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Character analysis and the integration of molecular and morphological data in an understanding of sand dollar phylogeny.

Reconciling discordant morphological and molecular phylogenies remains a problem in modern systematics. By examining conflicting DNA-hybridization and morphological phylogenies of sand dollars, I show that morphological criteria may be used to help evaluate the reliability of molecular phylogenies where they differ from morphological trees. All available criteria for assessing the reliability of DNA-hybridization phylogenies suggest that the sand dollar DNA-hybridization phylogeny is robust. Standard homology-recognition criteria are used to assess the a priori reliabilities of the morphological attributes associated with the node drawn into question by the DNA data, and it is shown that these attributes are among the least phylogenetically informative of all the morphological characters. Moreover, the questioned node has the smallest number of supporting characters, and most of these characters are associated with the food grooves, which suggests that they may be functionally correlated. Thus, on the basis of the analysis of the morphological data and given the robustness of the DNA tree, the DNA phylogeny is preferred. Further, paleobiogeographic data support the DNA tree rather than the morphological tree, and a plausible heterochronic mechanism has been proposed that may account for the homoplasious morphological evolution that must have occurred if the DNA tree is correct.

Animals↗

Nonequilibrium dynamics of the complex Ginzburg-Landau equation: analytical results.

We present a detailed analytical and numerical study of nonequilibrium dynamics for the complex Ginzburg-Landau equation. In particular, we characterize evolution morphologies using spiral defects. This paper is the first in a two-stage exposition. Here, we present analytical results for the correlation function arising from a single-spiral morphology. We also critically examine the utility of the Gaussian auxiliary field ansatz in characterizing a multispiral morphology. In the next paper of this exposition we will present detailed numerical results.

Journal Article↗

Nonequilibrium dynamics in the complex Ginzburg-Landau equation.

Results from a comprehensive analytical and numerical study of nonequilibrium dynamics in the two-dimensional complex Ginzburg-Landau equation have been presented. In particular, spiral defects have been used to characterize the domain growth law and the evolution morphology. An asymptotic analysis of the single-spiral correlation function shows a sequence of singularities-analogous to those seen for time-dependent Ginzburg-Landau models with O(n) symmetry, where n is even.

Journal Article↗

Anomalous self-assembly of gelatin in ethanol-water marginal solvent.

Light scattering, rheology, and atomic force microscope (AFM) studies have been performed on solutions of a polyampholyte (gelatin) prepared in water-ethanol marginal solvent. At ethanol concentration approximately 45+/-2% v/v anomalous aggregation led to formation of fractal (on hydrophilic substrates; glass, quartz and silicon) aggregate of polypeptide molecules having fractal dimension d(f) in 2D=1.60+/-0.08. The time evolution morphology of these self-assembled and self-organized structures formed on hydrophilic substrates was driven by selective ethanol evaporation and was observed by an AFM. These fractal aggregates eventually transformed into near-spherical clusters with fractal corona having same fractal dimension (d(f)=1.58+/-0.05) and finally, the corona separated and regular aggregates were formed. The kinetics of aggregation on substrates could be modeled through random sequential adsorption of particles with continuum power-law size distribution. The temporal growth of aggregate hydrodynamic radius R(h)(t) and scattered intensity I(s)(t) measured in the bulk were observed to exhibit; R(h)-t(z) and I(s)-t(z)-with z=1/d(f), giving a fractal dimension d(f) in 3D approximately equal to 2.6+/-0.2, which is discussed within the framework of Smoluchowski aggregation kinetics. This growth in R(h) is accompanied by narrowing down of the particle size distribution. Solution rheology at this ethanol concentration revealed minimum thixotropy and maximum infinite shear viscosity features.

Journal Article↗

Enhanced instability in thin liquid films by improved compatibility

We investigated experimentally the morphological evolution of thin polydimethylsiloxane films sandwiched between a silicon wafer and different bounding liquids with interfacial tensions varying by 2 orders of magnitude. It is shown that increasing the compatibility between film and bounding liquid by adding a few surfactant molecules results in a faster instability of shorter characteristic wavelength. Inversely, based on the characteristic parameters describing the instability we determined extremely small interfacial tensions with a remarkable accuracy.

Journal Article↗

Origin of the stability of Ge(105) on si: a new structure model and surface strain relaxation.

The structure of Ge(105)-(1 x 2) grown on Si(105) is examined by scanning tunneling microscopy (STM) and first-principles calculations. The morphology evolution with an increasing amount of Ge deposited documents the existence of a tensile surface strain in Si(105) and its relaxation with increasing coverage of Ge. A detailed analysis of high-resolution STM images and first-principles calculations produce a new stable model for the Ge(105)-(1 x 2) structure formed on the Si(105) surface that includes the existence of surface strain. It corrects the model developed from early observations of the facets of "hut" clusters grown on Si(001).

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Competing roughening mechanisms in strained heteroepitaxy: a fast kinetic Monte Carlo study.

We study the morphological evolution of strained heteroepitaxial films using kinetic Monte Carlo simulations in two dimensions. A novel Green's function approach, analogous to boundary integral methods, is used to calculate elastic energies efficiently. We observe island formation at low lattice misfit and high temperature that is consistent with the Asaro-Tiller-Grinfeld instability theory. At high misfit and low temperature, islands or pits form according to the nucleation theory of Tersoff and LeGoues.

Journal Article↗

Liquid-liquid transition in the molecular liquid triphenyl phosphite.

We found both nucleation-growth-type and spinodal-decomposition-type transformation from one liquid state to another in a "molecular liquid," triphenyl phosphite (TPP). Binodal and spinodal temperatures of this transition at ambient pressure were determined by the characteristics of morphological evolution, domain-growth kinetics, and rheological evolution. Furthermore, a distinct thermal signature of the glass transition of a second liquid was also detected in addition to that of an ordinary liquid. These findings strongly suggest the existence of a liquid-liquid transition; more precisely, a transformation of one supercooled liquid to a glassy state of another liquid, in TPP.

Journal Article↗

Kinetic roughening of ion-sputtered Pd(001) surface: beyond the Kuramoto-Sivashinsky model.

We investigate the kinetic roughening of Ar+ ion-sputtered Pd(001) surface both experimentally and theoretically. In situ real-time x-ray reflectivity and in situ scanning tunneling microscopy show that nanoscale adatom islands form and grow with increasing sputter time t. Surface roughness W(t) and lateral correlation length xi(t) follow the scaling laws W(t) approximately t(beta) and xi(t) approximately t(1/z) with the exponents beta approximately 0.20 and 1/z approximately 0.20, for an ion beam energy epsilon=0.5 keV, which is inconsistent with the prediction of the Kuramoto-Sivashinsky (KS) model. We thereby extend the KS model by applying the coarse-grained continuum approach of the Sigmund theory to the order of O(inverted Delta(4),h(2)), where h is the surface height, and derive a new term of the form inverted Delta(2)(inverted Delta h)(2) which plays a decisive role in describing the observed morphological evolution of the sputtered surface.

Journal Article↗

A new look at microbial leaching patterns on sulfide minerals.

Leaching patterns on sulfide minerals were investigated by high-resolution scanning electron microscopy (SEM). Our goal was to evaluate the relative contributions of inorganic surface reactions and reactions localized by attached cells to surface morphology evolution. Experiments utilized pyrite (FeS(2)), marcasite (FeS(2)) and arsenopyrite (FeAsS), and two iron-oxidizing prokaryotes in order to determine the importance of cell type, crystal structure, and mineral dissolution rate in microbially induced pit formation. Pyrite surfaces were reacted with the iron-oxidizing bacterium Acidithiobacillus ferrooxidans (at 25 degrees C), the iron-oxidizing archaeon 'Ferroplasma acidarmanus' (at 37 degrees C), and abiotically in the presence of Fe(3+) ions. In all three experiments, discrete bacillus-sized (1-2 µm) and -shaped (elliptical) pits developed on pyrite surfaces within 1 week of reaction. Results show that attaching cells are not necessary for pit formation on pyrite. Marcasite and arsenopyrite surfaces were reacted with A. ferrooxidans (at 25 degrees C) and 'F. acidarmanus' (at 37 degrees C). Cell-sized and cell-shaped dissolution pits were not observed on marcasite or arsenopyrite at any point during reaction with A. ferrooxidans, or on marcasite surfaces reacted with 'F. acidarmanus'. However, individual 'F. acidarmanus' cells were found within individual shallow (<0.5 µm deep) pits. The size and shape (round rather than elliptical) of the pits conformed closely to the shape of F. acidarmanus (cells) pits on arsenopyrite. We infer these pits to be cell-induced. We attribute the formation of pits readily detectable (by SEM) to the higher reactivity of arsenopyrite compared to pyrite and marcasite under the conditions the experiment was conducted. These pits contributed little to the overall surface topographical evolution, and most likely did not significantly increase surface area during reaction. Our results suggest that overall sulfide mineral dissolution may be dominated by surface reactions with Fe(3+) rather than by reactions at the cell-mineral interface.

Journal Article↗

Histopathologic and immunopathologic study of pyoderma gangrenosum.

Sixty-three patients with pyoderma gangrenosum were seen and studied at the Mayo Clinic from 1971 to 1980. Biopsies from the erythematous border or necrotic edge of the pyoderma gangrenosum lesions usually demonstrated a characteristic pathogenic morphologic evolution. The early lesions revealed mild to moderate perivascular lymphocytic infiltrate associated with endothelial swelling. The fully developed lesions demonstrated necrosis in addition to a dense lymphocytic infiltration surrounding as well as involving the blood vessels. Extravasation of erythrocytes and thrombosis sometimes were seen. Ulceration, infarction, and abscess formation were found in the later stages of evolution. Direct immunofluorescence results were positive in the blood vessels of 36 of 65 (55%) specimens. IgM, C3, and fibrin were found in the papillary and reticular dermal vessels. IgG and IgA were only occasionally present. Pyoderma gangrenosum appears to be a reactive process that is manifested as a vasculitis. Biopsy material from the advancing active erythematous border has early characteristic dermatopathologic findings of lymphocytic vasculitis. Cutaneous vascular immune deposits suggest an immune pathogenesis of either an immune complex disease or lymphocytotoxic reaction.

Biopsy↗

Extra-acral calcifying aponeurotic fibroma: a distinctive case with 23-year follow-up.

Calcifying aponeurotic fibroma (CAF) is an unusual but well-characterized soft tissue neoplasm that typically involves the digits of children and frequently recurs locally. This report describes a case from the subcutis of the lumbosacral region. A 26-year-old man initially presented at age 3 and developed three recurrences over a 23-year period each at approximately 8-year intervals (ages 10, 18, and 26). The microscopic findings in all recurrences showed a lobulated, poorly circumscribed proliferation of dense fibrous tissue containing epithelioid-like fibroblasts, multinucleated cells, and islands of metaplastic chondroid differentiation with focal calcification. Despite origin from an unusual anatomic site, this case reported herein demonstrates the classical morphologic features and clinical history of CAF which showed little in the way of morphologic evolution despite 23 years of persistence. The clinical and histologic features helpful in distinguishing CAF from infantile fibromatosis and soft tissue chondroma are discussed.

Adult↗

The root of angiosperm phylogeny inferred from duplicate phytochrome genes.

An analysis of duplicate phytochrome genes (PHYA and PHYC) is used to root the angiosperms, thereby avoiding the inclusion of highly diverged outgroup sequences. The results unambiguously place the root near Amborella (one species, New Caledonia) and resolve water lilies (Nymphaeales, approximately 70 species, cosmopolitan), followed by Austrobaileya (one species, Australia), as early branches. These findings bear directly on the interpretation of morphological evolution and diversification within angiosperms.

Apoproteins↗

Frog perspective on the morphological difference between humans and chimpanzees.

The body shapes of humans and chimpanzees were compared quantitatively by criteria chosen for their capacity to discriminate well among the body shapes of frogs. By these criteria, the difference in body shape between humans and chimpanzees was found to be greater than that between the most dissimilar pairs of frogs examined--that is, frogs classified in separate taxonomic suborders. Even though the morphological diffference between the two primates is large by frog standards, the biochemical differences between the structural genes of these two species are small. The results of this study give quantitative support to the proposal that morphological evolution and biochemical evolution in structural genes can proceed at independent rates.

Animals↗

Serological and histological follow up of chronic hepatitis B infection.

In order to study the clinical, serological, and morphological evolution of chronic hepatitis B virus infection in childhood, a prospective study has been carried out. A total of 90 children with a chronic infection were followed up for a mean (SD) of 3 (1.8) years. At the beginning of the study, 61 children were asymptomatic and 77 were household contacts of chronic carriers. Serologically 77 were hepatitis B e antigen (HBeAg) positive and 71 of them were positive to hepatitis B virus DNA. The mean alanine aminotransferase activities were higher among HBeAg positive patients than in antihepatitis B e (anti-HBe) positive ones. The most severe histological damage was also found among HBeAg positive patients. The annual seroconversion rate was 14%. A significant increase in the alanine aminotransferase activity was observed 13 (5.6) months before appearance of anti-HBe in the 85% of cases. Among anti-HBe positive patients, the alanine aminotransferase activities were normal in all except three (19%), two of whom had intrahepatic delta antigen. An increase in the histological activity was observed among patients who maintained HBeAg presence while an amelioration of liver damage was observed in anti-HBe carriers.

Adolescent↗

PID, a new member of the P1 bacteriophage group.

Phage P1D produces particles of essentially uniform head size and differs from P1 in its range and tail length. The dimensions of phage P1 are reassessed. The P1 phage group shows signs of morphological evolution.

Bacteriophage P1↗

Matching behavioral evolution to brain morphology.

A method is presented to test the relationship between a phylogenetic tree derived from brain morphology, and different hypotheses describing the evolution of a behavioral trait. This is a question of interest for evolutionary psychologists and behavioral biologists. The paper first discusses how hypotheses for behavioral evolution should be coded for such a comparison, then a triple-per-mutation test, originally proposed to compare independently obtained evolutionary trees, is used for the statistical assessment of each hypothesis. Non-parametric correlation coefficients computed between brain components and appropriately coded behavioral states can then be used to suggest what brain components are responsible for the development of the various states of the behavioral trait of interest. The procedure is illustrated with three different applications relating brain evolution to habitat selection in marsupials, locomotory specialization in primates, and trophic adaptation in bats.

Adaptation, Physiological↗