Habitat connectivity in reef fish communities and marine reserve design in Old Providence-Santa Catalina, Colombia

On the insular platform of Old Providence/Santa Catalina, Colombia, we compared nearshore lagoonal patch reefs to those on the northern bank distant from the islands to determine the importance of habitat connectivity to fish community structure. Nearshore patch reefs had greater proximity to mangrove, seagrass and rocky shore habitats, and they had significantly more individuals. Nearshore reefs also tended to have a greater total biomass, more species, a higher proportion of predators of mobile invertebrates and small fishes, and a lower proportion of herbivores. Biomass of snappers and grunts at nearshore sites was four times greater compared to bank sites, and was correlated with the amount of seagrass and sand/rubble habitat within 500 m of each patch reef. We also compared length-frequency distributions and abundances of grunts and snappers among all sites (deep and shallow forereefs, patch reefs and deep and shallow leeside slopes). The results were consistent with ontogenetic migrations from shallow sites, primarily seagrass and mangrove habitats, to deeper sites and to those further out on the bank. The evidence suggests that species differed in both distance and direction of dispersal, which may be affected by the abundance and distribution of preferred habitats. Marine reserves near the islands should target nearshore nursery areas and patch reefs harboring species of limited dispersal capability. Reserves on the northern bank would protect spawners of those species showing the greatest dispersal capability

Plasmonic gold nanodiscs using piezoelectric substrate birefringence for liquid sensing

This article presents the simulation, fabrication, and experimental characterization of a surface plasmonic resonance (SPR) sensor integrated with an acoustic sensing compatible substrate. The SPR sensor is designed to work in the visible region with gold nanodisc arrays fabricated on LiNbO3, which is both piezoelectric and birefringent. A linear relationship between resonance wavelength and varying liquid refractive indices were observed in experiments, and a sensitivity of 165 nm/refractive index unit was obtained. Polarization effects of the birefringent property of the Y-cut LiNbO3 substrate have been investigated, which can also be applied to X-cut LiNbO3. Our study demonstrates the feasibility of an SPR sensor device utilizing a birefringent substrate, which has acoustic wave compatibility and can pave the way toward much more robust and flexible biosensing device

Solving Non-Stationary Bandit Problems by Random Sampling from Sibling Kalman Filters

The multi-armed bandit problem is a classical optimization problem where an agent sequentially pulls one of multiple arms attached to a gambling machine, with each pull resulting in a random reward. The reward distributions are unknown, and thus, one must balance between exploiting existing knowledge about the arms, and obtaining new information. Dynamically changing (non-stationary) bandit problems are particularly challenging because each change of the reward distributions may progressively degrade the performance of any fixed strategy. Although computationally intractable in many cases, Bayesian methods provide a standard for optimal decision making. This paper proposes a novel solution scheme for bandit problems with non-stationary normally distributed rewards. The scheme is inherently Bayesian in nature, yet avoids computational intractability by relying simply on updating the hyper parameters of sibling Kalman Filters, and on random sampling from these posteriors. Furthermore, it is able to track the better actions, thus supporting non-stationary bandit problems. Extensive experiments demonstrate that our scheme outperforms recently proposed bandit playing algorithms, not only in non-stationary environments, but in stationary environments also. Furthermore, our scheme is robust to inexact parameter settings. We thus believe that our methodology opens avenues for obtaining improved novel solutions

Study of Cabibbo Suppressed Decays of the Ds Charmed-Strange Meson involving a KS

We study the decay of Ds meson into final states involving a Ks and report the discovery of Cabibbo suppressed decay modes Ds -> Kspi-pi+pi+ (179 +/- 36 events) and Ds -> Kspi+ (113 +/-26 events). The branching ratios for the new modes are Gamma(Ds -> Kspi-pi+pi+)/Gamma(Ds -> KsK-pi+pi+) = 0.18 +/- 0.04 +/- 0.05 and Gamma(Ds -> Kspi+)/Gamma(Ds -> KsK+) = 0.104 +/- 0.024 +/- 0.013.Comment: 11 pages, 6 figure

Can forest management based on natural disturbances maintain ecological resilience?

Given the increasingly global stresses on forests, many ecologists argue that managers must maintain ecological resilience: the capacity of ecosystems to absorb disturbances without undergoing fundamental change. In this review we ask: Can the emerging paradigm of natural-disturbance-based management (NDBM) maintain ecological resilience in managed forests? Applying resilience theory requires careful articulation of the ecosystem state under consideration, the disturbances and stresses that affect the persistence of possible alternative states, and the spatial and temporal scales of management relevance. Implementing NDBM while maintaining resilience means recognizing that (i) biodiversity is important for long-term ecosystem persistence, (ii) natural disturbances play a critical role as a generator of structural and compositional heterogeneity at multiple scales, and (iii) traditional management tends to produce forests more homogeneous than those disturbed naturally and increases the likelihood of unexpected catastrophic change by constraining variation of key environmental processes. NDBM may maintain resilience if silvicultural strategies retain the structures and processes that perpetuate desired states while reducing those that enhance resilience of undesirable states. Such strategies require an understanding of harvesting impacts on slow ecosystem processes, such as seed-bank or nutrient dynamics, which in the long term can lead to ecological surprises by altering the forest's capacity to reorganize after disturbance

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Partonic flow and ϕ\phi-meson production in Au+Au collisions at sNN\sqrt{s_{NN}} = 200 GeV

We present first measurements of the $\phi$-meson elliptic flow ($v_{2}(p_{T})$) and high statistics $p_{T}$ distributions for different centralities from $\sqrt{s_{NN}}$ = 200 GeV Au+Au collisions at RHIC. In minimum bias collisions the $v_{2}$ of the $\phi$ meson is consistent with the trend observed for mesons. The ratio of the yields of the $\Omega$ to those of the $\phi$ as a function of transverse momentum is consistent with a model based on the recombination of thermal $s$ quarks up to $p_{T}\sim 4$ GeV/$c$, but disagrees at higher momenta. The nuclear modification factor ($R_{CP}$) of $\phi$ follows the trend observed in the $K^{0}_{S}$ mesons rather than in $\Lambda$ baryons, supporting baryon-meson scaling. Since $\phi$-mesons are made via coalescence of seemingly thermalized $s$ quarks in central Au+Au collisions, the observations imply hot and dense matter with partonic collectivity has been formed at RHIC.Comment: 6 pages, 4 figures, submit to PR

Inclusive cross section and double helicity asymmetry for \pi^0 production in p+p collisions at sqrt(s)=200 GeV: Implications for the polarized gluon distribution in the proton

The PHENIX experiment presents results from the RHIC 2005 run with polarized proton collisions at sqrt(s)=200 GeV, for inclusive \pi^0 production at mid-rapidity. Unpolarized cross section results are given for transverse momenta p_T=0.5 to 20 GeV/c, extending the range of published data to both lower and higher p_T. The cross section is described well for p_T < 1 GeV/c by an exponential in p_T, and, for p_T > 2 GeV/c, by perturbative QCD. Double helicity asymmetries A_LL are presented based on a factor of five improvement in uncertainties as compared to previously published results, due to both an improved beam polarization of 50%, and to higher integrated luminosity. These measurements are sensitive to the gluon polarization in the proton, and exclude maximal values for the gluon polarization.Comment: 375 authors, 7 pages, 3 figures. Submitted to Phys. Rev. D, Rapid Communications. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of open charm production in dd+Au collisions at sNN\sqrt{s_{NN}}=200 GeV

We present the first comprehensive measurement of $D^{0}, D^{+}, D^{*+}$ and their charge conjugate states at mid-rapidity in $d$+Au collisions at $\sqrt{s_{_{NN}}}$=200 GeV using the STAR TPC. The directly measured open charm multiplicity distribution covers a broad transverse momentum region of 0$<p_{T}<11$ GeV/$c$. The measured $dN/dy$ at mid-rapidity for $D^{0}$ is $0.0265\pm 0.0036 (stat.) \pm 0.0071 (syst.)$ and the measured $D^{*+}/D^{0}$ and $D^{+}/D^{0}$ ratios are approximately equal with a magnitude of $0.40\pm 0.09(stat.) \pm 0.13(syst.)$. The total $c\bar{c}$ cross section per nucleon-nucleon collision extracted from this study is $1.18 \pm 0.21(stat.) \pm 0.39(syst.)$mb. The direct measurement of open charm production is consistent with STAR single electron data. This cross section is higher than expectations from PYTHIA and other pQCD calculations. The measured $p_{T}$ distribution is harder than the pQCD prediction using the Peterson fragmentation function.Comment: Quark Matter 2004 Proceeding