Common genetic variants influence human subcortical brain structures

The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08×10 -33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

Using genome-Wwide complex trait analysis to quantify 'missing heritability' in Parkinson's disease

Genome-wide association studies (GWASs) have been successful at identifying single-nucleotide polymorphisms (SNPs) highly associated with common traits; however, a great deal of the heritable variation associated with common traits remains unaccounted for within the genome. Genome-wide complex trait analysis (GCTA) is a statistical method that applies a linear mixed model to estimate phenotypic variance of complex traits explained by genome-wide SNPs, including those not associated with the trait in a GWAS. We applied GCTA to 8 cohorts containing 7096 case and 19 455 control individuals of European ancestry in order to examine the missing heritability present in Parkinson's disease (PD). We meta-analyzed our initial results to produce robust heritability estimates for PD types across cohorts. Our results identify 27% (95% CI 17-38, P = 8.08E - 08) phenotypic variance associated with all types of PD, 15% (95% CI -0.2 to 33, P = 0.09) phenotypic variance associated with early-onset PD and 31% (95% CI 17-44, P = 1.34E - 05) phenotypic variance associated with late-onset PD. This is a substantial increase from the genetic variance identified by top GWAS hits alone (between 3 and 5%) and indicates there are substantially more risk loci to be identified. Our results suggest that although GWASs are a useful tool in identifying the most common variants associated with complex disease, a great deal of common variants of small effect remain to be discovered. © Published by Oxford University Press 2012.

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

Revision of JANAF (1985) data for C2H2(g)

There is an error in the JANAF (1985) data on the standard enthalpy, Gibbs energy and equilibrium constant for the formation of C2H2 (g) from elements. The error has arisen on account of an incorrect expression used for computing these parameters from the heat capacity, entropy and the relative heat content. Presented in this paper are the corrected values of the enthalpy, the Gibbs energy of formation and the corresponding equilibrium constant.

Activities in the $FeTiO_{3}-NiTiO_{3}$ Solid Solution from Alloy-Oxide Equilibria at 1273 K

Nine tie-lines between Fe-Ni alloys and FeTiO3-NiTiO3 solid solutions were determined at 1273 K. Samples were equilibrated in evacuated quartz ampoules for periods up to 10 days. Compositions of the alloy and oxide phases at equilibrium were determined by energy-dispersive x-ray spectroscopy. X-ray powder diffraction was used to confirm the results. Attainment of equilibrium was verified by the conventional tie-line rotation technique and by thermodynamic analysis of the results. The tie-lines are skewed toward the FeTiO3 corner. From the tie-line data and activities in the Fe-Ni alloy phase available in the literature, activities of FeTiO3 and NiTiO3 in the ilmenite solid solution were derived using the modified Gibbs-Duhem technique of Jacob and Jeffes [K.T. Jacob and J.H.E. Jeffes, An Improved Method for Calculating Activities from Distribution Equilibria, High Temp. High Press., 1972, 4, p 177-182]. The components of the oxide solid solution exhibit moderate positive deviations from Raoult's law. Within experimental error, excess Gibbs energy of mixing for the FeTiO3-NiTiO3 solid solution at 1273 K is a symmetric function of composition and can be represented as: Delta G(E) = 8590 (+/- 200) X-FeTiO3 X-NiTiO3 J/mol Full spectrum of tie-lines and oxygen potentials for the three-phase equilibrium involving Fe-Ni alloys, FeTiO3-NiTiO3 solid solutions, and TiO2 at 1273 K were computed using results obtained in this study and data available in the literature.

Growing length and time scales in glass-forming liquids

The glass transition, whereby liquids transform into amorphous solids at low temperatures, is a subject of intense research despite decades of investigation. Explaining the enormous increase in relaxation times of a liquid upon supercooling is essential for understanding the glass transition. Although many theories, such as the Adam-Gibbs theory, have sought to relate growing relaxation times to length scales associated with spatial correlations in liquid structure or motion of molecules, the role of length scales in glassy dynamics is not well established. Recent studies of spatially correlated rearrangements of molecules leading to structural relaxation, termed ``spatially heterogeneous dynamics,'' provide fresh impetus in this direction. A powerful approach to extract length scales in critical phenomena is finite-size scaling, wherein a system is studied for sizes traversing the length scales of interest. We perform finite-size scaling for a realistic glass-former, using computer simulations, to evaluate the length scale associated with spatially heterogeneous dynamics, which grows as temperature decreases. However, relaxation times that also grow with decreasing temperature do not exhibit standard finite-size scaling with this length. We show that relaxation times are instead determined, for all studied system sizes and temperatures, by configurational entropy, in accordance with the Adam-Gibbs relation, but in disagreement with theoretical expectations based on spin-glass models that configurational entropy is not relevant at temperatures substantially above the critical temperature of mode-coupling theory. Our results provide new insights into the dynamics of glass-forming liquids and pose serious challenges to existing theoretical descriptions.

Dynamical Transition of Water in the Grooves of DNA Duplex at Low Temperature

At low temperature (below its freezing/melting temperature), liquid water under confinement is known to exhibit anomalous dynamical features. Here we study structure and dynamics of water in the grooves of a long DNA duplex using molecular dynamics simulations with TIP5P potential at low temperature. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both the major and the minor grooves of a DNA duplex. The transition occurs at a slightly higher temperature (TGL ≈ 255 K) than the temperature at which the bulk water is found to undergo a dynamical transition, which for the TIP5P potential is at 247 K. Groove water, however, exhibits markedly different temperature dependence of its properties from the bulk. Entropy calculations reveal that the minor groove water is ordered even at room temperature, and the transition at T ≈ 255 K can be characterized as a strong-to-strong dynamical transition. Confinement of water in the grooves of DNA favors the formation of a low density four-coordinated state (as a consequence of enthalpy−entropy balance) that makes the liquid−liquid transition stronger. The low temperature water is characterized by pronounced tetrahedral order, as manifested in the sharp rise near 109° in the O−O−O angle distribution. We find that the Adams−Gibbs relation between configurational entropy and translational diffusion holds quite well when the two quantities are plotted together in a master plot for different region of aqueous DNA duplex (bulk, major, and minor grooves) at different temperatures. The activation energy for the transfer of water molecules between different regions of DNA is found to be weakly dependent on temperature.

Adsorption isotherms for neutral organic compounds-A hierarchy in modelling: Part II

A two-state model allowing for size disparity between the solvent and the adsorbate is analysed to derive the adsorption isotherm for electrosorption of organic compounds. Explicity, the organic adsorbate is assumed to occupy "n" lattice sites at the interface as compared to "one" by the solvent. The model parameters are the respective permanent and induced dipole moments apart from the nearest neighbour distance. The coulombic interactions due to permanent and induced dipole moments, discreteness of charge effects, and short-range and specific substrate interactions have all been incorporated. The adsorption isotherm is then derived using mean field approximation (MFA) and is found to be more general than the earlier multi-site versions of Bockris and Swinkels, Mohilner et al., and Bennes, as far as the entropy contributions are concerned. The role of electrostatic forces is explicity reflected in the adsorption isotherm via the Gibbs energy of adsorption term which itself is a quadratic function of the electrode charge-density. The approximation implicit in the adsorption isotherm of Mohilner et al. or Bennes is indicated briefly.

Determination of the thermodynamic properties of xMgO + (1 x)MnO (s, sln) from a solid-electrolyte galvanic cell in the temperature range 1163 to 1318 K

The thermodynamic activities of MgO in the NaCl-type solid solutions which can exist in xMgO + (1 x)MnO have been determined in the temperature range 1163 to 1318 K from a solid-state galvanic cell incorporating MgF2 as the solid electrolyte. The activities of MnO have been calculated by a graphical Gibbs-Duhem integration method. The activities of both the components exhibit positive deviations from ideality over the entire composition range. The excess molar enthalpies are found to be positive. Further, xMgO + (1 - x)MnO does not conform to regular-solution behaviour. The origin of the excess thermodynamic properties is discussed in relation to the cationic size disparity and the crystal-field effects.

Phase relations in the system Ta-Rh-O and thermodynamic properties of TaRhO4

Phase relations in the system Ta-Rh-O were determined by analysis of quenched samples corresponding to thirteen compositions inside the ternary triangle after equilibration at 1273 K. All the Ta-Rh alloys were found to be in equilibrium with Ta2O5. Only one ternary oxide TaRhO4 was detected. Based on phase relations in the ternary system, a solid-state electrochemical cell, incorporating calcia-stabilized zirconia as the electrolyte, was designed to measure the standard Gibbs energy of formation (Delta G degrees, J mol(-1)) of TaRhO4 in the temperature range from 900 to 1300 K. For the reaction, 1/2 beta-Ta2O5 + 1/2 Rh2O3(ortho) -> TaRhO4 Delta G degrees = -42993 + 5.676T (+/- 85) The calculated decomposition temperatures of TaRhO4 are 1644 +/- 5K in pure O-2 and 1543 +/- 5K in air at a total pressure p(o) = 0.1 MPa. Thermodynamic properties of TaRhO4 at 298.15K have been evaluated from the results. The limited experimental thermodynamic data for Rh-rich alloys available in the literature are in fair accord with Miedema's model. The Gibbs energies of formation of the different phases in the binary system Ta-Rh were estimated based on these inputs, consistent with the binary phase diagram. Based on the thermodynamic information on the stability of various phases, an oxygen potential diagram for the system Ta-Rh-O at 1273K was constructed. Also presented are temperature-composition diagrams for the ternary system at constant oxygen partial pressures (po(2)/p(o) = 0.212 and 10(-6)) calculated form the basic data.

Phase relations between Al2O3---Cr2O3 and FeAl2O4---FeCr2O4 solid solutions at 1823 K

Tie-lines between the corundum and spinel solid solutions have been determined experimentally at 1823 K. Next, activities of FeCr2O4 and FeAl2O4 in the spinel solid solution were determined by combining the tie-line data with literature values for the activities of Cr2O3 and Al2O3 in the corundum phase. Activities and the Gibbs energy of mixing for the spinel solid solution were also obtained from a model based on cation distribution between nonequivalent crystallographic sites in the oxide lattice. The difference between the Gibbs energy of mixing obtained experimentally and from the model has been attributed to a strain enthalpy term which is relatively unchanged in magnitude from the reported at 1373 K. The integral enthalpy of mixing obtained from experimental data at 1373 and 1823 K using the second law is compared with the model result.

Spinel-Corundum Phase Equilibria in the Systems Mn-Cr-Al-O and Co-Cr-Al-O at 1373 K

The tie lines delineating ion-exchange equilibria between MCr2O4-MAl2O4 spinel solid solution, where M is either Mn or Co, and Cr2O3-Al2O3 solid solution with the corundum structure were determined at 1373 K by electron microprobe and E0AX point count analysis of the oxide phases equilibrated with metallic Co and Au-5% Mn. The component activities in the spinel solid solutions are derived from the tie lines and the thernodynamic data for Cr2O3-Al2O3 soiid solutions available hi the literature. The Gibbs free energies of mixing calculated from the experimental data are discussed in relation to the values derived from the cation distribution a.odel based on the site preference energies and assuming random mixing on both tetrahedral and octahedral sites. Positive deviations from ideality observed in this study suggest a miscibility gap for both series of spinel solid solutions at low temperatures in the absence of oxidation.

Thermodynamic properties of Pb2PtO4 and PbPt2O4 and phase equilibria in the system Pb–Pt–O

The compounds Pb2PtO4 and PbPt2O4 were synthesized from an intimate mixture of yellow PbO and Pt metal powders by heating under pure oxygen gas at 973 K for periods up to 600 ks with intermediate grinding and recompacting. Both compounds were found to decompose on heating in pure oxygen to PbO and Pt, apparently in conflict with the requirements for equilibrium phase relations in the ternary system Pb–Pt–O. The oxygen chemical potential corresponding to the three-phase mixtures, Pb2PtO4 + PbO + Pt and PbPt2O4 + PbO + Pt were measured as a function of temperature using solid-state electrochemical cells incorporating yttria-stabilized zirconia as the solid electrolyte and pure oxygen gas at 0.1 MPa pressure as the reference electrode. The standard Gibbs free energies of formation of the ternary oxides were derived from the measurements. Analysis of the results indicated that the equilibrium involving three condensed phases Pb2PtO4 + PbO + Pt is metastable. Under equilibrium conditions, Pb2PtO4 should have decomposed to a mixture of PbO and PbPt2O4. Measurement of the oxygen potential corresponding to this equilibrium decomposition as a function of temperature indicated that decomposition temperature in pure oxygen is 1014(±2) K. This was further confirmed by direct determination of phase relations in the ternary Pb–Pt–O by equilibrating several compositions at 1023 K for periods up to 850 ks and phase identification of quenched samples using X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Only one ternary oxide PbPt2O4 was stable at 1023 K under equilibrium conditions. Alloys and intermetallic compounds along the Pb–Pt binary were in equilibrium with PbO.

High temperature stability of oxysulfides containing Ce3+ and Y3+ ions

Standard Gibbs energies of formation of oxysulfides of cerium and yttrium from their respective oxedes were determined using solid oxide galvanic cells incorporating calcia-stabilized zirconia as the electrolyte in the temperature range 870–1120 K. The sulfur potential over the electrode containing the oxide and oxysulfide was fixed by a buffer mixture of Ag + Ag2S. A small amount of CaH2 was added to the buffer to generate an equilibrium ratio of H2S and H2 species in a closed system containing the buffer and the electrode. The sulfur potential is transmitted to the electrode via the gas phase. The results can be summarized by the equations 2left angle bracketCeO2right-pointing angle bracket+1/2(S2)→left angle bracketCe2O2Sright-pointing angle bracket+(O2) ΔG°=430600−109·7T(±400)J mol−1 left angle bracketY2O3right-pointing angle bracket+1/2(S2)→left angle bracketY2O2Sright-pointing angle bracket+1/2(O2) ΔG°=114780−1·45T(±200)J mol−1 The values are compared with data reported in the literature. The stability field diagram for the Ce---O---S system has been developed using the results of this study for Ce2O2S and data for other phases from the literature.

Vapour composition and activities in Mg-Zn liquid alloy at 923 K

Vapour species effusing from a magnesia Knudsen cell containing Mg-Zn alloy at 923 K were condensed on a water cooled copper plate. The equilibrium composition of the vapour phase over the alloy was determined from chemical analysis of the condensate. The activity coefficients of both components in the alloy have been derived from the data using a modified Gibbs-Duhem relation. The ratio of saturation vapour pressures of pure Zn and Mg obtained from the analysis of alloy data agree well with values from the literature, providing an internal check on the accuracy of data obtained in this study. Both components of the alloy exhibit negative deviations from Raoult's law. The concentration-concentration structure factor of Bhatia and Thomton at zero wave vector, evaluated from the measurements, indicate the presence of MgZn2 type complex in the liquid state. The associated regular solution model has been used for the thermodynamic description of liquid Mg-Zn alloys.