Effects of quenched impurities on surface diffusion, spreading, and ordering of O/W(110)

We study how quenched impurities affect the surfacediffusion and ordering of strongly interactingadsorbate atoms on surfaces. To this end, we carry out Monte Carlo simulations for a lattice-gas model of O/W(110), including small concentrations of immobile impurities which block their adsorption sites. We examine the behavior of the diffusion coefficients and order parameters as a function of coverage corresponding to various ordered phases at low temperatures. The effects of impurities are examined under both equilibrium and nonequilibrium conditions, and the results are compared to recent studies on a completely clean surface. We find that even minute impurity concentrations affect the diffusion behavior considerably in equilibrium. The effects are strongest in ordered phases and close to phase boundaries, where quenched impurities lead to a reduction of order, which in turn leads to significant changes in the collective diffusion and phase behavior. As the impurity concentration is increased to a level of a few percent of the total surface area, the reduction in order becomes particularly prominent at high coverages. Further studies under nonequilibrium conditions reveal that nonequilibrium effects are strong in the absence of impurities, while for surfaces covered by impurities the nonequilibrium effects are relatively weaker.Peer reviewe

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Political Scienc

Intersite comparison of interannual nearshore bar behavior

Long-term (>years) bathymetric data sets collected in six multiple near-shore sandbar systems were analyzed with complex empirical orthogonal function analysis to quantify intersite differences and similarities in cyclic offshore progressive bar behavior. The observations came from a 37-year annually sampled data set of four regions along the Dutch coast (spanning 70 km of coastline), an 18-year fortnightly to monthly sampled data set at Duck, North Carolina (alongshore extent ~1 km), and a 7-year daily sampled data set of a single cross-shore profile at the Hasaki coast of Japan. The first complex mode, typically representing 50–70% of the total depth variance, described the long-term offshore progressive behavior and allowed for an objective separation of the barred part of the profile from the shoreward- and seaward-located nonbarred parts by considering a threshold bar amplitude below which the spatial results from the first mode were not considered reliable. The sandbars at the six examined sites share common lengths and nondimensional amplitude characteristics, which can be described by a negatively skewed Gaussian function. The absolute amplitude dimensions and the cycle return intervals differ, however, considerably between the sites. The key geometric parameters that steer this intersite variation are the time-averaged mean depths at the shoreward and seaward side of the bar zone (dshore and dsea, respectively) as well as their difference dbz. The degree to which intersite differences in dshore, dsea, and dbz are related linearly to intersite differences in bulk statistics of external forcings (wave, tide, sediment, and bed profile characteristics) is inconclusive

Observations of nearshore crescentic sandbars

The temporal and spatial variability of crescentic sandbars is analyzed with hourly long-term (months) video observations collected at four barred sites and are qualitatively compared to the temporal and spatial variability predicted by hypotheses underpinning existing approaches and models for crescentic bar formation (edge-wave template model, linear stability analysis, and nonlinear models). The observations, coming from the single barred beaches at Duck (North Carolina, USA) and Miyazaki (Kyushu, Japan), and from the double-barred beaches at the northern Gold Coast (Queensland, Australia) and Noordwijk (Netherlands), show that crescentic sandbar wavelength and amplitude variations over space and time are very common. For instance, at any moment in time, the wavelength of the smallest and longest crescentic bar can differ by a factor of 2. Temporal changes in wavelength and amplitude result from merging and splitting of individual crescents, causing the ‘‘final’’ configuration of a crescentic sandbar system to be very different from the initial configuration. The Gold Coast data indicate that these intrinsically nonlinear interactions are an attempt of the crescentic bar system to self-organize into a more uniform pattern, as splitting is usually confined to the longest crescentic bar observed, whereas merging usually combines the smallest crescentic bars into a longer bar. The observed spatial and temporal crescentic bar behavior contrasts qualitatively with behavior predicted from the edge-wave template model and implies that the predictive skill of linear stability models is limited. Nonlinear models are potentially better suited for a comparison against these field observations; several suggestions to improve these models, and hence to facilitate a data-model comparison, are made

The Genome of the Netherlands:design, and project goals

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean = 53 years; SD = 16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.</p

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with ‘true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05–0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r2, increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results

WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary and environmental factors regulating TL are currently widely investigated, however, their relative contribution to TL variability is still understudied. We have used whole genome sequencing data of 250 family trios from the Genome of the Netherlands project to perform computational measurement of TL and a series of regression and genome-wide association analyses to reveal TL inheritance patterns and associated genetic factors. Our results confirm that TL is a largely heritable trait, primarily with mother’s, and, to a lesser extent, with father’s TL having the strongest influence on the offspring. In this cohort, mother’s, but not father’s age at conception was positively linked to offspring TL. Age-related TL attrition of 40 bp/year had relatively small influence on TL variability. Finally, we have identified TL-associated variations in ribonuclease reductase catalytic subunit M1 (RRM1 gene), which is known to regulate telomere maintenance in yeast. We also highlight the importance of multivariate approach and the limitations of existing tools for the analysis of TL as a polygenic heritable quantitative trait

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals