bluuebunny/crossref_metadata_2025 huggingface dataset:
Shot noise in the graphene-based double-barrier structures
Authors: Zhu Rui , Guo Yong
Published: December 2007

The authors investigated shot noise properties in the graphene-based double barriers. The shot noise with the Fano factor equal to 1∕3 is found to occur at all conductance minimums including the Dirac point, which is a combined result of Klein tunneling, resonant tunneling, and quasiparticle chirality. The similarity in the shot noise suppression between graphene and diffusive metals is interpreted by the collective contribution from noiseless open channels and Poissonian-noise closed ones in the transmission spectra. It is also found that the Fano factor shows abrupt increase when the energy gap in the dispersion is larger than 1meV.
Quantum-dot thermometry
Authors: Hoffmann E. A. , Nakpathomkun N. , Persson A. I. , Linke H. , Nilsson H. A. , Samuelson L.
Published: December 2007

We present a method for the measurement of a temperature differential across a single quantum dot that has transmission resonances that are separated in energy by much more than the thermal energy. We determine numerically that the method is accurate to within a few percent across a wide range of parameters. The proposed method measures the temperature of the electrons that enter the quantum dot and will be useful in experiments that aim to test theory which predicts that quantum dots are highly efficient thermoelectrics.
Trains of envelope solitons in nonlinear left-handed transmission line media
Authors: Kozyrev Alexander B. , van der Weide Daniel W.
Published: December 2007

We report the experimental observation of the self-generated stationary trains of envelope solitons in the left-handed nonlinear transmission line metamaterials. The trains of both bright or dark solitons, as well as switching between them, have been experimentally demonstrated in short transmission lines exhibiting strong and fast nonlinearity and strong anomalous dispersion, when pumped with a continuous wave signal.
Planar focusing antenna design by using coordinate transformation technology
Authors: Kong Fanmin , Wu Bae-Ian , Kong Jin Au , Huangfu Jiangtao , Xi Sheng , Chen Hongsheng
Published: December 2007

The coordinate transformation by using form-invariant transformations of Maxwell equations has led to an approach for designing devices with anisotropic metamaterial. In this paper, we present the design methodology for a low profile planar focusing antenna based on the transformation of a parabolic antenna. The electromagnetic behavior of the planar antenna is simulated by a two-dimensional finite element method and the results show that the planar antenna has the same performances as the parabolic antenna. The coordinate transformation technology provides an alternative design method to the conventional antennas.
Electrically pumped ZnO film ultraviolet random lasers on silicon substrate
Authors: Ma Xiangyang , Chen Peiliang , Li Dongsheng , Zhang Yuanyuan , Yang Deren
Published: December 2007

The electrically pumped ultraviolet (UV) random lasing in c-axis oriented ZnO polycrystalline films has been demonstrated. For this demonstration, a metal-oxide-semiconductor structure of Au∕SiOx(x<2)∕ZnO film was fabricated on a silicon substrate. With ever-higher forward bias where the negative voltage was connected to the silicon substrate, the UV electroluminescence from such a ZnO-based device transformed from the spontaneous emission to the random lasing in the ZnO film. It is believed that the recurrent scattering and interference of the enough strong electroluminescent UV light in the in-plane random cavities formed in the ZnO film leads to electrically pumped UV random lasing.
Molecular beam epitaxy of GaBiAs on (311)B GaAs substrates
Authors: Henini M. , Ibáñez J. , Schmidbauer M. , Shafi M. , Novikov S. V. , Turyanska L. , Molina S. I. , Sales D. L. , Chisholm M. F. , Misiewicz J.
Published: December 2007

We report the growth by molecular beam epitaxy of GaBixAs1−x epilayers on (311)B GaAs substrates. We use high-resolution x-ray diffraction (HRXRD), transmission electron microscopy, and Z-contrast imaging to characterize the structural properties of the as-grown material. We find that the incorporation of Bi into the GaBiAs alloy, as determined by HRXRD, is sizably larger in the (311)B epilayers than in (001) epilayers, giving rise to reduced band-gap energies as obtained by optical transmission spectroscopy.
Spring constant tuning of active atomic force microscope probes using electrostatic spring softening effect
Authors: Torun H. , Sarangapani K. K. , Degertekin F. L.
Published: December 2007

The authors describe a method to electrically adjust the spring constant of an active atomic force microscopy (AFM) probe using electrostatic spring softening effect. The probe consists of a clamped membrane with interferometric displacement sensing and integrated electrostatic actuation. Using the bias voltage on the integrated electrostatic actuator, the spring constant of the probe is reduced electrically. This increases the force sensitivity of the probe without significant dimensional change, therefore not affecting its noise level. The sensitivity improvement for force spectroscopy is demonstrated by capturing force curves using the membrane probe while it is in interaction with an AFM tip.
A method for fabricating dislocation-free tensile-strained SiGe films via the oxidation of porous Si substrates
Authors: Kim Jeehwan , Li Biyun , Xie Ya-Hong
Published: December 2007

A method for fabricating tensile-strained SiGe films via the oxidation of porous Si substrates with thin SiGe overlayers is reported. A 100nm thick Si0.77Ge0.23 film on a porous Si substrate is fabricated through self-limiting anodization of a heavily doped p-type Si substrate with an epitaxially grown intrinsic Si0.77Ge0.23 overlayer. The pseudomorphic Si0.77Ge0.23 film originally under 0.94% compressive strain on the porous Si substrate becomes completely relaxed by low temperature (500°C) oxidation of the porous Si substrate. Continued oxidation introduces an additional 0.71% tensile strain in the Si0.77Ge0.23 layer without the introduction of dislocations or cracks.
Breakup of a flow-focused emulsion jet for the production of matrix-structured microcapsules
Authors: He Yinghe
Published: December 2007

To achieve a better control of particle performances, significant research efforts have been directed toward the production of structured particles with a very narrow size distribution, or monodisperse “designer” particles. This paper presents a method for the production of monodisperse microspheres with a matrix structure. The technique is based on the application of flow focusing to the breakup of an emulsion jet in a liquid environment using an in-house designed and fabricated macroscopic device. Through the variation of flow conditions, the device is capable of producing matrix-structured monodisperse microcapsules in a size range of 20–200μm.
Capacitance characteristics of back-illuminated Al0.42Ga0.58N∕Al0.40Ga0.60N heterojunction p-i-n solar-blind UV photodiode
Authors: Cheng C. J. , Si J. J. , Zhang X. F. , Ding J. X. , Lu Z. X. , Sun W. G. , Sang L. W. , Qin Z. X , Zhang G. Y.
Published: December 2007

Capacitance-voltage and capacitance-frequency characteristics of Al0.42Ga0.58N∕Al0.40Ga0.60N heterojunction p-i-n photodiode are investigated. The slopes of the 1∕C2-V plot were nearly the same at 100Hz, 1KHz, 10KHz, and 100KHz, slightly smaller at 1MHz. A depletion region width of 63.6nm calculated under zero bias for this diode was smaller than that of the intrinsic region, which showed that the intrinsic region was depleted partly under zero bias. The difference between the capacitance measured at low and high frequencies could be due to the high resistivity of the intrinsic region.
Image effects on the transport of intense nonaxisymmetric charged beams
Authors: Pakter Renato , Levin Yan , Rizzato Felipe B.
Published: December 2007

The effect of conducting pipes on the equilibrium of intense nonaxisymmetric continuous beams of charged particles is investigated. For a cylindrical pipe and an elliptical beam, we obtain an exact closed form analytical expression for the electrostatic potential. Using a variational principle, we then explore the distortions that equilibrium beams suffer due to the conducting channel. Finally, we present an exact proof that despite the nonlinear forces acting on beams of arbitrary cross section inside conducting pipes of arbitrary shape, the density of these beams remains homogeneous and their cross sectional area remains the same as the one in free space.
Atomic-layer-deposited nanostructures for graphene-based nanoelectronics
Authors: Xuan Y. , Wu Y. Q. , Shen T. , Qi M. , Capano M. A. , Cooper J. A. , Ye P. D.
Published: January 2008

Graphene is a hexagonally bonded sheet of carbon atoms that exhibits superior transport properties with a velocity of 108cm∕s and a room-temperature mobility of >15000cm2∕Vs. How to grow gate dielectrics on graphene with low defect states is a challenge for graphene-based nanoelectronics. Here, we present the growth behavior of Al2O3 and HfO2 films on highly ordered pyrolytic graphite (HOPG) by atomic layer deposition (ALD). To our surprise, large numbers of Al2O3 and HfO2 nanoribbons, with dimensions of 5–200nm in width and >50μm in length, are observed on HOPG surfaces at growth temperature between 200 and 250°C. This is due to the large numbers of step edges of graphene on HOPG surfaces, which serve as nucleation sites for the ALD process. These Al2O3 and HfO2 nanoribbons can be used as hard masks to generate graphene nanoribbons or as top-gate dielectrics for graphene devices. This methodology could be extended to synthesize insulating, semiconducting, and metallic nanostructures and their combinations.
Size-dependent ferroelectric behaviors of BaTiO3 nanowires
Authors: Hong Jiawang , Fang Daining
Published: January 2008

Landau-Ginsburg-Devonshire theory is introduced to investigate the size-dependent ferroelectric properties of BaTiO3 nanowires, with the consideration of polarization orienting along the radial direction. It is shown that the Curie temperature, mean polarization, and area enclosed by hysteresis loop decrease with the reducing diameter of the nanowire. However, this size effect becomes obvious only when the diameter is below 20nm. Above this, the ferroelectric behaviors of nanowires are almost the same as those of bulk materials. Furthermore, there exists a temperature-dependent critical diameter for BaTiO3 nanowire below which the hysteresis loops vanish and it is 3.6nm at room temperature.
Femtosecond lasers prepare to break out of the laboratory
Authors: Ouellette Jennifer
Published: January 2008

The latest compact systems promise big benefits in a diverse array of practical applications, particularly in the biological and medical arenas.
Fermi, Pasta, Ulam, and a mysterious lady
Authors: Dauxois Thierry
Published: January 2008

The computations for the first-ever numerical experiment were performed by a young woman named Mary Tsingou. After decades of omission, it is time to recognize her contribution.
Behavioral tradeoff in estuarine larvae favors seaward migration over minimizing visibility to predators
Authors: Morgan Steven G. , Anastasia Jean R.
Published: January 2008

The ability of microscopic larvae to control their fate and replenish populations in dynamic marine environments has been a long-running topic of debate of central importance to understanding the ecology and evolution of life in the sea and managing resources in a changing global environment. After decades of research documenting behaviors that keep larvae close to natal populations, it is becoming apparent that larval behaviors in a broader spectrum of species promote long-distance migrations to offshore nursery grounds. Larvae must exert considerable control over their movements. We now show that larval emigration from estuaries is favored even over minimizing visibility to predators. An endogenous tidal vertical migration that would expedite seaward migration of
Uca pugilator
larvae was maintained experimentally across two tidal regimes. The periodicity of the rhythm doubled to match the local tidal regime, but larvae ascended to the surface during the daytime rather than at night. This process would conserve larval emigration but increase the visibility to predators across part of the species range. The periodicity of tidal vertical migration by
Sesarma cinereum
larvae failed to double and was inappropriately timed relative to both environmental cycles in the absence of a diel cycle. The timing system regulating tidally timed behaviors in these two species of crabs evidently differed. Phenotypic plasticity can conserve larval transport of both species when tidal and diel cycles are present. It may be widespread in the sea where diverse habitats are encountered across extensive species ranges.
Slow-wave sleep and the risk of type 2 diabetes in humans
Authors: Tasali Esra , Leproult Rachel , Ehrmann David A. , Van Cauter Eve
Published: January 2008

There is convincing evidence that, in humans, discrete sleep stages are important for daytime brain function, but whether any particular sleep stage has functional significance for the rest of the body is not known. Deep non-rapid eye movement (NREM) sleep, also known as slow-wave sleep (SWS), is thought to be the most “restorative” sleep stage, but beneficial effects of SWS for physical well being have not been demonstrated. The initiation of SWS coincides with hormonal changes that affect glucose regulation, suggesting that SWS may be important for normal glucose tolerance. If this were so, selective suppression of SWS should adversely affect glucose homeostasis and increase the risk of type 2 diabetes. Here we show that, in young healthy adults, all-night selective suppression of SWS, without any change in total sleep time, results in marked decreases in insulin sensitivity without adequate compensatory increase in insulin release, leading to reduced glucose tolerance and increased diabetes risk. SWS suppression reduced delta spectral power, the dominant EEG frequency range in SWS, and left other EEG frequency bands unchanged. Importantly, the magnitude of the decrease in insulin sensitivity was strongly correlated with the magnitude of the reduction in SWS. These findings demonstrate a clear role for SWS in the maintenance of normal glucose homeostasis. Furthermore, our data suggest that reduced sleep quality with low levels of SWS, as occurs in aging and in many obese individuals, may contribute to increase the risk of type 2 diabetes.
A chemical genomics screen highlights the essential role of mitochondria in HIF-1 regulation
Authors: Lin Xiaoyu , David Caroline A. , Donnelly Jennifer B. , Michaelides Mike , Chandel Navdeep S. , Huang Xiaoli , Warrior Usha , Weinberg Frank , Tormos Kathryn V. , Fesik Stephen W. , Shen Yu
Published: January 2008

Hypoxia-inducible factor-1 (HIF-1) plays an essential role in tumor development and progression by regulating genes that are vital for proliferation, glycolysis, angiogenesis, and metastasis. To identify strategies of targeting the HIF-1 pathway, we screened a siRNA library against the entire druggable genome and a small-molecule library consisting of 691,200 compounds using a HIF-1 reporter cell line. Although the siRNA library screen failed to reveal any druggable targets, the small-molecule library screen identified a class of alkyliminophenylacetate compounds that inhibit hypoxia-induced HIF-1 reporter activity at single-digit nanomolar concentrations. These compounds were found to inhibit hypoxia but not deferoxamine-induced HIF-1α protein stabilization. Further analysis indicated that the alkyliminophenylacetate compounds likely inhibit the HIF-1 pathway through blocking the hypoxia-induced mitochondrial reactive oxygen species (ROS) production. Strikingly, all of the nonalkyliminophenylacetate HIF-1 inhibitors identified from the small-molecule library screen were also found to target mitochondria like the alkyliminophenylacetate compounds. The exclusive enrichment of mitochondria inhibitors from a library of >600,000 diverse compounds by using the HIF-1 reporter assay highlights the essential role of mitochondria in HIF-1 regulation. These results also suggest that targeting mitochondrial ROS production might be a highly effective way of blocking HIF-1 activity in tumors.
Endometriomas are more frequent on the left side
Authors: SZNURKOWSKI JACEK J. , EMERICH JANUSZ
Published: December 2007

Objective. To investigate whether asymmetry exists in the left‐ and right‐distribution of ovarian cystic lesions in women with endometriosis. Methods. We evaluated operative reports of women who underwent surgical treatment of endometrioma (n = 253) from January 1999 to December 2003. We included only those cases that had not been previously operated on (n = 234). Data of all operative findings consisted of a written report and a diagram, fulfilling the revised American Fertility Society Classification of endometriosis. Results. Endometrioma was found in the left ovary in 113 women, in the right ovary in 67, and bilaterally in 54. Left ovarian unilateral endometrioma was found more frequently (62.8%) than right endometrioma (p<0.001, odds ratio (OR) 2.8, 95% confidence interval (CI) 1.9, 4.4). The frequencies of left and right ovarian endometrioma were compared with the expected 50% using Pearson's χ2‐test. The results confirmed asymmetry (p = 0.001). We found 4 cases of ovarian cancer associated with left endometrioma without histological proof of transition. Conclusion. Our results confirm a left lateral predisposition of endometrioma. This predisposition may be caused by the presence of the sigmoid colon in the left side of the pelvis, which decreases peritoneal fluid movement. Our findings may support the transplantation theory of the origin for endometriosis.
Consanguinity and the risk of hyperemesis gravidarum in Norway
Authors: GRJIBOVSKI ANDREJ M , VIKANES ÅSE , STOLTENBERG CAMILLA , MAGNUS PER
Published: December 2007

Background. Hyperemesis gravidarum (HG) is a condition that occurs in the first half of pregnancy, and is manifested by severe vomiting, electrolyte disturbances and weight loss. Previous studies have suggested the potential role of genetic factors in the aetiology of HG. We hypothesise that consanguineous relations between parents increase the risk of HG due to the increased risk of homozygosity in HG‐associated alleles in a fetus. Moreover, we examine whether ethnic variations in the occurrence of HG can be attributed to consanguinity. Methods. All Norwegian, Pakistani and Turkish primiparous women with singleton pregnancies registered in the Norwegian Medical Birth Registry (MBRN) from 1967 to 2005 comprised the sample. Data on HG and potential confounders were obtained from MBRN. Multiple logistic regression was used to study associations between the degrees of relationship between women and their partners and the prevalence of HG. Crude and adjusted odds ratios (OR) with 95% confidence intervals (CI) were calculated. Results. The prevalence of HG was 0.9, 2.2 and 1.9% in Norwegian, Pakistani and Turkish women, respectively. Norwegian (OR =0.93; 95% CI: 0.42–2.09), Pakistani (OR =1.08; 95% CI: 0.68–1.74) and Turkish (OR =1.08; 95% CI: 0.44–2.67) women related to their partners as first cousins had similar risks of HG as non‐related women after adjustment for potential confounders. Conclusions. Consanguinity was not associated with HG in this study. The differences in the occurrence of HG between Norwegian, Pakistani and Turkish women are not attributed to consanguinity.
Seroprevalence and genital DNA prevalence of HPV types 6, 11, 16 and 18 in a cohort of young Norwegian women: study design and cohort characteristics
Authors: SKJELDESTAD FINN EGIL , MEHTA VINAY , SINGS HEATHER L. , ØVRENESS TORBJØRN , TURPIN JENNIFER , SU LING , SKJELDESTAD FINN EGIL , MEHTA VINAY , SINGS HEATHER L. , ØVRENESS TORBJØRN , TURPIN JENNIFER , SU LING , BOERCKEL PATRICIA , ROBERTS CHRISTINE , BRYAN JANINE , JANSEN KATHRIN U. , SKJELDESTAD FINN EGIL , MEHTA VINAY , SINGS HEATHER L. , ØVRENESS TORBJØRN , TURPIN JENNIFER , SU LING , BOERCKEL PATRICIA , ROBERTS CHRISTINE , BRYAN JANINE , JANSEN KATHRIN U. , ESSER MARK T. , LIAW KAI‐LI
Published: December 2007

Background. Long‐term efficacy evaluations of a quadrivalent HPV type 6/11/16/18 vaccine are ongoing in the Nordic region. As there are limited epidemiological data on HPV infection in Norway, we determined prevalence and identified sociobehavioural correlates of HPV 6/11/16/18 infection in young Norwegian women. Methods. Norwegian (n = 898) women, aged 16–24 years, were enrolled in a 4‐year prospective study. At enrolment and at 6‐month intervals thereafter, an interview on behavioural data and a gynaecological examination were undertaken. Genital samples were tested for the L1, E6 and E7 genes of HPV‐6/11/16/18, and serum anti‐HPV‐6/11/16/18 levels were measured using a competitive Luminex immunoassay (cLIA). Results. DNA and seroprevalence of HPV 6, 11, 16 or 18 ranged from 0.9 to 16.3% and 2.6 to 16.2%, respectively; and most infected women (∼75%) were infected with only 1 type. Of the HPV DNA positive cases, 54.3, 50.0, 47.3 and 38.5% had detectable HPV 6, 11, 16 or 18 antibodies, respectively. More than 50% of the high‐grade cervical intraepithelial neoplasia (CIN) cases were HPV‐16 or HPV‐18 DNA positive. Lifetime number of partners was the strongest and only predictor of sero‐ and DNA‐positivity across the 4 HPV types. Conclusion. Given the high prevalence of HPV infection among young women with mostly single‐type infection, and the fact that type‐specific HPV screening is not recommended prior to the administration of the quadrivalent HPV vaccine, our data suggest the importance of widespread, rather than targeted, immunisation.
Analysis of 127 peripartum hypoxic brain injuries from closed claims registered by the Danish Patient Insurance Association
Authors: HOVE LARS DAHLGAARD , BOCK JOHANNES , CHRISTOFFERSEN JENS KROGH , HEDEGAARD MORTEN
Published: December 2007

Background. One of the most feared complications in medicine is hypoxic brain damage to a newborn. The authors investigated the circumstances of registered peripartum hypoxic brain injuries in order to identify potential opportunities to improve patient safety and prevent injuries. Methods. The authors retrospectively investigated peripartum hypoxic brain injuries registered by the Danish Patient Insurance Association. Results. From 1992 to 2004, 127 approved claims concerning peripartum hypoxic brain injuries were registered and subsequently analysed. Thirty‐eight newborns died, and a majority of the 89 surviving children suffered from major handicaps, primarily cerebral palsy. In 69 of the cases, misinterpretation of or late action on an abnormal cardiotocography (CTG) were the reasons for the majority of the hypoxic brain injuries. Conclusions. All injuries could potentially have been avoided using established obstetric practice. CTGs are often misinterpreted. In the authors’ opinion, education and training in CTG interpretation is essential. The use of ST‐analysis of the fetus ECG (STAN) could probably reduce the number of these injuries.
Principles of atomic friction: from sticking atoms to superlubric sliding
Authors: Hölscher Hendrik , Schirmeisen André , Schwarz Udo D
Published: December 2007

Tribology—the science of friction, wear and lubrication—is of great importance for all technical applications where moving bodies are in contact. Nonetheless, little progress has been made in finding an exact atomistic description of friction since Amontons proposed his empirical macroscopic laws over three centuries ago. The advent of new experimental tools such as the friction force microscope, however, enabled the investigation of frictional forces occurring at well-defined contacts down to the atomic scale. This research field has been established as nanotribology. In the present article, we review our current understanding of the principles of atomic-scale friction based on recent experiments using friction force microscopy.
Using light to study boundary lubrication: spectroscopic study of confined fluids
Authors: Bae Sung Chul , Wong Janet S , Kim Minsu , Jiang Shan , Hong Liang , Granick Steve
Published: December 2007

Several instrumental developments to examine the spectroscopic response of molecularly thin fluids confined between mica sheets are described. They are predicated on using a redesigned surface forces apparatus where dielectric coatings, transparent to light at needed optical wavelengths, retain the ability to measure interferometric thickness at other optical wavelengths. Examples of recent measurements are presented using confocal laser Raman spectroscopy to evaluate how molecules orient as well as to perform chemical imaging. Other examples are presented using confocal fluorescence recovery after photobleaching to evaluate translational diffusion of confined polymer melts. The advantage of separating the mechanical average (force and friction) from direct information about structure and mobility at the molecular level is stressed.
Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation
Authors: Nakagawa Takeya , Kajitani Takuya , Togo Shinji , Masuko Norio , Ohdan Hideki , Hishikawa Yoshitaka , Koji Takehiko , Matsuyama Toshifumi , Ikura Tsuyoshi , Muramatsu Masami , Ito Takashi
Published: January 2008

Transcriptional initiation is a key step in the control of mRNA synthesis and is intimately related to chromatin structure and histone modification. Here, we show that the ubiquitylation of H2A (ubH2A) correlates with silent chromatin and regulates transcriptional initiation. The levels of ubH2A vary during hepatocyte regeneration, and based on microarray expression data from regenerating liver, we identified USP21, a ubiquitin-specific protease that catalyzes the hydrolysis of ubH2A. When chromatin is assembled in vitro, ubH2A, but not H2A, specifically represses the di- and trimethylation of H3K4. USP21 relieves this ubH2A-specific repression. In addition, in vitro transcription analysis revealed that ubH2A represses transcriptional initiation, but not transcriptional elongation, by inhibiting H3K4 methylation. Notably, ubH2A-mediated repression was not observed when H3 Lys 4 was changed to arginine. Furthermore, overexpression of USP21 in the liver up-regulates a gene that is normally down-regulated during hepatocyte regeneration. Our studies revealed a novel mode of trans-histone cross-talk, in which H2A ubiquitylation controls the di- and trimethylation of H3K4, resulting in regulation of transcriptional initiation.
The Protein Data Bank: a historical perspective
Authors: Berman Helen M.
Published: December 2007

The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.
Fascinating quasicrystals
Authors: Steurer Walter , Deloudi Sofia
Published: December 2007

It took Dan Shechtman more than two years to get his discovery of an Al–Mn phase with icosahedral diffraction symmetryandsharp Bragg reflections published. A paradigm shift had to take place before this novel ordering state of matter – seemingly contradicting crystallographic laws – could be accepted. Today, more than 25 years later, the existence of quasicrystals is beyond doubt. However, not everything is settled yet. All the factors governing formation, growth, stability and structure of quasicrystals are still not fully understood, nor is it resolved whether their structures are strictly or only on average quasiperiodic, and it is still an open question why only quasicrystals with 5-, 8-, 10- and 12-fold rotational symmetry have been experimentally observed so far. These points will be addressed in this review article.
Powder crystallography on macromolecules
Authors: Margiolaki I. , Wright J. P.
Published: December 2007

Following the seminal work of Von Dreele, powder X-ray diffraction studies on proteins are being established as a valuable complementary technique to single-crystal measurements. A wide range of small proteins have been found to give synchrotron powder diffraction profiles where the peak widths are essentially limited only by the instrumental resolution. The rich information contained in these profiles, combined with developments in data analysis, has stimulated research and development to apply the powder technique to microcrystalline protein samples. In the present work, progress in using powder diffraction for macromolecular crystallography is reported.
Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS
Authors: Stuhrmann Heinrich B.
Published: December 2007

Methods of contrast variation are tools that are essential in macromolecular structure research. Anomalous dispersion of X-ray diffraction is widely used in protein crystallography. Recent attempts to extend this method to native resonant labels like sulfur and phosphorus are promising. Substitution of hydrogen isotopes is central to biological applications of neutron scattering. Proton spin polarization considerably enhances an existing contrast prepared by isotopic substitution. Concepts and methods of nuclear magnetic resonance (NMR) become an important ingredient in neutron scattering from dynamically polarized targets.
Busting out of crystallography's Sisyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distribution
Authors: Cranswick Lachlan Michael David
Published: December 2007

The history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. In practice, this involves practising crystallographers communicating their thoughts to the crystallographic program authors, in the hope that new procedures will be implemented within their software. Against this background, the development of small-molecule single-crystal and powder diffraction software is traced. Starting with the analogue machines and the use of Hollerith tabulators of the late 1930's, it is shown that computing developments have been science led, with new technologies being harnessed to solve pressing crystallographic problems. The development of software is also traced, with a final caution that few of the computations now performed daily are really understood by the program users. Unless a sufficient body of people continues to dismantle and re-build programs, the knowledge encoded in the old programs will become as inaccessible as the knowledge of how to build the Great Pyramid at Giza.
The search for a structural basis for therapeutic intervention against the SARS coronavirus
Authors: Bartlam Mark , Xue Xiaoyu , Rao Zihe
Published: December 2007

The 2003 outbreak of severe acute respiratory syndrome (SARS), caused by a previously unknown coronavirus called SARS-CoV, had profound social and economic impacts worldwide. Since then, structure–function studies of SARS-CoV proteins have provided a wealth of information that increases our understanding of the underlying mechanisms of SARS. While no effective therapy is currently available, considerable efforts have been made to develop vaccines and drugs to prevent SARS-CoV infection. In this review, some of the notable achievements made by SARS structural biology projects worldwide are examined and strategies for therapeutic intervention are discussed based on available SARS-CoV protein structures. To date, 12 structures have been determined by X-ray crystallography or NMR from the 28 proteins encoded by SARS-CoV. One key protein, the SARS-CoV main protease (Mpro), has been the focus of considerable structure-based drug discovery efforts. This article highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.
Stability of ferroic phases in the highly piezoelectric Pb(ZrxTi1−x)O3ceramics
Authors: Pandey Dhananjai , Singh Akhilesh Kumar , Baik Sunggi
Published: December 2007

The morphotropic phase boundary in the phase diagram of the technologically important Pb(ZrxTi1−x)O3(PZT) ceramics has been traditionally believed to separate ferroelectric tetragonal and rhombohedral phase regions. This old picture has come under close scrutiny during the last eight years following the discovery of new monoclinic phases in theCmandCcspace groups. This article presents a brief overview of these discoveries in which the use of multiple diffraction probes (X-ray, electron, neutron diffraction) in conjunction with physical property measurements has played a crucial role. A new phase diagram of PZT showing the stability fields of these structures below room temperature is also presented.
Buried water molecules in helical transmembrane proteins
Authors: Renthal Robert
Published: December 2007

Buried water molecules (having no contact with bulk solvent) in 30 helical transmembrane (TM) protein structures were identified. The average amount of buried water in helical TM proteins is about the same as for all water‐soluble (WS) proteins, but it is greater than the average for helical WS proteins. Buried waters in TM proteins make more polar contacts, and are more frequently found contacting helices than in WS proteins. The distribution of the buried water binding sites across the membrane profile shows that the sites to some extent reflect protein function. There is also evidence for asymmetry of the sites, with more in the extracellular half of the membrane. Many of the buried water contact sites are conserved across families of proteins, including family members having different functions. This suggests that at least some buried waters play a role in structural stabilization. Disease‐causing mutations, which are known to result in misfolded TM proteins, occur at buried water contact sites at a higher than random frequency, which also supports a stabilizing role for buried water molecules.
The biochemistry and biology of extracellular plant lipid‐transfer proteins (LTPs)
Authors: Yeats Trevor H. , Rose Jocelyn K.C.
Published: December 2007

Plant lipid‐transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a role in intracellular lipid transport is considered unlikely, based on their extracellular localization. A number of other biological roles, including antimicrobial defense, signaling, and cell wall loosening, have been proposed, but conclusive evidence is generally lacking, and these functions are not well correlated with in vitro activity or structure. A survey of sequenced plant genomes suggests that the two biochemically characterized families of LTPs are phylogenetically restricted to seed plants and are present as substantial gene families. This review aims to summarize the current understanding of LTP biochemistry, as well as the evidence supporting the proposed in vivo roles of these proteins within the emerging post‐genomic framework.
Clinical Experiences with Laparoscopic Colectomy
Authors: MUKAI Masaya , SADAHIRO Sotaro , TOKUNAGA Nobuhiro , ISHIDA Hideki , MAKUUCHI Hiroyasu , TAJIMA Tomoo , MITOMI Toshio
Published: December 2007

Abstract: The indications for laparoscopic colon resection and the associated complications are discussed herein. This procedure was indicated for patients with benign disease or malignant disease with invasion limited to the submucosal layer. The subjects consisted of 14 cases with submucosal tumor invasion diagnosed preoperative, three with submucosal invasion clarified by endoscopic polypectomy, three with adenomas larger than 2 cm in diameter strongly suspected of being focal submucosal tumor invasion considered unsuitable for endoscopic mucosal resection and one with Crohn's disease with ileus. Two cases in whom laparoscopic surgery was not appropriate were included in this series. In one case with a superficial elevated lesion (Ma type), 15 mm in diameter, a diagnosis of moderately differentiated adenocarcinoma of the cecum was made preoperatively, but subserosal tumor invasion of the colonic wall with negative lymph node metastasis (nO) was revealed by examination of the resected specimen. The histology of the second superficial elevated lesion (Ha+lie type), which had a central depression, 13 mm in diameter and located above Bauhin's valve, was a well differentiated adenocarcinoma of which the cancerous portion invaded the proper muscle with positive lymph node metastasis (n1). Complications occurred in four cases. There were two cases of intraoperative vascular injury necessitating conversion to a standard laparotomy. One case with complete transection of the left ureter by End‐GIA later underwent reoperation. The other case with minor leakage at the anastomotic site was managed with conservative therapy. In both of these cases the depth of tumor invasion had been incorrectly assessed as representing small elevated lesions, 15 mm in diameter, in the right colon. Furthermore, the cases who experienced complications had left colonic lesions. These results suggest that preoperative ultrasonic‐endoscopy should be conducted as extensively as possible and that a good bloodless visual field appears to be necessary to avoid injuring adjacent organs.
The Superiority of Laparoscopic Examination in Predicting Hepatocellular Carcinoma after Inteferon Therapy for Chronic Type C Hepatitis
Authors: ARASE Yasuji , MURASHIMA Naoya , CHAYAMA Kazuaki , TSUBOTA Akihito , KOIDA Isao , SUZUKI Yukihiko , IKEDA Kenji , SAITOH Satoshi , KOBAYASHI Masaaki , KUMADA Hiromitsu , KOBAYASHI Mariko
Published: December 2007

Abstract: To explain the appearance rates of hepatocellular carcinoma (HCC) in patients treated with interferon (IFN) and to assess the risk factors for hepatocellular carcinogenesis, we studied 442 patients with chronic type C hepatitis for one to 7.6 years (median 2.8 years). Of these 442 patients, 135 (30.5%) showed a complete response with persistent HCV‐RNA negativity for more than six months after completing IFN therapy. During the observation period, HCC developed in 16 patients. We divided the patients into three groups based on laparoscopic findings of the liver surface : smooth, irregular, and nodular. The cumulative appearance rates of HCC in these three liver types were zero, 6.6% and 14%, respectively, at the end of the fifth year. As to the efficacy of IFIM, the HCC appearance rate in patients who responded was lower than that in patients who did not (p<0.05). However, multivariate Cox regression analysis showed that the laparoscopic findings correlated most strongly with liver carcinogenesis. Therefore, we conclude that laparoscopic findings before IFN therapy are significantly associated with liver carcinogenesis over the short term observation period after IFN therapy.
A Clinical Study of Acute Pancreatitis following Endoscopic Retrograde Cholangiopancreatography
Authors: ONO Ken , KOBAYASHI Shigeru , SAKAMOTO Kazuhiro , HAYASHIDA Yasuo , SAKAKIBARA Noburu
Published: December 2007

Abstract: Endoscopic retrograde cholangiopancreatography (ERCP) has been established as a safe and effective examination for patients with pancreatobiliary diseases. Pancreatitis following ERCP is an extremely rare complication. However, once pancreatitis occurs, patients may deteriorate developing a severe condition. This study was designed to investigate the cause of this pancreatitis with the aim of minimizing complications.

Six hundred and forty‐nine patients underwent ERCP in our clinic, from January 1990 to December 1994. Six patients developed acute pancreatitis following the examination. Amounts of contrast medium used, examination durations, pancreatic duct diameters, the existence of chronic pancreatitis, the presence of para‐papillary diverticulum, and the use of a brushing procedure on the pancreatic duct are discussed in this study. There was no significant difference in the amount of contrast medium used, examination duration or pancreatic duct diameter. Chronic pancreatitis was not related to the occurrence of acute pancreatitis following ERCP (p = 0.1352). The presence of para‐papillary diverticulum was associated with a tendency to develop pancreatitis (p=0.0989). Use of the brushing procedure correlated significantly with the occurrence of acute pancreatitis (p= 0.0081). This technique is one of the most important methods of diagnosing pancreatic malignancy, and should be done with great care in examining cases of suspected malignancy.
Malignant Paraganglioma of the Stomach
Authors: KONISHI Kazuo , NOZU Fumihiko , AKITA Yasushi , KURAHASHI Toshinori , YOSHIKAWA Nozomi , MITAMURA Keiji , SAKAMOTO Osamu , ASAKAWA Yoshio , SUZUKI Kyouji , TAKAYAMA Noboru , INOUE Norio , SAKUMA Hideo
Published: December 2007

Abstract: We report a case of malignant paraganglioma of the stomach. A gastric endoscopic examination on a 67‐year‐old female, performed for follow‐up purposes, revealed an irregularly elevated lesion with a central ulcer on the lesser curvature of the lower body. The lesion showed characteristics of both an epithelial tumor and a submucosal tumor by endoscopy and radiography. The biopsy specimen suggested that the lesion was a malignant poorly differentiated tumor. On abdominal ultrasonography and computed tomography, several space occupying lesions were found in both lobes of the liver. Therefore, this case was diagnosed as having an advanced gastric cancer with liver metastases and underwent distal gastrectomy. Postoperatively, a final diagnosis of gastric paraganglioma was made by histological and immunohistochemical findings (positive for Grimelius, neuron specific enolase and other stains). These findings also revealed lymph node metastases. To date, only seven cases of gastric paraganglioma have been reported. Furthermore, two cases of malignant gastric paraganglioma have also been described in the literature. This is the first case of malignant gastric paraganglioma evaluated in detail by endoscopic and radiographic examinations.
Color Doppler‐enhanced Endoscopic Ultrasonographic Diagnosis of Upper Gastrointestinal Submucosal Lesions
Authors: IWASE Hiroaki , KUSUGAMP Kazuo , SUGA Shoji , KYOKANE Kazuhiro , YAMAGUCHP Takeo
Published: December 2007

Abstract: We investigated the usefulness of color Doppler‐enhanced endoscopic ultrasonography for the assessment of upper gastrointentinal tract submucosal lesions. The subjects were 61 patients with endoscopically detected lesions : five extraluminal, four solitary varices, 26 leiomyomas, seven leiomyosarcomas, five aberrant pancreata, five cysts, three granular cell tumors, three lipomas, two schwannomas and one fibroma. Lesions were confirmed by surgery, biopsy or angiography, as appropriate. The ultrasonographic appearance of the lesions and their locations within the five‐layered structure of the wall are described. For leiomyomatous tumors less than 5 cm including leiomysarcoma, the presence of turbulent, pulsatile flow, as demonstrated on fast Fourier transform analysis, was associated with a sensitivity of 100% (7/7) and a specificity of 77.8% (7/9). We speculate that the flow pattern is related to abnormal vessels in the malignant tumors. Evaluation of the ultrasonographic characteristics of leiomyomatous tumors utilizing the pulsatile wave pattern may allow the diagnosis of leiomyosarcoma. Color Doppler‐enhanced endoscopic ultrasonography is potentially useful in the preoperative diagnosis of submucosal lesions involving the upper gastrointestinal tract.
Changes in Gastric Mucosal Blood Flow during Healing of EMR‐Induced Ulcer
Authors: HASHIMOTO Tomoyuki , ADACHI Kyoichi
Published: December 2007

Abstract: We used the laser Doppler method to study the difference in gastric mucosal blood flow changes between peptic ulcer (65 cases) and artificial ulcer caused by endoscopic mucosal resection (35 cases) during their respective healing processes. At each endoscopic ulcer stage, blood flow at the ulcer margin and that in the surrounding mucosa were measured. In the artificial ulcer, which heals easily, blood flow at the ulcer margin was still high at the scarring stage as compared with that in the corresponding area of a peptic ulcer, which is prone to relapse. Moreover, the blood flow ratio (blood flow at the ulcer margin/blood flow in the surrounding mucosa) at the S1 stage in artificial ulcers was significantly higher than that in peptic ulcers (p<0.05). These results suggest that blood flow in the SI stage is an important aspect of ulcer healing and relapse.
Usefulness of Intraductal Ultrasonography (IDUS) for Diagnosing Mucin‐producing Pancreatic Tumors
Authors: OZAWA Fumiaki , MURATA Yoko , IMAIZUMP Toshihide , HARADA Nobuhiko , HATORI Takashi , TOKI Fumitake , SUZUKI Shigeru , TAKASAKI Ken
Published: December 2007

Abstract: While it is very important to detect protruded lesions in order to determine the optimal treatment modality for mucin‐producing tumors of the pancreas (MPT), it can be very difficult to discriminate between mucinous substance and tumor. Intraductal ultrasonography (IDUS) (2.0 mm diameter, 15 or 20 MHz) was performed in five MPT cases. The sizes of the tumors were 2, 5, 12, 12 and 30 mm. Histological findings of the resected specimens demonstrated adenocarcinoma in two cases, adenoma in one, and hyperplasia in one. IDUS visualized all tumors, i. e. the visualization rate was 100%. The visualization rate for US and CT was 40% with 12 and 30 mm tumors, and that for EUS was 60% with 2, 12, and 30 mm tumors. We found IDUS to be a very useful method for visualizing small protruded lesions in MPT.
Three‐dimensional Ultrasonography Using Ultrasonic Probes by the Transpapillary Approach for Diagnosis of Pancreatobiliary Diseases
Authors: KANEMAKP Naoto , NAKAZAWA Saburo , INUI Kazuo , YOSHINO Junji , YAMACHIKA Hitoshi , OKUSHIMA Kazumu , NAKAMURA Yuta , YAMAO Kenji
Published: December 2007

Abstract: Three‐dimensional (3D) intraductal ultrasonography (IDUS) is more useful than two‐dimensional IDUS for the diagnosis of pancreatobiliary disease. We investigated the advantages and disadvantages of the transpapillary approach for 3D‐IDUS using a newly developed system for pancreatobiliary application. In total 12 patients with a sufficiently wide orifice were examined, bile duct (BD) scanning being successful in 100% of attempted cases and main pancreatic duct (MPD) scanning in 85.7%. In all cases, acceptable radial and linear images were obtained and 3D diagnosis was accomplished. However, several primary problems were experienced; 1) The 3D probe is relatively inflexible, having a thick shaft and a long tip, such that insertion into the BD or MPD can be somewhat difficult; 2) Clear images of the BD or MPD wall were not always obtained because of artifacts produced by the 3D probe itself; 3) In some cases, linear images could not be reconstructed with BD or MPD scanning despite sufficiently clear radial scan images. In the future, development of new 3D probes with more flexible and thinner shafts, and shorter tips, should considerably enhance the diagnostic capacity of IDUS for the pancreatobiliary system.