Leveraging wall-sized high-resolution displays for comparative genomics analyses of copy number variation

The scale of comparative genomics data frequently overwhelms current data visualization methods on conventional (desktop) displays. This paper describes two types of solution that take advantage of wall-sized high-resolution displays (WHirDs), which have orders of magnitude more display real estate (i.e., pixels) than desktop displays. The first allows users to view detailed graphics of copy number variation (CNV) that were output by existing software. A WHirD's resolution allowed a 10× increase in the granularity of bioinformatics output that was feasible for users to visually analyze, and this revealed a pattern that had previously been smoothed out from the underlying data. The second involved interactive visualization software that was innovative because it uses a music score metaphor to lay out CNV data, overcomes a perceptual distortion caused by amplification/deletion thresholds, uses filtering to reduce graphical data overload, and is the first comparative genomics visualization software that is designed to leverage a WHirD's real estate. In a field evaluation, a clinical user discovered a fundamental error in the way their data had been processed, and established confidence in the software by using it to 'find' known genetic patterns in hepatitis C-driven hepatocellular cancer

Finite strain Landau theory of high pressure phase transformations

The properties of materials near structural phase transitions are often successfully described in the framework of Landau theory. While the focus is usually on phase transitions, which are induced by temperature changes approaching a critical temperature T-c, here we will discuss structural phase transformations driven by high hydrostatic pressure, as they are of major importance for understanding processes in the interior of the earth. Since at very high pressures the deformations of a material are generally very large, one needs to apply a fully nonlinear description taking physical as well as geometrical nonlinearities (finite strains) into account. In particular it is necessary to retune conventional Landau theory to describe such phase transitions. In Troster et al (2002 Phys. Rev. Lett. 88 55503) we constructed a Landau-type free energy based on an order parameter part, an order parameter-(finite) strain coupling and a nonlinear elastic term. This model provides an excellent and efficient framework for the systematic study of phase transformations for a wide range of materials up to ultrahigh pressures

The nonlinear anomalous lattice elasticity associated with the high-pressure phase transition in spodumene: A high precission static compression study

The high-pressure behavior of the lattice elasticity of spodumene, LiAlSi2O6, was studied by static compression in a diamond-anvil cell up to 9.3 GPa. Investigations by means of single-crystal XRD and Raman spectroscopy within the hydrostatic limits of the pressure medium focus on the pressure ranges around similar to 3.2 and similar to 7.7 GPa, which have been reported previously to comprise two independent structural phase transitions. While our measurements confirm the well-established first-order C2/c-P2(1)/c transformation at 3.19 GPa (with 1.2% volume discontinuity and a hysteresis between 0.02 and 0.06 GPa), both unit-cell dimensions and the spectral changes observed in high-pressure Raman spectra give no evidence for structural changes related to a second phase transition. Monoclinic lattice parameters and unit-cell volumes at in total 59 different pressure points have been used to re-calculate the lattice-related properties of spontaneous strain, volume strain, and the bulk moduli as a function of pressure across the transition. A modified Landau free energy expansion in terms of a one component order parameter has been developed and tested against these experimentally determined data. The Landau solution provides a much better reproduction of the observed anomalies than any equation-of-state fit to data sets truncated below and above P (tr), thus giving Landau parameters of K (0) = 138.3(2) GPa, K' = 7.46(5), lambda (V) = 33.6(2) GPa, a = 0.486(3), b = -29.4(6) GPa and c = 551(11) GPa

Discontinuous evolution of single-crystal elastic constants as a function of pressure through the C2/c <-> P2(1)/c phase transition in spodumene (LiAlSi2O6)

A Landau free energy expansion in one order parameter has been developed to describe the first-order C2/c ↔ P21/c phase transition at high pressures in spodumene (LiAlSi2O6). The complete set of elastic constants required for this model was determined at ambient conditions by resonant ultrasound spectroscopy. Other coefficients in the 246 expansion were calibrated using lattice parameter data from the literature, which had been collected by following the transition in a diamond anvil cell. The complete calibration leads to predictions of significant, abrupt changes in elastic constants at the transition point, 3.19 GPa, which have then been tested against ultrasonic data obtained in situ at high pressures in a uniaxial split cylinder apparatus. Velocities of compressional waves in three mutually perpendicular directions through single crystals of spodumene were measured and used to extract elastic constant data. The transition, indeed, causes large, abrupt changes of single-crystal elastic constants with increasing pressure. Steep increases in attenuation were also observed in the vicinity of the transition point for two directions and over a broader pressure interval in the third direction. The Landau expansion reproduces the general form of the elastic anomalies, even though it does not do as well for spontaneous strain variations. If this type of transition occurred in mantle pyroxenes (or in any other mantle phase), it would be expected to leave a distinctive signature in seismic velocity profiles of the Earth's interior

Towards a better public housing service for people with mental illness: The importance of intersectoral linkage

Objective: To discuss issues relevant to the equitable delivery of public housing services to people with mental illness. Strategies adopted by Queensland Department of Housing to address these issues and to improve services are described, and matters of particular relevance to mental health professionals are highlighted. Conclusions: Formal interagency service agreements between the Departments of Health, Housing and Disability Services, appropriate training programs, and case conferencing strategies can enhance the delivery of appropriate housing services to people with mental illness. Promotion of active interagency collaboration by mental health professionals will facilitate these strategies

Structural evolution of (Ca0.35Sr0.65)TiO3 perovskite at high pressures

Lattice parameters of a synthetic powder sample of Ca0.35Sr0.65TiO3 perovskite have been determined by the method of Le Bail refinement, using synchrotron X-ray diffraction patterns collected at pressures up to 15.5 GPa with a membrane-driven diamond anvil cell. At ambient conditions, diffraction data were consistent with the I4/mcm structure reported previously in the literature for the same composition. Diffraction data collected at high pressures were consistent with tetragonal (or, at least, pseudo-tetragonal) lattice geometry, and no evidence was found for the development of any of the orthorhombic structures identified in other studies of (Ca,\ud Sr)TiO3 perovskites. Additional weak reflections, which could not be accounted for by the normal I4/mcm perovskite structure, were detected in diffraction patterns collected at pressures of 0.9–2.5 GPa, and above 13.5 GPa, however. Small anomalies in the evolution of unit cell volume and tetragonal strain were observed near 3 GPa, coinciding approximately with breaks in slope with increasing pressure\ud of bulk and shear moduli for a sample with the same composition which had previously been reported. The anomalies could be due either to new tetragonal2tetragonal/pseudo-tetragonal phase transitions or to subtle changes in compression mechanism of the tetragonal perovskite structure

Designing a metal-binding site in the scaffold of Escherichia coli KDO8PS

KDO8PS (3-deoxy-d-manno-octulosonate-8-phosphate synthase) and DAH7PS (3-deoxy-d-arabino-heptulosonic acid-7-phosphate synthase) enzymes catalyse analogous condensation reactions between phosphoenolpyruvate and arabinose 5-phosphate or erythrose 4-phosphate, respectively. All known DAH7PS and some of KDO8PS enzymes (Aquifex aeolicus KDO8PS) require a metal ion for activity whereas another class of KDO8PS (including Escherichia coli KDO8PS) does not. Based on sequence alignment of all known KDO8PS and DAH7PS enzymes, we identified a single amino acid residue that might define the metal dependence of KDO8PS activity. One of the four metal-binding residues, a cysteine, is conserved only among metal-binding KDO8PS and DAH7PS enzymes and is replaced by an asparagine residue in other KDO8PS enzymes. We introduced a metal binding site into E.coli KDO8PS by a single N26C and a double M25P N26C mutation, which led to an increased k(cat) of the enzymes in the presence of activating Mn(2+) ions. The M25P N26C mutant of E.coli KDO8PS had a value of k(cat)/K(M) in the presence of Mn(2+) ions four times higher than A.aeolicus KDO8PS. KDO8PS and DAH7PS may have evolved from a common ancestor protein that required a divalent metal ion for activity. A non-metal-binding KDO8PSs may have evolved from an ancestor protein that was able to bind Mn(2+) but no longer required Mn(2+) to function and eventually lost one of metal-binding residues

Ultralow-frequency elastic response in

We present novel low-frequency (0.1\un{Hz}–50\un{Hz}) measurements of the complex elastic susceptibility of \chem{KMn} $_{1-x}$ \chem{Ca} x \chem{F_3} (x=0, 0.003, 0.018). An ultraslow relaxational process in pure \chem{KMnF_3} just below T_{\ab{c}}=186 \un{K} is discovered and explained by a refined heat diffusion model. In addition, a giant softening (superelasticity) due to domain wall motion is found. In contrast to the case of \chem{SrTiO_3} and also of pure \chem{KMnF_3}, we find a ferroelastic domain freezing in the mixed crystals with 0.3% \chem{Ca} substitution. The dispersion displays a Cole-Davidson–like behaviour with an additional logarithmic low-frequency contribution in agreement with the theoretical results for weak pinning of elastic interfaces in crystals with randomly distributed impurities