The effect of cation order on the elasticity of omphacite from atomistic calculations

Omphacite, a clinopyroxene mineral with two distinct crystallographic sites, M1 and M2, and composition intermediate between diopside and jadeite, is abundant throughout the Earth's upper mantle, and is the dominant mineral in subducted oceanic crust. Unlike the end-members, omphacite exists in two distinct phases, a P2/n ordered phase at low temperature and a high-temperature C2/c disordered phase. The crystal structure and full elastic constants tensor of ordered P2/n omphacite have been calculated to 15 GPa using plane-wave density functional theory. Our results show that several of the elastic constants, notably C11, C12, and C13 deviate from linear- mixing between diopside and jadeite. The anisotropy of omphacite decreases with increasing pressure and, at 10 GPa, is lower than that of either diopside or jadeite. The effect of cation disorder is investigated through force-field calculations of the elastic constants of Special Quasirandom Structures supercells with simulated disorder over the M2 sites only, and over both cation sites. These show that cation order influences the elasticity, with some components displaying particular sensitivity to order on a specific cation site. C11, C12, and C66 are sensitive to disorder on M1, while C22 is softened substantially by disorder on M2, but insensitive to disorder on M1. This shows that the elasticity of omphacite is sensitive to the degree of disorder, and hence the temperature. We expect these results to be relevant to other minerals with order-disorder phase transitions, implying that care must be taken when considering the effects of composition on seismic anisotropy

Interactions between bare and protonated Mg vacancies and dislocation cores in MgO

Water can be incorporated into the lattice of mantle minerals in the form of protons charge-balanced by the creation of cation vacancies. These protonated vacancies, when they interact with dislocations, influence strain rates by affecting dislocation climb, pinning the dislocation, and, potentially, by altering the Peierls barrier to glide. We use atomic scale simulations to investigate segregation of Mg vacancies to atomic sites within the core regions of dislocations in MgO. Energies are computed for bare and V′′Mg protonated Mg vacancies occupying atomic sites close to ½ 〈110〉 screw dislocations, and ½ 〈110〉 {100} and ½ 〈110〉 {110} edge dislocations. These are compared with energies for equivalent defects in the bulk lattice to determine segregation energies for each defect. Mg vacancies preferentially bind to ½ 〈110〉 {100} edge dislocations, with calculated minimum segregation energies of − 3.54 eV for and − 4.56 eV for 2HxMg . The magnitudes of the minimum segregation energies calculated for defects binding to ½ 〈110〉 {110} edge or ½ 〈110〉 screw dislocations are considerably lower. Interactions with the dislocation strain field lift the threefold energy degeneracy of the 2HxMg defect in MgO. These calculations show that Mg vacancies interact strongly with dislocations in MgO, and may be present in sufficiently high concentrations to affect dislocation mobility in both the glide- and climb-controlled creep regimes

Lubrication of dislocation glide in forsterite by Mg vacancies: insights from Peierls-Nabarro modeling

Dislocation glide is an important contributor to the rheology of olivine under conditions of high stress and low to moderate temperature, such as occur in mantle wedges. Interactions between point defects and dislocation core may alter the Peierls stress, σp, and has been suggested that vacancy-related defects may selectively enhance glide on certain slip systems, changing the olivine deformation fabric. In this study, the Peierls-Nabarro model, parameterized by generalized stacking fault (GSF) energies calculated atomistically using empirical interatomic potentials, is used to determine the effect of bare Mg vacancies on the Peierls stresses of [100](010) and [001](010) dislocations in forsterite. Mg vacancies considerably reduce GSF energies and, consequently, σp for dislocations gliding on (010) in olivine. The magnitude of this decrease depends strongly on dislocation and the type of the lattice site, with vacant M2 sites producing the largest reduction of σp. The [001](010) slip system is found to be more sensitive than the [100](010) slip system to the presence of vacancies. Although, at ambient pressure, σp is lower for [100](010) than [001](010) edge dislocations, dσp/dP is greater for [100](010) dislocations, resulting in a change in the preferred slip system at 1.5 GPa. By preferentially lubricating [001](010) glide, Mg vacancies reduce the pressure at which this cross-over occurs. An M2 vacancy concentration at the glide plane of 0.125 defects/site is sufficient to reduce cross-over to 0.7 GPa. This may account for the existence of the B-type olivine deformation fabric in the corners of mantle wedges

Lubrication of dislocation glide in MgO by hydrous defects

Water-related defects, principally in the form of protonated cation vacancies, are potentially able to weaken minerals under high-stress or low-temperature conditions by reducing the Peierls stress required to initiate dislocation glide. In this study, we use the Peierls-Nabarro (PN) model to determine the effect of protonated Mg vacancies on the 1/2{110} and 1/2{100} slip systems in MgO. This PN model is parameterized using generalized stacking fault energies calculated using plane-wave density functional theory, with and without protonated Mg vacancies present at the glide plane. It found that these defects increase dislocation core widths and reduce the Peierls stress over the entire pressure range 0-125 GPa. Furthermore, 1/2{110} slip is found to be more sensitive to the presence of protonated vacancies which increases in the pressure at which {100} becomes the easy glide plane for 1/2 screw dislocations. These results demonstrate, for a simple mineral system, that water-related defects can alter the deformation behavior of minerals in the glide-creep regime by reducing the stress required to move dislocations by glide. (Mg, Fe)O is the most anisotropic mineral in the Earth's lower mantle, so the differential sensitivity of the major slip systems in MgO to hydrous defects has potential implications for the interpretation of the seismic anisotropy in this region

The influence of channel anion identity on the high-pressure crystal structure, compressibility, and stability of apatite

The material properties of the common phosphate mineral apatite are influenced by the identity of the channel anion, which is usually F−, Cl−, or (OH)−. Density functional theory calculations have been used to determine the effect of channel anion identity on the compressibility and structure of apatite. Hydroxyapatite and fluorapatite are found to have similar zero pressure bulk moduli, of 79.2 and 82.1 GPa, respectively, while chlorapatite is considerably more compressible, with K₀=55.0 GPa. While the space groups of hydroxyapatite and fluorapatite do not change between 0 and 25 GPa, symmetrization of the Cl− site in chlorapatite at ~7.5 GPa causes the space group to change from P2₁/b to P6₃/m. Examination of the valence electron density distribution in chlorapatite reveals that this symmetry change is associated with a change in the coordination of the Cl− anion from threefold to sixfold coordinated by Ca. We also calculate the pressure at which apatite decomposes to form tuite, a calcium orthophosphate mineral, and find that the transition pressure is sensitive to the identity of the channel anion, being lowest for fluorapatite (13.8 GPa) and highest for chlorapatite (26.9 GPa). Calculations are also performed within the DFT-D2 framework to investigate the influence of dispersion forces on the compressibility of apatite minerals

Peierls-Nabarro modeling of dislocations in UO₂

Under conditions of high stress or low temperature, glide of dislocations plays an important role in the deformation of UO2. In this paper, the Peierls-Nabarro model is used to calculate the core widths and Peierls stresses of ½ edge and screw dislocations gliding on {100}, {110}, and {111}. The energy of the inelastic displacement field in the dislocation core is parameterized using generalized stacking fault energies, which are calculated atomistically using interatomic potentials. We use seven different interatomic potential models, representing the variety of different models available for UO2. The different models broadly agree on the relative order of the strengths of the different slip systems, with the 1/2{100} edge dislocation predicted to be the weakest slip system and 1/2{110} the strongest. However, the calculated Peierls stresses depend strongly on the interatomic potential used, with values ranging between 2.7 and 12.9 GPa for glide of 1/2{100} edge dislocations, 16.4–32.3 GPa for 1/2{110} edge dislocations, and 6.8–13.6 GPa for 1/2{111} edge dislocations. The glide of 1/2 screw dislocations in UO2 is also found to depend on the interatomic potential used, with some models predicting similar Peierls stresses for glide on {100} and {111}, while others predict a unique easy glide direction. Comparison with previous fully atomistic calculations show that the Peierls-Nabarro model can accurately predict dislocation properties in UO2

Phosphodiesterase-induced cAMP degradation restricts hepatitis B virus infection

Hepatitis B virus (HBV) entry into hepatocytes is mediated via a high affinity interaction between the preS1 glycoprotein and sodium/bile acid cotransporting polypeptide (NTCP). To date, in vitro model systems rely on high multiplicities of infection to achieve infection of cell lines overexpressing human NTCP. This study investigates a novel regulatory pathway for NTCP trafficking to the cell surface, induced by DMSO-mediated cellular differentiation. DMSO rapidly induces high cell surface expression of NTCP and results in increased susceptibility of cells to HBV infection. Additionally, DMSO treatment induces actin, as well as tubulin reshaping within the cells. We show that direct disruption of the actin and tubulin network directly enhances NTCP expression and the subsequent susceptibility of cells to HBV infection. DMSO induces these changes via alterations in the levels of cyclic (c)AMP, which participates in the observed actin rearrangements. Blocking of phosphodiesterases (PDEs), which degrade accumulated cAMP, had the same effect as DMSO differentiation and demonstrates that DMSO prevents phosphodiesterase-mediated cAMP degradation. This identifies adenylate cyclase as a novel target for blocking the entry of HBV via targeting the cell surface accumulation of NTCP

The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z.

BACKGROUND: Sex-determining systems have evolved independently in vertebrates. Placental mammals and marsupials have an XY system, birds have a ZW system. Reptiles and amphibians have different systems, including temperature-dependent sex determination, and XY and ZW systems that differ in origin from birds and placental mammals. Monotremes diverged early in mammalian evolution, just after the mammalian clade diverged from the sauropsid clade. Our previous studies showed that male platypus has five X and five Y chromosomes, no SRY, and DMRT1 on an X chromosome. In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping. RESULTS: Chromosome painting reveals a meiotic chain of nine sex chromosomes in the male echidna and establishes their order in the chain. Two of those differ from those in the platypus, three of the platypus sex chromosomes differ from those of the echidna and the order of several chromosomes is rearranged. Comparative gene mapping shows that, in addition to bird autosome regions, regions of bird Z chromosomes are homologous to regions in four platypus X chromosomes, that is, X1, X2, X3, X5, and in chromosome Y1. CONCLUSION: Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Comparison of depression and anxiety symptom networks in reporters and non-reporters of lifetime trauma in two samples of differing severity

Background: Reported trauma is associated with differences in the course and outcomes of depression and anxiety. However, no research has explored the association between reported trauma and patterns of clinically relevant symptoms of both depression and anxiety. / Methods: We used network analysis to investigate associations between reported trauma and depression and anxiety symptom interactions in affected individuals from the Genetic Links to Anxiety and Depression (GLAD) Study (n = 17720), and population volunteers from the UK Biobank (n = 11120). Participants with current moderate symptoms of depression or anxiety were grouped into reporters and non-reporters of lifetime trauma. Networks of 16 depression and anxiety symptoms in the two groups were compared using the network comparison test. / Results: In the GLAD Study, networks of reporters and non-reporters of lifetime trauma did not differ on any metric. In the UK Biobank, the symptom network of reporters had significantly greater density (7.80) than the network of non-reporters (7.05). / Limitations: The data collected in the GLAD Study and the UK Biobank are self-reported with validated or semi-validated questionnaires. / Conclusions: Reported lifetime trauma was associated with stronger interactions between symptoms of depression and anxiety in population volunteers. Differences between reporters and non-reporters may not be observed in individuals with severe depression and/or anxiety due to limited variance in the presentation of disorder

A systematic review and meta-synthesis of the impact of low back pain on people's lives

Copyright @ 2014 Froud et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Background - Low back pain (LBP) is a common and costly problem that many interpret within a biopsychosocial model. There is renewed concern that core-sets of outcome measures do not capture what is important. To inform debate about the coverage of back pain outcome measure core-sets, and to suggest areas worthy of exploration within healthcare consultations, we have synthesised the qualitative literature on the impact of low back pain on people’s lives. Methods - Two reviewers searched CINAHL, Embase, PsycINFO, PEDro, and Medline, identifying qualitative studies of people’s experiences of non-specific LBP. Abstracted data were thematic coded and synthesised using a meta-ethnographic, and a meta-narrative approach. Results - We included 49 papers describing 42 studies. Patients are concerned with engagement in meaningful activities; but they also want to be believed and have their experiences and identity, as someone ‘doing battle’ with pain, validated. Patients seek diagnosis, treatment, and cure, but also reassurance of the absence of pathology. Some struggle to meet social expectations and obligations. When these are achieved, the credibility of their pain/disability claims can be jeopardised. Others withdraw, fearful of disapproval, or unable or unwilling to accommodate social demands. Patients generally seek to regain their pre-pain levels of health, and physical and emotional stability. After time, this can be perceived to become unrealistic and some adjust their expectations accordingly. Conclusions - The social component of the biopsychosocial model is not well represented in current core-sets of outcome measures. Clinicians should appreciate that the broader impact of low back pain includes social factors; this may be crucial to improving patients’ experiences of health care. Researchers should consider social factors to help develop a portfolio of more relevant outcome measures.Arthritis Research U