Analysis of deciduous tree species dynamics after a severe ice storm using SORTIE model simulations

Ice storms are frequent natural disturbance events in hardwood forests of eastern Canada and the United States, but their effects on forest dynamics are not well understood. Our objectives were to characterize short- and long-term tree species dynamics after a severe ice storm, and to assess the influence of spatial distribution of trees on these dynamics. SORTIE, a spatially explicit individual tree-based forest model, was used to simulate the effects of a severe ice storm on 300 years old stands. Crown radius was reduced and tree mortality was increased for a 5-year period following the ice storm disturbance. To investigate the influence of the spatial distribution of trees, we repeated the same experiment in a uniformly distributed stand where we systematically assigned coordinates of all trees, saplings and seedlings before the ice storm was modeled. Our results showed that six types of dynamics can be adopted by a species following an ice storm and that spatial distribution of trees influenced the species responses. In summary, we found that a combination of factors, namely, species density and spatial distribution, shade tolerance, growth rate, extent of canopy openness and canopy loss resulting from the ice storm, determine how tree species respond to ice storm disturbance

Propagation on networks: an exact alternative perspective

By generating the specifics of a network structure only when needed (on-the-fly), we derive a simple stochastic process that exactly models the time evolution of susceptible-infectious dynamics on finite-size networks. The small number of dynamical variables of this birth-death Markov process greatly simplifies analytical calculations. We show how a dual analytical description, treating large scale epidemics with a Gaussian approximations and small outbreaks with a branching process, provides an accurate approximation of the distribution even for rather small networks. The approach also offers important computational advantages and generalizes to a vast class of systems.Comment: 8 pages, 4 figure

Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics

Motivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera. Contact: [email protected] Supplementary informatio

MS 2053.7-0449: Confirmation of a bimodal mass distribution from strong gravitational lensing

We present the first strong lensing study of the mass distribution in the cluster MS 2053-04 based on HST archive data. This massive, X-ray luminous cluster has a redshift z=0.583, and it is composed of two structures that are gravitationally bound to each other. The cluster has one multiply imaged system constituted by a double gravitational arc. We have performed a parametric strong lensing mass reconstruction using NFW density profiles to model the cluster potential. We also included perturbations from 23 galaxies, modeled like elliptical singular isothermal sphere, that are approximately within 1'x1' around the cluster center. These galaxies were constrained in both the geometric and dynamical parameters with observational data. Our analysis predicts a third image which is slightly demagnified. We found a candidate for this counter-image near the expected position and with the same F702W-F814W colors as the gravitational arcs in the cluster. The results from the strong lensing model shows the complex structure in this cluster, the asymmetry and the elongation in the mass distribution, and are consistent with previous spectrophotometric results that indicate that the cluster has a bimodal mass distribution. Finally, the derived mass profile was used to estimate the mass within the arcs and for comparison with X-ray estimates.Comment: To be published in ApJ (accepted

Maternal Smoking During Pregnancy and Offspring Birth Weight: A Genetically-Informed Approach Comparing Multiple Raters

Maternal smoking during pregnancy (SDP) is a significant public health concern with adverse consequences to the health and well-being of the fetus. There is considerable debate about the best method of assessing SDP, including birth/medical records, timeline follow-back approaches, multiple reporters, and biological verification (e.g., cotinine). This is particularly salient for genetically-informed approaches where it is not always possible or practical to do a prospective study starting during the prenatal period when concurrent biological specimen samples can be collected with ease. In a sample of families (N = 173) specifically selected for sibling pairs discordant for prenatal smoking exposure, we: (1) compare rates of agreement across different types of report—maternal report of SDP, paternal report of maternal SDP, and SDP contained on birth records from the Department of Vital Statistics; (2) examine whether SDP is predictive of birth weight outcomes using our best SDP report as identified via step (1); and (3) use a sibling-comparison approach that controls for genetic and familial influences that siblings share in order to assess the effects of SDP on birth weight. Results show high agreement between reporters and support the utility of retrospective report of SDP. Further, we replicate a causal association between SDP and birth weight, wherein SDP results in reduced birth weight even when accounting for genetic and familial confounding factors via a sibling comparison approac

Missouri mothers and their children: A family study of the effects of genetics and the prenatal environment

The Missouri Mothers and Their Children Study was specifically designed to critically investigate prenatal environmental influences on child attention problems and associated learning and cognitive deficits. The project began as a pilot study in 2004 and was formally launched in 2008. Participants in the study were initially identified via the Department of Vital Statistics birth record database. Interview and lab-based data were obtained from (1) mothers of Missouri-born children (born 1998–2005), who smoked during one pregnancy but not during another pregnancy, (2) biological fathers when available, and (3) the children [i.e., full sibling pairs discordant for exposure to maternal smoking during pregnancy (SDP)]. This within-mother, between-pregnancy contrast provides the best possible methodological control for many stable maternal and familial confounding factors (e.g., heritable and socio-demographic characteristics of the mother that predict increased probability of SDP). It also controls for differences between mothers who do and do not smoke during pregnancy, and their partners, that might otherwise artifactually create, or alternatively mask, associations between SDP and child outcomes. Such a design will therefore provide opportunities to determine less biased effect sizes while also allowing us to investigate (on a preliminary basis) the possible contribution of paternal or other second-hand smoke exposure during the pre-, peri- and postnatal periods to offspring outcome. This protocol has developed a cohort that can be followed longitudinally through periods typically associated with increased externalizing symptoms and substance use initiation

The effect of smoking during pregnancy on severity and directionality of externalizing and internalizing symptoms: A genetically informed approach

The objective was to examine the association between maternal smoking during pregnancy (SDP) and (I) severity and (II) directionality of externalizing and internalizing symptoms in a sample of sibling pairs while rigorously controlling for familial confounds. The Missouri Mothers and Their Children Study is a family study (N = 173 families) with sibling pairs (aged 7 to 16 years) who are discordant for exposure to SDP. This sibling comparison study is designed to disentangle the effects of SDP from familial confounds. An SDP severity score was created for each child using a combination of SDP indicators (timing, duration, and amount). Principal component analysis of externalizing and internalizing behavior, assessed with the Child Behavior Checklist and Teacher Report Form, was used to create symptom severity and directionality scores. The variance in severity and directionality scores was primarily a function of differences between siblings (71% and 85%, respectively) rather than differences across families (29% and 15%, respectively). The severity score that combines externalizing and internalizing symptom severity was not associated with SDP. However, a significant within-family effect of SDP on symptom directionality (b = 0.07

Analysis of electron-positron momentum spectra of metallic alloys as supported by first-principles calculations

Electron-positron momentum distributions measured by the coincidence Doppler broadening method can be used in the chemical analysis of the annihilation environment, typically a vacancy-impurity complex in a solid. In the present work, we study possibilities for a quantitative analysis, i.e., for distinguishing the average numbers of different atomic species around the defect. First-principles electronic structure calculations self-consistently determining electron and positron densities and ion positions are performed for vacancy-solute complexes in Al-Cu, Al-Mg-Cu, and Al-Mg-Cu-Ag alloys. The ensuing simulated coincidence Doppler broadening spectra are compared with measured ones for defect identification. A linear fitting procedure, which uses the spectra for positrons trapped at vacancies in pure constituent metals as components, has previously been employed to find the relative percentages of different atomic species around the vacancy [A. Somoza et al. Phys. Rev. B 65, 094107 (2002)]. We test the reliability of the procedure by the help of first-principles results for vacancy-solute complexes and vacancies in constituent metals.Comment: Submitted to Physical Review B on September 19 2006. Revised version submitted on November 8 2006. Published on February 14 200