Introducing a unified magnetic space-group symbol.

The two commonly used systems of magnetic space-group (MSG) symbols, with accompanying numbers and settings, are those of Belov-Neronova-Smirnova (BNS) and Opechowski-Guccione (OG). The symbols from both systems have been used for several decades now. Both have advantages and disadvantages. Both present challenges of interpretation to novice and expert users alike, which can inhibit understanding and lead to errors in published magnetic structures. To address each of these challenges going forward, a new unified (UNI) MSG symbol is introduced, which combines a modified BNS symbol with essential information from the OG symbol.

S-adenosyl-L-methionine (SAMe) halts the autoimmune response in patients with primary biliary cholangitis (PBC) via antioxidant and S-glutathionylation processes in cholangiocytes.

S-adenosyl-L-methionine is an endogenous molecule with hepato-protective properties linked to redox regulation and methylation. Here, the potential therapeutic value of SAMe was tested in 17 patients with PBC, a cholestatic disease with autoimmune phenomena targeting small bile ducts. Nine patients responded to SAMe (SAMe responders) with increased serum protein S-glutathionylation. That posttranslational protein modification was associated with reduction of serum anti-mitochondrial autoantibodies (AMA-M2) titers and improvement of liver biochemistry. Clinically, SAMe responders were younger at diagnosis, had longer duration of the disease and lower level of serum S-glutathionylated proteins at entry. SAMe treatment was associated with negative correlation between protein S-glutathionylation and TNFα. Furthermore, AMA-M2 titers correlated positively with INFγ and FGF-19 while negatively with TGFß. Additionally, cirrhotic PBC livers showed reduced levels of glutathionylated proteins, glutaredoxine-1 (Grx-1) and GSH synthase (GS). The effect of SAMe was also analyzed in vitro. In human cholangiocytes overexpressing miR-506, which induces PBC-like features, SAMe increased total protein S-glutathionylation and the level of γ-glutamylcysteine ligase (GCLC), whereas reduced Grx-1 level. Moreover, SAMe protected primary human cholangiocytes against mitochondrial oxidative stress induced by tBHQ (tert-Butylhydroquinone) via raising the level of Nrf2 and HO-1. Finally, SAMe reduced apoptosis (cleaved-caspase3) and PDC-E2 (antigen responsible of the AMA-M2) induced experimentally by glycochenodeoxycholic acid (GCDC). These data suggest that SAMe may inhibit autoimmune events in patients with PBC via its antioxidant and S-glutathionylation properties. These findings provide new insights into the molecular events promoting progression of PBC and suggest potential therapeutic application of SAMe in PBC.

Unexpected phase transition sequence in the ferroelectric Bi4Ti3O12.

The high-temperature phase behaviour of the ferroelectric layered perovskite Bi4Ti3O12 has been re-examined by high-resolution powder neutron diffraction. Previous studies, both experimental and theoretical, had suggested conflicting structural models and phase transition sequences, exacerbated by the complex interplay of several competing structural instabilities. This study confirms that Bi4Ti3O12 undergoes two separate structural transitions from the aristotype tetragonal phase (space group I4/mmm) to the ambient-temperature ferroelectric phase (confirmed as monoclinic, B1a1). An unusual, and previously unconsidered, intermediate paraelectric phase is suggested to exist above T C with tetragonal symmetry, space group P4/mbm. This phase is peculiar in displaying a unique type of octahedral tilting, in which the triple perovskite blocks of the layered structure alternate between tilted and untilted. This is rationalized in terms of the bonding requirements of the Bi3+ cations within the perovskite blocks.

Automatic calculation of symmetry-adapted tensors in magnetic and non-magnetic materials: a new tool of the Bilbao Crystallographic Server.

Two new programs, MTENSOR and TENSOR, hosted on the open-access website known as the Bilbao Crystallographic Server, are presented. The programs provide automatically the symmetry-adapted form of tensor properties for any magnetic or non-magnetic point group or space group. The tensor is chosen from a list of 144 known tensor properties gathered from the scientific literature or, alternatively, the user can also build a tensor that possesses an arbitrary intrinsic symmetry. Four different tensor types are considered: equilibrium, transport, optical and nonlinear optical susceptibility tensors. For magnetically ordered structures, special attention is devoted to a detailed discussion of the transformation rules of the tensors under the time-reversal operation 1'. It is emphasized that for non-equilibrium properties it is the Onsager theorem, and not the constitutive relationships, that indicates how these tensors transform under 1'. In this way it is not necessary to restrict the validity of Neumann's principle. New Jahn symbols describing the intrinsic symmetry of the tensors are introduced for several transport and optical properties. In the case of some nonlinear optical susceptibilities of practical interest, an intuitive method is proposed based on simple diagrams, which allows easy deduction of the action of 1' on the susceptibilities. This topic has not received sufficient attention in the literature and, in fact, it is usual to find published results where the symmetry restrictions for such tensors are incomplete.

Molecular dynamics simulations of the structure of mixtures of protic ionic liquids and monovalent and divalent salts at the electrochemical interface.

We perform molecular dynamics simulations of mixtures of a prototypical protic ionic liquid, ethylammonium nitrate, with lithium or magnesium nitrate (LiNO3/Mg(NO3)2) confined between two graphene walls. The structure of the system is analyzed by means of ionic density profiles, angular orientations of ethylammonium cations close to the wall and the lateral structure of the first layer close to the graphene wall. All these results are compared to those of the corresponding aprotic ionic liquid systems, analyzing the influence of the graphene wall charge in the structure of the protic and aprotic mixtures. Moreover, vibrational densities of states are calculated for the salt cations close to the walls. Finally, we investigate the structure of the mixture with Li salt near the interface using ab initio density functional theory, and the results are compared with those obtained by classical molecular dynamics simulations.

GADDLE Maps: General Algorithm for Discrete Object Deformations Based on Local Exchange Maps.

A new method for switching between structures consisting of equivalent discrete and flexible objects with different particle representation and object configuration, including different resolution levels (number of particles per object), is reported. The method is fully general since it does not require any extra code nor additional database elements for new systems. It is based on a Monte Carlo sampling of the configurational space for each object type of the target system. The sampling is controlled by a Metropolis acceptance criterion of movements (translations, rotations, and relative deformations of the object configuration) that uses the generalized distance between the sets of particles at both representations. For Gaussian distributed distances, such a minimization procedure is equivalent to an optimization of χ2 in a maximum likelihood method. This provides sound statistical support since the method leads to the most probable configuration of the system at each representation. The configurations obtained in this way are then used to create resolution exchange maps for each object type, which allows the extrapolation of the conversion to every object configuration throughout the whole system. As an example, the method is here tested with several molecular dynamics simulated systems (ionic liquids, cyclodextrins, cell-penetrating peptides, cyclic peptides, lipid bilayers, vesicles, heterogeneous organic molecules, DNA, and solvated proteins) for different resolution force fields (GROMOS, AMBER, OPLS, MARTINI) using GROMACS. In this context, the method can be applied to map structures described by any other pair of force fields, as well as to homogeneous and heterogeneous systems with many different molecules. The method is proved to be highly efficient since the time required for the mapping is practically independent of the number of molecules in the target system.

Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures.

This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement, between graphene sheets. By means of molecular dynamics simulations, the adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces, and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The confinement effect on the structure and dynamics of the mixtures is thoroughly analyzed using the density and the potential of mean force profiles, as well as by the vibrational densities of the states of water molecules near the graphene surface. The orientation of water molecules and the water-induced structural transitions in the layer closest to the graphene surface are also discussed.

Symmetry conditions for type II multiferroicity in commensurate magnetic structures.

Type II multiferroics are magnetically ordered phases that exhibit ferroelectricity as a magnetic induced effect. We show that in single-k magnetic phases the presence in the paramagnetic phase of non-symmorphic symmetry combined with some specific type of magnetic propagation vector can be sufficient for the occurrence of this type of multiferroic behaviour. Other symmetry scenarios especially favourable for spin driven multiferroicity are also presented. We review and classify known type II multiferroics under this viewpoint. In addition, some other magnetic phases which due to their symmetry properties can exhibit type II multiferroicity are pointed out.

Crystallographic and magnetic structure of the perovskite-type compound BaFeO2.5: unrivaled complexity in oxygen vacancy ordering.

We report here on the characterization of the vacancy-ordered perovskite-type structure of BaFeO2.5 by means of combined Rietveld analysis of powder X-ray and neutron diffraction data. The compound crystallizes in the monoclinic space group P2(1)/c [a = 6.9753(1) Å, b = 11.7281(2) Å, c = 23.4507(4) Å, ß = 98.813(1)°, and Z = 28] containing seven crystallographically different iron atoms. The coordination scheme is determined to be Ba7(FeO4/2)1(FeO3/2O1/1)3(FeO5/2)2(FeO6/2)1 = Ba7Fe([6])1Fe([5])2Fe([4])4O17.5 and is in agreement with the (57)Fe Mössbauer spectra and density functional theory based calculations. To our knowledge, the structure of BaFeO2.5 is the most complicated perovskite-type superstructure reported so far (largest primitive cell, number of ABX2.5 units per unit cell, and number of different crystallographic sites). The magnetic structure was determined from the powder neutron diffraction data and can be understood in terms of "G-type" antiferromagnetic ordering between connected iron-containing polyhedra, in agreement with field-sweep and zero-field-cooled/field-cooled measurements.

Brillouin-zone database on the Bilbao Crystallographic Server.

The Brillouin-zone database of the Bilbao Crystallographic Server (http://www.cryst.ehu.es) offers k-vector tables and figures which form the background of a classification of the irreducible representations of all 230 space groups. The symmetry properties of the wavevectors are described by the so-called reciprocal-space groups and this classification scheme is compared with the classification of Cracknell et al. [Kronecker Product Tables, Vol. 1, General Introduction and Tables of Irreducible Representations of Space Groups (1979). New York: IFI/Plenum]. The compilation provides a solution to the problems of uniqueness and completeness of space-group representations by specifying the independent parameter ranges of general and special k vectors. Guides to the k-vector tables and figures explain the content and arrangement of the data. Recent improvements and modifications of the Brillouin-zone database, including new tables and figures for the trigonal, hexagonal and monoclinic space groups, are discussed in detail and illustrated by several examples.

Monophosphate tungsten bronzes with pentagonal tunnels: reinvestigation through the peephole of the superspace.

The large family of monophosphate tungsten bronzes with pentagonal tunnels (MPTBp), (PO2)4(WO3)2m with m ranging from 4 to 14, can be considered as modular structures via a description with (PO2)2(WO3)m modules related together by a symmetry operation and alternating along the z axis. Following the success of the application of the superspace for the description of the lillianites homologous series, a (3+1)-dimensional superspace model is efficiently defined to unify the structural analysis of the MPTBp. The (3+1)-dimensional model reveals hidden common characteristics such as the symmetry. An evaluation of the model for six well known members of the series was carried out from experimental data collected to this aim.

A fast method for the quantitation of key metabolites of the methionine pathway in liver tissue by high-resolution mass spectrometry and hydrophilic interaction ultra-performance liquid chromatography.

We developed an assay for the extraction and simultaneous quantitation of five key metabolites of the methionine metabolic pathway in liver tissue. The metabolites included were 5'-methylthioadenosine, methionine, homocysteine, S-adenosyl-L-homocysteine, and S-adenosyl-L-methionine. The metabolites were extracted using a bead-based homogenization method, and quantitation was carried out using hydrophilic interaction chromatography and time-of-flight mass spectrometry. The extraction procedure was optimized by testing the effect of various solvent combinations. The chromatographic method was optimized for peak shape, signal intensity, and carry-over. With a total chromatographic run time of 5 min, this assay is suitable for the analysis of large sample sets. Time-of-flight mass spectrometry provided high mass accuracy which, combined with isotope pattern matching and use of chemical standards, guarantees high specificity. Moreover, by operating the mass spectrometer in enhanced duty cycle mode the signal strength for the analytes increased three- to tenfold in comparison with the generic full-scan mode. For quantitation, a matrix-spiked calibration method was used. The lowest analyte levels detected and quantified using our method were within the range of concentrations found in the liver. The inter-day coefficients of variance for the analytes were between 5 and 15% in pooled tissue samples. Interestingly, the CVs between individual liver tissue aliquots were about twice as high. Additional experiments suggested that this higher variability was caused by uneven distribution of the analytes within the liver. In conclusion, an optimized and robust assay is now available for the extraction and quantification of key metabolites in the methionine metabolic pathway.

Spanish human proteome project: dissection of chromosome 16.

The Chromosome 16 Consortium forms part of the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a chromosome-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). A Spanish consortium of 16 laboratories was organized into five working groups: Protein/Antibody microarrays, protein expression and Peptide Standard, S/MRM, Protein Sequencing, Bioinformatics and Clinical healthcare, and Biobanking. The project is conceived on a multicenter configuration, assuming the standards and integration procedures already available in ProteoRed-ISCIII, which is encompassed within HUPO initiatives. The products of the 870 protein coding genes in chromosome 16 were analyzed in Jurkat T lymphocyte cells, MCF-7 epithelial cells, and the CCD18 fibroblast cell line as it is theoretically expected that most chromosome 16 protein coding genes are expressed in at least one of these. The transcriptome and proteome of these cell lines was studied using gene expression microarray and shotgun proteomics approaches, indicating an ample coverage of chromosome 16. With regard to the B/D section, the main research areas have been adopted and a biobanking initiative has been designed to optimize methods for sample collection, management, and storage under normalized conditions and to define QC standards. The general strategy of the Chr-16 HPP and the current state of the different initiatives are discussed.

[Alcoholic ketoacidosis and reversible neurological complications due to hypophosphataemia]. / Cetoacidosis alcohólica y complicaciones neurológicas reversibles de la hipofosfatemia.

A 57-year-old man with chronic alcoholism was admitted to our hospital due to disturbance of consciousness and polyradiculitis. Laboratory examination revealed metabolic acidosis, hypokalemia and hypophosphataemia. Alcoholic ketoacidosis is a common disorder in alcoholic patients. All patients present with a history of heavy alcohol misuse, preceding a bout of particularly excesive intake, which had been terminated by nausea, vomiting and abdominal pain. The most important laboratory results are: normal or low glucose level, metabolic acidosis with a raised anion GAP, low or absent blood alcohol level and urinary ketones. The greatest threats to patients are: hypovolemia, hypokaliemia, hypoglucemia and acidosis. Alcohol abuse may result in a wide range of electrolyte and acid-base disorders including hypophosphataemia, hypomagnesemia, hypocalcemia, hypokalemia, metabolic acidosis and respiratory alkalosis. Disturbance of consciousness in alcoholic patients is observed in several disorders, such drunkenness, Wernicke encephalopathy, alcohol withdrawal syndrome, central pontine myelinolysis, hepatic encephalopathy, hypoglucemia and electrolyte disorders.

Compositional uniformity, domain patterning and the mechanism underlying nano-chessboard arrays.

We propose that systems exhibiting compositional patterning at the nanoscale, so far assumed to be due to some kind of ordered phase segregation, can be understood instead in terms of coherent, single phase ordering of minority motifs, caused by some constrained drive for uniformity. The essential features of this type of arrangement can be reproduced using a superspace construction typical of uniformity-driven orderings, which only requires the knowledge of the modulation vectors observed in the diffraction patterns. The idea is discussed in terms of a simple two-dimensional lattice-gas model that simulates a binary system in which the dilution of the minority component is favoured. This simple model already exhibits a hierarchy of arrangements similar to the experimentally observed nano-chessboard and nano-diamond patterns, which are described as occupational modulated structures with two independent modulation wavevectors and simple step-like occupation modulation functions.

Structure refinement and superspace description of the system Bi(2(n + 2))Mo(n)O(6(n + 1)) (n = 3, 4, 5 and 6).

The system Bi(2(n + 2))Mo(n)O(6(n + 1)) is described within the superspace formalism. Two superspace models are proposed for the different members of this family, depending on the parity of the parameter n. The superspace model for the odd members is constructed through the embedding of the cationic distribution of the member with n = 3, and the modification of a superspace model previously proposed for the compound Bi(2)MoO(6). However, this model cannot be applied to the even members of the family. Performing the appropriate transformations, a suitable superspace model for the even members is obtained. The atomic structure of the different compounds of the family have been refined through the Rietveld method combining synchrotron X-ray and neutron powder diffraction data.

Unified (3 + 1)-dimensional superspace description of the 2212-type stair-like [Bi2Sr3Fe2O9]m[Bi4Sr6Fe2O16] family of compounds.

The (3 + 1)-dimensional superspace approach is applied to describe and refine a series of sheared compounds related to layered high T(c) superconducting oxides. Two commensurate members (m = 4, 5) of the 2212 stair-like [Bi(2)Sr(3)Fe(2)O(9)](m)[Bi(4)Sr(6)Fe(2)O(16)] family of compounds, previously studied using single-crystal diffraction data, are analyzed. A common average unit cell has been identified and a composition-dependent modulation wavevector is proposed. The model is built using only three independent atomic domains, one for the metal atoms and two for the O atoms. The three Sr, Bi and Fe species are described using close-connected crenel-like functions forming a continuous atomic domain along the internal space. The two oxygen domains are represented by crenel functions and the displacive modulation functions are built up by Legendre polynomials recently implemented in the program JANA2006. Surprisingly, the results of the refinements show a striking similarity of the displacive modulations for the two compounds analyzed, indicating that a unique model can be used to describe the correlations between the atomic displacements of the 2212 stair-like series. This final model is then applied to predict the structure of new members of the family.

Magnetic superspace groups and symmetry constraints in incommensurate magnetic phases.

Superspace symmetry has been for many years the standard approach for the analysis of non-magnetic modulated crystals because of its robust and efficient treatment of the structural constraints present in incommensurate phases. For incommensurate magnetic phases, this generalized symmetry formalism can play a similar role. In this context we review from a practical viewpoint the superspace formalism particularized to magnetic incommensurate phases. We analyse in detail the relation between the description using superspace symmetry and the representation method. Important general rules on the symmetry of magnetic incommensurate modulations with a single propagation vector are derived. The power and efficiency of the method is illustrated with various examples, including some multiferroic materials. We show that the concept of superspace symmetry provides a simple, efficient and systematic way to characterize the symmetry and rationalize the structural and physical properties of incommensurate magnetic materials. This is especially relevant when the properties of incommensurate multiferroics are investigated.

Obesity-dependent metabolic signatures associated with nonalcoholic fatty liver disease progression.

Our understanding of the mechanisms by which nonalcoholic fatty liver disease (NAFLD) progresses from simple steatosis to steatohepatitis (NASH) is still very limited. Despite the growing number of studies linking the disease with altered serum metabolite levels, an obstacle to the development of metabolome-based NAFLD predictors has been the lack of large cohort data from biopsy-proven patients matched for key metabolic features such as obesity. We studied 467 biopsied individuals with normal liver histology (n=90) or diagnosed with NAFLD (steatosis, n=246; NASH, n=131), randomly divided into estimation (80% of all patients) and validation (20% of all patients) groups. Qualitative determinations of 540 serum metabolite variables were performed using ultraperformance liquid chromatography coupled to mass spectrometry (UPLC-MS). The metabolic profile was dependent on patient body-mass index (BMI), suggesting that the NAFLD pathogenesis mechanism may be quite different depending on an individual's level of obesity. A BMI-stratified multivariate model based on the NAFLD serum metabolic profile was used to separate patients with and without NASH. The area under the receiver operating characteristic curve was 0.87 in the estimation and 0.85 in the validation group. The cutoff (0.54) corresponding to maximum average diagnostic accuracy (0.82) predicted NASH with a sensitivity of 0.71 and a specificity of 0.92 (negative/positive predictive values=0.82/0.84). The present data, indicating that a BMI-dependent serum metabolic profile may be able to reliably distinguish NASH from steatosis patients, have significant implications for the development of NASH biomarkers and potential novel targets for therapeutic intervention.