bluuebunny/crossref_metadata_2025 huggingface dataset:
Can correct protein models be identified?
Authors: Wallner Björn , Elofsson Arne
Published: April 2003

The ability to separate correct models of protein structures from less correct models is of the greatest importance for protein structure prediction methods. Several studies have examined the ability of different types of energy function to detect the native, or native‐like, protein structure from a large set of decoys. In contrast to earlier studies, we examine here the ability to detect models that only show limited structural similarity to the native structure. These correct models are defined by the existence of a fragment that shows significant similarity between this model and the native structure. It has been shown that the existence of such fragments is useful for comparing the performance between different fold recognition methods and that this performance correlates well with performance in fold recognition. We have developed ProQ, a neural‐network‐based method to predict the quality of a protein model that extracts structural features, such as frequency of atom–atom contacts, and predicts the quality of a model, as measured either by LGscore or MaxSub. We show that ProQ performs at least as well as other measures when identifying the native structure and is better at the detection of correct models. This performance is maintained over several different test sets. ProQ can also be combined with the Pcons fold recognition predictor (Pmodeller) to increase its performance, with the main advantage being the elimination of a few high‐scoring incorrect models. Pmodeller was successful in CASP5 and results from the latest LiveBench, LiveBench‐6, indicating that Pmodeller has a higher specificity than Pcons alone.
The crystal structure of augmenter of liver regeneration: A mammalian FAD‐dependent sulfhydryl oxidase
Authors: Wu Chia‐Kuei , Dailey Tamara A. , Dailey Harry A. , Wang Bi‐Cheng , Rose John P.
Published: April 2003

The crystal structure of recombinant rat augmenter of liver regeneration (ALRp) has been determined to 1.8 Å. The protein is a homodimer, stabilized by extensive noncovalent interactions and a network of hydrogen bonds, and possesses a noncovalently bound FAD in a motif previously found only in the related protein ERV2p. ALRp functions in vitro as a disulfide oxidase using dithiothreitol as reductant. Reduction of the flavin by DTT occurs under aerobic conditions resulting in a spectrum characteristic of a neutral semiquinone. This semiquinone is stable and is only fully reduced by addition of dithionite. Mutation of either of two cysteine residues that are located adjacent to the FAD results in inactivation of the oxidase activity. A comparison of ALRp with ERV2p is made that reveals a number of significant structural differences, which are related to the in vivo functions of these two proteins. Possible physiological roles of ALR are examined and a hypothesis that it may serve multiple roles is proposed.
Analytical Formulation of Friction Interface Elements for Analysis of Nonlinear Multi-Harmonic Vibrations of Bladed Disks
Authors: Petrov E. P. , Ewins D. J.
Published: April 2003

An analytical formulation for the vectors of contact forces and the stiffness matrix of the nonlinear friction contact interface is developed for the analysis of multi-harmonic vibrations in the frequency domain. The contact interface elements provided here an exact description of friction and unilateral contact forces at the interacting surfaces, taking into account the influence of the variable normal load on the friction forces, including the extreme cases of separation of the two surfaces. Initial gaps and interferences at the contact nodes, which affect the normal force, as well as the unilateral action of the normal force at the contact surface, are all included in the model. The accurate calculation of the force vector and the tangent stiffness matrix provides a very reliable and fast convergence of the iteration process used in the search for the amplitudes of nonlinear vibrations of bladed disks. Numerical investigations demonstrate excellent performance with respect to speed, accuracy and stability of computation.
An Experimental and Computational Study of the Formation of a Streamwise Shed Vortex in a Turbine Stage
Authors: Pullan Graham , Denton John , Dunkley Michael
Published: April 2003

Shear layers shed by aircraft wings roll up into vortices. A similar, though far less common, phenomenon can occur in the wake of a turbomachine blade. This paper presents experimental data from a new single-stage turbine that has been commissioned at the Whittle Laboratory. Two low-aspect ratio stators have been tested with the same rotor row. Surface flow visualization illustrates the extremely strong secondary flows present in both NGV designs. These secondary flows lead to conventional passage vortices, but also to an intense vortex sheet which is shed from the trailing edge of the blades. Pneumatic probe traverses show how this sheet rolls up into a concentrated vortex in the second stator design, but not in the first. A simple numerical experiment is used to model the shear layer instability and the effects of trailing edge shape and exit yaw angle distribution are investigated. It is found that the latter has a strong influence on shear layer rollup: inhibiting the formation of a vortex downstream of NGV 1 but encouraging it behind NGV 2.
Evidence for the Exposure of Water Ice on Titan's Surface
Authors: Griffith Caitlin A. , Owen Tobias , Geballe Thomas R. , Rayner John , Rannou Pascal
Published: April 2003

The smoggy stratosphere of Saturn's largest moon, Titan, veils its surface from view, except at narrow wavelengths centered at 0.83, 0.94, 1.07, 1.28, 1.58, 2.0, 2.9, and 5.0 micrometers. We derived a spectrum of Titan's surface within these “windows” and detected features characteristic of water ice. Therefore, despite the hundreds of meters of organic liquids and solids hypothesized to exist on Titan's surface, its icy bedrock lies extensively exposed.
Nota Bene: A Call to Arms
Authors: Martineau Monique
Published: April 2003

The Chicago Guide to Communicating Science
. Scott L. Montgomery. University of Chicago Press, Chicago, 2003. 240 pp. $40, £28. ISBN 0-226-53484-7. Paper, $15, £10.50. ISBN 0-226-53485-5.

Montgomery provides detailed and practical advice for presenting science in a wide range of formats, including conference talks, research papers, review articles, and interviews with the media. Rather than focusing on rules and warnings, he stresses the adaptation of good models of expression.
EXTENDED ENSEMBLE MONTE CARLO
Authors: IBA YUKITO
Published: April 2003

"Extended Ensemble Monte Carlo" is a generic term that indicates a set of algorithms, which are now popular in a variety of fields in physics and statistical information processing. Exchange Monte Carlo (Metropolis-Coupled Chain, Parallel Tempering), Simulated Tempering (Expanded Ensemble Monte Carlo) and Multicanonical Monte Carlo (Adaptive Umbrella Sampling) are typical members of this family. Here, we give a cross-disciplinary survey of these algorithms with special emphasis on the great flexibility of the underlying idea. In Sec. 2, we discuss the background of Extended Ensemble Monte Carlo. In Secs. 3, 4 and 5, three types of the algorithms, i.e., Exchange Monte Carlo, Simulated Tempering, Multicanonical Monte Carlo, are introduced. In Sec. 6, we give an introduction to Replica Monte Carlo algorithm by Swendsen and Wang. Strategies for the construction of special-purpose extended ensembles are discussed in Sec. 7. We stress that an extension is not necessary restricted to the space of energy or temperature. Even unphysical (unrealizable) configurations can be included in the ensemble, if the resultant fast mixing of the Markov chain offsets the increasing cost of the sampling procedure. Multivariate (multicomponent) extensions are also useful in many examples. In Sec. 8, we give a survey on extended ensembles with a state space whose dimensionality is dynamically varying. In the appendix, we discuss advantages and disadvantages of three types of extended ensemble algorithms.
A MODERN INTRODUCTION TO QUARKONIUM THEORY
Authors: GRINSTEIN BENJAMIN
Published: April 2003

Recent advances in lattice and continuum QCD have given us new insights into quarkonium physics. These sets of lectures are intend for the uninitiated. We first give a physical picture of quarkonium and describe the hybrids states established in lattice QCD. Then we give an unorthodox presentation of Nonrelativistic QCD (NRQCD) including a novel method for the application of spin-symmetries. Finally we describe the prototypical application of NRQCD: cancellation of infrared divergences in decays of P wave quarkonia.
THE WALL OF THE CAVE
Authors: POLYAKOV A. M.
Published: April 2003

In this article old and new relations between gauge fields and strings are discussed. We add new arguments that the Yang–Mills theories must be described by the noncritical strings in the five-dimensional curved space. The physical meaning of the fifth dimension is that of the renormalization scale represented by the Liouville field. We analyze the meaning of the zigzag symmetry and show that it is likely to be present if there is a minimal supersymmetry on the world sheet. We also present the new string backgrounds which may be relevant for the description of the ordinary bosonic Yang–Mills theories. The article is written on the occasion of the 40th anniversary of the IHES.
EXACT RESULTS IN GAUGE THEORIES: PUTTING SUPERSYMMETRY TO WORK
Authors: SHIFMAN M.
Published: April 2003

Powerful methods based on supersymmetry allow one to find exact solutions to certain problems in strong coupling gauge theories. The inception of some of these methods (holomorphy in the gauge coupling and other chiral parameters, in conjunction with instanton calculations) dates back to the 1980's. I describe the early exact results — the calculation of the β function and the gluino condensate — and their impact on the subsequent developments. A brief discussion of the recent breakthrough discoveries where these results play a role is given.
SYNTHESIS OF ELECTRONIC CIRCUITS FOR SIMULATING NONLINEAR DYNAMICS
Authors: ITOH MAKOTO
Published: April 2003

In this paper, we present a unified approach for synthesizing nonlinear circuits. That is, we synthesize electronic circuits for simulating nonlinear dynamics. One advantage of our approach is that we can directly synthesize nonlinear circuits from ordinary differential equations. A large variety of chaotic nonlinear systems (Chua's circuit, hyperchaotic system, Lorenz system, Rössler system, etc.) are realized by using several analog circuit elements.
THE sp HYBRID BONDING OF C, N AND O TO THE fcc(001) SURFACE OF NICKEL AND RHODIUM
Authors: SUN CHANG Q.
Published: April 2003

This brief review focuses on the nature, kinetics, dynamics and consequences of the sp-orbital hybrid bonding of C, N and O to the Ni/Rh(001) surfaces which give rise to the same kind of "radial and then the p4g clock" reconstruction. It is identified that the "radial" and the subsequent "clock" reconstruction result from the adsorbate–substrate bond formation with sp-orbital hybridization, and that the driving force behind the reconstruction originates from the electrostatic interaction along the <11> direction. At the initial stage, A-1 (A=C, N or O adsorbate) sinks into the fourfold hollow site and forms one bond with a B (B = Ni or Rh host atom) underneath, giving rise to an AB5 cluster with four dipoles at the surface. As A-1 evolves into the hybridized-A-n (n=4, 3, 2), the AB5 cluster evolves into an AB4 tetrahedron. Meanwhile, the AB4 tetrahedron redefines three of the four surface dipoles as B+, B2+, B+/ dipole or Bdipole, depending on the valence value of the adsorbate. The electrostatic force arises upon repopulating the valence electrons, which creates rhombus strings along the <11> direction. With the presence of nonbonding lone pairs, the clock rotation on Ni(00l)-(2×2)p4g-2N-3 and Rh(00l)-(2×2)p4g-2O-2 surfaces is initiated by the alternate attraction and repulsion in the <11> direction and the rotation is stabilized by bond tension; whereas the clock rotation on the Ni(00l)-(2×2)p4g-2C-4 surface is driven by the nonequivalent electrostatic repulsion in the <11> direction and the rotation is balanced by strong bond compression. The findings so far have led to technical innovation for the adhesion between diamond and metals by designing a gradient TiCN transition layer to neutralize the bond stress.
CURRENT INDUCED TELEGRAPH NOISE IN CMR MANGANITES
Authors: YUZHELEVSKI Y. , DIKOVSKY V. , MARKOVICH V. , GORODETSKY G. , JUNG G. , SHULYATEV D. A. , MUKOVSKII YA. M.
Published: April 2003

Random telegraph fluctuations of the resistivity exceeding 10% have been observed in current induced low resistive metastable state of low-dopped La 1-x Ca x MnO 3 single crystal at temperatures below the Curie point. Telegraph amplitudes and average life-times depend on dc bias. Near the characteristic minimum in the resistance vs current curve the bias dependent duty cycle of the telegraph signal crosses 0.5. The pronounced telegraph fluctuations are tentatively associated with fluctuating conductivity of intrinsic tunnel barriers between ferromagnetic domains joined by antiferromagnetic insulating matrix in percolating paths of the phase separated manganite.
ON THE STATISTICAL ANALYSIS OF NOISE IN CHEMICAL SENSORS AND ITS APPLICATION FOR SENSING
Authors: SMULKO JANUSZ , GRANQVIST CLAES-GÖRAN , KISH LASZLO B.
Published: April 2003

Resistance noise data from a single gas sensor can be utilized to identify gas mixtures. We calculated the power spectral density. higher order probability densities and the bispectrum function of the recorded noise samples; these functions are sensitive to different natural vapors and can be employed to select a proper detection criterion for gas composites and odors.
A MULTIMODE SIMULATION MODEL OF MODE-COMPETITION LOW-FREQUENCY NOISE IN SEMICONDUCTOR LASERS
Authors: AHMED MOUSTAFA , YAMADA MINORU , ABDULRHMANN SALAH
Published: April 2003

A multimode model is proposed to simulate the mode-competition low-frequency noise in semiconductor lasers taking account of the possible mechanisms of nonlinear gain saturation. A new technique is reported to generate the Langevin noise sources that induce spontaneous-emission fluctuations in dynamics of the lasing modes. The model is applied to simulate the intensity noise in AlGaAs lasers. Agreement of the simulated noise results with the experimental measurements is found. Correlation of the noise characteristics with dynamics of the mode competition is newly introduced. The low-frequency noise is enhanced when the dynamics exhibit mode hopping or a jittering single mode, and is suppressed when the stable single-mode operation is achieved.
Intravenous Itraconazole followed by Oral Itraconazole for the Treatment of Amphotericin-B-Refractory Invasive Pulmonary Aspergillosis
Authors: Caillot D.
Published: April 2003

The efficacy and safety of 2 weeks of intravenous itraconazole (200 mg twice daily for 2 days, then 200 mg once daily for 12 days) followed by 12 weeks of oral itraconazole capsules 200 mg twice daily were evaluated in a multicentre, open trial in 31 immunocompromised patients with invasive pulmonary aspergillosis (IPA). We report on a subset of 21 patients who had amphotericin-B-refractory IPA. All patients had haematological malignancies, 10 patients had failed prophylaxis, 12 patients had failed empirical therapy and 2 patients had failed treatment of confirmed infection with amphotericin B. By the second day of treatment, all patients assessed (n = 12) had trough plasma concentrations of itraconazole greater than 250 ng/ml. Mean trough plasma concentrations increased throughout the intravenous and oral treatment periods. Of the 10 patients who completed the 14 weeks of therapy, 9 (90%) had a complete or partial response and the remaining patient had stable disease. Overall, 11 of the 21 patients (52%) had a complete or partial response at their last assessment and three additional patients had stable disease. During intravenous treatment, 18 patients (86%) experienced adverse events; during oral treatment, 11 patients (52%) experienced adverse events. Most adverse events were not related to itraconazole treatment and all were expected in this patient population. In conclusion, intravenous itraconazole followed by oral itraconazole is an effective and well-tolerated treatment for amphotericin-B-refractory IPA.
Homogeneous Immunoglobulins following Allogeneic Bone Marrow Transplantation
Authors: Hajdu Melinda , Puskás Éva , Sipos Andrea , Barta Anikó , Pálóczi Katalin , Uher Ferenc
Published: April 2003

Homogeneous immunoglobulins are frequently detected in the serum of patients undergoing allogeneic bone marrow transplantation (BMT). The aim of the present study was to further characterize the incidence of this phenomenon and its correlations with laboratory and clinical data. Serum samples were gathered from 29 patients undergoing allogeneic or syngeneic BMT for chronic myeloid leukemia (CML), and serial protein (IgG, IgA and IgM) quantification, electrophoresis and immunofixation were performed. Transient mono- or oligoclonal gammopathies were observed in 23 out of 29 patients between days 20 and 1,750 following transplantation. The presence of homogeneous immunoglobulins was not correlated with the following clinical parameters: graft-versus-host disease, bacterial sepsis, Epstein-Barr virus or cytomegalovirus infection or invasive fungal infection. Therefore, the development of mono- or oligoclonal immunoglobulins may represent a complex disorder of B cell regeneration which may be caused by an intrinsic B cell defect, or a failure in the regenerating T cell system, or both, manifesting itself in a restricted antibody diversity after allogeneic BMT.
Vascular Risk Factors, Cognition and Dementia Incidence over 6 Years in the Sydney Older Persons Study
Authors: Piguet Olivier , Grayson David A. , Creasey Helen , Bennett Hayley P. , Brooks William S. , Waite Louise M. , Broe G. Anthony
Published: April 2003

The specific contributions of factors associated with an increased risk of stroke to cognitive decline and vascular dementia in elderly people remain somewhat unclear. We investigated the prevalence of vascular risk factors (RFs) and their role on the incidence of dementia, cognitive decline and death over a 6-year period in a sample of 377 non-demented community dwellers aged 75 years and over at the time of study entry. Presence and history of vascular RFs and cognitive decline over 6 years were ascertained using direct interviews, medical and cognitive examinations. Hypertension and history of heart disease were very common affecting about 50% of the participants. At 6 years, 114 (30%) participants had died, and 63 (16.7%) met diagnostic criteria for dementia. Hypertension was significantly associated with a greater cognitive decline but not with dementia. Smoking and stroke diagnosis showed a significant positive association with death. Reported hypercholesterolaemia was found to be associated with a protective effect for the development of dementia, for cognitive decline and for death over the 6-year period. All other associations were non-significant. Figures of dementia incidence are similar to previous studies in contrast to the lack of anticipated effects of the vascular RFs. The results indicate that in very old participants, the impact of vascular RFs changes with time and may no longer contribute to the development of dementia and cognitive decline.
Effects of a New Immunotherapeutic Agent (CG5601) on Endotoxin-Induced Uveitis
Authors: Porstmann A.U. , Zwingenberger K. , Pleyer U. , Baatz H.
Published: April 2003

CG5601 is a novel immunomodulatory substance showing anti-inflammatory properties comparable to thalidomide. To investigate the anti-inflammatory effects of CG5601 in endotoxin-induced uveitis (EIU) and to evaluate its influence on leukocyte-endothelium interaction, the anterior chamber inflammatory reaction was assessed and intravital fluorescence microscopy was carried out at 2, 4, 8 and 24 h. Lewis rats received an intraperitoneal injection of CG5601 (200 mg/kg b.w.) at the time of lipopolysaccharide injection. At 8 and 24 h, CG5601 inhibited the cell migration and protein concentration in the aqueous humor compared to untreated EIU (p < 0.0001). There was no significant difference between nontreated animals and vehicle controls. The treatment of CG5601 reduced the number of rolling leukocytes. At early time points (2 and 4 h), inhibition of rolling leukocyte flux was significant (p < 0.005). The rise of serum TNF-α levels in EIU at 2 h was reduced. CG5601 exerts potent anti-inflammatory effects in EIU.
Electroretinographic Changes in Eyes of Patients with BRCA1 Gene Mutation
Authors: Lubiński Wojciech , Górski Bogdan , Szych Zbigniew , Penkala Krzysztof , Palacz Olgierd , Lubiński Jan
Published: April 2003

Aim: To assess the retinal function in BRCA1 gene mutation carriers and to evaluate the clinical significance of its potential alterations. Patients and Methods: Flash electroretinogram (ERG) was studied in 15 unaffected patients (30 eyes) with constitutional BRCA1 gene mutation. Routine ophthalmological examination was additionally performed in the oldest, unaffected 15 patients and in 15 breast cancer patients being carriers of BRCA1 mutation. Results: In ERGs, in the maximal response, a-wave (p < 0.03) and b-wave (p < 0.05) amplitudes were reduced. In the cone single-flash response, the amplitude of a-wave (p < 0.007) was also reduced. In the oscillatory potentials (OPs), increased amplitude of OP2 (p < 0.03), and increased latencies of OP3 (p < 0.0009) and OP4 (p < 0.03) were obtained. BRCA1 carriers even at old age or after treatment of breast cancer have not presented increased frequency of abnormalities detectable by routine ophthalmological examination. Conclusion: It can be hypothesized that dysfunction of rods, cones and inner retinal layers is present in asymptomatic carriers of BRCA1 gene mutation; however, this does not have clinical consequences.
Suction-Assisted One-Piece Self-Retaining Wide-Angle Contact Lens for Vitrectomy
Authors: Shah Vinay A. , Chalam K.V.
Published: April 2003

Introduction: We have developed a suction-assisted one-piece self-retaining wide-angle contact lens for vitrectomy. Design: The wide-angle contact lens is a one-piece lens without the case, making it lightweight. The contact inferior surface is enhanced by four quadrant plate extensions. A metal housing is attached to the side of the plate extension with an opening at the inferior surface. A negative suction device is attached to the housing of the lens. Method of Use: A drop of viscoelastic is placed between the lens and the cornea. Suction created by a syringe device holds the contact lens on the cornea. Conclusion: This specially designed lens is lightweight and eliminates the need for a skilled assistant to stabilize the contact lens. It provides a stable well-centered view of the peripheral fundus during vitreous surgery.
The Effect of Cingulate Cortex Lesions on Task Switching and Working Memory
Authors: Rushworth M. F. S. , Hadland K. A. , Gaffan D. , Passingham R. E.
Published: April 2003

Anatomic interconnections between the prefrontal and anterior cingulate cortices suggest that these areas may have similar functions. Here we report the effect of anterior cingulate removal on task switching, error monitoring, and working memory. Neuroimaging studies have implicated the cingulate cortex in all these processes. Six macaques were taught task switching (TS) and delayed alternation (DA) paradigms. TS required switching between two conditional response tasks with mutually incompatible response selection rules. DA required alternation between two identically covered food-well positions. In the first set of experiments, anterior cingulate lesions did not consistently impair TS or DA performance. One animal performed worst on both TS and DA and in this animal the cingulate sulcus lesion was most complete. In the second set of experiments, we confirmed that larger anterior cingulate lesions, which included the sulcus, consistently impaired TS but only led to a mild and equivocal impairment of DA. The TS error pattern, however, did not suggest an impairment of TS per se. The consequence of a cingulate lesion is, therefore, distinct to that of a prefrontal lesion. TS error distribution analyses provided some support for a cingulate role in monitoring responses for errors and subsequent correction but the pattern of reaction time change in TS was also indicative of a failure to sustain attention to the task and the responses being made.
The Right Hemisphere Involvement in the Processing of Morphologically Derived Words
Authors: Marangolo Paola , Incoccia Chiara , Pizzamiglio Luigi , Sabatini Umberto , Castriota-Scanderbeg Alessandro , Burani Cristina
Published: April 2003

It is widely documented that the left hemisphere is dominant in all complex linguistic tasks, including the processing of inflectional morphology. Both in Italian and in other languages, patients with brain damage with a selective deficit in derivational morphology have never been reported. Here we present the unusual case of two patients with very similar right-hemisphere lesions, who in the absence of aphasic disorders showed a selective inability in producing derivational morphology. Although both patients were unimpaired in producing verb infinitives, they both showed a selective deficit in producing nouns derived from verbs. This difficulty was not present in deriving nouns from other grammatical categories, such as adjectives. Interestingly, both patients mostly substituted the derived noun with the past participle of the verb. This pattern of results documents for the first time a right-hemisphere contribution in the domain of derivational morphology.
Marked Potentiation of the Dominant Negative Action of a Mutant Thyroid Hormone Receptor β in Mice by the Ablation of One Wild-Type β Allele
Authors: Suzuki H. , Zhang X.-Y. , Forrest D. , Willingham M. C. , Cheng S.-Y.
Published: April 2003

Mutations in the thyroid hormone receptor (TR) β gene result in resistance to thyroid hormone (RTH), characterized by reduced sensitivity of tissues to thyroid hormone. To understand which physiological TR pathways are affected by mutant receptors, we crossed mice with a dominantly negative TRβ mutation (TRβPV) with mice carrying a TRβ null mutation (TRβ−/−) to determine the consequences of the TRβPV mutation in the absence of wild-type TRβ. TRβPV/− mice are distinct from TRβ+/− mice that did not show abnormalities in thyroid function tests. TRβPV/− mice are also distinct from TRβPV/+ and TRβ−/− mice in that the latter shows mild dysfunction in the pituitary-thyroid axis, whereas the former exhibit very severe abnormalities, including extensive papillary hyperplasia of the thyroid epithelium, indistinguishable from that observed in TRβPV/PV mice. Similar to TRβPV/PV mice, TRβPV/− mice exhibited impairment in weight gain. Moreover, the abnormal regulation patterns of T3-target genes in the tissues of TRβPV/− and TRβPV/PV mice were strikingly similar. Using TR isoforms and PV-specific antibodies in gel shift assays, we found that in vivo, PV competed with TRα1 for binding to thyroid hormone response elements in TRβPV/− mice as effectively as in TRβPV/PV mice. Thus, the actions of mutant TRβ are markedly potentiated by the ablation of the second TRβ allele, suggesting that interference with wild-type TRα1-mediated gene regulation by mutant TRβ leads to severe RTH.
A New Open Metal-Organic Framework [Zn8(GeO4)(C8H4O4)6]n, Constructed by Heterometallic Cluster Zn8(GeO4) Secondary Building Units
Authors: Chen Jinxi , Liu Zhicheng , Yu Ting , Chen Zhenxia , Sun Jinyu , Weng Linhong , Tu Bo , Zhao Dongyuan
Published: April 2003

A new interpenetrating three dimensional open metal–organic framework [Zn8(GeO4)(C8H4O4)6]n, constructed by Zn8(GeO4) secondary building units is reported. It is a rare example of metal–organic frameworks based on the heterometallic cluster secondary building units. Thermogravimetric analysis shows that it is thermally stable up to 320 °C.
The Iberian Peninsula thermal low
Authors: Hoinka Klaus P. , Castro Manuel DE
Published: April 2003

Statistics of the thermal low above the Iberian Peninsula are presented for the period between 1979 and 1993, based on gridded data from the European Centre for Medium‐Range Weather Forecasts reanalysis project. The sample of days with a thermal low above the Iberian Peninsula was selected objectively using criteria applied to mean‐sea‐level pressure and 925 hPa geopotential fields. The synoptic‐ and regional‐scale horizontal structure is characterized by the climatology of the 500 hPa geopotential and mean‐sea‐level pressure distributions. The diurnal evolution of the mean‐sea‐level pressure is portrayed by mean fields at 00, 06, 12 and 18 U TC. The climatological vertical structure of the thermal low is shown by relation to meridional and zonal cross‐sections passing through the thermal low's centre. The diurnal evolution of the divergence, relative vorticity, potential temperature and vertical velocity is investigated. Statistics are presented also for the monthly frequency, geographical location, vertical extent and intensity of the Iberian thermal low. Copyright © 2003 Royal Meteorological Society
Assimilation of GOME total‐ozone satellite observations in a three‐dimensional tracer‐transport model
Authors: Eskes H. J. , Velthoven P. F. J. Van , Valks P. J. M. , Kelder H. M.
Published: April 2003

A data‐assimilation scheme to assimilate the Global Ozone Monitoring Experiment (GOME) total‐ozone data is described. The corresponding software (called TM3DAM) has been operational since early 2000 and is used to produce daily ozone analyses and five‐day ozone forecasts. The model is a tracer‐transport model with a parametrized description of stratospheric gas‐phase and heterogeneous ozone chemistry. It is driven by operational meteorological fields from the ECMWF numerical weather‐prediction model. TM3DAM analyses near‐real‐time level‐2 ozone data from the GOME instrument on the ESA ERS‐2 satellite. The focus of this paper is on the data‐assimilation aspects and the analysis results. The assimilation approach is based on the Kalman‐filter equations and provides detailed and realistic maps of the forecast error. The analysis scheme is nevertheless computationally efficient. The forecast‐minus‐observation statistics, accumulated over a two‐year period, are described in detail. A comparison with TOMS and Brewer observations shows good agreement. Copyright © 2003 Royal Meteorological Society
Fine‐needle aspiration of synovial sarcoma: Criteria for diagnosis: Retrospective reexamination of 37 cases, including ancillary diagnostics. A Scandinavian sarcoma group study
Authors: Åkerman Måns , Ryd Walter , Skytting Björn
Published: April 2003

The cytologic criteria of synovial sarcoma in fine‐needle aspirates were defined by a retrospective examination of 37 primary tumors. Irrespective of subtype, a typical pattern at low power was found, provided the yield was rich. The typical pattern was a mixture of dispersed cells with the presence of striped nuclei and cell‐tight tumor tissue fragments with irregular borders. Often a branching network of vessels was present in the fragments, imitating a true vascular tumor. Except in poorly differentiated synovial sarcomas, the tumor cells were, small to medium in size, with rounded, ovoid, or fusiform bland nuclei with inconspicuous nucleoli. In the biphasic variant, small glandular‐ or acinar‐like structures were present, although not in all cases. In the poorly differentiated type, however, the cellular pleomorphism was marked with the presence of cells with irregular nuclei and rhabdomyoblast‐like cells, corresponding to the pleomorphic variant. The Ewing's sarcoma‐like and the atypical spindle cell variants of poorly differentiated synovial sarcoma were not diagnosed in the material. An unequivocal diagnosis of sarcoma is possible when the yield is rich. However, ancillary diagnostics are necessary for a correct diagnosis, to avoid important pitfalls, such as other sarcomas with bland tumor cells and vessel‐rich tumor fragments, in particular, solitary fibrous tumor and true hemangiopericytoma. Electron microscopic and/or molecular genetic analyses were better diagnostic adjuncts than immunocytochemistry. Diagn. Cytopathol. 2003;28:232–238. © 2003 Wiley‐Liss, Inc.
Scrape cytology of the ovaries: Potential role in intraoperative consultation of ovarian lesions
Authors: Khunamornpong Surapan , Siriaunkgul Sumalee
Published: April 2003

Intraoperative diagnosis of ovarian lesions can be achieved by gross examination with the help of frozen sections and/or cytologic examination. Various cytologic techniques, including imprint, fine‐needle aspiration, and scrape, may be used. In this study, we evaluated the application of scrape cytology in the diagnosis of ovarian lesions occurring during a 16‐mo period at one institution. The cytologic diagnosis was primarily based on findings in air‐dried, Diff‐Quik‐stained smears in correlation with clinical and intraoperative findings. In total, 131 histologically proven ovarian lesions, including 13 nonneoplastic lesions, 47 benign tumors, 17 epithelial tumors of low malignant potential (LMP), and 54 malignant tumors (35 primary, 1 leukemia, and 18 metastases), were cytologically examined. The accuracy of scrape cytology was 95% in the benign, 47% in the LMP, and 98% in the malignant group. In the LMP group, the false‐negative rate was 12%, while the deferred rate and false‐positive rate were 24% and 18%, respectively. There was no misdiagnosis between the benign and malignant categories. The histologic subtypes were correctly predicted in 78% of cases. There were limitations of scrape cytology in the diagnosis of LMP and mucinous tumors, which require histologic architectural evaluation and adequate histologic sampling. Scrape cytology is a simple, rapid, and inexpensive adjunctive technique that should be used in intraoperative consultation for ovarian lesions. Diagn. Cytopathol. 2003;28:250–257. © 2003 Wiley‐Liss, Inc.
Study of the Rh2(OAc)4‐ or BF3·OEt2‐Mediated Reaction of Thioacetic S‐Acid with α‐Diazocarbonyl Compounds
Authors: Yao Wengang , Liao Mingyi , Zhang Xiaomei , Xu Hao , Wang Jianbo
Published: April 2003

The Rh2(OAc)4‐catalyzed reaction of methyl aryldiazoacetates with thioacetic S‐acid gives exclusively the S−H insertion products in high yields, while the corresponding reaction mediated by BF3·OEt2 gives O‐esters. The mechanism of the reaction is discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003
Protective effect of a polyherbal formulation (Immu‐21) against cyclophosphamide‐induced mutagenicity in mice
Authors: Jena G. B. , Nemmani Kumar V. S. , Kaul C. L. , Ramarao P.
Published: April 2003

The object was to evaluate the effects of a polyherbal formulation, Immu‐21, against cyclophosphamide (CP)‐induced chromosomal aberrations (CA) and micronuclei (MN) in mice. CP alone (40 mg/kg, i.p.) produced classical as well as non‐classical chromosomal aberrations in mice, and the incidence of CA was signiﬁcantly more in the CP treated group when compared with that of the control group. Immu‐21, which contains extracts of Ocimum sanctum, Withania somnifera, Emblica officinalis and Tinospora cordifolia, was given at 100 mg/kg, daily, over 7 days, and 30 mg/kg daily over 14 days and inhibited both CP‐induced classical and non‐classical chromosomal aberrations (∼40%–60% of control). A significant increase in MN was also observed in bone marrow erythrocytes of mice treated with CP, and pretreatment with Immu‐21 also signiﬁcantly reduced these. Cytotoxicity was evaluated by estimating the ratio of polychromatic erythrocytes (PCEs) to normochromatic erythrocytes (NCEs). The present results indicate that chronic treatment with Immu‐21 prevented CP‐induced genotoxicity in mice. Copyright © 2003 John Wiley & Sons, Ltd.
Trypsin inhibitory effect of wedelolactone and demethylwedelolactone
Authors: Syed Samiulla D. , Deepak Mundkinajeddu , Yogisha Shivanna , Chandrashekar Arun P. , Muddarachappa Keerthi A. , D'Souza Prashanth , Agarwal Amit , Venkataraman B. V.
Published: April 2003

Wedelolactone (WL) and demethylwedelolactone (DWL) isolated from Eclipta alba were tested in the trypsin inhibition bioassay (in vitro). Both compounds showed potent activity. IC50 values of WL and DWL were found to be 2.9 and 3.0 µg/mL respectively. Copyright © 2003 John Wiley & Sons, Ltd.
Possible involvement of the transcription factor ISGF3γ in virus‐induced expression of the IFN‐β gene
Authors: Kawakami Takatoshi , Matsumoto Masahito , Sato Mitsuharu , Harada Hisashi , Taniguchi Tadatsugu , Kitagawa Motoo
Published: April 2003

Two virus‐inducible transcription factors, IRF‐1 and IRF‐2 have been identified as an activator and a repressor, respectively, of the type I interferon (IFN) genes. Recent studies with mice carrying null mutations for the IRF‐1 or IRF‐2 alleles have revealed the existence of IRF‐1‐dependent and ‐independent pathways mediating IFN‐β gene induction. Here we report that the expression of an IRF family member ISGF3γ is induced upon viral infection in IRF‐1‐/‐, IRF‐2‐/‐ embryonic fibroblasts. Furthermore, ISGF3γ can bind to a virus‐inducible promoter element in the IFN‐β gene. These results suggest that ISGF3γ or complex containing ISGF3γ is involved in the IRF‐1‐independent pathway mediating IFN‐β gene regulation.
The three‐dimensional solution structure of a constrained peptidomimetic in water and in chloroform observation of solvent induced hydrophobic cluster
Authors: Lee Min S. , Gardner Benjamin , Kahn Michael , Nakanishi Hiroshi
Published: April 2003

A large number of protein‐protein interactions involve turn or loop regions. The excised linear peptides from these regions reveal complex conformational averaging. To circumvent this motional averaging and to stabilize the β‐turn conformation, extensive effort has been devoted to the design of constrained peptidomimetics. Here, we report the three‐dimensional solution structure of a 12‐membered cyclic peptidomimetic. The structures were calculated from NMR studies performed in chloroform and in water at 263 and 278K, respectively. This 12‐membered cyclic scaffolding is part of a program to design and to construct conformationally stable β‐turn peptidomimetics. The impact of the surrounding environment on the conformation of this constrained peptidomimetic is discussed. The general structural features of the cyclic mimetic are retained in both environments; however, the formation of a hydrophobic patch in the aqueous solvent is evident.
New and specific nucleoside diphosphate glucose substrates for glycogenin
Authors: Alonso Miriam D. , Lagzdins Erik J. , Lomako Joseph , Lomako Wieslawa M. , Whelan William J.
Published: April 2003

Glycogenin, the autocatalytic, self‐glucosylating primer for glycogen synthesis by glycogen synthase, is presumed, in vivo, to use UDP‐glucose as the source of the glucose residues it adds to itself. When we tested its ability to utilize other nucleoside diphosphate glucoses, it emerged that purine nucleotides are not utilized but two pyrimidine nucleotides are used, in addition to UDP‐glucose. These are CDP‐glucose and TDP‐glucose. CDP‐glucose is utilized at 70% of the rate of UDP‐glucose. While there is no evidence that CDP‐glucose is a natural substrate for glycogenin, it has the advantage over UDP‐glucose in that it can be used specifically to detect and assay glycogenin in the presence of glycogen synthase because CDP‐glucose, unlike UDP‐glucose, is not a substrate for the synthase.
Cloning and expression of an isoform of the rat μ opioid receptor (rMOR1B) which differs in agonist induced desensitization from rMOR1
Authors: Zimprich Alexander , Simon Tatiana , Höllt Volker
Published: April 2003

A novel rat μ opioid receptor (rMOR1B) has been isolated. It shows identity to the recently published sequence of rMOR1 [Chen, et al., Mol. Pharmacol., 44 (1993) 8–12] up to amino acid 386 and differs only in length and amino acid composition at the very carboxy‐terminal tail. Both μ opioid receptor isoforms, when stably expressed in CHO‐K1 cells, show similar affinities to opioid compounds and are equally effective in the inhibition of forskolin‐induced cAMP formation. Reverse transcription polymerase chain reaction (RT‐PCR) revealed that rMOR1B displays a similar distribution as rMOR1 in various rat brain areas. Studies measuring the inhibition of adenylate cyclase in cells that had been pre‐exposed to the μ opioid agonist DAMGO indicated that rMOR1B is much more resistant to agonist‐induced desensitization than rMOR1.
Suppression of nitric oxide toxicity in islet cells by α‐tocopherol
Authors: Burkart Volker , Groβ-Eick Anne , Bellmann Kerstin , Radons Jürgen , Kolb Hubert
Published: April 2003

We show here that preincubation of pancreatic islet cells with α‐tocopherol significantly improves their resistance to toxic doses of nitric oxide (NO). No protection was afforded by other antioxidants such as vitamin C or glutathione‐monoethyl ester. The pathway of NO induced islet cell death involves DNA damage and excessive activation of poly(ADP‐ribose)polymerase leading to irreversible depletion of intracellular NAD+. α‐Tocopherol was found to interfere at early steps of this pathway, by preventing the occurrence of DNA strand breaks. This indicates that α‐tocopherol directly interacts with NO or its reactive intermediates. We conclude that α‐tocopherol is not only part of the cellular defence system against oxygen radicals but also protects eukaryotic cells from NO toxicity.
Phosphatidylcholine‐phospholipase C mediates the induction of nerve growth factor in cultured glial cells
Authors: Laviada Inés D. , Baudet Cristel , Galve-Roperh Ismael , Naveilhan Philippe , Brachet Philippe
Published: April 2003

Addition of phosphatidylcholine‐hydrolyzing phospholipase C (PC‐PLC) to cultured glial cells increased the levels of nerve growth factor (NGF) mRNA and the amount of cell‐secreted NGF. The effect of PC‐PLC was 2.5 times higher than that elicited by 4β‐phorbol 12β‐myristate 13α‐acetate. In cells in which protein kinase C (PKC) was fully inhibited or downregulated, the effect of PC‐PLC was reduced ‐ though still evident ‐ and similar to that exerted by sphingosine. Results thus indicate that PC‐PLC induces the synthesis of NGF by glial cells by a PKC‐dependent and PKC‐independent mechanisms.
Human lymphoblast and erythrocyte multicatalytic proteases: differential peptidase activities and responses to the 11S regulator
Authors: Ustrell V. , Realini C. , Pratt G. , Rechsteiner M.
Published: April 2003

The multicatalytic protease (MCP) or 20S proteasome was purified from human red blood cells and two lymphoblastoid cell lines, 721.45 which constitutively expresses protease subunits LMP2 and LMP7, and 721.174 in which genes for these subunits are deleted. Each MCP was assayed using a series of fluorogenic peptides. The hydrophobic peptides gGGF‐MCA, sRPFHLLVY‐MCA and sLY‐MCA were particularly good substrates for 721.45 MCP as compared to the enzyme from 721.174 and red blood cells. In addition, hydrolysis of gGGF‐MCA and sLY‐MCA was activated by human red blood cell and recombinant regulators to a greater extent using MCP from 721.45 lymphoblasts. Thus, LMP2/LMP7 and regulator appear to act synergistically in the enhanced degradation of gGGF‐MCA and sLY‐MCA by the multicatalytic protease.
Molecular cloning of a 74‐kDa regulatory subunit (B″ or δ) of human protein phosphatase 2A
Authors: Tanabe Osamu , Nagase Terumasa , Murakami Takehiko , Nozaki Hideto , Usui Hirofumi , Nishito Yasumasa , Hayashi Hideyuki , Kagamiyama Hiroyuki , Takeda Masao
Published: April 2003

Based on amino acid sequence data of a 74‐kDa regulatory subunit (B″ or δ) of a human heterotrimeric protein phosphatase 2A, a cDNA encoding the subunit was isolated from a human cerebral cortex library. The cDNA had an open reading frame encoding an M
r 66 138 protein of 570 amino acids. Bacterial expression of the cDNA yielded a protein immunoreactive with antisera specific to the 74‐kDa subunit. The predicted primary structure of the subunit had no similarity to already reported sequences of PP2A regulatory subunits including A, B, and PR72. Potential phosphorylation sites for protein kinases A and C, a bipartite motif of putative nuclear localization signal, an SH3 accessible proline‐rich domain, and a unique PQ repeat were found in the sequence. The subunit mRNA of about 2.9 kb was ubiquitously expressed in rat tissues.
Genetic diversity of flagellins of Pseudomonas aeruginosa
Authors: Spangenberg Claudia , Heuer Thomas , Bürger Christiane , Tümmler Burkhard
Published: April 2003

Physical genome analysis of the virulence‐associated fliC locus in 20 Pseudomonas aeruginosa strains by mapping and sequencing revealed groups of heterologous a‐type (1164 bp; 1185 bp) and highly conserved b‐type (1467 bp) flagellin genes. Whereas only two synonymous nucleotide substitutions were detected in eight b‐type fliC sequences, the 12 a‐type sequences exhibited 57 nucleotide substitutions, of which 39 occurred within a variable central region. Although a‐type and b‐type flagellins differ by 35% in their primary structure, they share strong homology in their predicted features, implying that the polymorphic proteins fold into similar structures during polymerization of the flagella.
High ciliary neuronotrophic specific activity in rat peripheral nerve
Authors: Williams Lawrence R. , Manthorpe Marston , Barbin Gilles , Nieto‐Sampedro Manuel , Cotman Carl W. , Varon Silvio
Published: April 2003

Ciliary neuronotrophic factors (CNTFs) are proteins defined by their ability to promote the survival in tissue culture of chick embryo ciliary ganglionic neurons. CNTF activity has been reported in several source materials. Among these sources, the highest specific activity, i.e. 16,000 TU/mg, has been found in the intraocular tissue innervated by the ciliary ganglionic neurons. We now report that extracts of adult rat peripheral nerve and spinal nerve roots contain CNTF at a specific activity equal to or greater than the intraocular tissue. Equally high concentrations of CNTF activity are found in both motor and sensory nerves. The possible cellular source(s) of this mammalian CNTF is discussed.
A culture model for age‐related human neurofibrillary pathology
Authors: Cole Gregory M. , Wu Ken , Timiras Paola S.
Published: April 2003

Cloned human neuroblastoma cells have been induced to differentiate with retinoic acid whereupon they form an extensive network of processes and pseudoganglia. Ultrastructural examination shows these processes often contain assembled neurofilaments arranged parallel to microtubules in orderly arrangements characteristic of normal neurons. Perturbation of these differentiated, ganglion like cells with agents such as aluminum, zinc, and possibly leupeptin results in apparent neurofibrillary pathologies as evidenced by neurofilament specific immunofluorescent microscopy. A quantitative increase in neurofilament‐specific antibody binding induced by aluminum and leupeptin were verified by flow cytometry with a fluorescence activated cell sorter. The utility of this system in screening agents for their capacity to produce neurofibrillary lesions characteristic of age‐related human disorders is discussed.