7- and 3-mm wavelength quasar observations from the VLBA and simulated 1.3-mm Event Horizon Telescope observations of Sgr A* and M87. Consistent with past studies, we find that polarimetric MEM can produce superior resolution compared to the standard CLEAN algorithm when imaging smooth and compact source distributions. As an imaging framework, MEM is highly adaptable, allowing a range of constraints on polarization structure. Polarimetric MEM is thus an attractive choice for image reconstruction with the EHT.Comment: 19 pages, 9 figures. Accepted for publication in ApJ. Imaging code available at https://github.com/achael/eht-imaging

Relative Astrometry of Compact Flaring Structures in Sgr A* with Polarimetric VLBI

We demonstrate that polarimetric interferometry can be used to extract precise spatial information about compact polarized flares of Sgr A*. We show that, for a faint dynamical component, a single interferometric baseline suffices to determine both its polarization and projected displacement from the quiescent intensity centroid. A second baseline enables two-dimensional reconstruction of the displacement, and additional baselines can self-calibrate using the flare, enhancing synthesis imaging of the quiescent emission. We apply this technique to simulated 1.3-mm wavelength observations of a "hot spot" embedded in a radiatively inefficient accretion disk around Sgr A*. Our results indicate that, even with current sensitivities, polarimetric interferometry with the Event Horizon Telescope can achieve ~5 microarcsecond relative astrometry of compact flaring structures near Sgr A* on timescales of minutes.Comment: 9 Pages, 4 Figures, accepted for publication in Ap

The effect of calcium binding on adhesion and pilus biogenesis in the PilC family of proteins

Pseudomonas aeruginosa is an opportunistic pathogen prevalent in people on immunosuppressants, recent open wounds, or cystic fibrosis patients. P. aeruginosa attaches to the host cell via polar type IV pili (tfp). These tfp are composed of many proteins including the major pilus subunit PilA, retraction protein PilT, and one focus of this dissertation, 1163 residue protein PilY1. PilY1 shares homology to other bacterial adhesion and pilus biogenesis proteins such as the PilC family of proteins in Neisseria gonorrhoeae, Neisseria meningitidis, and Kingella kingae thus, it is often characterized as a pilus biogenesis protein and the P. aeruginosa adhesin. However, no known mechanism for either situation had been elucidated. In this study, we have identified two calcium binding sites which affect both functional pilus biogenesis and adhesion to host cells. In addition, we have also located an RGD (integrin binding motif) that mediates PilY1 binding to integrin. The C-terminal most PilY1 calcium binding site (CBS) was found from residues 851-859 in PAK and is conserved in other strains of P. aeruginosa. This CBS is also conserved in the PilC proteins over 100 different bacteria. We found, through mutating the bidentate aspartic acid in vitro and in vivo, that this CBS controlled functional pilus biogenesis with the calcium bound and unbound states corresponding to pilus extension and retraction respectfully. We also characterized the homologous CBSs in N. gonorrhoeae and K. kingae finding similar results. Upon further examination, we also located separate CBS from residues 600-608. This site was in close proximity to an RGD. This CBS was conserved in other strains of P. aeruginosa, but not in other bacteria. We found that purified PilY1 bound integrin in an RGD dependent manner. Furthermore, we found that this interaction was mediated by the calcium bound states of both CBSs. Here, we demonstrate that P. aeruginosa PilY1 uses calcium to mediate both functional pilus biogenesis factor and adhesion to host cells. Future studies will hopefully include exploiting both calcium binding domains to prevent pilus formation and binding to host cells and characterizing the in vivo effects of these three sites

Star Formation at z=2.481 in the Lensed Galaxy SDSS J1110+6459, I: Lens Modeling and Source Reconstruction

Using the combined resolving power of the Hubble Space Telescope and gravitational lensing, we resolve star-forming structures in a z~2.5 galaxy on scales much smaller than the usual kiloparsec diffraction limit of HST. SGAS J111020.0+645950.8 is a clumpy, star forming galaxy lensed by the galaxy cluster SDSS J1110+6459 at z = 0.659, with a total magnification ~30x across the entire arc. We use a hybrid parametric/non-parametric strong lensing mass model to compute the deflection and magnification of this giant arc, reconstruct the light distribution of the lensed galaxy in the source plane, and resolve the star formation into two dozen clumps. We develop a forward-modeling technique to model each clump in the source plane. We ray trace the model to the image plane, convolve with the instrumental point spread function (PSF), and compare with the GALFIT model of the clumps in the image plane, which decomposes clump structure from more extended emission. This technique has the advantage, over ray tracing, by accounting for the asymmetric lensing shear of the galaxy in the image plane and the instrument PSF. At this resolution, we can begin to study star formation on a clump-by-clump basis, toward the goal of understanding feedback mechanisms and the buildup of exponential disks at high redshift.Comment: 19 pages, 12 figures, accepted to Ap

Modeling Seven Years of Event Horizon Telescope Observations with Radiatively Inefficient Accretion Flow Models

An initial three-station version of the Event Horizon Telescope, a millimeter-wavelength very-long baseline interferometer, has observed Sagittarius A* (Sgr A*) repeatedly from 2007 to 2013, resulting in the measurement of a variety of interferometric quantities. Of particular importance, there is now a large set of closure phases, measured over a number of independent observing epochs. We analyze these observations within the context of a realization of semi-analytic radiatively inefficient disk models, implicated by the low luminosity of Sgr A*. We find a broad consistency among the various observing epochs and between different interferometric data types, with the latter providing significant support for this class of models of Sgr A*. The new data significantly tighten existing constraints on the spin magnitude and its orientation within this model context, finding a spin magnitude of $a=0.10^{+0.30+0.56}_{-0.10-0.10}$, an inclination with respect to the line of sight of $\theta={60^\circ}^{+5^\circ+10^\circ}_{-8^\circ-13^\circ}$, and a position angle of $\xi={156^\circ}^{+10^\circ+14^\circ}_{-17^\circ-27^\circ}$ east of north. These are in good agreement with previous analyses. Notably, the previous $180^\circ$ degeneracy in the position angle has now been conclusively broken by the inclusion of the closure phase measurements. A reflection degeneracy in the inclination remains, permitting two localizations of the spin vector orientation, one of which is in agreement with the orbital angular momentum of the infrared gas cloud G2 and the clockwise disk of young stars. This possibly supports a relationship between Sgr A*'s accretion flow and these larger-scale features.Comment: 16 pages, 11 figures, accepted to Ap