The role of antiphase boundaries during ion sputtering and solid phase epitaxy of Si(001)

The Si(001) surface morphology during ion sputtering at elevated temperatures and solid phase epitaxy following ion sputtering at room temperature has been investigated using scanning tunneling microscopy. Two types of antiphase boundaries form on Si(001) surfaces during ion sputtering and solid phase epitaxy. One type of antiphase boundary, the AP2 antiphase boundary, contributes to the surface roughening. AP2 antiphase boundaries are stable up to 973K, and ion sputtering and solid phase epitaxy performed at 973K result in atomically flat Si(001) surfaces.Comment: 16 pages, 4 figures, to be published in Surface Scienc

Temporal variation in abundance and diversity of butterflies in Bornean rain forests: opposite impacts of logging recorded in different seasons

We used traps baited with fruit to examine how the temporal variation of butterflies within primary forest in Sabah, Borneo differed between species. In addition, we compared patterns of temporal variation in primary and selectively logged forest, and we tested the hypothesis that selective logging has different recorded impacts on species diversity of adults during the wet monsoon period and the drier remaining half of the year. Species of Satyrinae and Morphinae had significantly less-restricted flight periods than did species of Nymphalinae and Charaxinae, which were sampled mainly during the drier season. especially in primary forest. Species diversity of adults was significantly higher during the drier season in primary forest, but did not differ between seasons in logged forest. As a consequence, logging had opposite recorded impacts on diversity during wetter and drier seasons: primary forest had significantly higher diversity than logged forest during the drier season but significantly lower diversity than logged forest during the wetter monsoon season. The results of this study have important implications for the assessment of biodiversity in tropical rain forests, particularly in relation to habitat disturbance: short-term assessments that do not take account of seasonal variation in abundance are likely to produce misleading results, even in regions where the seasonal variation in rainfall is not that great

Preparation of atomically clean and flat Si(100) surfaces by low-energy ion sputtering and low-temperature annealing

Si(100) surfaces were prepared by wet-chemical etching followed by 0.3-1.5keV Ar ion sputtering, either at elevated or room temperature. After a brief anneal under ultrahigh vacuum conditions, the resulting surfaces were examined by scanning tunneling microscopy. We find that wet-chemical etching alone cannot produce a clean and flat Si(100) surface. However, subsequent 300eV Ar ion sputtering at room temperature followed by a 973K anneal yields atomically clean and flat Si(100) surfaces suitable for nanoscale device fabrication.Comment: 13 pages, 3 figures, to be published in Applied Surface Scienc

Comparative study of dimer vacancies and dimer-vacancy lines on Si(001) and Ge(001)

Although the clean Si(001) and Ge(001) surfaces are very similar, experiments to date have shown that dimer-vacancy (DV) defects self-organize into vacancy lines (VLs) on Si(001), but not on Ge(001). In this paper, we perform empirical-potential calculations aimed at understanding the differences between the vacancies on Si(001) and Ge(001). We identify three energetic parameters that characterize the DVs on the two surfaces: the formation energy of a single DV, the attraction between two DVs in adjacent dimer rows, and the strain sensitivity of the formation energy of DVs and VLs. At the empirical level of treatment of the atomic interactions (Tersoff potentials), all three parameters are favorable for the self-assembly of DVs on the Si(001) surface rather than on Ge(001). The most significant difference between the defects on Si(001) and on Ge(001) concerns the formation energy of single DVs, which is three times larger in the latter case. By calculating the strain-dependent formation energies of DVs and VLs, we propose that the experimental observation of self-assembly of vacancies on clean Ge(001) could be achieved by applying compressive strains of the order of 2%.Comment: 3 tables, 4 figures, to appear in Surface Scienc

Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained via masstrapping, many of which will be new species, could be incorporated routinely in phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures via mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from ~500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined, only minor topological changes are induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, whilst the ecological sample expands the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA ‘superbarcodes’ for testing hypotheses regarding global patterns of diversity

Nonlinear Measures for Characterizing Rough Surface Morphologies

We develop a new approach to characterizing the morphology of rough surfaces based on the analysis of the scaling properties of contour loops, i.e. loops of constant height. Given a height profile of the surface we perform independent measurements of the fractal dimension of contour loops, and the exponent that characterizes their size distribution. Scaling formulas are derived and used to relate these two geometrical exponents to the roughness exponent of a self-affine surface, thus providing independent measurements of this important quantity. Furthermore, we define the scale dependent curvature and demonstrate that by measuring its third moment departures of the height fluctuations from Gaussian behavior can be ascertained. These nonlinear measures are used to characterize the morphology of computer generated Gaussian rough surfaces, surfaces obtained in numerical simulations of a simple growth model, and surfaces observed by scanning-tunneling-microscopes. For experimentally realized surfaces the self-affine scaling is cut off by a correlation length, and we generalize our theory of contour loops to take this into account.Comment: 39 pages and 18 figures included; comments to [email protected]

Prolonged Effect of Omeprazole on the 14 C-Urea Breath Test

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73649/1/j.1572-0241.1996.tb08294.x.pd

Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression

Copyright © 2009 The Authors. Copyright © ECOGRAPHY 2009.A major focus of geographical ecology and macro ecology is to understand the causes of spatially structured ecological patterns. However, achieving this understanding can be complicated when using multiple regressions, because the relative importance of explanatory variables, as measured by regression coefficients, can shift depending on whether spatially explicit or non-spatial modelling is used. However, the extent to which coefficients may shift and why shifts occur are unclear. Here, we analyze the relationship between environmental predictors and the geographical distribution of species richness, body size, range size and abundance in 97 multi-factorial data sets. Our goal was to compare standardized partial regression coefficients of non-spatial ordinary least squares regressions (i.e. models fitted using ordinary least squares without taking autocorrelation into account; “OLS models” hereafter) and eight spatial methods to evaluate the frequency of coefficient shifts and identify characteristics of data that might predict when shifts are likely. We generated three metrics of coefficient shifts and eight characteristics of the data sets as predictors of shifts. Typical of ecological data, spatial autocorrelation in the residuals of OLS models was found in most data sets. The spatial models varied in the extent to which they minimized residual spatial autocorrelation. Patterns of coefficient shifts also varied among methods and datasets, although the magnitudes of shifts tended to be small in all cases. We were unable to identify strong predictors of shifts, including the levels of autocorrelation in either explanatory variables or model residuals. Thus, changes in coefficients between spatial and non-spatial methods depend on the method used and are largely idiosyncratic, making it difficult to predict when or why shifts occur. We conclude that the ecological importance of regression coefficients cannot be evaluated with confidence irrespective of whether spatially explicit modelling is used or not. Researchers may have little choice but to be more explicit about the uncertainty of models and more cautious in their interpretation