Closure statistics in interferometric data

Interferometric visibilities, reflecting the complex correlations between signals recorded at antennas in an interferometric array, carry information about the angular structure of a distant source. While unknown antenna gains in both amplitude and phase can prevent direct interpretation of these measurements, certain combinations of visibilities called closure phases and closure amplitudes are independent of antenna gains and provide a convenient set of robust observables. However, these closure quantities have subtle noise properties and are generally both linearly and statistically dependent. These complications have obstructed the proper use of closure quantities in interferometric analysis, and they have obscured the relationship between analysis with closure quantities and other analysis techniques such as self calibration. We review the statistics of closure quantities, noting common pitfalls that arise when approaching low signal-to-noise due to the nonlinear propagation of statistical errors. We then develop a strategy for isolating and fitting to the independent degrees of freedom captured by the closure quantities through explicit construction of linearly independent sets of quantities along with their noise covariance in the Gaussian limit, valid for moderate signal-to-noise, and we demonstrate that model fits have biased posteriors when this covariance is ignored. Finally, we introduce a unified procedure for fitting to both closure information and partially calibrated visibilities, and we demonstrate both analytically and numerically the direct equivalence of inference based on closure quantities to that based on self calibration of complex visibilities with unconstrained antenna gains.Comment: 31 pages, 17 figure

Response of the benthic food web to short- and long-term nutrient 1 enrichment in saltmarsh mudflats

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Marine Ecology Progress Series 474 (2013): 27-41, doi:10.3354/meps10090.We examined the responses of biota at or near the base of the benthic food web to nutrient enrichment in salt marsh mudflats in Plum Island estuary (Massachusetts, USA). To simulate eutrophication, nitrate and phosphate loading rates were increased 10- to 15-fold in creeks fertilized for 2 mo (i.e. short-term enrichment) or 6 yr (chronic enrichment). We found that benthic invertebrate community structure was not altered by nutrient enrichment, although the abundance of epifaunal, but not infaunal, grazers increased. Short-term enrichment had no effect on the food web, but significant changes were detected with chronic enrichment. Grazing experiments with 15N-enriched bacteria and 13C-enriched benthic algae revealed higher per capita ingestion rates of benthic microalgae by nematodes, copepods and hydrobiid snails in the creek with chronic nutrient enrichment where isotope composition also indicated that algae increased in dietary importance. The fraction of bacterial biomass grazed was not affected by nutrient enrichment; however, the fraction of benthic algal biomass grazed increased by 235% with chronic enrichment. This higher grazing pressure was partly the result of dietary changes (increases in per capita feeding rate or a change in selection) but was mostly due to an increased abundance of the grazing consumer with the highest biomass, the snail Nassarius obsoletus. This increased top-down control partially masked the bottom-up effects of nutrient enrichment on algal biomass and helps explain the slow and inconsistent response of microalgal biomass to chronic nutrient enrichment previously observed in this estuary. Our research shows that eutrophication may subtly affect benthic food webs before large, sustained increases in algal biomass are observed.Pierre-Yves Pascal conducted this research while being supported by a 563 postdoctoral fellowship funded by the Department of Energy Office of Biological and 564 Environmental Research Award DE-FG02-05ER64070 and the Louisiana State University 565 College of Science. This material is based upon work supported by the National Science 566 Foundation under Grant Nos. 0213767 and 9726921

The Effects of Malignant Transformation on Susceptibility of Human Urothelial Cells to CD40-Mediated Apoptosis

Background: The tumor necrosis factor (TNF) superfamily of ligands and receptors mediates immune cell survival. Some members possess a death domain, a protein motif that functions to transmit apoptotic signals, whereas others, such as CD40, do not. CD40 is expressed by both normal and malignant epithelial cells. To investigate the functional significance of this expression, we studied the effects of ligation of CD40, Fas, and TNF receptors (TNFRs) on the proliferation and survival of normal and malignant human urothelial cells and urothelial cells with disabled p53 function. Methods: Normal and malignant human urothelial cells were cultured with soluble TNF family agonists (CD40 ligand [CD40L], TNF-α, anti-Fas antibody, or cocultured with mouse fibroblasts stably transfected with plasmids that caused the cells to constitutively express CD40L or CD32; cell proliferation was estimated by an [3H]thymidine incorporation assay, and apoptosis was determined by Annexin V staining and by a DNA fragmentation assay. Messenger RNA levels for CD40 and potential downstream effector molecules were quantified by polymerase chain reaction-based and ribonuclease protection assays, respectively, and nuclear factor (NF) κB nuclear translocation was detected by immunofluorescence. All statistical tests were two-sided. Results: Soluble trimeric CD40L inhibited the growth of normal and malignant urothelial cells but did not induce apoptosis. Cell surface-presented CD40L induced massive apoptosis in CD40-positive transitional cell carcinoma cells but not in normal urothelial cells. Normal cells underwent CD40L-mediated apoptosis only in the presence of other TNFR agonists. An agonistic anti-CD40 antibody presented on the surface of CD32-transfected fibroblasts also induced apoptosis in transitional cell carcinoma cells and in normal urothelial cells. Apoptotic responses of tumor (but not normal) cells to soluble agonists were enhanced by blocking protein synthesis. Karyotypically normal urothelial cells with disabled p53 function underwent apoptosis during coculture with CD40L-expressing fibroblasts alone but were not additionally sensitive to additional TNFR agonists. Conclusions: Susceptibility to CD40 ligation-induced apoptosis may be a novel mechanism for eliminating neoplastically transformed urothelial cells. Loss of CD40 expression may be an important adaptive mechanism for transitional cell carcinoma development and progressio

Frictionless bead packs have macroscopic friction, but no dilatancy

The statement of the title is shown by numerical simulation of homogeneously sheared packings of frictionless, nearly rigid beads in the quasistatic limit. Results coincide for steady flows at constant shear rate γ in the limit of small γ and static approaches, in which packings are equilibrated under growing deviator stresses. The internal friction angle ϕ, equal to 5.76 $\pm$ 0.22 degrees in simple shear, is independent on the average pressure P in the rigid limit. It is shown to stem from the ability of stable frictionless contact networks to form stress-induced anisotropic fabrics. No enduring strain localization is observed. Dissipation at the macroscopic level results from repeated network rearrangements, like the effective friction of a frictionless slider on a bumpy surface. Solid fraction Φ remains equal to the random close packing value ≃ 0.64 in slowly or statically sheared systems. Fluctuations of stresses and volume are observed to regress in the large system limit, and we conclude that the same friction law for simple shear applies in the large psystem limit if normal stress or density is externally controlled. Defining the inertia number as I = γ m/(aP), with m the grain mass and a its diameter, both internal friction coefficient $\mu$∗ = tan ϕ and volume 1/Φ increase as powers of I in the quasistatic limit of vanishing I, in which all mechanical properties are determined by contact network geometry. The microstructure of the sheared material is characterized with a suitable parametrization of the fabric tensor and measurements of connectivity and coordination numbers associated with contacts and near neighbors.Comment: 19 pages. Additional technical details may be found in v

Evaluating the Social Costs of Fishing Activities in A Deliberative Perspective

The ECOST project aims to develop a new approach for the evaluation of fishing activities and policies in order to contribute to a better management of aquatic resources which affect sustainable development in coastal zones around the world. It has to be seen from the wider perspective of equipping public decisionmakers and society with the appropriate tools and methods needed to take into account, not only immediate economic and social profits, but also the costs engendered by fishing activities, which relate as much to ecosystems as to societies. The novelty and originality of the suggested approach doesn’t rely on the concept chosen for the analysis, the social cost, but on the way it is built and mobilised to deliberate on the evaluation of fishing activities. As Fisheries activity is a complex system, characterized by reciprocal interactions between fisheries activity and the harvested resource, it is difficult to define the effects of such activities in the society. The social cost is thus defined as an articulation between the frontiers of what is feasible? and the assessment of members of the society concerning what will be judged desirable? (O’Connor 2004). We propose an evaluation process defining the performance issue related to fishery metiers, a set of indicators and a method to assess the social cost using the Kerbabel Deliberation Matrix framework.Keywords: Fisheries Economics, Integrated Modeling Approach of Social and Environmental Interactions in Support of Marine Resource Management, Modeling and Economic TheoryKeywords: Fisheries Economics, Integrated Modeling Approach of Social and Environmental Interactions in Support of Marine Resource Management, Modeling and Economic Theor

The fables of pity: Rousseau, Mandeville and the animal-fable

Copyright @ 2012 Edinburgh University PressPrompted by Derrida’s work on the animal-fable in eighteenth-century debates about political power, this article examines the role played by the fiction of the animal in thinking of pity as either a natural virtue (in Rousseau’s Second Discourse) or as a natural passion (in Mandeville’s The Fable of the Bees). The war of fables between Rousseau and Mandeville – and their hostile reception by Samuel Johnson and Adam Smith – reinforce that the animal-fable illustrates not so much the proper of man as the possibilities and limitations of a moral philosophy that is unable to address the political realities of the state

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure

A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular clusters. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices $(0.7 < \Gamma <1.4)$ and clear evidence for an exponential cut-off in the range 1.0-2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices $(1.0 < \Gamma < 1.7)$, however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600-4700 MSPs in Galactic globular clusters, commensurate with previous estimates. The observation of high-energy gamma-ray emission from a globular cluster thus provides a reliable independent method to assess their millisecond pulsar populations that can be used to make constraints on the original neutron star X-ray binary population, essential for understanding the importance of binary systems in slowing the inevitable core collapse of globular clusters.Comment: Accepted for publication in A&A. Corresponding authors: J. Kn\"odlseder, N. Webb, B. Pancraz

Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry

Construction of artificial higher order protein complexes allows sampling of structural architectures and functional features not accessible by classical monomeric proteins. Here, we combine in silico modelling with expanded genetic code facilitated strain promoted azide-alkyne cycloaddition to construct artificial complexes that are structurally integrated protein dimers and demonstrate functional synergy. Using fluorescent proteins sfGFP and Venus as models, homodimers and heterodimers are constructed that switched ON once assembled and display enhanced spectral properties. Symmetrical crosslinks are found to be important for functional enhancement. The determined molecular structure of one artificial dimer shows that a new long-range polar network comprised mostly of organised water molecules links the two chromophores leading to activation and functional enhancement. Single molecule analysis reveals the dimer is more resistant to photobleaching spending longer times in the ON state. Thus, genetically encoded bioorthogonal chemistry can be used to generate truly integrated artificial protein complexes that enhance function