Solution of organic crystal structures from powder diffraction by combining simulated annealing and direct methods

Theab initiocrystal structure solution from powder diffraction data can be attemptedviadirect methods. If heavy atoms are present, they are usually correctly located; then some crystal chemical information can be exploited to complete the partial structure model. Organic structures are more resistant to direct methods; as an alternative, their molecular geometry is used as prior information for Monte Carlo methods. In this paper, a new procedure is described which combines the information contained in the electron density map provided by direct methods with a Monte Carlo method which uses simulated annealing as a minimization algorithm. A figure of merit has been designed based on the agreement between the experimental and calculated profiles, and on the positions of the peaks in the electron density map. The procedure is completely automatic and has been included inEXPO; its performance has been validated and tested for a set of known molecular structures.

Completion of crystal structure by powder diffraction data: a new method for locating atoms with polyhedral coordination

Ab initiocrystal structure solutionviapowder diffraction data is often incomplete: frequently, the heavy atoms are correctly located but the light-atom positions are usually unreliable. The recently developed procedurePOLPO[Altomareet al.(2000).J. Appl. Cryst.33, 1305–1310], implemented in theEXPOprogram [Altomareet al.(1999).J. Appl. Cryst.32, 339–340], aims at completing a partial structure model provided by direct methods by exploiting the prior information on the polyhedral coordination of the located atoms (tetrahedral or octahedral) and their connectivity. ThePOLPOprocedure requires that all the cations are correctly labelled and rightly located. This condition does not always occur, particularly when the data quality is poor. A new method is described which is able to locate missing cations and surrounding anions when the cation coordination is tetrahedral or octahedral. The procedure has been successfully checked on different test structures.

Angiogenesis and hereditary hemorrhagic telangiectasia. Rendu-Osler-Weber disease

To date much of the recent work on pathological angiogenesis has focused on inflammatory diseases, diabetes and cancer in particular. Hereditary hemorrhagic telangiectasia or Rendu-Osler-Weber disease provides an example of the genetic disorder of angiogenesis in which a multisystemic angiodysplasia is responsible for severe hemorrhage. The disease pathogenesis is partially explained by a defect in the TGF-beta signaling system, although in more recent works a possible role of other vascular growth factors has been proposed. This paper provides a model of an aberrant angiogenesis in which multiple vascular growth factors could be involved in a diffuse angiodysplasia.

Real-space technique applied to crystal structure determination from powder data

Real-space techniques used for phase extension and refinement in the modern direct procedures forab initiocrystal structure solution of proteins have been optimized for application to powder diffraction data. The new process has been implemented in a modified version ofEXPO[Altomareet al.(1999).J.Appl.Cryst.32, 339–340]. The method is able to supply a structural model that is more complete than that provided by the standardEXPOprogram. The model is then refinedviaa diagonal least-squares procedure, but only when the ratio of the number of observations to the number of structure parameters to be refined is larger than a given threshold.

Peak labelling in electron density maps from powder data: the use of crystal chemical information

Direct methods applied to powder diffraction data often provide electron density maps of which the quality is usually affected by systematic and/or random phase errors, by amplitude truncation effects in the series representation of the electron density,etc. The frequent incorrect labelling of the peaks can strongly affect the efficiency of the procedures used for crystal structure refinement. For example, the success of alternative techniques, such asPOLPO[Altomareet al. (2000).J. Appl. Cryst.33, 1305–1310], requires that all the heavy atoms be positioned and exactly labelled.

A random procedure for the decomposition of a powder pattern inEXPO

The main obstacle toab initiocrystal structure solution by powder data is the lack of accuracy in the single Bragg integrated intensity estimates. The two-stage method proves powerful for solving crystal structures from powder data: in the first stage, the integrated intensities and, consequently, the structure-factor moduli, are extracted from the pattern for each reflection; in the second stage, direct methods may be applied to estimate the phases of the structure factors. The greater the accuracy of the integrated intensities, the more efficient the phasing procedure. A new procedure is described, aiming at overcoming the tendency of the Le Bail algorithm [Le Bailet al.(1988).Mater. Res. Bull.23, 447–452] to equipartition the intensities of strongly overlapping reflections. It proves to be efficient for lowering the phase error in the phasing process. The procedure has been implemented in theEXPOprogram [Altomareet al.(1999).J. Appl. Cryst.32, 339–340].

Simultaneous monitoring of glucose and lactate by an interference and cross-talk free dual electrode amperometric biosensor based on electropolymerized thin films

An interference and cross-talk free dual electrode amperometric biosensor integrated with a microdialysis sampling system is described, for simultaneous monitoring of glucose and lactate by flow injection analysis. The biosensor is based on a conventional thin layer flow-through cell equipped with a Pt dual electrode (parallel configuration). Each Pt disk was modified by a composite bilayer consisting of an electrosynthesised overoxidized polypyrrole (PPYox) anti-interference membrane covered by an enzyme entrapping gel, obtained by glutaraldehyde co-crosslinking of glucose oxidase or lactate oxidase with bovine serum albumin. The advantages of covalent immobilization techniques were coupled with the excellent interference-rejection capabilities of PPYox. Ascorbate, cysteine, urate and paracetamol produced lactate or glucose bias in the low micromolar range; their responses were, however, completely suppressed when the sample was injected through the microdialysis unit. Under these operational conditions the flow injection responses for glucose and lactate were linear up to 100 and 20 mM with typical sensitivities of 9.9 (+/- 0.1) and 7.2 (+/- 0.1) nA/mM. respectively. The shelf-lifetime of the biosensor was at least 2 months. The potential of the described biosensor was demonstrated by the simultaneous determination of lactate and glucose in untreated tomato juice samples; results were in good agreement with those of a reference method.

A model of social stress in dominant mice: effects on sociosexual behaviour

The possibility of socially stressing the dominant/aggressive member of a pair of male mice is tested. Male mice (NMRI outbreed strain) were housed in pairs to assess dominant and subordinate roles by agonistic interactions and urine-marking test. Social stress for dominant males consisted in 30 min/day of exposure to their subordinate partner interacting with a female in the adjacent compartment of the cage, for 9 days. Results showed that dominance status was maintained. Behavioural observations indicated that neither the subordinates nor the dominant males habituated to this experimental procedure. At the end of the chronic stress, dominant animals were given the opportunity to interact for 30 min with a female in their compartment. Results indicated that stressed dominants showed impairment in their sexual behaviour and were more oriented towards the physical environment in comparison with control dominants. The behavioural response to apomorphine (0.25 mg/kg) indicated an alteration of the dopaminergic functioning in socially stressed dominant mice. This study suggests that the characteristics of the stressor and the effects of the chronic social stress could be different, according to male social status.

Flow injection analysis of L-lactate in milk and yoghurt by on-line microdialysis and amperometric detection at a disposable biosensor

A disposable lactate biosensor able to operate in flow injection analysis is described and characterized. The biosensing layer, obtained by glutaraldehyde co-crosslinking of lactate oxidase with bovine serum albumin, was cast on an underlying electropolymerized layer of overoxidized polypyrrole. The resulting biosensor was interference-free and showed a K'M value of 2.4 mmol l-1 and a maximum current density of 440 microA cm-2. When integrated in a flow injection analysis system, a sensitivity of 300 +/- 10 nA mmol-1 l, a linear response up to 1 mmol l-1 and detection limits in the low micromolar range were obtained. The introduction of a microdialysis membrane-based sampler reduced the sensitivity to 7.9 +/- 0.2 nA mmol-1 l and extended the linear range up to 50 mmol l-1 lactate. The anti-interference characteristics of the biosensor permitted lactate determination in untreated milk and diluted yoghurt samples.

Quanto: a Rietveld program for quantitative phase analysis of polycrystalline mixtures

Quantitative determination of phase abundance in a multicomponent polycrystalline mixture is a basic goal in materials characterization. Because of several advantages compared with traditional techniques, the Rietveld method has been increasingly applied to this task. Further progress in this direction would be to carry out the analysis automatically. The new Rietveld packageQuantois devoted to the automatic estimation of the weight fraction of each crystalline phase in a mixture. The amorphous content can be estimated by means of the internal-standard method. Corrections for preferred orientation and microabsorption effects are available. A user-friendly graphical interface facilitates interaction. A data bank including several organic and inorganic phases is supplied with the program.

The effect of the eradication of Helicobacter pylori infection on hemorrhage because of duodenal ulcer

The cost of a recurrently bleeding duodenal ulcer (DU) is very high, both from a human and an economic point-of-view. Helicobacter pylori infection plays an important role in the pathogenesis of DU disease and its complications, such as bleeding. Cure of H. pylori infection is recommended in patients with DU and its complications, although in the latter case, the most efficient management is not yet a defined issue. In particular, acid secretion inhibitors may not contribute to long-term cure. Our aims were to ascertain whether the recurrence of bleeding because of DU could be prevented by H. pylori eradication and whether long-term inhibition of gastric acid output is needed to prevent recurrence. Eighty-four patients (65 men; mean age, 55.1 years), who had bled because of recurrent DU, were followed after the cure of H. pylori infection. None of the patients were on therapy with nonsteroidal antiinflammatory drugs. Successful cure of H. pylori was determined by gastroscopy, histology, and serology performed at 3, 6, 12, 24, and 48 months after the eradication treatment. A 13C urea breath test was performed when the results of serology were unclear and also at recurrence of DU or bleeding. After the antibiotic treatment, 46 patients stopped all medications, whereas 38 continued long-term therapy with histamine type 2 receptor antagonists. During a mean follow-up period of 47.2 months (range, 37-65 months), recurrence of DU at endoscopy was observed in three patients in each group (p = 0.56), but none bled again. We conclude that H. pylori eradication prevents DU recurrence and rebleeding, that reinfection rate by H. pylori after cure was nil at 4 years, and that long-term inhibition of acid secretion may not improve outcome after cure of H. pylori, even in patients whose DU was complicated by hemorrhage.

Completion of crystal structures from powder data: the use of the coordination polyhedra

Direct methods applied to powder diffraction data often provide well located heavy atoms and unreliable light-atom positions. The completion of the crystal structure is then not always straightforward and may require a considerable amount of user intervention. The heavy-atom connectivity provided by the trial solution may be used to guess the nature of the coordination polyhedra. A Monte Carlo procedure is described which, in the absence of a well defined structural model, is able to locate the light atoms correctly under the restraints of the experimental heavy-atom connectivity model. The correctness of the final model is assessed by criteria based on the agreement between the whole experimental diffraction pattern and the calculated one. The procedure requires little CPU computing time and has been implemented as a routine ofEXPO[Altomareet al.(1999).J. Appl. Cryst.32, 339–340]. The method has proved to be sufficiently robust against the distortion of the coordination polyhedra and has been successfully applied to some test structures.

A video-polygraphic analysis of the cataplectic attack

OBJECTIVES AND METHODS

To perform a video-polygraphic analysis of 11 cataplectic attacks in a 39-year-old narcoleptic patient, correlating clinical manifestations with polygraphic findings. Polygraphic recordings monitored EEG, EMG activity from several cranial, trunk, upper and lower limbs muscles, eye movements, EKG, thoracic respiration.

RESULTS

Eleven attacks were recorded, all of them lasting less than 1 min and ending with the fall of the patient to the ground. We identified, based on the video-polygraphic analysis of the episodes, 3 phases: initial phase, characterized essentially by arrest of eye movements and phasic, massive, inhibitory muscular events; falling phase, characterized by a rhythmic pattern of suppressions and enhancements of muscular activity, leading to the fall; atonic phase, characterized by complete muscle atonia. Six episodes out of 11 were associated with bradycardia, that was maximal during the atonic phase.

CONCLUSIONS

Analysis of the muscular phenomena that characterize cataplectic attacks in a standing patient suggests that the cataplectic fall occurs with a pattern that might result from the interaction between neuronal networks mediating muscular atonia of REM sleep and neural structures subserving postural control.

New techniques for indexing:N-TREORinEXPO

Indexing of a powder diffraction pattern is still a critical point in procedures aiming at solving crystal structures from powder data. New code has been associated to the programTREOR90 in order to define an efficient peak search procedure, to modify the crystallographic decisions coded intoTREOR90 to make it more exhaustive, to refine the selected unit cell automatically, and to make the entire procedure user friendly,viaa graphical interface. The new program, calledN-TREOR, has been integrated into the packageEXPOto create a suite of programs able to provide a structural model from the analysis of the experimental pattern.N-TREORis also available as a stand-alone program.

[The emergency treatment of aneurysms of the supra-aortic trunks and of the internal carotid]

In the last 10 years, four patients with aneurysms of the supraaortic trunks and the internal carotid artery have been operated in emergency at Department of Vascular Surgery of University of Bari. The first case was a mycotic aneurysm of the carotid bifurcation, the second an aneurysm of internal carotid artery interesting the retropharynx, the third a post-operatory pseudoaneurysm of common carotid in a patient affected by Takayasu's disease and the last an atherosclerotic aneurysm of the innominate artery. Clinical picture suggested an immediate surgical treatment in all patients. Different procedure were used depending on size and localization of each lesion. Results in all cases have been satisfactory. The aneurysms of supraaortic trunks and of internal carotid artery are very rare; therefore when clinical picture is dramatic or quickly worsening, emergency treatment is mandatory in order to reduce mortality risk and minimize complications.

Synthesis, X-ray powder structure, and magnetic properties of the new, weak ferromagnet iron(II) phenylphosphonate

A new molecule-based weak ferromagnet of formula Fe[C6H5PO3].H2O was synthesized. It was characterized by thermogravimetric analysis and UV-visible and infrared spectroscopy, and the magnetic properties were studied using a superconducting quantum interference device magnetometer. The crystal structure of the compound was determined "ab initio" from X-ray powder diffraction data and refined by the Rietveld method. The crystals of Fe[C6H5PO3].H2O are orthorhombic, space group Pmn2(1), with a = 5.668(8) A, b = 14.453(2) A, c = 4.893(7) A, and Z = 2. The title compound is isostructural with the previously reported lamellar M[C6H5PO3].H2O, M = Mn(II), Zn(II), and Cd(II). The inorganic layers are made of Fe(II) ions octahedrally coordinated by five phosphonate oxygen atoms and one from oxygen of the water molecule. These layers are then separated by bilayers of the phenyl groups, and van der Waals contacts are established between them. The refinement has shown that the phenyl rings are disordered in the lattice. The oxidation state of the metal ion is +2, and the electronic configuration is d6 (S = 2) high-spin, as determined from dc magnetic susceptibility measurements from 150 K to room temperature. Below 100 K, the magnetic moment of Fe[C6H5PO3].H2O rises rapidly to a maximum at TN = 21.5 K, and then it decreases again. The peak at TN is associated with the 3D antiferromagnetic long-range ordering. Below the critical temperature, the title compound behaves as a "weak" ferromagnet, which represents the third type of magnetic materials characterized by having a finite zero-field magnetization, ferromagnets and ferrimagnets being the other two types. The large coercive field (i.e., 6400 G) observed in the hysteresis loop at T = 10 K is rare in molecule-based materials; it can be ascribed to a pronounced spin-orbit coupling for the 5T2g ground state of the Fe(II) ion in the octahedral environment.

Solving crystal structures from powder data. V. Located molecular fragment and powder-pattern decomposition

In direct procedures for crystal structure solution from powder data, information on the location and orientation of a molecular fragment may readily become available. Such information may be used retrospectively to improve the powder-pattern decomposition, with favourable effects on the phasing process. A method is described by which accurate estimation of a large number of structure-factor moduli is possible by exploiting the prior partial structural information.

Takayasu's arteritis: a cell-mediated large-vessel vasculitis

Takayasu's arteritis is an idiopathic, systemic inflammatory disease, typically involving the aorta and its main branches. Cell-mediated autoimmunity has been strongly implicated in its pathogenesis. Early or active-stage pathology consists of continuous or patchy granulomatous inflammation, which progresses to intimal and adventitial fibrosis and scarring of the media. Multiple focal or segmental stenoses result and aneurysms may occasionally occur. Clinical presentation is heterogeneous, ranging from asymptomatic to catastrophic. In some patients, constitutional signs and symptoms indicating a systemic inflammatory response are observed, usually in the early stages. Specific features reflect arterial involvement, and result from end-organ or limb ischemia; they include vascular, neurological, cardiac, and pulmonary manifestations. The course of Takayasu's arteritis usually extends for many years with varying degrees of activity. Takayasu's arteritis has a worldwide distribution, with the greatest prevalence in eastern countries. Women of reproductive age are preferentially affected, but the illness is being recognized with increasing frequency in males. Variable phenotypes are recently emerging in different ethnic groups. Diagnosis is based on clinical features and vascular imaging studies that document typical patterns of stenoses or aneurysms of the aorta and its primary branches. Assessment of the activity of Takayasu's arteritis is imprecise, in that clinical features and acute-phase reactants do not accurately reflect active blood vessel inflammation. High-dose corticosteroids alone or a cytotoxic agent in addition to a corticosteroid may be effective in treating active disease. Critical lesions may require correction by surgery or interventional radiology.

EXPO: a program for full powder pattern decomposition and crystal structure solution

EXPOis the integration of two programs,EXTRAandSIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition.EXPOalso allows preliminary cycles of Rietveld refinement.