DNA methylation profiling of the human major histocompatibility complex: A pilot study for the Human Epigenome Project

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data

Dimensional Crossover in the Large N Limit

We consider dimensional crossover for an $O(N)$ Landau-Ginzburg-Wilson model on a $d$-dimensional film geometry of thickness $L$ in the large $N$-limit. We calculate the full universal crossover scaling forms for the free energy and the equation of state. We compare the results obtained using ``environmentally friendly'' renormalization with those found using a direct, non-renormalization group approach. A set of effective critical exponents are calculated and scaling laws for these exponents are shown to hold exactly, thereby yielding non-trivial relations between the various thermodynamic scaling functions.Comment: 25 pages of PlainTe

SO(5) superconductor in a Zeeman magnetic field: Phase diagram and thermodynamic properties

In this paper we present calculations of the SO(5) quantum rotor theory of high-T$_{c}$ superconductivity in Zeeman magnetic field. We use the spherical approach for five-component quantum rotors in three-dimensional lattice to obtain formulas for critical lines, free energy, entropy and specific heat and present temperature dependences of these quantities for different values of magnetic field. Our results are in qualitative agreement with relevant experiments on high-T$_{c}$ cuprates.Comment: 4 pages, 2 figures, to appear in Phys. Rev. B, see http://prb.aps.or

Object knowledge modulates colour appearance

We investigated the memory colour effect for colour diagnostic artificial objects. Since knowledge about these objects and their colours has been learned in everyday life, these stimuli allow the investigation of the influence of acquired object knowledge on colour appearance. These investigations are relevant for questions about how object and colour information in high-level vision interact as well as for research about the influence of learning and experience on perception in general. In order to identify suitable artificial objects, we developed a reaction time paradigm that measures (subjective) colour diagnosticity. In the main experiment, participants adjusted sixteen such objects to their typical colour as well as to grey. If the achromatic object appears in its typical colour, then participants should adjust it to the opponent colour in order to subjectively perceive it as grey. We found that knowledge about the typical colour influences the colour appearance of artificial objects. This effect was particularly strong along the daylight axis

RATAN-600 7.6-cm Deep Sky Strip Surveys at the Declination of the SS433 Source During the 1980-1999 Period. Data Reduction and the Catalog of Radio Sources in the Right-Ascension Interval 7h < R.A. < 17h

We use two independent methods to reduce the data of the surveys made with RATAN-600 radio telescope at 7.6 cm in 1988-1999 at the declination of the SS433 source. We also reprocess the data of the "Cold" survey (1980-1981). The resulting RCR (RATAN COLD REFINED) catalog contains the right ascensions and fluxes of objects identified with those of the NVSS catalog in the right-ascension interval 7h < R.A. < 17h. We obtain the spectra of the radio sources and determine their spectral indices at 3.94 and 0.5 GHz. The spectra are based on the data from all known catalogs available from the CATS, Vizier, and NED databases, and the flux estimates inferred from the maps of the VLSS and GB6 surveys. For 245 of the 550 objects of the RCR catalog the fluxes are known at two frequencies only: 3.94 GHz (RCR) and 1.4 GHz (NVSS). These are mostly sources with fluxes smaller than 30 mJy. About 65% of these sources have flat or inverse spectra (alpha > -0.5). We analyze the reliability of the results obtained for the entire list of objects and construct the histograms of the spectral indices and fluxes of the sources. Our main conclusion is that all 10-15 mJy objects found in the considered right-ascension interval were already included in the decimeter-wave catalogs.Comment: 26 pages, 18 figure

A generalized spherical version of the Blume-Emery-Griffits model with ferromagnetic and antiferromagnetic interactions

We have investigated analitycally the phase diagram of a generalized spherical version of the Blume-Emery-Griffiths model that includes ferromagnetic or antiferromagnetic spin interactions as well as quadrupole interactions in zero and nonzero magnetic field. We show that in three dimensions and zero magnetic field a regular paramagnetic-ferromagnetic (PM-FM) or a paramagnetic-antiferromagnetic (PM-AFM) phase transition occurs whenever the magnetic spin interactions dominate over the quadrupole interactions. However, when spin and quadrupole interactions are important, there appears a reentrant FM-PM or AFM-PM phase transition at low temperatures, in addition to the regular PM-FM or PM-AFM phase transitions. On the other hand, in a nonzero homogeneous external magnetic field $H$, we find no evidence of a transition to the state with spontaneous magnetization for FM interactions in three dimensions. Nonethelesss, for AFM interactions we do get a scenario similar to that described above for zero external magnetic field, except that the critical temperatures are now functions of $H$. We also find two critical field values, $H_{c1}$, at which the reentrance phenomenon dissapears and $H_{c2}$ ($H_{c1}\approx 0.5H_{c2}$), above which the PM-AFM transition temperature vanishes.Comment: 21 pages, 6 figs. Title changed, abstract and introduction as well as section IV were rewritten relaxing the emphasis on spin S=1 and Figs. 5 an 6 were improved in presentation. However, all the results remain valid. Accepted for publication in Phys. Rev.

Sound symbolism in synesthesia: evidence from a lexical-gustatory synesthete

Synesthesia is a condition in which perceptual or cognitive stimuli (e.g., a written letter) trigger atypical additional percepts (e.g., the color yellow). Although these cross-modal pairings appear idiosyncratic in that they superficially differ from synesthete to synesthete, underlying patterns do exist and these can, in some circumstances, reflect the cross-modal intuitions of nonsynesthetes (e.g., higher pitch sounds tend to be "seen" in lighter colors by synesthetes and are also paired to lighter colors by nonsynesthetes in cross-modal matching tasks). We recently showed that grapheme-color synesthetes are more sensitive to sound symbolism (i.e., cross-modal sound-meaning correspondences) in natural language compared to nonsynesthetes. Accordingly, we hypothesize that sound symbolism may be a guiding force in synesthesia to dictate what types of synesthetic experiences are triggered by words. We tested this hypothesis by examining the cross-modal mappings of lexical-gustatory synesthete, JIW, for whom words trigger flavor experiences. We show that certain phonological features (e.g., front vowels) systematically trigger particular categories of taste (e.g., bitter) in his synesthesia. Some of these associations agree with sound symbolic patterns in natural language. This supports the view that synesthesia may be an exaggeration of cross-modal associations found in the general population and that sound symbolic properties of language may arise from similar mechanisms as those found in synesthesia

Avoided Critical Behavior in O(n) Systems

Long-range frustrating interactions, even if their strength is infinitesimal, can give rise to a dramatic proliferations of ground or near-ground states. As a consequence, the ordering temperature can exhibit a discontinuous drop as a function of the frustration. A simple model of the doped Mott insulator, where the short-range tendency of the holes to phase separate competes with long-range Coulomb effects, exhibits this "avoided critical" behavior. This model may serve as a paradigm for many other systems.Comment: 4 pages, 2 figure