Use of Ψ<Superscript>α</Superscript>-ETOs in the unified treatment of electronic attraction,electric field and electric field gradient multicenter integrals of screened Coulomb potentials over Slater orbitals

In this study, using complete orthonormal sets of -ETOs (where =1, 0, –1, –2, ...)introduced by the author, a large number of series expansion formulae for the multicenter electronic attraction (EA), electric field (EF) and electric field gradient (EFG) integrals of the Yukawa-like screened Coulomb potentials (SCPs) is presented through the new central and noncentral potentials and the overlap integrals with the same screening constants. The final results obtained are valid for arbitrary locations of STOs and their parameters.An erratum to this article can be found at     

Comparative wood anatomy of epacrids (Styphelioideae,Ericaceae s.L.)

The wood anatomy of 16 of the 37 genera within the epacrids (Styphelioideae, Ericaceae s.l.) is investigated by light and scanning electron microscopy. Several features in the secondary xylem occur consistently at the tribal level: arrangement of vessel-ray pits, distribution of axial parenchyma, ray width, and the presence and location of crystals. The primitive nature of Prionoteae and Archerieae is supported by the presence of scalariform perforation plates with many bars and scalariform to opposite vessel pitting. The wood structure of Oligarrheneae is similar to that of Styphelieae, but the very narrow vessel elements, exclusively uniseriate rays and the lack of prismatic crystals in Oligarrheneae distinguish these two tribes. The secondary xylem of Monotoca tamariscina indicates that it does not fit in Styphelieae; a position within Oligarrheneae is possible. Like most Cosmelieae, all Richeeae are characterized by exclusively scalariform perforation plates with many bars, a very high vessel density and paratracheal parenchyma, although they clearly differ in ray width (exclusively uniseriate rays in Cosmelieae vs. uniseriate and wide multiseriate rays in Richeeae). Several wood anatomical features confirm the inclusion of epacrids in Ericaceae s.l. Furthermore, there are significant ecological implications. The small vessel diameter and high vessel frequency in many epacrids are indicative of a high conductive safety to avoid embolism caused by freeze-thaw cycles, while the replacement of scalariform by simple vessel perforation plates and an increase in vessel diameter would suggest an increased conductive efficiency, which is especially found in mesic temperate or tropical Styphelieae.     

Matching unrelated stimuli with same discriminative functions: training order effects

Previous research has shown that after training simple discriminations (A1+/A2−, B1+/B2−), bringing these tasks under conditional control (J1–A1, J2–A2) leads to transfer of discriminative control (J1+/J2−) and to generalized matching on the basis of same discriminative functions (e.g. J1–B1, J2–B2). The same occurs when conditional discriminations are trained (D1–E1, D2–E2; F1–G1, F2–G2). When the subjects are then trained to demonstrate correct relations (D1–E1, D2–E2) when given X1 and to demonstrate incorrect relations when given X2 (XD–E), transfer of discriminative control (X1+/X2−) and generalized matching on the basis of same discriminative functions emerges (e.g. X1F1–G1, X2F1–G2). The present study investigated if these performances are dependent on the training and/or testing order. In Experiment 1, the lower-order contingency tasks were trained before the higher-order contingency tasks (A1+/A2−, B1+/B2− before J–A, and D–E, F–G before XD–E). Half the subjects received the J–B test before the more complex XF–G test (Condition A), while for the other subjects, this testing order was reversed (Condition B). Finally, all subjects received additional tests in which they were given the opportunity to demonstrate the discriminative properties of the J and X stimuli (J1+/J2−, X1+/X2−), and to match the A, J, and X stimuli with newly introduced stimuli of same discriminative properties (e.g. J1-POLITE, J2-RUDE). Experiment 2 was the same except that the training order was reversed (J–A before A1+/A2−, B1+/B2−, and XD–E before D–E, F–G). The results were affected by the training order but not by the testing order. Transfer of discriminative functions and generalized matching on the basis of same functions only occurred reliably when the lower-order contingency tasks were trained first. A stimulus-control account of the data is offered.     

Improved protein-ligand docking using GOLD

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol.     

The contribution of ancestry,chance, and past and ongoing selection to adaptive evolution

The relative contributions of ancestry, chance, and past and ongoing election to variation in one adaptive (larval feeding rate) and one seemingly nonadaptive (pupation height) trait were determined in populations ofDrosophila melanogaster adapting to either low or high larval densities in the laboratory. Larval feeding rates increased rapidly in response to high density, and the effects of ancestry, past selection and chance were ameliorated by ongoing selection within 15–20 generations. Similarly, in populations previously kept at high larval density, and then switched to low larval density, the decline of larval feeding rate to ancestral levels was rapid (15-20 generations) and complete, providing support for a previously stated hypothesis regarding the costs of faster feeding inDrosophila larvae. Variation among individuals was the major contributor to variation in pupation height, a trait that would superficially appear to be nonadaptive in the environmental context of the populations used in this study because it did not diverge between sets of populations kept at low versus high larval density for many generations. However, the degree of divergence among populations (FST) for pupation height was significantly less than expected for a selectively neutral trait, and we integrate results from previous studies to suggest that the variation for pupation height among populations is constrained by stabilizing selection, with a flat, plateau-like fitness function that, consequently, allows for substantial phenotypic variation within populations. Our results support the view that the genetic imprints of history (ancestry and past selection) in outbreeding sexual populations are typically likely to be transient in the face of ongoing selection and recombination. The results also illustrate the heuristic point that different forms of selection-for example directional versus stabilizing selection—acting on a trait in different populations may often not be due to differently shaped fitness functions, but rather due to differences in how the fitness function maps onto the actual distribution of phenotypes in a given population. We discuss these results in the light of previous work on reverse evolution, and the role of ancestry, chance, and past and ongoing selection in adaptive evolution.     

Sensitivity analyses for ecological regression

In many ecological regression studies investigating associations between environmental exposures and health outcomes, the observed relative risks are in the range 1.0-2.0. The interpretation of such small relative risks is difficult due to a variety of biases--some of which are unique to ecological data, since they arise from within-area variability in exposures/confounders. The potential for residual spatial dependence, due to unmeasured confounders and/or data anomalies with spatial structure, must also be considered, though it often will be of secondary importance when compared to the likely effects of unmeasured confounding and within-area variability in exposures/confounders. Methods for addressing sensitivity to these issues are described, along with an approach for assessing the implications of spatial dependence. An ecological study of the association between myocardial infarction and magnesium is critically reevaluated to determine potential sources of bias. It is argued that the sophistication of the statistical analysis should not outweigh the quality of the data, and that finessing models for spatial dependence will often not be merited in the context of ecological regression.     

Divergent selection drives the adaptive radiation of crossbills

Abstract Knowledge of how phenotype influences fitness is necessary if we are to understand the basis of natural selection and how natural selection contributes to adaptive radiations. Here I quantify selection on a wild population of red crossbills ( Loxia curvirostra complex) in the South Hills, Idaho. Bill depth is the target of selection and selection on bill depth is stabilizing. I then show how fitness is related to both bill depth and performance. I use these and previously published relationships to estimate a fitness surface for five species of red crossbills that are part of an ongoing adaptive radiation in western North America. The fitness surface for crossbills has distinct peaks and valleys, with each crossbill species residing on or very near the summits. This work strongly supports a key tenet of the ecological theory of adaptive radiations; namely, divergent selection for utilizing alternative resources is the ultimate cause of adaptive radiations.     

Multilocus models of sympatric speciation: Bush versus Rice versus Felsenstein

Abstract. In populations of phytophagous insects that use the host plant as a rendezvous for mating, divergence in host preference could lead to sympatric speciation. Speciation requires the elimination of "generalist" genotypes, that is, those with intermediate host preference. This could occur because such genotypes have an inherent fitness disadvantage, or because preference alleles become associated with alleles that are oppositely selected on the two hosts. Although the former mechanism has been shown to be plausible, the latter mechanism has not been studied in detail. I consider a multilocus model (the "Bush model") in which one set of biallelic loci affects host preference, and a second set affects viability on the hosts once chosen. Alleles that increase viability on one host decrease viability on the other, and all loci are assumed to be unlinked. With moderately strong selection on the viability loci, preference alleles rapidly become associated with viability alleles, and the population splits into two reproductively isolated host specialist populations. The conditions for speciation to occur in this model, as measured by the strength of selection required, are somewhat more stringent than in a model in which preference and viability are controlled by the same loci (one-trait model). In contrast, the conditions are much less stringent than in a model in which speciation requires buildup of associations between viability loci and loci controlling a host-independent assortative mating trait (canonical two-trait model). Moreover, in the one-trait model, and to a lesser extent the Bush model, the strength of selection needed to initiate speciation is only slightly greater than that needed to complete it. This indicates that documenting instances of sympatric species that are reproductively isolated only by host or habitat preference would provide evidence for the plausibility of sympatric speciation in nature.     

Predictive Validity of Discriminant Analysis for Genetic Data

We examined the predictive validity of the results using discriminant analysis to distinguish statistically among two or more populations with a large sample of random amplified polymorphic DNA (RAPD) loci, but a small sample of genotypes from each population. We compared and contrasted results from randomized data with results from real data of three studies by 100 randomized shuffling of genotypes into various populations. We generally obtained substantial differences between results from randomized data compared to those from the real data in several characteristics of discriminant analysis. We showed that a high level of correctly classified percentage is also obtainable in the analysis of randomized data, mainly with a low number of populations. However, the correctly classified percentage obtained from the real data was generally significantly higher than the percentage obtained from the randomized data. We suggested that the high level of real differences in allele frequencies of the RAPD polymorphic loci clearly distinguished the various populations and that the populations differ significantly in their RAPD contents in accordance with ecological heterogeneity. We obtained either no or a low level of difference between the correct classification rate obtained by the leaving-one-out procedure and that obtained from the original data, attributed to a low number of loci selected by the stepwise method. The results strengthen and support our conclusion and lead us to focus on the discriminant analysis by selecting only low numbers of discriminating variables.     

A theoretical framework of ecological phase transitions for characterizing tree-grass dynamics

This paper describes a theoretical framework of ecological phase transitions for modeling tree-grass dynamics and analyzing the shifts or phase transitions from one vegetation structure to another in the southern Texas landscape. This framework implements the integration of percolation theory, fractal geometry and phase transition theory as a method for modeling the spatial patterns of tree-grass dynamics, and nonlinear Markov non-equilibrium thermodynamic stability theory as a method for characterizing temporal tree-grass dynamics and phase transition. An historical sequence of aerial photographs at a Prosopis - thornscrub savanna parkland site in southern Texas was used to determine the parameters of the models. The preliminary analytical result accords well with current understanding and field survey of vegetation dynamics in the southern Texas landscape. The potential of such approaches and other relevant theories such as self-organized criticality and synergetics to vegetation dynamics is also discussed.