Evolution of a fluorinated green fluorescent protein

The fluorescence of bacterial cells expressing a variant (GFPm) of the green fluorescent protein (GFP) was reduced to background levels by global replacement of the leucine residues of GFPm by 5,5,5-trifluoroleucine. Eleven rounds of random mutagenesis and screening via fluorescence-activated cell sorting yielded a GFP mutant containing 20 amino acid substitutions. The mutant protein in fluorinated form showed improved folding efficiency both in vivo and in vitro, and the median fluorescence of cells expressing the fluorinated protein was improved {approx}650-fold in comparison to that of cells expressing fluorinated GFPm. The success of this approach demonstrates the feasibility of engineering functional proteins containing many copies of abiological amino acid constituents

Pentaquark searches at FOCUS

We find no evidence for high-energy photoproduction of pentaquarks at 1540 MeV/$c^2$, 1862 MeV/$c^2$, or 3099 MeV/$c^2$ using decay modes $pK_S^0$, $\Xi^-\pi^-$, and $D^{(*)-}p$, respectively.Comment: Proceedings from talk at 2004 DPF Meeting at University of California, Riversid

Modelos jerárquicos de marcaje–recaptura: un marco para la inferencia de procesos demográficos

The development of sophisticated mark–recapture models over the last four decades has provided fundamental tools for the study of wildlife populations, allowing reliable inference about population sizes and demographic rates based on clearly formulated models for the sampling processes. Mark–recapture models are now routinely described by large numbers of parameters. These large models provide the next challenge to wildlife modelers: the extraction of signal from noise in large collections of parameters. Pattern among parameters can be described by strong, deterministic relations (as in ultrastructural models) but is more flexibly and credibly modeled using weaker, stochastic relations. Trend in survival rates is not likely to be manifest by a sequence of values falling precisely on a given parametric curve; rather, if we could somehow know the true values, we might anticipate a regression relation between parameters and explanatory variables, in which true value equals signal plus noise. Hierarchical models provide a useful framework for inference about collections of related parameters. Instead of regarding parameters as fixed but unknown quantities, we regard them as realizations of stochastic processes governed by hyperparameters. Inference about demographic processes is based on investigation of these hyperparameters. We advocate the Bayesian paradigm as a natural, mathematically and scientifically sound basis for inference about hierarchical models. We describe analysis of capture–recapture data from an open population based on hierarchical extensions of the Cormack–Jolly–Seber model. In addition to recaptures of marked animals, we model first captures of animals and losses on capture, and are thus able to estimate survival probabilities (i.e., the complement of death or permanent emigration) and per capita growth rates f (i.e., the sum of recruitment and immigration rates). Covariation in these rates, a feature of demographic interest, is explicitly described in the model.El desarrollo de sofisticados modelos de marcaje–recaptura a lo largo de las últimas cuatro décadas ha proporcionado herramientas fundamentales para el estudio de poblaciones de fauna silvestre, lo que ha permitido inferir con fiabilidad los tamaños poblacionales y las tasas demográficas a partir de modelos claramente formulados para procesos estocásticos. En la actualidad, los modelos de marcaje–recaptura se describen de forma rutinaria mediante una extensa serie de parámetros. Dichos modelos representan el siguiente reto al que deberán enfrentarse los modeladores de fauna silvestre: discriminar las señales del ruido en amplias series de parámetros. La pauta que encontramos en los parámetros puede describirse mediante sólidas relaciones deterministas (como en los modelos ultraestructurales), pero resulta más flexible y creíble si se modela utilizando relaciones estocásticas más débiles. No es probable que la tendencia en las tasas de supervivencia se manifieste por una secuencia de valores hallados concretamente en una curva paramétrica dada; por ello, si pudiéramos llegar a conocer los valores reales, podríamos prever una relación de regresión entre parámetros y variables explicativas, de forma que el valor verdadero equivaldría a la señal más el ruido. Los modelos jerárquicos proporcionan un marco útil para la inferencia acerca de series de parámetros relacionados. Así, en lugar de interpretar los parámetros como cantidades fijas, pero desconocidas, los interpretamos como realizaciones de procesos estocásticos regidos por hiperparámetros. La inferencia acerca de los procesos demográficos se basa en la investigación de dichos hiperparámetros. Por este motivo, defendemos el paradigma bayesiano como una base natural, matemática y científicamente sólida para la inferencia acerca de modelos jerárquicos. En el presente estudio describimos el análisis de datos de captura–recaptura obtenidos a partir de una población abierta basada en ampliaciones jerárquicas del modelo de Cormack–Jolly–Seber. Además de las recapturas de animales marcados, también modelamos las primeras capturas de animales y de pérdidas durante la captura, lo que nos permitió estimar las probabilidades de supervivencia de (es decir, el complemento de la muerte o la emigración permanente) y las tasas de crecimiento per cápita f (es decir, la suma de las tasas de reclutamiento y de migración). En el modelo se describe explícitamente la covariación en estas tasas, que constituye una característica de interés demográfico

On thinning of chains in MCMC

1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology. 2. We have noted that many authors routinely ‘thin’ their simulations, discarding all but every kth sampled value; of the studies we surveyed with details on MCMC implementation, 40% reported thinning. 3. Thinning is often unnecessary and always inefficient, reducing the precision with which features of the Markov chain are summarised. The inefficiency of thinning MCMC output has been known since the early 1990’s, long before MCMC appeared in ecological publications. 4. We discuss the background and prevalence of thinning, illustrate its consequences, discuss circumstances when it might be regarded as a reasonable option and recommend against routine thinning of chains unless necessitated by computer memory limitations

Long-Distance Contributions to D^0-D^0bar Mixing Parameters

Long-distance contributions to the $D^0$-$\bar D^0$ mixing parameters $x$ and $y$ are evaluated using latest data on hadronic $D^0$ decays. In particular, we take on two-body $D \to PP$ and $VP$ decays to evaluate the contributions of two-body intermediate states because they account for $\sim 50$ of hadronic $D^0$ decays. Use of the diagrammatic approach has been made to estimate yet-observed decay modes. We find that $y$ is of order a few $\times 10^{-3}$ and $x$ of order $10^{-3}$ from hadronic $PP$ and $VP$ modes. These are in good agreement with the latest direct measurement of $D^0$-$\bar D^0$ mixing parameters using the $D^0 \to K_S \pi^+\pi^-$ and $K_S K^+ K^-$ decays by BaBar. We estimate the contribution to $y$ from the $VV$ modes using the factorization model and comment on the single-particle resonance effects and contributions from other two-body modes involving even-parity states.Comment: 18 pages and 1 figure; footnotes and references added; to appear in Phys. Rev.

Estimating age from recapture data: integrating incremental growth measures with ancillary data to infer age-at-length

Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models overlook variation in growth rates of individuals and consider growth parameters as population parameters. More recent models have taken advantage of hierarchical structuring of parameters and Bayesian inference methods to allow for variation among individuals as functions of environmental covariates or individual-specific random effects. Here, we describe hierarchical models in which growth curves vary as individual-specific stochastic processes, and we show how these models can be fit using capture–recapture data for animals of unknown age along with data for animals of known age. We combine these independent data sources in a Bayesian analysis, distinguishing natural variation (among and within individuals) from measurement error. We illustrate using data for African dwarf crocodiles, comparing von Bertalanffy and logistic growth models. The analysis provides the means of predicting crocodile age, given a single measurement of head length. The von Bertalanffy was much better supported than the logistic growth model and predicted that dwarf crocodiles grow from 19.4 cm total length at birth to 32.9 cm in the first year and 45.3 cm by the end of their second year. Based on the minimum size of females observed with hatchlings, reproductive maturity was estimated to be at nine years. These size benchmarks are believed to represent thresholds for important demographic parameters; improved estimates of age, therefore, will increase the precision of population projection models. The modeling approach that we present can be applied to other species and offers significant advantages when multiple sources of data are available and traditional aging techniques are not practical

QCD sum rules for the anti-charmed pentaquark

We present a QCD sum rule analysis for the anti-charmed pentaquark state with and without strangeness. While the sum rules for most of the currents are either non-convergent or dominated by the $DN$ continuum, the one for the non-strange pentaquark current composed of two diquarks and an antiquark, is convergent and has a structure consistent with a positive parity pentaquark state after subtracting out the $DN$ continuum contribution. Arguments are presented on the similarity between the result of the present analysis and that based on the constituent quark models, which predict a more stable pentaquark states when the antiquark is heavy.Comment: 19 pages, 8 figures, REVTex, revised version,new figures added and references update

MiniBooNE

The physics motivations, design, and status of the Booster Neutrino Experiment at Fermilab, MiniBooNE, are briefly discussed. Particular emphasis is given on the ongoing preparatory work that is needed for the MiniBooNE muon neutrino to electron neutrino oscillation appearance search. This search aims to confirm or refute in a definitive and independent way the evidence for neutrino oscillations reported by the LSND experiment.Comment: 3 pages, no figures, to appear in the proceedings of the 9th International Conference on Astroparticle and Underground Physics (TAUP 2005), Zaragoza, Spain, 10-14 Sep 200