Crystallographic Criteria Research Articles

HLA-DQ heterodimers in hematopoietic cell transplantation

AbstractHLA-DQ heterodimers increase the susceptibility to autoimmune diseases, but their role in hematopoietic cell transplantation is unknown. We tested the hypothesis that outcome after HLA-matched and HLA-DQ–mismatched hematopoietic cell transplantation is influenced by HLA-DQ heterodimers. Heterodimers were defined in 5164 HLA-matched and 520 HLA-DQ–mismatched patients and their transplant donors according to well-established crystallographic criteria. Group 1 (G1) heterodimers are any DQA1*02/03/04/05/06α paired with any DQB1*02/03/04β. Group 2 (G2) heterodimers are DQA1*01α paired with any DQB1*05/06β. Multivariable models identified significantly higher relapse risk in G1G2 and G2G2 compared with G1G1 HLA-matched patients with malignant disease; risk increased with an increasing number of G2 molecules. In HLA-DQ–mismatched transplantation for malignant diseases, matching or mismatching for G2 increased relapse risk. G2 lowered disease-free survival after both HLA-matched and HLA-DQ–mismatched transplantation. A paradigm based on HLA-DQ heterodimers provides a functional definition of the hematopoietic cell transplantation barrier and a means to lower risks for future patients.

Влияние кислородной нестехиометрии на фазовое расслоение, структуру и магнитные свойства сложного оксида NdSr2Mn2O7 ± 

To create different oxygen nonstoichiometry in oxide samples of NdSr2Mn2O7 + δ, we have used a two-step method of synthesis, which makes it possible to achieve different oxygen nonstoichiometry of the samples. Oxygen nonstoichiometry is formed by two methods: quenching at certain temperatures and annealing at certain values of oxygen partial pressure. The value of oxygen nonstoichiometry is determined by the mass of oxygen emitted from the sample during the decomposition of samples of NdSr2Mn2O7 + δ to simple oxides. We have determined oxygen nonstoichiometry in NdSr2Mn2O7 + δ when recording external parameters such as pressure and temperature. The study of samples of NdSr2Mn2O7 + δ using thermogravimetry and X-rays revealed phase separation—two phases with the same cation composition, having different oxygen content. By example of a sample of NdSr2Mn2O7 + δ tempered from 1000°C and having oxygen nonstoichiometry of +0.09, we have proposed a crystallographic criterion of manifestation of phase separation in Ruddlesden–Popper (R–P) phases—a sharp change in the manganese-oxygen bond lengths. Measurements of the electrical dc resistance in the samples of NdSr2Mn2O7 have been performed in the temperature range of 5–300 K and magnetic fields up to 7 T using the standard 4-probe method. A magnetoresistive effect up to 400% was found in the studied oxides, which is nonlinearly dependent on their oxygen nonstoichiometry.

Symmetry in Recognition of Supramolecular Synthons–Competition between Hydrogen Bonding and Coordination Bond in Multinuclear CuII–4f Complexes with Bicompartmental Schiff Base Ligand

Classic Cu–O coordination bonds in 1 or elongated semi-coordination ones in 2 and 3 were applied to construct CuII–4f complexes composed of trinuclear subunits linked through μ-NO3− ions with formulae given as [Cu2Tm(H2tehy)2]2(NO3)6·H2O, (1), {[Cu2Ho(H2tehy)2(NO3)2][Cu2Ho(H2tehy)2(H2O)2]}(NO3)4·2H2O, (2), and {[Cu2Er(H2tehy)2(H2O)]2([Cu2Er(H2tehy)2(NO3)]2}(NO3)10·2H2O·4CH3OH, (3), where H2tehy = C19H20N2O4 is a tetrahydroxy Schiff base ligand. Topological analysis showed that the same characteristic motif of coordination accompanied by hydrogen bonds involving the uncoordinated nitrate oxygen atom and ligand’s phenoxy O atoms is responsible for linking trinuclear subunits into a hexanuclear one as well as for bridging the hexanuclear coordination units in 3 into a 1D supramolecular polymer, with the Cu–O distance being 3.19(1) Å, much longer than the limit of a semi-coordination bond (3.07 Å). The Cambridge Structural Database was used to discuss issues of crystallographic criteria (distance and angular preferences) for the assessment of the stabilizing or destabilizing effect of hydrogen bonding on coordination. The presented results show that the symmetrically repeated arrangement of molecules may provide a useful tool for identifying higher order non-covalently bonded supramolecular aggregates. The complexes 1–3 have been characterized by X-ray diffraction, FTIR, and thermal analysis. The magnetic studies indicated the ferromagnetic interaction between CuII and HoIII ions.

Special interphase orientation relationships and locked lamellar growth in thin In-In2Bi eutectics

Lamellar eutectic alloys have two main types (floating or locked) of growth patterns depending on the orientations of the two eutectic phases. Recent theoretical studies have suggested that the existence of locked lamellar patterns is linked to that of deep minima in the surface energy plot of the interphase boundaries [Ghosh et al., Phys. Rev. E 91, 022407 (2015)]. We present an experimental study aiming at testing this prediction. We used a near-eutectic In-In2Bi alloy that solidifies into a tetragonal phase ε (In-11.5 at%Bi) and a hexagonal phase δ (In2Bi). Thin samples of this alloy were solidified using a rotating directional solidification stage and analyzed for crystallographic texture by X-ray diffraction. A series of large eutectic grains with low (1 to 3°) mosaic spreads were found to contain either of the following coincidence relationships: A={21¯1¯0}δ∥{111}ε or E={11¯02}δ∥{111}ε. A-type eutectic grains exhibited a locked type of growth, and E-type eutectic grains a floating type of growth. Given that according to standard crystallographic criteria A-type interphase boundaries have a much smaller surface energy than E-type ones, these findings are in agreement with the theoretical predictions.

PDB_REDO: constructive validation, more than just looking for errors.

Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.

Characterisation of magnesium oxide and its interface with α-Mg in Mg–Al-based alloys

Magnesium oxide (MgO) films and particles have been collected by pressurised filtration of a Mg-8.6wt%Al-0.67wt%Zn (AZ91D) alloy melt. The morphology of the oxides and their interfaces with the α-Mg phase were investigated by high-resolution transmission electron microscopy. It was found that the oxide films consisted of large numbers of sub-micrometre-sized MgO particles, and that melt shearing can effectively break up the oxide films and disperse the oxide particles. For the first time, orientation relationships (ORs) of OR I: [1 1 1]MgO∼2° from (0 0 0 1)α-Mg and (0 1 1)MgO //[2 1 1 0)α-Mg; and OR II: (1 1 1)MgO//(1 1 0 1)α-Mg and [0 1 1]MgO//[1 2 1 1]α-Mg, were observed between the MgO particles and the α-Mg matrix. The calculated Bramfitt planar disregistries were 5.5% and 2.5% for the two ORs, respectively, indicating good lattice matching between MgO and α-Mg at the interface. With the evidence of grain refinement effect observed in the sheared AZ91D magnesium alloy, the possibility of MgO particles to act as potent nucleants for heterogeneous nucleation of α-Mg grains is discussed in terms of the crystallographic criterion.

Advanced Electron Microscopy Investigation of Ceria–Zirconia‐Based Catalysts

AbstractThe potentials of advanced transmission and scanning transmission electron microscopy in nanostructural studies of ceria–zirconia mixed oxides are overviewed. The crystallographic criteria that allow us to discriminate the different CeO2–ZrO2 polymorphs and the nanocrystal size range within which they can be applied are discussed. The combined use of high resolution electron microscopy (HREM) and high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) to detect disorder–order transitions in the cation sublattice of this family of oxides and the size limit down to which each of them can be used for that purpose are also analyzed. Criteria to discriminate, on the basis of HREM images, the oxygen arrangement of the so called κ‐Ce2Zr2O8 phase from that of an oxidized pyrochlore Ce2Zr2O8 phase are presented and applied to the interpretation of experimental HREM images. HAADF‐STEM tomography studies and detailed analysis of HAADF‐STEM images establish both the crystallographic and compositional features of the surfaces of the mixed oxides that give enhanced redox activity. These findings allow deeper understanding of the influence of different thermal ageing pretreatments on the redox behavior of this family of mixed oxides. Novel characterization data do evidence that this model does not only fruitfully apply to binary ceria–zirconia oxides but also to more complex ternary oxides containing terbium.

Experimental Study on the Origin of Cremated Bone Apatite Carbon

Bones that have undergone burning at high temperatures (i.e. cremation) no longer contain organic carbon. Lanting et al. (2001) proposed that some of the original structural carbonate, formed during bioapatite formation, survives. This view is based on paired radiocarbon dating of cremated bone apatite and contemporary charcoal. However, stable carbon isotope composition of carbonate in cremated bones is consistently light compared to the untreated material and is closer to the δ13C values seen in C3 plant material. This raises the question of the origin of carbonate carbon in cremated bone apatite. That is, does the isotope signal reflect an exchange of carbon with the local cremation atmosphere and thus with carbon from the burning fuel, or is it caused by isotopic fractionation during cremation?To study the changes in carbon isotopes (14C, 13C) of bone apatite during burning up to 800 °, a modern bovine bone was exposed to a continuous flow of an artificial atmosphere (basically a high-purity O2/N2 gas mix) under defined conditions (temperature, gas composition). To simulate the influence of the fuel carbon available under real cremation conditions, fossil CO2 was added at different concentrations. To yield cremated bone apatite properties similar to archaeological cremated bones, in terms of crystallographic criteria, water vapor had to be added to the atmosphere in the oven. Infrared vibrational spectra reveal large increases in crystal size and loss of carbonate upon cremation. The isotope results indicate an effective carbon exchange between bone apatite carbonate and CO2 in the combustion gases depending on temperature and CO2 concentration. 14C dates on archaeological cremated bone apatite may thus suffer from an old-wood effect. Paired 13C and 14C values indicate that in addition to this exchange, isotope fractionation between CO2 and carbonate, and admixture of carbon from other sources such as possibly collagen or atmospheric CO2, may play a role in determining the final composition of the apatite carbonate.

Deformation twinning and twinning related fracture in coarse-grained α-uranium

An investigation of deformation twinning in coarse-grained α-uranium was conducted within the heat-affected zone of weld specimens tested in tension. Twins and twin interactions were studied both at fracture surfaces and sub-surface, using transmission electron microscopy (TEM) and electron backscatter diffraction (EBSD). The fracture surface plane was identified using TEM of foils cut from the fracture surface using a focused ion beam. Intersecting twins found in these foils were also analyzed. EBSD was also used to analyze twins and twin interactions at and below the fracture surface. Fracture parallel to {1 7 2} twin planes and {1 7 2} twin crossings were observed, in agreement with previous optical/Laue diffraction studies. Previously unobserved crossings of {1 7 2} twins by {1 1 2} twins were also frequently observed. These twin interactions are interpreted in terms of previously established crystallographic criteria for twin crossings.

Second-order junctions and strain hardening in bcc and fcc crystals

Axial ternary junctions, which were recently discovered by Bulatov et al. [V.V. Bulatov et al., Nature 440 (2006) 1174], as well as zigzag ternary configurations, were classified according to crystallographic criteria in face-centered cubic (fcc) and body-centered cubic (bcc) metals. The determination of their average strength by dislocation dynamics simulations shows that ternary configurations induce a significant Taylor hardening in bcc crystals, but not in fcc crystals. In both cases, these configurations should enhance strain hardening through their contribution to the storage rate of dislocations.

Solution Growth and Characterisation of L-alanine Single Crystals

Single crystals of L-alanine have been grown from buffered aqueous solutions and characterised as to their optical quality via wavefront distortion analysis, electrooptical response and harmonic generation efficiency. Refraction indices as well as phase matching loci were found in satisfactory agreement with previously published data for crystals grown in non buffered solution. Estimates for the electro-optical response are reported for the first time. The experimentally observed crystal habit is discussed in terms of morphological importance (M.I.), which was found to be in disagreement with the predictions of crystallographic criteria based on the interplanar distance d hkl , on the periodic bond chains (PBC) and the attachment energy E att . This disagreement is tentatively attributed to the presence of impurities and non-appropriate supersaturation conditions.

Experimental approach of a crystallographic cleavage criterion in a cast aged duplex stainless steel

The stress state distribution in an aged duplex steel is determined in each phase and is then correlated to local damage mechanisms. The measurements are performed at the grain scale because the studied material contains coarse grains up to one millimetre in size. A single-crystal specific X-ray method is required to determine the stress tensor. During in situ loading, the mechanical state determined in the ferritic crystal is associated with both the plastic flow and the damage mechanism observation. The coupling of the techniques makes it possible to establish that for the studied aged material, the stress normal to a {100} plane value of 465 MPa can be considered as a crystallographic criterion for cleavage propagation. The comparison of this value with the Cottrell's model seems to be good but the number of dislocations in the pile-up must be verified experimentally.

Basic Thermoluminescence Properties of Micas: Muscovite, Sericite and Phlogopite

Natural thermoluminescence (TLN) as well as gamma and beta induced thermoluminescence (TLI) were studied in a set of micas with the general formula (K, Na) X n AlSi 3 O 10 (OH,F) 2 , where X corresponds to Al 3+ , Mn 2+ , Mn 3+ , Fe 2+ , Fe 3+ , Mg 2+ , Ti 4+ or Li + , depending on the mica type. These minerals are classified according to crystallographic criteria in dioctahedral (D-micas as muscovite and sericite) and trioctahedral (T-micas like phlogopite and lepidolite). The results provide evidence of the presence of several thermoluminescence (TL) glow peaks induced after laboratory trituration (triboluminescence) of the non-irradiated mica samples. A gamma or beta irradiation of these minerals reveals the presence of a new peak located in the low temperature region (160°C), and a higher TL intensity of the curves. TL 3-D emission spectra of the non-irradiated mica samples does not produce significant signal, but after a gamma irradiation several bands are found in the blue and orange part of the spectrum: 315 nm, 475 nm, 590 nm, 600 nm and 720 nm.

Noncrystallographic Calcite Dendrites from Hot-Spring Deposits at Lake Bogoria, Kenya

ABSTRACT Complex calcite crystals are an integral component of precipitates that form around the orifices of the Loburu and Mawe Moto hot springs on the shores of Lake Bogoria, Kenya. Two types of large (up to 4 cm long) noncrystallographic dendrites are important components of these deposits. Feather dendrites are characterized by multiple levels of branching with individual branches developed through crystal splitting and spherulitic growth. Scandulitic (from Latin meaning shingle) dendrites are formed of stacked calcite crystals and are generally more compact than feather dendrites. These developed through the incremental stacking of rectangular-shaped calcite crystals that initially grew as skeletal crystals. Feather and scandulitic dendrites precipitated from the same waters in the same springs. The difference in morphology is therefore related to microenvironments in which they grew. Feather dendrites grew in any direction in pools of free-standing water provided that they were in constant contact with the solute. Conversely, scandulitic dendrites grew on rims of dams where water flowed over the surface in concert with the pulses of spring water. Thus, each calcite crystal in these dendrites represents one episode of crystal growth. The orientation of the component crystals in scandulitic dendrites is controlled by the topography of the dam or surface, not crystallographic criteria. The noncrystallographic dendrites formed from spring waters with initial temperatures of 90-99°C. Surficial water cooling, loss of CO2, and presence of other elements that can interfere with crystal growth contributed to the formation of these unusual crystals.

Phase equilibria in the Ln-Mn-O system ( Ln = Pr, Nd) and general aspects of the stability of the perovskite phase LnMeO 3

Phase equilibria in the Pr-Mn-O and Nd-Mn-O systems have been studied between 1100 and 1500 K and in atmospheres with an oxygen partial pressure ranging between 10 −15 and 1 atm. LnMnO 3 and LnMn 2O 5 have been found to form in both systems. PrMn 2O 5 was synthesized for the first time and has the orthorhombic DyMn 2O 5-type structure with cell parameters: a = 7.51, b = 8.63 and c = 5.69 Å. The thermodynamic stability of complex oxides was studied using TG and emf measurements in a galvanic cell with solid electrolytes. The equilibrium oxygen pressure, the standard Gibbs potential of the decomposition reactions 3LnMn 2O 5 = 3LnMnO 3 + Mn 3O 4 + O 2 and LnMnO 3 = 1 2 Ln 2O 3 + MnO + 1 4 O 2 , and the standard Gibbs potential of the formation of the ternary oxides have been calculated. The variation of LnMeO 3 stability for the rare earth manganates, and for the 3 d-transition metal (Cr, Mn, Co, Ni, Cu) compounds for a given rare earth element is discussed based on geometrical crystallographic criteria and the outer 3 d n electron configurations.

Control of Texture During Vapor Deposition of Al on (111) Si

The growth of Al on (111) Si single crystal substrates by various techniques usually leads to films with (111) texture, sometimes with a small (100) component. Using X-ray diffraction and electron microscopy, the present study shows that the (100) texture component can be enhanced to the point of forming an oriented (100) continuous tricrystal structure. The formation of this texture is shown to be related the presence of Cu. It is concluded that an understanding of heteroepitaxy must take into account the effect of chemistry in addition to the crystallographic criteria of lattice matching.

Low energy grain boundaries in silver and copper close to the melting point

Crystallographic parameters of low energy grain boundaries in silver and copper in the temperature range 0.8-0.996 T m have been studied. The investigations have been carried out by sintering single crystalline spheres to single crystalline plates having surfaces parallel to low index planes. In the above temperature range the most important energy cusps were found to be associated with [110] tilt boundaries. This result indicates that the parallelity of close packed rows of atoms from both grains surfaces leads to low energy grain boundary structures. The distribution of misorientation angles for low energy [1 1 0] tilt boundaries is almost continuous at 0.8 T m. At higher temperatures the spheres select some orientations as more preferred than others. This set of orientations is smaller than predicted according to recent geometrical criteria for low energy boundaries. It can be interpreted in terms of grain boundary faceting in such a way that it contains compact structural units of low energy. There seems to be no connection between the type of structural units in the grain boundary and the present crystallographic criteria. This is the reason why these criteria fail to select between nonsymmetrical boundaries of higher and lower energy.

Development of new technologies for solid‐state polymerization. A conceptual and experimental approach

AbstractA review of an extensive study on the preparation and solid‐state reactivity of squareplanar NiX2L2 complexes is presented, where X = Cl, Br, I, or NCS and L = P(CH2CH2CN)3. Physical, chemical, and crystallographic criteria have been evaluated for such complexes, from the viewpoints of the properties and reactivity of the squareplanar monomer and the analogous octahedral polymer. Factors such as nearest‐neighbor interactions, nucleation, temperature, doping, polymorphism, and crystal symmetry greatly influence the course of the thermal solid‐state reactions. The reactions per se are characterized by chemical and crystallographic specificity, stereodirectionality, highly anisotropic front motion in single crystals, and reversibility. In a series of preliminary, related experiments, the radiation‐induced polymerization of salts and complexes of β‐acryloxypropionic acid and propiolic acid has been studied; there is a great variation in reactivity among these species. Many of the reactive phases have short contacts between neighboring molecules which would appear to satisfy topochemical criteria for reaction in the solid state.

Criteria of choice of the helix type in crystalline dextran

A reduction in the water content in dextran samples crystallized from water-salt solution results in transformation of the crystal lattice of the polymer-salt complex due to stretching of the polysaccharide chains. A right helix of the 5 2 type has been selected as the most preferential for crystalline dextran on the basis of energy, thermodynamic and crystallographic criteria. It is concluded that maximally stretched helices with the lowest (for the theoretically possible isoenergic conformers) symmetry and a minimal diameter are realized in polysaccharide crystals.

Computer averaging of electron micrographs of 40S ribosomal subunits.

An enhanced lateral view of the 40S ribosomal subunit of HeLa cells has been obtained by computer averaging of single particles visualized in the electron microscope. Application of crystallographic criteria to independent averages shows that the reproducibility of the result is comparable to that obtained for thin, stained protein crystals by conventional Fourier filtration methods.