Full real-space analysis of a dodecagonal quasicrystal

The atomically resolved real-space structure of a long-range-ordered dodecagonal quasicrystal is determined based on scanning tunnelling microscopy. For the BaTiO3-derived oxide quasicrystal which spontaneously forms on a Pt(111) surface, 8100 atomic positions have been determined and are compared with an ideal Niizeki–Gähler tiling. Although the Niizeki–Gähler tiling has a complex three-element structure, the abundance of the triangle, square and rhomb tiling elements in the experimental data closely resembles the ideal frequencies. Similarly, the frequencies of all possible next-neighbour tiling combinations are, within the experimental uncertainty, identical to the ideal tiling. The angular and orientational distributions of all individual tiling elements show the characteristics of the dodecagonal quasicrystal. In contrast, the analysis of the orientation of characteristic and more complex tiling combinations indicates the partial decomposition of the quasicrystal into small patches with locally reduced symmetry. These, however, preserve the long-range quasicrystal coherence. The symmetry reduction from dodecagonal to sixfold is assigned to local interaction with the threefold substrate. It leads to atomic flips which preserve the number of quasicrystal tiling elements

Two-dimensional wetting layer structures of reduced ternary oxides on Ru(0001) and Pt(111)

Long-range ordered structures of reduced oxide films with monolayer thickness derived from BaTiO3 and SrTiO3 on Ru(0001) and Pt(111) are investigated by scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED). Upon ultrahigh vacuum annealing at 1100 K, a hexagonal phase is observed for BaTiO3 on Ru(0001), which forms similarly from SrTiO3 on Pt(111). At higher temperatures, a triangle–square tiling called σ-phase develops in the BaTiO3/Ru(0001) system, with a unit cell rotation of 15° against the Ru(0001) substrate. Furthermore, it is shown that this 15° rotated σ-phase also forms in the BaTiO3/Pt(111) system in addition to the already known 8° rotated σ-phase. The results emphasize a strong flexibility in the structural parameters of the reduced oxide wetting layers in response to the substrate interaction strength

Macroscopic superposition states of ultracold bosons in a double-well potential

We present a thorough description of the physical regimes for ultracold bosons in double wells, with special attention paid to macroscopic superpositions (MSs). We use a generalization of the Lipkin-Meshkov-Glick Hamiltonian of up to eight single particle modes to study these MSs, solving the Hamiltonian with a combination of numerical exact diagonalization and high-order perturbation theory. The MS is between left and right potential wells; the extreme case with all atoms simultaneously located in both wells and in only two modes is the famous NOON state, but our approach encompasses much more general MSs. Use of more single particle modes brings dimensionality into the problem, allows us to set hard limits on the use of the original two-mode LMG model commonly treated in the literature, and also introduces a new mixed Josephson-Fock regime. Higher modes introduce angular degrees of freedom and MS states with different angular properties.Comment: 15 pages, 8 figures, 1 table. Mini-review prepared for the special issue of Frontiers of Physics "Recent Progresses on Quantum Dynamics of Ultracold Atoms and Future Quantum Technologies", edited by Profs. Lee, Ueda, and Drummon

Improving the forecast for biodiversity under climate change

Acknowledgments: This paper originates from the “Ecological Interactions and Range Evolution Under Environmental Change” and “RangeShifter” working groups, supported by the Synthesis Centre of the German Centre for Integrative Biodiversity Research (DFG-FZT-118), DIVERSITAS, and its core projects bioDISCOVERY and bioGENESIS. Supported by the Canada Research Chair, Natural Sciences and Engineering Research Council of Canada, and Quebec Centre for Biodiversity Science (A.G.); the University of Florida Foundation (R.D.H.); KU Leuven Research Fund grant PF/2010/07, ERA-Net BiodivERsA TIPPINGPOND, and Belspo IAP SPEEDY (L.D.M.); European Union Biodiversity Observation Network grant EU-BON-FP7-308454 (J.-B.M. and G.P.); KU Leuven Research Fund (J.P.); and NSF grants DEB-1119877 and PLR-1417754 and the McDonnell Foundation (M.C.U.).Peer reviewedPostprin

Forward-time simulation of realistic samples for genome-wide association studies

<p>Abstract</p> <p>Background</p> <p>Forward-time simulations have unique advantages in power and flexibility for the simulation of genetic samples of complex human diseases because they can closely mimic the evolution of human populations carrying these diseases. However, a number of methodological and computational constraints have prevented the power of this simulation method from being fully explored in existing forward-time simulation methods.</p> <p>Results</p> <p>Using a general-purpose forward-time population genetics simulation environment, we developed a forward-time simulation method that can be used to simulate realistic samples for genome-wide association studies. We examined the properties of this simulation method by comparing simulated samples with real data and demonstrated its wide applicability using four examples, including a simulation of case-control samples with a disease caused by multiple interacting genetic and environmental factors, a simulation of trio families affected by a disease-predisposing allele that had been subjected to either slow or rapid selective sweep, and a simulation of a structured population resulting from recent population admixture.</p> <p>Conclusions</p> <p>Our algorithm simulates populations that closely resemble the complex structure of the human genome, while allows the introduction of signals of natural selection. Because of its flexibility to generate different types of samples with arbitrary disease or quantitative trait models, this simulation method can simulate realistic samples to evaluate the performance of a wide variety of statistical gene mapping methods for genome-wide association studies.</p

An Evolutionary Framework for Association Testing in Resequencing Studies

Sequencing technologies are becoming cheap enough to apply to large numbers of study participants and promise to provide new insights into human phenotypes by bringing to light rare and previously unknown genetic variants. We develop a new framework for the analysis of sequence data that incorporates all of the major features of previously proposed approaches, including those focused on allele counts and allele burden, but is both more general and more powerful. We harness population genetic theory to provide prior information on effect sizes and to create a pooling strategy for information from rare variants. Our method, EMMPAT (Evolutionary Mixed Model for Pooled Association Testing), generates a single test per gene (substantially reducing multiple testing concerns), facilitates graphical summaries, and improves the interpretation of results by allowing calculation of attributable variance. Simulations show that, relative to previously used approaches, our method increases the power to detect genes that affect phenotype when natural selection has kept alleles with large effect sizes rare. We demonstrate our approach on a population-based re-sequencing study of association between serum triglycerides and variation in ANGPTL4

Novel Association of ABO Histo-Blood Group Antigen with Soluble ICAM-1: Results of a Genome-Wide Association Study of 6,578 Women

While circulating levels of soluble Intercellular Adhesion Molecule 1 (sICAM-1) have been associated with diverse conditions including myocardial infarction, stroke, malaria, and diabetes, comprehensive analysis of the common genetic determinants of sICAM-1 is not available. In a genome-wide association study conducted among 6,578 participants in the Women's Genome Health Study, we find that three SNPs at the ICAM1 (19p13.2) locus (rs1799969, rs5498 and rs281437) are non-redundantly associated with plasma sICAM-1 concentrations at a genome-wide significance level (P<5×10−8), thus extending prior results from linkage and candidate gene studies. We also find that a single SNP (rs507666, P = 5.1×10−29) at the ABO (9q34.2) locus is highly correlated with sICAM-1 concentrations. The novel association at the ABO locus provides evidence for a previously unknown regulatory role of histo-blood group antigens in inflammatory adhesion processes

Distinct in vitro binding properties of the anti-CD20 small modular immunopharmaceutical 2LM20-4 result in profound and sustained in vivo potency in cynomolgus monkeys

Objectives. To characterize the in vitro binding and effector function properties of CD20-directed small modular immunopharmaceutical (SMIP) 2LM20-4, and to compare its in vivo B-cell depletion activity with the mutated 2LM20-4 P331S [no in vitro complement-dependent cytotoxicity (CDC)] and rituximab in cynomolgus monkeys

Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder

Psychiatric disorders are thought to have a complex genetic pathology consisting of interplay of common and rare variation. Traditionally, pedigrees are used to shed light on the latter only, while here we discuss the application of polygenic risk scores to also highlight patterns of common genetic risk. We analyze polygenic risk scores for psychiatric disorders in a large pedigree (n similar to 260) in which 30% of family members suffer from major depressive disorder or bipolar disorder. Studying patterns of assortative mating and anticipation, it appears increased polygenic risk is contributed by affected individuals who married into the family, resulting in an increasing genetic risk over generations. This may explain the observation of anticipation in mood disorders, whereby onset is earlier and the severity increases over the generations of a family. Joint analyses of rare and common variation may be a powerful way to understand the familial genetics of psychiatric disorders