An algorithm for series expansions based on hierarchical rate equations

We propose a computational method to obtain series expansions in powers of time for general dynamical systems described by a set of hierarchical rate equations. The method is generally applicable to problems in both equilibrium and nonequilibrium statistical mechanics such as random sequential adsorption, diffusion-reaction dynamics, and Ising dynamics. New result of random sequential adsorption of dimers on a square lattice is presented.Comment: LaTeX, 9 pages including 1 figur

Behaviors of Adult \u3ci\u3eAgrilus Planipennis\u3c/i\u3e (Coleoptera: Buprestidae)

A 2-year study was conducted in Canada (2003) and the United States (2005) to better understand searching and mating behaviors of adult Agrilus planipennis Fairmaire. In both field and laboratory, adults spent more time resting and walking than feeding or flying. The sex ratio in the field was biased towards males, which tended to hover around trees, likely looking for mates. There was more leaf feeding damage within a tree higher in the canopy than in the lower canopy early in the season, but this difference disappeared over time. In choice experiments, males attempted to mate with individuals of both sexes, but they landed more frequently on females than on males. A series of sexual behaviors was observed in the laboratory, including: exposure of the ovipositor/genitalia, sporadic jumping by males, attempted mating, and mating. Sexual behaviors were absent among 1-3 day-old beetles, but were observed regularly in 10-12 day-old beetles. Females were seen exposing their ovipositor, suggestive of pheromone-calling behavior. No courtship was observed prior to mating. Hovering, searching, and landing behaviors suggest that beetles most likely rely on visual cues during mate finding, although host-plant volatiles and/or pheromones might also be involved

A Survey of Laboratory Programs for First Year Medical Students

Basic science courses offered to freshmen medical students have been traditionally taught by didactic presentations and laboratory work. Various factors have prompted many departments to either markedly reduce the time allotted for the traditional, but more vulnerable, laboratory phase of these courses or drastically alter the content of the laboratory programs. Information concerning the desirability for such changes is incomplete and no evaluation has been developed to determine the effectiveness of change. Before beginning any further alterations in the laboratory programs at the Medical College of Virginia, it seemed desirable to determine anew what we wish to teach in the laboratory. This problem was approached in part by surveying the attitudes of other anatomy, biochemistry, and physiology departments

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let

\u3ci\u3eAnoplophora Glabripennis\u3c/i\u3e Within-Tree Distribution, Seasonal Development, and Host Suitability in China and Chicago

Established populations of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae), were first reported in the United States in New York in 1996, Illinois in 1998, and New Jersey in 2002. A federal quarantine and an eradication program were implemented in 1997, involving tree surveys and removal of infested trees. We recorded the number of A. glabripennis life stages found at several locations along the main trunk and major branches of naturally infested trees in China (species of Populus, Salix, and Ulmus) and Chicago, Illinois (species of Acer, Fraxinus, and Ulmus) during 1999 to 2002. Typically, A. glabripennis initiated attack near the crown base along both the trunk and main branches. The one exception to this pattern was on Populus trees in China that had branches along the entire trunk, in which case A. glabripennis initiated attack along the lower trunk. Larvae were the dominant overwintering stage in both countries. A host suitability index for A. glabripennis was calculated for each tree with the formula: (number of living life stages + number of exit holes) / number of oviposition pits. The mean host suitability index was higher on Populus and Salix than Ulmus in China, and generally higher on Acer and Ulmus than Fraxinus in Chicago. Eleven genera of trees (N = 1465 trees) were infested by A. glabripennis in Chicago; in decreasing order of tree frequency they included Acer, Ulmus, Fraxinus, Aesculus, Betula, Salix, Celtis, Malus, Pyrus, Sorbus, and Tilia. When the proportion of each genus of infested street trees (N = 958 trees in 7 genera) was compared to its proportion of all Chicago street trees based on a 2003 inventory (N = 539,613 trees in 45 genera), A. glabripennis showed a significant preference to infest the genera Acer and Ulmus. Based on our results, inspectors should focus their efforts on upper trunks and lower branches of Acer and Ulmus trees

Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling

Citation: Rife, T. W., Wu, S. Y., Bowden, R. L., & Poland, J. A. (2015). Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling. Bmc Genomics, 16, 7. https://doi.org/10.1186/s12864-015-1404-9Background: In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of these objectives. Results: We have developed spiked genotyping-by-sequencing (sGBS), which combines targeted amplicon sequencing with reduced representation genotyping-by-sequencing. To minimize the cost of targeted assays, we utilize a small percent of sequencing capacity available in runs of GBS libraries to "spike" amplified targets of a priori alleles tagged with a different set of unique barcodes. This open platform allows multiple, single-target loci to be assayed while simultaneously generating a whole-genome profile. This dual-genotyping approach allows different sets of samples to be evaluated for single markers or whole genome-profiling. Here, we report the application of sGBS on a winter wheat panel that was screened for converted KASP markers and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34. Conclusions: The flexibility and low-cost of sGBS will enable a range of applications across genetics research. Specifically in breeding applications, the sGBS approach will allow breeders to obtain a whole-genome profile of important individuals while simultaneously targeting specific genes for a range of selection strategies across the breeding program

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Why is the DNA Denaturation Transition First Order?

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d=2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let

Denaturation of Heterogeneous DNA

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second order melting transition in the simplest (Peyrard-Bishop) model. However, sequence heterogeneity is dramatically amplified upon adopting a more realistic treatment of the backbone stiffness. The model yields features of ``multi-step melting'' similar to those observed in experiments.Comment: 4 pages, LaTeX, text and figures also available at http://matisse.ucsd.edu/~hw

Maintaining Social Connections in Dementia: A Qualitative Synthesis

The clinical symptoms of dementia include difficulty with speech, poor short-term memory, and changes in behavior. These symptoms can affect how the person with dementia understands and performs in social interactions. This qualitative review investigated how people with mild to moderate dementia managed social connections. A systematic search of social science databases retrieved 13 articles; data were synthesized using thematic analysis. Results established the work undertaken by people with dementia to maintain and present a social persona seen as socially acceptable. Interpretations are contextualized within Goffman and Sabat's theories on "self." People with dementia were agentic in impression management: undertaking work to maintain recognized social roles, while being aware of when their illness led to others discrediting them. Wider recognition of strategies used to maintain a social self could inform interventions designed to increase capability and confidence in co-managing social connections following dementia diagnosis