bluuebunny/crossref_metadata_2025 huggingface dataset:
Dust rotation effects on dust-acoustic surface waves in a Lorentzian plasma
Authors: Lee Myoung-Jae
Published: December 2007

The dispersion relation for a dust-acoustic surface wave is obtained for the semi-bounded dusty plasma containing elongated and rotating charged dust particles. The plasma equilibrium velocity distribution function is taken to be Lorentzian. Dust particles are assumed to be cold. The results show that the phase velocity of the dust-acoustic surface wave propagating at the plasma-vacuum interface is suppressed by the rotation of dust particles in the case that kxλD≲1, where kxλD is the scaled wave number. In addition, the increase of the spectral index κ in the Lorentzian distribution function is found to decrease the phase velocity of the wave. It is interesting to note that the frequency of the phase velocity remains constant as the wave number increases. In contrast, the rotation effect on group velocity of the surface wave diminishes as the wave number approaches either zero or infinity, although the increase of the magnitude of angular frequency reduces the group velocity at all wave numbers. The influence of κ on the group velocity is discussed.
Three-dimensional homogeneous Lorentzian metrics with prescribed Ricci tensor
Authors: Calvaruso Giovanni
Published: December 2007

We introduce a system of partial differential equations, whose solutions permit to determine explicitly locally homogeneous Lorentzian metrics in R3 having the prescribed admissible Ricci tensor. Solutions of this system are presented for all the different models of homogeneous Lorentzian three spaces.
Description of all conformally invariant differential operators, acting on scalar functions
Authors: Nikolov Petko , Valchev Tihomir
Published: December 2007

We present an algorithm to obtain all conformally invariant differential operators acting on scalar functions and taking values on scalar functions as well. There are two cases under consideration: Operators acting on functions defined on the Euclidean space R4 and on the Minkowski space. In both cases each conformally invariant operator of order k is nonlinear and is a function of a finite set of functionally independent invariant operators of order up to k. In particular, the second order independent operators are only three and we give their explicit realization. The applied technique is based on the jet bundle formalism, analysis of the group action, and a dimensional reduction. As a simple illustration of this method we consider the case of differential operators between analytic functions on C which are invariant under the action of the modular group. A power series which generates all functionally independent invariant operators is derived.
Distinct atomic structures of the Ni-Nb metallic glasses formed by ion beam mixing
Authors: Tai K. P. , Wang L. T. , Liu B. X.
Published: December 2007

Four Ni-Nb metallic glasses are obtained by ion beam mixing and their compositions are measured to be Ni77Nb23, Ni55Nb45, Ni31Nb69, and Ni15Nb85, respectively, suggesting that a composition range of 23–85 at. % of Nb is favored for metallic glass formation in the Ni-Nb system. Interestingly, diffraction analyses show that the structure of the Nb-based Ni31Nb69 metallic glass is distinctly different from the structure of the Nb-based Ni15Nb85 metallic glass, as the respective amorphous halos are located at 2θ≈38 and 39 deg. To explore an atomic scale description of the Ni-Nb metallic glasses, an n-body Ni-Nb potential is first constructed with an aid of the ab initio calculations and then applied to perform the molecular dynamics simulation. Simulation results determine not only the intrinsic glass forming range of the Ni-Nb system to be within 20–85 at. % of Nb, but also the exact atomic positions in the Ni-Nb metallic glasses. Through a statistical analysis of the determined atomic positions, a new dominant local packing unit is found in the Ni15Nb85 metallic glass, i.e., an icositetrahedron with a coordination number to be around 14, while in Ni31Nb69 metallic glasses, the dominant local packing unit is an icosahedron with a coordination number to be around 12, which has been reported for the other metallic glasses. In fact, with increasing the irradiation dose, the Ni31Nb69 metallic glasses are formed through an intermediate state of face-centered-cubic-solid solution, whereas the Ni15Nb85 metallic glass is through an intermediate state of body-centered-cubic-solid solution, suggesting that the structures of the constituent metals play an important role in governing the structural characteristics of the resultant metallic glasses.
Field modulation of light transmission through ferrofluid film
Authors: Li Jian , Liu Xiaodong , Lin Yueqiang , Bai Lang , Li Qiang , Chen Xianming , Wang Anrong
Published: December 2007

The intensity of light transmitted through a thin ferrofluid film could be modulated by an applied magnetic field. After the magnet was switched on, the light transmission coefficient decreased first to a minimum value, then raised up to a stable level, forming a valley in the time section. The stronger the applied magnetic field is, or the higher the particle volume fraction is, the lower the valley value of light transmission coefficient. After the magnetic field was switched off, the final stable value of light transmission coefficient was affected by the remanence of magnet. The relaxation process of light transmission through the ferrofluid film could be repeated by continuously switching on and off the magnet, but the highest transmission values and the lowest transmission values can be stable without drift only after many cycles. The behavior of light transmission coefficient should be related with the particle chains’ forming, lengthening, moving, and breaking in the ferrofluid film.
Sign of tunneling magnetoresistance in CrO2-based magnetic tunnel junctions
Authors: Leo Titus , Kaiser Christian , Yang Hyunsoo , Parkin Stuart S. P. , Sperlich Martin , Güntherodt Gernot , Smith David J.
Published: December 2007

Half-metallic ferromagnets are potentially useful as electrodes in magnetic tunnel junctions (MTJs) because of the possibility for 100% spin polarization near the Fermi energy. We report tunneling magnetoresistance (TMR) behavior of MTJs having epitaxial CrO2(100) as one electrode, CoFe as second electrode, and MgO as tunnel barrier, i.e., TiO2(100)∕CrO2(100)∕MgO∕CoFe. When CrO2 is exposed to air, several monolayers of oxide surface decompose and negative MR is observed. Conversely, sample surfaces protected by thin Mg layers show small but positive MR consistent with intrinsic spin polarization. Thus, the TMR sign can be reversed simply by subtle modifications to the CrO2∕MgO interface.
Effects of magnetic field gradient on ion beam current in cylindrical Hall ion source
Authors: Tang Deli , Zhao Jie , Wang Lisheng , Pu Shihao , Cheng Changming , Chu Paul K.
Published: December 2007

The effects of the magnetic gradient on the ion beam current in an end Hall-type ion source with a magnetic mirror field are investigated. In a cylindrical Hall ion source in which a cylindrical magnetic ring other than a regular magnetic pole is shortened and centrally inserted, a mirror magnetic field profile can be formed around the annular anode. A positive-negative variable magnetic gradient is shown experimentally to enhance ionization; the ionization efficiency is substantially affected by the different magnetic gradient. The high ionization results in 60% efficiency in the conversion of discharge current to ion beam current. The experimental results and interpretation of the effects are presented in this paper.
Multilayered coatings with alternate ZrN and TiAlN superlattices
Authors: Li D. J. , Cao M. , Deng X. Y. , Sun X. , Chang W. H. , Lau W. M.
Published: December 2007

Zr N ∕ Ti Al N multilayers with various modulation periods and ratios were grown by ion beam assisted deposition. The nanoscale multilayered modulation was confirmed by Auger electron spectroscopy. All multilayers possess higher hardness than the rule-of-mixture value of monolithic coatings. These properties critically depend on both modulation period and ratio. The multilayer with modulation period of 6.5nm and ratio of 2:3 displays the highest hardness (>30GPa) and critical fracture load (53.3mN). These improvements in properties are likely the result of nanoscale strain optimization as the evolution of layer crystallinity finally reaches the formation of (111) textures in all layers.
Enhancement of diffraction for biosensing applications via Bloch surface waves
Authors: Liscidini Marco , Sipe J. E.
Published: December 2007

We propose a biosensor based on the diffraction of Bloch surface waves (BSWs) in periodic dielectric stacks. Significant enhancement of diffraction efficiency by a biomolecule grating placed on the multilayer is predicted when a BSW is excited through a prism in the Kretschmann configuration. Numerical calculations for BSW in a Si∕SiO2 dielectric stack show an increase of diffraction intensity up to three orders of magnitude with respect to the case of surface plasmon wave enhancement. The mechanism that leads to large field confinement and the absence of absorption losses in the dielectric system make this solution flexible and suitable to different grating periods.
Multiwavelength Sŏlc filters based on χ(2) nonlinear quasiperiodic photonic crystals with Fibonacci sequences
Authors: Kee Chul-Sik , Lee Jongmin , Lee Yeung Lak
Published: December 2007

We demonstrate that a χ(2) nonlinear quasiperiodic photonic crystal can act as a multiwavelength Sŏlc filter. The χ(2) nonlinear quasiperiodic photonic crystal consists of two building blocks A and B, in which each containing a pair of antiparallel poled domains, arranged as a Fibonacci sequence. The filtering wavelengths are analyzed with the Fibonacci sequence parameters such as the quasiperiodic indices and the average lattice parameter. The filtering efficiency can be tuned by the lengths of poled domains.
A stable blue host material for organic light-emitting diodes
Authors: Kim Myeong-Suk , Choi Byoung-Ki , Lee Tae-Woo , Shin Dongwoo , Kang Sung Kee , Kim Jong Min , Tamura Shinichiro , Noh Taeyong
Published: December 2007

We have developed a high performance fluorescent host material, 6-anthracene-9-yl-2,3-di-p-tolyl benzo[b]thiophene (ATB), for blue organic light-emitting diodes. ATB formed a stable amorphous solid state film with a high glass transition temperature (Tg=116°C). The multilayer devices fabricated using ATB as a blue host material showed higher power efficiency (6.4lm∕W at 1000cd∕m2) than the conventional device using 2-tert-butyl-9,10-di(2-naphthyl)anthracene (TBADN) (4.3lm∕W at 1000cd∕m2). The half lifetime of the ATB device (6480h at 1000cd∕m2) was also enhanced compared to the TBADN device (5341h at 1000cd∕m2).
A statistical method for determining intrinsic electronic transport properties of self-assembled alkanethiol monolayer devices
Authors: Song Hyunwook , Lee Takhee , Choi Nak-Jin , Lee Hyoyoung
Published: December 2007

We present a statistical method to investigate the electronic transport of molecular devices. Electrical characterizations are performed with subsequent statistical analysis on 6745 molecular devices with nanometer-scale junction diameter. The comprehensive temperature-variable current-voltage measurements are also performed to elucidate the dominant charge conduction mechanism responsible for intrinsic molecular transport properties. The entity of data acquired represents a reliable basis for statistical analysis, which consequently provides an objective criterion to determine the most probable transport characteristics of molecular devices.
Energetics and metastability of the adenine dication observed in proton-adenine collisions
Authors: Moretto-Capelle Patrick , Le Padellec Arnaud , Brière Guillaume , Massou Sophie , Franceries Frédéric
Published: December 2007

We present here a study that deals with the correlated fragmentation of a doubly charged adenine molecular target induced by a 100keV proton beam. We have elucidated part of the dissociation dynamics for several channels and have obtained the corresponding kinetic energy released values. We have extracted activation energies by combining our experimental data with computations using the ab initio GAMESS code. We have observed metastability patterns against fragmentation, for which we have extracted the temporal mechanism (one or two steps). Subsequently, we have obtained lifetimes in the 100–200ns range. In the simplest case of two-body fragmentation with the emission of mass 28, the determination of transition states and reaction paths has showed that emission of the H–C–N–H fragment is preferred to that of C–N–H2. From the calculated activation barriers and lifetimes, we have deduced an equivalent temperature of the dication that we have compared with the existing models.
Dielectric properties of Ba0.6Sr0.4TiO3 thin films using Pb0.3Sr0.7TiO3 buffer layers
Authors: Wang Sheng-Xiang , Hao Jian-Hua , Wu Zhen-Ping , Wang Dan-Yang , Zhuo Yue , Zhao Xing-Zhong
Published: December 2007

Ba 0.6 Sr 0.4 Ti O 3 (BST) thin films buffered with Pb0.3Sr0.7TiO3 (PST) at each side of the interface contact with electrodes (PST/BST/PST) were deposited on Pt∕Ti∕SiO2∕Si substrates. The dielectric properties of the films were measured using planar Pt∕PST∕BST∕PST∕Pt∕Ti∕SiO2∕Si capacitor structures. The existence of a PST layer between the BST and Pt electrode can improve the dielectric properties of the BST film. The loss tangent of the multilayered films annealed at 750°C was found to be 0.016 at 1MHz and room temperature. The films showed a ∼31.7% tunability of the permittivity at an applied bias field of 0.85MV∕cm. This suggests that such films have potential applications for integrated device applications.
Hysteretic behavior in weakly coupled double-dot transport in the spin blockade regime
Authors: Iñarrea J. , Lopez-Monis C. , MacDonald A. H. , Platero G.
Published: December 2007

Double quantum dot systems in the spin blockade regime exhibit leakage currents that have been attributed to the hyperfine interaction. We model weakly coupled double-dot transport using a rate equation approach which accounts for hyperfine flip-flop transitions. The rate equations allow us to self-consistently obtain the time evolution for electronic charge occupations and for the nuclei polarizations in each dot. We analyze the current in the spin blockade region as a function of magnetic field and observe hysteretic behavior for fields corresponding to the crossing between triplet and singlet states.
Concentration of chemokines in peripheral blood in first trimester of diabetic pregnancy
Authors: WENDER‐OZEGOWSKA E. , MICHAŁOWSKA‐WENDER G. , ZAWIEJSKA A. , PIETRYGA M. , BRAZERT J. , WENDER M.
Published: December 2007

Background. Several types of regulators (i.e. chemokines and metalloproteinases) are considered to play a crucial role in pregnancy by local modulation of the immune system at the level of peripheral leukocytes. The aim of this study was to determine whether changes in chemokines (interferon‐gamma‐inducible protein (IP‐10), monocyte chemotactic peptide‐1 (MCP‐1), cytokines regulated upon activation normal T cell expressed and secreted (RANTES) and matrix metalloproteinase‐9 (MMP‐9)) concentrations in diabetic patients could affect the course of pregnancy. Methods. The study group consisted of 65 diabetics in the first trimester of pregnancy. Some 47 pregnancies were successfully continued to delivery, 18 were terminated with spontaneous miscarriages. Twenty healthy women matched for gestational age served as a control group. Results. Glycated haemoglobin (HbA1C), vascular complications and lipoproteins (cholesterol, HDL‐cholesterol, low density lipoprotein (LDL)‐cholesterol and triglicerides) concentrations in maternal blood did not influence the chemokines concentrations. Lower RANTES level and higher MMP‐9 concentrations were found in diabetic women. MCP‐1 and RANTES levels differed significantly between pregnancies with good and poor perinatal outcome. A logistic regression model revealed that not only duration of diabetes, age of patients, HbA1C and insulin requirements, but also MMP‐9, RANTES, MCP‐1 and LDL‐cholesterol levels seem to be involved in first trimester metabolism. Conclusions. Our results suggest the possible role of chemokines in early pregnancy development, especially in well‐controlled diabetic patients, when hyperglycaemia is unlikely to be the main reason for an unfavourable outcome. Our results show that MCP‐1 and RANTES might serve as predictive factors for an unfavourable outcome in diabetic pregnancy, whereas MMP‐9 seems to be a marker of immunological changes related to mild hyperglycaemia. However, the open question of how the modulation of chemokines concentrations might be applied to prevent miscarriage in diabetic patients remains.
Stage I small cell carcinoma of the endometrium: survival and management options
Authors: KORCUM AYLIN FIDAN , AKSU GAMZE , OZDOGAN MUSTAFA , ERDOGAN GULGUN , TASKIN OMUR
Published: December 2007

Small cell carcinoma (SCC) of the endometrium is a rare but aggressive disease with early systemic involvement. Patient survival is short. To date, no effective treatment protocol has been established. Surgery, radiotherapy, and chemotherapy have been used either alone or in combination. The case of a patient with stage IB endometrial SCC is presented with an overview based on all reported cases of SCC of the endometrium and its treatment with particular reference to stage I cases.
Preinduction cervical ripening with prostaglandin E2 at preterm
Authors: MELAMED NIR , YOGEV YARIV , HADAR ERAN , HOD MOSHE , BEN‐HAROUSH AVI
Published: December 2007

Objective. To evaluate the efficacy of prostaglandin E2 (PGE2) for cervical ripening at preterm and to identify factors predicting ripening failure. Design. A retrospective study of women admitted for preinduction cervical ripening with PGE2 vaginal tablets at preterm (n = 444). PGE2 vaginal tablets were administered at 6–8 h intervals until cervical ripening was achieved (Bishop score ≥7) or ripening failed (Bishop score <7 after administration of 4 PGE2 tablets). Data were compared with a control group of women admitted for preinduction cervical ripening with PGE2 vaginal tablets at term (n = 1,029). A multivariate logistic regression analysis was performed to detect factors predicting ripening failure. Results. Women at preterm required a significantly higher number of PGE2 tablets compared to women at term (2.0±1.1 versus 1.6±0.9, p<0.001). Overall rates of ripening failure and caesarean section due to failed induction were significantly higher in preterm than term gestations (11.4 versus 1.1% and 9.7 versus 0.4%, p <0.001), and were inversely related to gestational age. Nulliparity, lower gestational age at delivery, lack of cervical dilatation, and higher maternal age were significant predictors of ripening failure at preterm. Conclusion. The use of PGE2 for preinduction cervical ripening at preterm may be associated with an increased risk of ripening failure and caesarean section compared with term gestations. This information may be useful when consulting women regarding the available options when premature delivery is necessary.
Ultrasonographic assessment of tape location following tension‐free vaginal tape and transobturator tape procedure
Authors: LONG CHENG‐YU , HSU CHUN‐SHUO , LO TSIA‐SHU , LIU CHENG‐MIN , CHEN YUNG‐HUNG , TSAI EING‐MEI
Published: December 2007

Background. The purpose of this study was to perform an ultrasonographic comparison of tension‐free vaginal tape (TVT) and the TVT‐obturator (TVT‐O) procedure in women with stress urinary incontinence (SUI). Methods. We retrospectively reviewed 159 women with SUI undergoing either TVT (n = 91) or TVT‐O (n = 68). All subjects underwent perineal ultrasonographies, pelvic examination, urinalyses, 1‐h pad tests, multichannel urodynamic studies and a personal interview using the Bristol Female Lower Urinary Tract Symptoms Questionnaire before and 1 year after surgery. Results. At rest or during Valsalva, the middle of the TVT‐O tape localised more distally than the TVT on ultrasound (p<0.01). A higher rate of urethral kinking during straining was observed in the TVT group compared with the TVT‐O group after surgery (86.9 versus 23.9%, p<0.01). Mean operative time was significantly shorter in the TVT‐O group (16.2 versus 28.6 min, p<0.01). The rate of objective cure was comparable for the TVT and TVT‐O groups (94.5 versus 88.2%, p<0.05). However, subjective cure rate was significantly lower for the TVT‐O than the TVT group (82.4 versus 93.4%, p = 0.042). There was no statistical difference between the 2 groups regarding patient characteristics and complication rates. Conclusions. TVT‐O tape results in a less acute angle and localises to a more distal part of the urethra, resulting in less urethral compression and a lower rate of urethral dynamic kinking.
Group B streptococcal carriage in Sweden: a national study on risk factors for mother and infant colonisation
Authors: HÅKANSSON STELLAN , AXEMO PIA , BREMME KATARINA , BRYNGELSSON ANNA‐LENA , WALLIN MARIE CARLSSON , EKSTRÖM CARL‐MAGNUS , GRANLUND MARGARETA , JACOBSSON BO , KÄLLÉN KARIN , SPETZ EVA , TESSIN INGEMAR ,   SWEDISH WORKING GROUP FOR THE PREVENTION OF PERINATAL GROUP B STREPTOCOCCAL INFECTIONS
Published: December 2007

Background. To study group B streptococcus (GBS) colonisation in parturients and infants in relation to obstetric outcome and to define serotypes and antibiotic resistance in GBS isolates acquired. Methods. A population‐based, national cohort of parturients and their infants was investigated. During 1 calendar week in 2005 all women giving birth (n = 1,754) were requested to participate in the study. Results. A total of 1,569 mother/infant pairs with obstetric and bacteriological data were obtained. Maternal carriage rate was 25.4% (95% confidence interval (CI): 23.3–27.6). In GBS‐positive mothers with vaginal delivery and no intrapartum antibiotics, the infant colonisation rate was 68%. Some 30% of infants were colonised after acute caesarean section, and 0% were colonised after an elective procedure. Duration of transport of maternal recto/vaginal swabs of more than 1 day impeded culture sensitivity. Infant mMales were more frequently colonised than females (76.9 versus 59.8%, odds ratio (OR): 2.16; 95% CI: 1.27–3.70), as were infants born after rupture of membranes ≥24 h (p =0.039). Gestational age, birth weight and duration of labor did not significantly influence infant colonisation. Some 30% of parturients with at least one risk factor for neonatal disease received intrapartum antibiotics. The most common GBS serotypes were type III and V. Some 5% of the isolates were resistant to clindamycin and erythromycin, respectively. Conclusions. Maternal GBS prevalence and infant transfer rate were high in Sweden. Males were more frequently colonised than females. The sensitivity of maternal cultures decreased with the duration of sample transport. Clindamycin resistance was scarce. The use of intrapartum antibiotics was limited in parturients with obstetric risk factors for early onset group B streptococcal disease.
Using surface force apparatus, diffusion and velocimetry to measure slip lengths
Authors: Bouzigues C.I , Bocquet L , Charlaix E , Cottin-Bizonne C , Cross B , Joly L , Steinberger A , Ybert C , Tabeling P
Published: December 2007

Determining the slip lengths for liquids flowing close to smooth walls is challenging. The reason lies in the fact that the scales that must be addressed range between a few and hundreds of nanometres. Several techniques have been used over the last few years. Here, we consider three of them based on surface force apparatus, diffusion and velocimetry, respectively. The descriptions offered here incorporate recent instrumental progress made in the field.
Friction between solids
Authors: Harrison Judith A , Gao Guangtu , Schall J.David , Knippenberg M. Todd , Mikulski Paul T
Published: December 2007

The theoretical examination of the friction between solids is discussed with a focus on self-assembled monolayers, carbon-containing materials and antiwear additives. Important findings are illustrated by describing examples where simulations have complemented experimental work by providing a deeper understanding of the molecular origins of friction. Most of the work discussed herein makes use of classical molecular dynamics (MD) simulations. Of course, classical MD is not the only theoretical tool available to study friction. In view of that, a brief review of the early models of friction is also given. It should be noted that some topics related to the friction between solids, i.e. theory of electronic friction, are not discussed here but will be discussed in a subsequent review.
The interpretation and analysis of diffuse scattering using Monte Carlo simulation methods
Authors: Welberry T. R. , Goossens D. J.
Published: December 2007

Studies of diffuse scattering had a prominent place in the first issue ofActa Crystallographica60 years ago at a time when conventional crystallography (determination of the average structure from Bragg peaks) was in its infancy. Since that time, conventional crystallography has developed enormously while diffuse-scattering analysis has seemingly lagged well behind. The paper highlights some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering and plots the progress that has been made. With the advent of the latest X-ray and neutron sources, area detectors and the ever-increasing power of computers, most disorder problems are now tractable. Two recent contrasting examples are described which highlight what can be achieved by current methods.
A short history ofSHELX
Authors: Sheldrick George M.
Published: December 2007

An account is given of the development of theSHELXsystem of computer programs fromSHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation inSHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long.SHELXLis the most widely used program for small-molecule refinement andSHELXSandSHELXDare often employed for structure solution despite the availability of objectively superior programs.SHELXLalso finds a niche for the refinement of macromolecules against high-resolution or twinned data;SHELXPROacts as an interface for macromolecular applications.SHELXC,SHELXDandSHELXEare proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines forhigh-throughputphasing. This paper could serve as a general literature citation when one or more of the open-sourceSHELXprograms (and the Bruker AXS versionSHELXTL) are employed in the course of a crystal-structure determination.
Does mathematical crystallography still have a role in the XXI century?
Authors: Nespolo Massimo
Published: December 2007

Mathematical crystallography is the branch of crystallography dealing specifically with the fundamental properties of symmetry and periodicity of crystals, topological properties of crystal structures, twins, modular and modulated structures, polytypes and OD structures, as well as the symmetry aspects of phase transitions and physical properties of crystals. Mathematical crystallography has had its most evident success with the development of the theory of space groups at the end of the XIX century; since then, it has greatly enlarged its applications, but crystallographers are not always familiar with the developments that followed, partly because the applications sometimes require some additional background that the structural crystallographer does not always possess (as is the case, for example, in graph theory). The knowledge offered by mathematical crystallography is at present only partly mirrored inInternational Tables for Crystallographyand is sometimes still enshrined in more specialist texts and publications. To cover this communication gap is one of the tasks of the IUCr Commission on Mathematical and Theoretical Crystallography (MaThCryst).
The charge flipping algorithm
Authors: Oszlányi Gábor , Sütő András
Published: December 2007

This paper summarizes the current state of charge flipping, a recently developed algorithm ofab initiostructure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.
On wine, chirality and crystallography
Authors: Derewenda Zygmunt S.
Published: December 2007

As the first centennial of X-ray diffraction is inevitably drawing closer, it is tempting to reflect on the impact that this fascinating discipline has had on natural sciences and how it has changed the world we live in. Also, next year is the 160th anniversary of the fateful April afternoon when Louis Pasteur separated D- from L-tartrate crystals, an event that many science historians recognize as the birth of stereochemistry, and the first step that the barely nascent field of crystallography took on the road to elucidate a fundamental phenomenon of chemistry and biology – chirality. Many great minds – Pasteur, Van 't Hoff, Fischer, Lord Kelvin, the Braggs, Astbury and Bijvoet, to mention just a few – contributed along the way. But one central inanimate character was there at all times – an inconspicuous somewhat obscure organic compound found in wine: tartaric acid. This is the story of its contribution to science.
High-pressure crystallography
Authors: Katrusiak Andrzej
Published: December 2007

Since the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure–property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.
An easy non-invasive X-ray diffraction method to determine the composition of Na-pyroxenes from high-density `greenstone' implements
Authors: Giustetto Roberto , Chiari Giacomo , Compagnoni Roberto
Published: December 2007

A large number of polished stone implements from Palaeolithic to Bronze Age sites of Northern Italy and Southern France are made of high-pressure (HP) metamorphic rocks (eclogite and related rocks), mainly consisting of Na-pyroxene (jadeite to omphacite) from the metamorphic belt of the Western Alps. The standard archaeometric study of prehistoric stone implements follows a procedure that is invasive, expensive and time-consuming. Since Na-pyroxenes may show a large compositional range, a thorough study of the variations affecting thedhklvalues, obtained by X-ray diffraction, of three selected reflections as a function of different chemical composition was carried out, in order to determine the chemistry of Na-pyroxene isomorphic mixtures and roughly evaluate their relative amounts. These reflections (\bar221, 310, 002) are sharp, intense and sensitive to the variation of pyroxene chemical composition. Using suchdhklvalues measured on pyroxenes of known chemistry, a Ca-pyroxene(Di)–jadeite(Jd)–aegirine(Ae) compositional diagram was constructed, from which the composition of an unknown pyroxene can be estimated within an error of about 5%. When the size of the object is relatively small and a flat polished surface is present, the proposed analytical procedure becomes totally non-invasive. The data obtained shed light on the provenance sources of such implements and the prehistoric trade routes.
Structure determination from powder diffraction data
Authors: David W. I. F. , Shankland K.
Published: December 2007

Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.
The MEM/Rietveld method with nano-applications – accurate charge-density studies of nano-structured materials by synchrotron-radiation powder diffraction
Authors: Takata Masaki
Published: December 2007

Structural studies of materials with nano-sized spaces, called nano-structured materials, have been carried out by high-resolution powder diffraction. Our developed analytical method, which is the combination of the maximum-entropy method (MEM) and Rietveld refinement, the so-called MEM/Rietveld method, has been successfully applied to the analysis of synchrotron-radiation (SR) powder diffraction data measured at SPring-8, a third-generation SR light source. In this article, structural studies of nano-porous coordination polymers and endohedral metallofullerenes are presented with the advanced technique of SR powder experiment. The structure of the adsorbed guest molecule in the coordination polymer and encapsulated atoms in the fullerene cage are clearly revealed by the MEM charge density. The methodology of MEM/Rietveld analysis is also presented.
Characterizing the Mycobacterium tuberculosis Rv2707 protein and determining its sequences which specifically bind to two human cell lines
Authors: Chapeton‐Montes Julie A. , Plaza David F. , Curtidor Hernando , Forero Martha , Vanegas Magnolia , Patarroyo Manuel E. , Patarroyo Manuel A.
Published: December 2007

The Rv2707 gene encoding a putative alanine‐ and leucine‐rich protein was found to be present in all Mycobacterium tuberculosis complex strains (by PCR) and its transcription was shown by RT‐PCR in all but M. bovis and M. microti. Antibodies raised against Rv2707 peptides specifically recognized the native protein by Western blot and were able to locate this protein on the M. tuberculosis membrane by immunoelectron microscopy. A549 and U937 cells lines were used in binding assays involving synthetic peptides covering the whole Rv2707 protein. High A549 cell‐binding peptide 16083 (281QEEWPAPATHAHRLGNWLKAY300) was identified. Peptides 16072 (61LFGPDTLPAIEKSALSTAHSY80) and 16084 (301RIGVGTTTYSSTAQHSAVAA320) presented high specific binding to both A549 and U937 cells. Cross‐linking assays revealed that peptide 16084 specifically bound to a 40‐kDa and a 50‐kDa U937 cell membrane protein. High activity binding peptides (HABPs) 16083 and 16084 were able to inhibit M. tuberculosis invasion of A549 cells. Our results suggest that these sequences could be part of the binding sites used by the bacillus for interacting with target cells, and thus represent good candidates to be tested in a future subunit‐based, multiepitope, antituberculosis vaccine.
LTHREADER: Prediction of extracellular ligand–receptor interactions in cytokines using localized threading
Authors: Pulim Vinay , Bienkowska Jadwiga , Berger Bonnie
Published: December 2007

Identification of extracellular ligand–receptor interactions is important for drug design and the treatment of diseases. Difficulties in detecting these interactions using high‐throughput experimental techniques motivate the development of computational prediction methods. We propose a novel threading algorithm, LTHREADER, which generates accurate local sequence‐structure interface alignments and integrates various statistical scores and experimental binding data to predict interactions within ligand–receptor families. LTHREADER uses a profile of secondary structure and solvent accessibility predictions with residue contact maps to guide and constrain alignments. Using a decision tree classifier and low‐throughput experimental data for training, it combines information inferred from statistical interaction potentials, energy functions, correlated mutations, and conserved residue pairs to predict interactions. We apply our method to cytokines, which play a central role in the development of many diseases including cancer and inflammatory and autoimmune disorders. We tested our approach on two representative families from different structural classes (all‐α and all‐β proteins) of cytokines. In comparison with the state‐of‐the‐art threader RAPTOR, LTHREADER generates on average 20% more accurate alignments of interacting residues. Furthermore, in cross‐validation tests, LTHREADER correctly predicts experimentally confirmed interactions for a common binding mode within the 4‐helical long‐chain cytokine family with 75% sensitivity and 86% specificity with 40% gain in sensitivity compared to RAPTOR. For the TNF‐like family our method achieves 70% sensitivity with 55% specificity with 70% gain in sensitivity. LTHREADER combines information from multiple complex templates when such data are available. When only one solved structure is available, a localized PSI‐BLAST approach also outperforms standard threading methods with 25%–50% improvements in sensitivity.
Identification of transient hub proteins and the possible structural basis for their multiple interactions
Authors: Higurashi Miho , Ishida Takashi , Kinoshita Kengo
Published: December 2007

Proteins that can interact with multiple partners play central roles in the network of protein–protein interactions. They are called hub proteins, and recently it was suggested that an abundance of intrinsically disordered regions on their surfaces facilitates their binding to multiple partners. However, in those studies, the hub proteins were identified as proteins with multiple partners, regardless of whether the interactions were transient or permanent. As a result, a certain number of hub proteins are subunits of stable multi‐subunit proteins, such as supramolecules. It is well known that stable complexes and transient complexes have different structural features, and thus the statistics based on the current definition of hub proteins will hide the true nature of hub proteins. Therefore, in this paper, we first describe a new approach to identify proteins with multiple partners dynamically, using the Protein Data Bank, and then we performed statistical analyses of the structural features of these proteins. We refer to the proteins as transient hub proteins or sociable proteins, to clarify the difference with hub proteins. As a result, we found that the main difference between sociable and nonsociable proteins is not the abundance of disordered regions, in contrast to the previous studies, but rather the structural flexibility of the entire protein. We also found greater predominance of charged and polar residues in sociable proteins than previously reported.
Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate
Authors: Stump Matthew R. , Gloss Lisa M.
Published: December 2007

Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild‐type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB‐3A), was mutated to Tyr and Trp. Two Tyr‐to‐Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central α‐helix of the histone fold. Far‐UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two‐state, reversible processes, with ΔG°(H2O) values within 1 kcal/mol of the wild‐type dimers. The hPyA1 Trp variants fold by two‐state kinetic mechanisms like wild‐type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr‐32 and Tyr‐36) contribute to transition state structure. Like wild‐type hMfB, M35Y and M35W hMfB fold by a three‐state mechanism, with a stopped‐flow CD burst‐phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1.
Ultra‐high Magnification Endoscopic Observation of Carcinoma in situ of the Esophagus
Authors: INOUE Haruhiro , HONDA Tohru , NAGAI Kagami , KAWANO Tatsuyuki , YOSHINO Kunihide , TAKESHITA Kimiya , ENDO Mitsuo
Published: December 2007

Abstract: Super‐zooming observation of carcinoma in situ of the esophagus was achieved utilizing an ultra‐high magnification endoscope which has a 150X magnification capacity. Superficial flat and slightly depressed lesions (O‐llb and O‐llc according to the Japanese classification of esophageal cancer), usually observed as a well‐demarcated reddish patch, were revealed to be a composite of scattered red dots and a pinkish homogeneous background. Those red dots were disclosed to be intrapapillary capillary loop changes such as dilatation, meandering and caliber irregularities. These changes were never observed in normal mucosa or in the setting of esophagitis. These characteristic findings were confirmed histologically in the resected specimen.
An Improved Endoscopic Variceal Ligator for Esophagogastric Varix
Authors: SHIBUYA Susumu , KAWASHIMA Takahiko , CHIKAMORI Fumio , EDA Hiroyuki , AOYAGI Hiroyuki , TAKASE Yasuhiro , NAKAHARA Akira , FUKUTOMI Hisayuki , TANAKA Naomi
Published: December 2007

Abstract: We recently reported a 16.0 mm in length new type of instrument with an inner cylinder of 10.3 mm for endoscopic variceal ligation (EVL). This device is capable of shooting three elastic O bands consecutively in rapid succession without removing the endoscope. The aspirated volume of variceal tissue with the new instrument is larger than that obtained with the Stiegmann ligator. We performed EVL in 16 cases with esophageal varices and seven with solitary gastric varices. EVL was performed for prophylaxis in all cases. The esophageal varices disappeared in all 16 cases after ulcer formation. The procedure was performed once in 14 cases and twice in the remaining two. Three patients died of hepatic failure during the follow‐up period which ranged from four to 16 months. Six and 12 month cumulative recurrence rates were 30% and 48%, respectively. All gastric varices disappeared after a single EVL session. There was one variceal recurrence during the follow‐up period. Computed tomography and/ or arterioportography performed previously had shown patent gastro‐renal shunt in five cases. No changes in the shunts were observed after treatment. No serious complications attributable to EVL were encountered in this series. Therefore, this method is potentially useful for the treatment of not only esophageal varices but also gastric varices.
Absorbable and Sell‐expanding Esophageal Stent
Authors: INOUE Haruhiro , HIROSE Tadatsugu , NAGAI Kagami , KAWANO Tatsuyuki , YOSHINO Kunihide , ENDO Mitsuo
Published: December 2007

Abstract: A flexible self‐expanding esophageal stent, made entirely of absorbable materials, was recently developed by the authors. The new stent consists of two components: a rolled vicryl sheet (Vicryl woven mesh, Ethicon) which has a 20‐mm outer diameter, and a PDS string (PDS II, 1 ‐0. Ethicon) which runs spirally around the rolled sheet. The stent is almost equal in flexibility to the Ultraflex (Microvasive, USA) and its expanding force exceeds that of the Ultraflex. This stent was uneventfully placed in the porcine esophagus and then fully opened. This absorbable stent, incubated in 37°C saline, showed a gradual diminution of its expanding force over a period of more than two weeks. We conclude that this novel absorbable stent, which has characteristics comparable to those of a metallic stent, as well as certain other advantages, is applicable to clinical cases.
Early Gastric Cancer as a Possible Cause of Cauda Equina Syndrome and Disseminated Intravascular Coagulation
Authors: WEI Shu‐Chen , WONG Jau‐Min , CHEN Chi‐Long , CHENG Ann‐Lii , WANG Cheng‐Yi , WANG Teh‐Hong
Published: December 2007

Abstract: Early gastric cancer is an important gastric malignancy which is defined as adenocarcinoma confined to the mucosa or submucosa of the stomach with or without simultaneous metastases involving regional lymph nodes. The prognosis of early gastric cancer is generally good with a 5‐year survival rate of about 95%. Distant metastases and disseminated intravascular coagulation (DIC) usually occur in the advanced stage of gastric cancer but are relatively rare in early gastric cancer. Cauda equina syndrome has never before been reported as the initial presentation of gastric cancer, and to our knowledge, up to 1993, only 17 cases of early gastric cancer with synchronous liver metastases had been reported. Bone metastases with DIC and adrenal metastasis are both rare in early gastric cancer. Herein, we present a case of early gastric cancer with an initial presentation including cauda equina syndrome and DIC. Synchronous hepatic, adrenal gland, pulmonary, bone and bone marrow metastases were found two days after admission. The patient had a fulminant clinical course and died 45 days after the diagnosis. A small focus (0.8 × 0.5cm) of poorly differentiated adenocarcinoma located in the mucosa and submucosa at the gastric lower body with extensive lymphatic permeation around the primary focus and duodenum were noted at autopsy. Cancers with an unknown primary accounted for 4.9% of cancers presenting with disseminated intravascular coagulation. Our experience disclosed that early gastric cancer is a potential cause of cauda equina syndrome and disseminated intravascular coagulation.