The importance of habitat quality for marine reserve fishery linkages

We model marine reserve - fishery linkages to evaluate the potential contribution of habitat-quality improvements inside a marine reserve to fish productivity and fishery catches. Data from Mombasa Marine National Park, Kenya, and the adjacent fishery are used. Marine reserves increase total fish biomass directly by providing refuge from exploitation and indirectly by improving fish habitat in the reserve. As natural mortality of the fish stock decreases in response to habitat enhancement in the reserve, catches increase by up to 2.6 tonnes (t).km(-2).year(-1) and total fish biomass by up to 36 t.km(-2). However, if habitat-quality improvement reduces the propensity of fish to move out of the reserve, catches may fall by up to 0.9 t.km(-2).year(-1). Our results indicate that habitat protection in reserves can underpin fish productivity and, depending on its effects on fish movements, augment catches

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS.

Kaposi's sarcoma (KS) in HIV-infected individuals can have a wide range of clinical outcomes, from indolent skin tumors to a life-threatening visceral cancer. KS tumors contain endothelial-related cells and inflammatory cells that may be HIV-infected. In this study we tested if HIV evolutionary patterns distinguish KS tumor relatedness and progression. Multisite autopsies from participants who died from HIV-AIDS with KS prior to the availability of antiretroviral therapy were identified at the AIDS and Cancer Specimen Resource (ACSR). Two patients (KS1 and KS2) died predominantly from non-KS-associated disease and KS3 died due to aggressive and metastatic KS within one month of diagnosis. Skin and visceral tumor and nontumor autopsy tissues were obtained (n = 12). Single genome sequencing was used to amplify HIV RNA and DNA, which was present in all tumors. Independent HIV tumor clades in phylogenies differentiated KS1 and KS2 from KS3, whose sequences were interrelated by both phylogeny and selection. HIV compartmentalization was confirmed in KS1 and KS2 tumors; however, in KS3, no compartmentalization was observed among sampled tissues. While the sample size is small, the HIV evolutionary patterns observed in all patients suggest an interplay between tumor cells and HIV-infected cells which provides a selective advantage and could promote KS progression

The phase diagram of the lattice Calogero-Sutherland model

We introduce a {\it lattice} version of the Calogero Sutherland model adapted to describe $1/d^2$ pairwise interacting steps with discrete positions on a vicinal surface. The configurational free energy is obtained within a transfer matrix method. The full phase diagram for attractive and for repulsive interaction is deduced. For attraction, critical temperatures of faceting transitions are found to depend on step density.Comment: latex PRBCalogSuth.tex, 6 files, 4 pages [SPEC-S00/900

Confirmation of the \eps -- \eiso (Amati) relation from the X-ray flash XRF 050416A observed by Swift/BAT

We report Swift Burst Alert Telescope (BAT) observations of the X-ray Flash (XRF) XRF 050416A. The fluence ratio between the 15-25 keV and 25-50 keV energy bands of this event is 1.5, thus making it the softest gamma-ray burst (GRB) observed by BAT so far. The spectrum is well fitted by the Band function with E^{\rm obs}_{\rm peak} of 15.0_{-2.7}^{+2.3} keV. Assuming the redshift of the host galaxy (z = 0.6535), the isotropic-equivalent radiated energy E_{\rm iso} and the peak energy at the GRB rest frame (E^{\rm src}_{\rm peak}) of XRF 050416A are not only consistent with the correlation found by Amati et al. and extended to XRFs by Sakamoto et al., but also fill-in the gap of this relation around the 30 - 80 keV range of E^{\rm src}_{\rm peak}. This result tightens the validity of the E^{\rm src}_{\rm peak} - E_{\rm iso} relation from XRFs to GRBs. We also find that the jet break time estimated using the empirical relation between E^{\rm src}_{\rm peak} and the collimation corrected energy E_{\gamma} is inconsistent with the afterglow observation by Swift X-ray Telescope. This could be due to the extra external shock emission overlaid around the jet break time or to the non existence of a jet break feature for XRF, which might be a further challenging for GRB jet emission, models and XRF/GRB unification scenarios.Comment: 16 pages, 4 figures; accepted for publication in ApJ

The First Swift BAT Gamma-Ray Burst Catalog

We present the first Swift Burst Alert Telescope (BAT) catalog of gamma-ray bursts (GRBs), which contains bursts detected by the BAT between 2004 December 19 and 2007 June 16. This catalog (hereafter BAT1 catalog) contains burst trigger time, location, 90% error radius, duration, fluence, peak flux, and time averaged spectral parameters for each of 237 GRBs, as measured by the BAT. The BAT-determined position reported here is within 1.75' of the Swift X-ray Telescope (XRT)-determined position for 90% of these GRBs. The BAT T_90 and T_50 durations peak at 80 and 20 seconds, respectively. From the fluence-fluence correlation, we conclude that about 60% of the observed peak energies, Epeak, of BAT GRBs could be less than 100 keV. We confirm that GRB fluence to hardness and GRB peak flux to hardness are correlated for BAT bursts in analogous ways to previous missions' results. The correlation between the photon index in a simple power-law model and Epeak is also confirmed. We also report the current status for the on-orbit BAT calibrations based on observations of the Crab Nebula.Comment: 63 pages, 23 figures, Accepted in ApJS, Corrected for the BAT ground position, the image significance, and the error radius of GRB 051105, Five machine-readable tables are available at http://swift.gsfc.nasa.gov/docs/swift/results/bat1_catalog

Autocorrelation analysis for the unbiased determination of power-law exponents in single-quantum-dot blinking

We present an unbiased and robust analysis method for power-law blinking statistics in the photoluminescence of single nano-emitters, allowing us to extract both the bright- and dark-state power-law exponents from the emitters' intensity autocorrelation functions. As opposed to the widely-used threshold method, our technique therefore does not require discriminating the emission levels of bright and dark states in the experimental intensity timetraces. We rely on the simultaneous recording of 450 emission timetraces of single CdSe/CdS core/shell quantum dots at a frame rate of 250 Hz with single photon sensitivity. Under these conditions, our approach can determine ON and OFF power-law exponents with a precision of 3% from a comparison to numerical simulations, even for shot-noise-dominated emission signals with an average intensity below 1 photon per frame and per quantum dot. These capabilities pave the way for the unbiased, threshold-free determination of blinking power-law exponents at the micro-second timescale

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi’s Sarcoma during AIDS

Kaposi’s sarcoma (KS) in HIV-infected individuals can have a wide range of clinical outcomes, from indolent skin tumors to a life-threatening visceral cancer. KS tumors contain endothelial-related cells and inflammatory cells that may be HIV-infected. In this study we tested if HIV evolutionary patterns distinguish KS tumor relatedness and progression. Multisite autopsies from participants who died from HIV-AIDS with KS prior to the availability of antiretroviral therapy were identified at the AIDS and Cancer Specimen Resource (ACSR). Two patients (KS1 and KS2) died predominantly from non-KS-associated disease and KS3 died due to aggressive and metastatic KS within one month of diagnosis. Skin and visceral tumor and nontumor autopsy tissues were obtained (n=12). Single genome sequencing was used to amplify HIV RNA and DNA, which was present in all tumors. Independent HIV tumor clades in phylogenies differentiated KS1 and KS2 from KS3, whose sequences were interrelated by both phylogeny and selection. HIV compartmentalization was confirmed in KS1 and KS2 tumors; however, in KS3, no compartmentalization was observed among sampled tissues. While the sample size is small, the HIV evolutionary patterns observed in all patients suggest an interplay between tumor cells and HIV-infected cells which provides a selective advantage and could promote KS progression