Measurement of the differential cross section for the reaction gamman-->pi- p from deuterium.

We report a measurement of the differential cross section for the gamman-->pi- p process from the CLAS detector at Jefferson Laboratory in Hall B for photon energies between 1.0 and 3.5 GeV and pion center-of-mass (c.m.) angles (thetac.m.) between 50 degrees and 115 degrees. We confirm a previous indication of a broad enhancement around a c.m. energy ([sqrt]s) of 2.1 GeV at thetac.m.=90 degrees in the scaled differential cross section s7dsigma/dt and a rapid falloff in a center-of-mass energy region of about 400 MeV following the enhancement. Our data show an angular dependence of this enhancement as the suggested scaling region is approached for thetac.m. from 70 degrees to 105 degrees.

Lack of cross-scale linkages reduces robustness of community-based fisheries management.

Community-based management and the establishment of marine reserves have been advocated worldwide as means to overcome overexploitation of fisheries. Yet, researchers and managers are divided regarding the effectiveness of these measures. The "tragedy of the commons" model is often accepted as a universal paradigm, which assumes that unless managed by the State or privatized, common-pool resources are inevitably overexploited due to conflicts between the self-interest of individuals and the goals of a group as a whole. Under this paradigm, the emergence and maintenance of effective community-based efforts that include cooperative risky decisions as the establishment of marine reserves could not occur. In this paper, we question these assumptions and show that outcomes of commons dilemmas can be complex and scale-dependent. We studied the evolution and effectiveness of a community-based management effort to establish, monitor, and enforce a marine reserve network in the Gulf of California, Mexico. Our findings build on social and ecological research before (1997-2001), during (2002) and after (2003-2004) the establishment of marine reserves, which included participant observation in >100 fishing trips and meetings, interviews, as well as fishery dependent and independent monitoring. We found that locally crafted and enforced harvesting rules led to a rapid increase in resource abundance. Nevertheless, news about this increase spread quickly at a regional scale, resulting in poaching from outsiders and a subsequent rapid cascading effect on fishing resources and locally-designed rule compliance. We show that cooperation for management of common-pool fisheries, in which marine reserves form a core component of the system, can emerge, evolve rapidly, and be effective at a local scale even in recently organized fisheries. Stakeholder participation in monitoring, where there is a rapid feedback of the systems response, can play a key role in reinforcing cooperation. However, without cross-scale linkages with higher levels of governance, increase of local fishery stocks may attract outsiders who, if not restricted, will overharvest and threaten local governance. Fishers and fishing communities require incentives to maintain their management efforts. Rewarding local effective management with formal cross-scale governance recognition and support can generate these incentives.

Cross-cultural variability of component processes in autobiographical remembering: Japan, Turkey, and the USA.

Although the underlying mechanics of autobiographical memory may be identical across cultures, the processing of information differs. Undergraduates from Japan, Turkey, and the USA rated 30 autobiographical memories on 15 phenomenological and cognitive properties. Mean values were similar across cultures, with means from the Japanese sample being lower on most measures but higher on belief in the accuracy of their memories. Correlations within individuals were also similar across cultures, with correlations from the Turkish sample being higher between measures of language and measures of recollection and belief. For all three cultures, in multiple regression analyses, measures of recollection were predicted by visual imagery, auditory imagery, and emotions, whereas measures of belief were predicted by knowledge of the setting. These results show subtle cultural differences in the experience of remembering.

RNA Virus Evolution: a Cross-scale, Disease Dynamic Perspective

RNA viruses are an important cause of global morbidity and mortality. The rapid evolutionary rates of RNA virus pathogens, caused by high replication rates and error-prone polymerases, can make the pathogens difficult to control. RNA viruses can undergo immune escape within their hosts and develop resistance to the treatment and vaccines we design to fight them. Understanding the spread and evolution of RNA pathogens is essential for reducing human suffering. In this dissertation, I make use of the rapid evolutionary rate of viral pathogens to answer several questions about how RNA viruses spread and evolve. To address each of the questions, I link mathematical techniques for modeling viral population dynamics with phylogenetic and coalescent techniques for analyzing and modeling viral genetic sequences and evolution. The first project uses multi-scale mechanistic modeling to show that decreases in viral substitution rates over the course of an acute infection, combined with the timing of infectious hosts transmitting new infections to susceptible individuals, can account for discrepancies in viral substitution rates in different host populations. The second project combines coalescent models with within-host mathematical models to identify driving evolutionary forces in chronic hepatitis C virus infection. The third project compares the effects of intrinsic and extrinsic viral transmission rate variation on viral phylogenies.

A Bayesian Dirichlet-Multinomial Test for Cross-Group Differences

Testing for differences within data sets is an important issue across various applications. Our work is primarily motivated by the analysis of microbiomial composition, which has been increasingly relevant and important with the rise of DNA sequencing. We first review classical frequentist tests that are commonly used in tackling such problems. We then propose a Bayesian Dirichlet-multinomial framework for modeling the metagenomic data and for testing underlying differences between the samples. A parametric Dirichlet-multinomial model uses an intuitive hierarchical structure that allows for flexibility in characterizing both the within-group variation and the cross-group difference and provides very interpretable parameters. A computational method for evaluating the marginal likelihoods under the null and alternative hypotheses is also given. Through simulations, we show that our Bayesian model performs competitively against frequentist counterparts. We illustrate the method through analyzing metagenomic applications using the Human Microbiome Project data.