Lattice Relaxation in Epitaxial BaTiO3_3 Thin Films

We have investigated the out-of-plane lattice relaxation related to the ferroelectric transitions in epitaxial BaTiO$_3$ (BTO) films using synchrotron X-ray diffraction. Under either compressive strain or tensile strain, there is evidence for two structural phase transitions as a function of temperature. The transition temperature $T_C$ is a strong function of strain, which can be as much as 100 K above the corresponding $T_C$ in bulk. Under compressive strain, the tetragonality of BTO unit cell implies that the polarization of the first ferroelectric phase is out-of-plane, while under tensile strain, the polarization is in-plane. The transitions at lower temperature may correspond to the $aa\to r$ or $c\to r$ transitions, following the notations by Pertsev \textit{et al}. The orientations of the domains are consistent with theoretical predictions.Comment: 4 pages, 3 figure

Neutron Scattering Study of Sr\u3csub\u3e2\u3c/sub\u3eCu\u3csub\u3e3\u3c/sub\u3eO\u3csub\u3e4\u3c/sub\u3eCl\u3csub\u3e2\u3c/sub\u3e

We report a neutron scattering study on the tetragonal compound Sr2Cu3O4Cl2, which has two-dimensional (2D) interpenetrating CuI and CuII subsystems, each forming a S=1/2 square lattice quantum Heisenberg antiferromagnet (SLQHA). The mean-field ground state is degenerate, since the intersubsystem interactions are geometrically frustrated. Magnetic neutron scattering experiments show that quantum fluctuations lift the degeneracy and cause a 2D Ising ordering of the CuII subsystem. Due to quantum fluctuations a dramatic increase of the CuI out-of-plane spin-wave gap is also observed. The temperature dependence and the dispersion of the spin-wave energy are quantitatively explained by spin-wave calculations which include quantum fluctuations explicitly. The values for the nearest-neighbor superexchange interactions between the CuI and CuII ions and between the CuII ions are determined experimentally to be JI−II=−10(2) meV and JII=10.5(5) meV, respectively. Due to its small exchange interaction JII, the 2D dispersion of the CuII SLQHA can be measured over the whole Brillouin zone with thermal neutrons, and a dispersion at the zone boundary, predicted by theory, is confirmed. The instantaneous magnetic correlation length of the CuII SLQHA is obtained up to a very high temperature, T/JII≈0.75. This result is compared with several theoretical predictions as well as recent experiments on the S=1/2 SLQHA

Critical Josephson Current in a Model Pb/YBa_2Cu_3O_7 Junction

In this article we consider a simple model for a c--axis Pb/YBa_2Cu_3O_{7-\delta} Josephson junction. The observation of a nonzero current in such a junction by Sun et al. [A. G. Sun, D. A. Gajewski, M. B. Maple, R. C. Dynes, Phys. Rev. Lett. 72, 2267 (1994)] has been taken as evidence against d--wave superconductivity in YBa_2Cu_3O_{7-\delta}. We suggest, however, that the pairing interaction in the CuO_2 planes may well be d--wave but that the CuO chains destroy the tetragonal symmetry of the system. We examine two ways in which this happens. In a simple model of an incoherent junction, the chains distort the superconducting condensate away from d_{x^2-y^2} symmetry. In a specular junction the chains destroy the tetragonal symmetry of the tunneling matrix element. In either case, the loss of tetragonal symmetry results in a finite Josephson current. Our calculated values of the critical current for specular junctions are in good agreement with the results of Sun and co-workers.Comment: Latex File, 21 pages, 6 figures in uuencoded postscript, In Press (Phys. Rev. B

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis.

BACKGROUND: The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we performed a high-level data integration of 14 whole-genome transcriptomics datasets from samples of intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information from the Reactome database. RESULTS: The results show an integrated response of the mouse intestinal mucosa to challenges with agents introduced orally that were expected to perturb homeostasis. We observed that a common set of pathways respond to different stimuli, of which the most reactive was the Regulation of Complement Cascade pathway. Altered expression of the Regulation of Complement Cascade pathway was verified in mouse organoids challenged with different stimuli in vitro. CONCLUSIONS: Results of the integrated transcriptomics analysis and data driven experiment suggest an important role of epithelial production of complement and host complement defence factors in the maintenance of homeostasis

The Hubbard model within the equations of motion approach

The Hubbard model has a special role in Condensed Matter Theory as it is considered as the simplest Hamiltonian model one can write in order to describe anomalous physical properties of some class of real materials. Unfortunately, this model is not exactly solved except for some limits and therefore one should resort to analytical methods, like the Equations of Motion Approach, or to numerical techniques in order to attain a description of its relevant features in the whole range of physical parameters (interaction, filling and temperature). In this manuscript, the Composite Operator Method, which exploits the above mentioned analytical technique, is presented and systematically applied in order to get information about the behavior of all relevant properties of the model (local, thermodynamic, single- and two- particle ones) in comparison with many other analytical techniques, the above cited known limits and numerical simulations. Within this approach, the Hubbard model is shown to be also capable to describe some anomalous behaviors of the cuprate superconductors.Comment: 232 pages, more than 300 figures, more than 500 reference

Calpain Cleavage Prediction Using Multiple Kernel Learning

Calpain, an intracellular -dependent cysteine protease, is known to play a role in a wide range of metabolic pathways through limited proteolysis of its substrates. However, only a limited number of these substrates are currently known, with the exact mechanism of substrate recognition and cleavage by calpain still largely unknown. While previous research has successfully applied standard machine-learning algorithms to accurately predict substrate cleavage by other similar types of proteases, their approach does not extend well to calpain, possibly due to its particular mode of proteolytic action and limited amount of experimental data. Through the use of Multiple Kernel Learning, a recent extension to the classic Support Vector Machine framework, we were able to train complex models based on rich, heterogeneous feature sets, leading to significantly improved prediction quality (6% over highest AUC score produced by state-of-the-art methods). In addition to producing a stronger machine-learning model for the prediction of calpain cleavage, we were able to highlight the importance and role of each feature of substrate sequences in defining specificity: primary sequence, secondary structure and solvent accessibility. Most notably, we showed there existed significant specificity differences across calpain sub-types, despite previous assumption to the contrary. Prediction accuracy was further successfully validated using, as an unbiased test set, mutated sequences of calpastatin (endogenous inhibitor of calpain) modified to no longer block calpain's proteolytic action. An online implementation of our prediction tool is available at http://calpain.org

The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution

Single-cell gene expression analyses of mammalian tissues have uncovered profound stage-specific molecular regulatory phenomena that have changed the understanding of unique cell types and signaling pathways critical for lineage determination, morphogenesis, and growth. We discuss here the case for a Pediatric Cell Atlas as part of the Human Cell Atlas consortium to provide single-cell profiles and spatial characterization of gene expression across human tissues and organs. Such data will complement adult and developmentally focused HCA projects to provide a rich cytogenomic framework for understanding not only pediatric health and disease but also environmental and genetic impacts across the human lifespan

Differential Effects of Early- and Late-Life Access to Carotenoids on Adult Immune Function and Ornamentation in Mallard Ducks (Anas platyrhynchos)

Environmental conditions early in life can affect an organism’s phenotype at adulthood, which may be tuned to perform optimally in conditions that mimic those experienced during development (Environmental Matching hypothesis), or may be generally superior when conditions during development were of higher quality (Silver Spoon hypothesis). Here, we tested these hypotheses by examining how diet during development interacted with diet during adulthood to affect adult sexually selected ornamentation and immune function in male mallard ducks (Anas platyrhynchos). Mallards have yellow, carotenoid-pigmented beaks that are used in mate choice, and the degree of beak coloration has been linked to adult immune function. Using a 2×2 factorial experimental design, we reared mallards on diets containing either low or high levels of carotenoids (nutrients that cannot be synthesized de novo) throughout the period of growth, and then provided adults with one of these two diets while simultaneously quantifying beak coloration and response to a variety of immune challenges. We found that both developmental and adult carotenoid supplementation increased circulating carotenoid levels during dietary treatment, but that birds that received low-carotenoid diets during development maintained relatively higher circulating carotenoid levels during an adult immune challenge. Individuals that received low levels of carotenoids during development had larger phytohemagglutinin (PHA)-induced cutaneous immune responses at adulthood; however, dietary treatment during development and adulthood did not affect antibody response to a novel antigen, nitric oxide production, natural antibody levels, hemolytic capacity of the plasma, or beak coloration. However, beak coloration prior to immune challenges positively predicted PHA response, and strong PHA responses were correlated with losses in carotenoid-pigmented coloration. In sum, we did not find consistent support for either the Environmental Matching or Silver Spoon hypotheses. We then describe a new hypothesis that should be tested in future studies examining developmental plasticity