bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure‐induced insulator–metal transition in a novel layer metalloorganic structure
Authors: Ovsyannikov Sergey V. , Shchennikov Vladimir V. , Titov Alexander N. , Uwatoko Yoshiya
Published: November 2006

A novel layer metalloorganic structure (Co(η5‐C5H5)2)0.25TiSe2has been synthesized by intercalation of the cobaltocene, Co(η5‐C5H5)2[bis(eta‐5‐cyclopentadienyl)cobalt] (a representative of the metallocenes M(η5‐C5H5)2where M – is a metal) into van‐der‐Waals gaps of TiSe2matrix. The papers reports a study of the electrical resistanceR, thermoelectric powerS(Seebeck effect), and contraction of a sample's thickness (compressibility) under almost continuous variation of quasihydrostatic pressurePwithin 0–20 GPa at room temperature. We observed a gradual decrease ofR(P) by ∼8 orders to 20 GPa. AboutP∼ 10 GPa we established both an abrupt change of dR/dPand inversion ofSfrom the electronic to the holes type of conductivity. ToP∼ 16 GPa the intercalate became a metal and exhibited a “close to zero”S, which was kept down to 8 GPa on decompression; all pressure‐induced changes were reversible. The synthesized compound (Co(η5‐C5H5)2)0.25TiSe2is a novel functional material for wide application. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural phase transformations in InP under pressure: A molecular‐dynamics study
Authors: Rino José Pedro , Branício Paulo S.
Published: November 2006

The pressure induced structural phase transformations of InP up to 100 GPa are investigated using molecular‐dynamics simulations. The calculated InP equation of state for the zincblende (ZB) phase at room temperature is in excellent agreement with experiments as well as several thermodynamic properties validating the interatomic potential employed in the simulations. Results show a sequence of dynamic structural transformations from ZB → rocksalt (RS) at 10 GPa, from RS → rhombohedral (RH) at 14 GPa, and from RH → CsCl at 70 GPa. The RS → RH transformation is a weakly first order transition while the other two transformations are typical first order transitions which present large volume drop and hysteresis in the reverse transformation. The RH intermediate phase between RS and CsCl was never considered for InP even though it was predicted for other materials. The ZB → RS transition uses a Pmm2 pathway while the RS → RH → CsCl is consistent with the Buerger mechanism which uses the R$ \bar 3 $m pathway. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Anisotropy analysis of the surface stress in Ag stepped surfaces with the modified embedded atom method
Authors: Shu Yu , Zhang Jian‐Min , Xu Ke‐Wei
Published: November 2006

The surface stresses in Ag stepped surfaces (910), (710), (510), (410), (310), (210), (320), (430) and (540) have been calculated by using the modified embedded atom method (MEAM). The surface stresses in the surface plane τxx (along the step edge) and τyy (normal to the step edge) have similar orders of magnitude as the surface energy. For surfaces having the (100) and (110) terraces, the change of τxx and τyy is very small and the variation of the surface energy is smooth. The stress τzz (normal to the surface plane) is always tensile in the unrelaxed state. The linear variation of the change in surface energy per unit change in elastic strain ${\partial \gamma\over \partial \varepsilon_{xx}}$, ${\partial \gamma\over \partial \varepsilon_{yy}}$ and ${\partial \gamma\over \partial \varepsilon_{zz}}$ (i.e. τxx − γ, τyy − γ and τzz) with the angle α between the (hk0) and (100) planes has a turning point corresponding to the (210) surface. The anisotropic ratio in the stepped surface having the (110) terrace is larger than that having the (100) terrace, and the wider the (110) terrace or the narrower the (100) terrace, the larger the ratio τyy/τxx. Copyright © 2006 John Wiley & Sons, Ltd.
Reaction of imidazole in gas phase at very low pressure with Cu foil and Cu oxides studied by X‐ray photoelectron spectroscopy
Authors: Hernández M. P. , Fernández‐Bertrán J. F. , Farías M. H. , Díaz J. A.
Published: November 2006

The gas‐phase reactions of imidazole with Cu foil, CuO and Cu2O powders at a pressure of 10−5 Torr are studied by means of X‐ray photoelectron spectroscopy (XPS) at room temperature for 1 h. The reactivity of gaseous imidazole is very intense with Cu foil, weak with CuO and nil with Cu2O. The reaction product on the Cu foil is cuprous imidazolate of oligomeric nature and with CuO is cupric imidazolate of very low molecular weight. Copyright © 2006 John Wiley & Sons, Ltd.
An approach to joint analysis of longitudinal measurements and competing risks failure time data
Authors: Elashoff Robert M. , Li Gang , Li Ning
Published: November 2006

Joint analysis of longitudinal measurements and survival data has received much attention in recent years. However, previous work has primarily focused on a single failure type for the event time. In this paper we consider joint modelling of repeated measurements and competing risks failure time data to allow for more than one distinct failure type in the survival endpoint which occurs frequently in clinical trials. Our model uses latent random variables and common covariates to link together the sub‐models for the longitudinal measurements and competing risks failure time data, respectively. An EM‐based algorithm is derived to obtain the parameter estimates, and a profile likelihood method is proposed to estimate their standard errors. Our method enables one to make joint inference on multiple outcomes which is often necessary in analyses of clinical trials. Furthermore, joint analysis has several advantages compared with separate analysis of either the longitudinal data or competing risks survival data. By modelling the event time, the analysis of longitudinal measurements is adjusted to allow for non‐ignorable missing data due to informative dropout, which cannot be appropriately handled by the standard linear mixed effects models alone. In addition, the joint model utilizes information from both outcomes, and could be substantially more efficient than the separate analysis of the competing risk survival data as shown in our simulation study. The performance of our method is evaluated and compared with separate analyses using both simulated data and a clinical trial for the scleroderma lung disease. Copyright © 2006 John Wiley & Sons, Ltd.
A residuals‐based transition model for longitudinal analysis with estimation in the presence of missing data
Authors: Koru‐Sengul Tulay , Stoffer David S. , Day Nancy L.
Published: November 2006

We propose a transition model for analysing data from complex longitudinal studies. Because missing values are practically unavoidable in large longitudinal studies, we also present a two‐stage imputation method for handling general patterns of missing values on both the outcome and the covariates by combining multiple imputation with stochastic regression imputation. Our model is a time‐varying autoregression on the past innovations (residuals), and it can be used in cases where general dynamics must be taken into account, and where the model selection is important. The entire estimation process was carried out using available procedures in statistical packages such as SAS and S‐PLUS. To illustrate the viability of the proposed model and the two‐stage imputation method, we analyse data collected in an epidemiological study that focused on various factors relating to childhood growth. Finally, we present a simulation study to investigate the behaviour of our two‐stage imputation procedure. Copyright © 2006 John Wiley & Sons, Ltd.
Kernel support for zero‐loss Internet service restart
Authors: Chang Da‐Wei , Tsai Chuan‐Ming , Li Wei‐Kou , Lee Tzu‐Rung
Published: November 2006

Owing to long serving time and huge numbers of clients, Internet services can easily suffer from transient faults. Although restarting a service can solve this problem, information of the on‐line requests will be lost owing to the service restart, which is unacceptable for many commercial or transaction‐based services. In this paper, we propose an approach to achieve the goal of zero‐loss restart for Internet services. Under this approach, a kernel subsystem is responsible for detecting the transient faults, retaining the I/O channels of the service, and managing the service restart flow. In addition, some straightforward modifications to the service should be made to take advantage of the kernel support. To demonstrate the feasibility of our approach, we implemented the subsystem in the Linux kernel. Moreover, we modified a Web server and a CGI program to take advantage of the kernel support. According to the experimental results, our approach incurs little runtime overhead (i.e. less than 3.2%). When the service crashes, it can be restarted quickly (i.e. within 210 μs) with no information loss. Furthermore, the performance impact due to the service crash is small. These results show that the approach can efficiently achieve the goal of zero‐loss restart for Internet services. Copyright © 2006 John Wiley & Sons, Ltd.
Profiling with AspectJ
Authors: Pearce David J. , Webster Matthew , Berry Robert , Kelly Paul H. J.
Published: November 2006

This paper investigates whether AspectJ can be used for efficient profiling of Java programs. Profiling differs from other applications of AOP (e.g. tracing), since it necessitates efficient and often complex interactions with the target program. As such, it was uncertain whether AspectJ could achieve this goal. Therefore, we investigate four common profiling problems (heap usage, object lifetime, wasted time and time‐spent) and report on how well AspectJ handles them. For each, we provide an efficient implementation, discuss any trade‐offs or limitations and present the results of an experimental evaluation into the costs of using it. Our conclusions are mixed. On the one hand, we find that AspectJ is sufficiently expressive to describe the four profiling problems and reasonably efficient in most cases. On the other hand, we find several limitations with the current AspectJ implementation that severely hamper its suitability for profiling. Copyright © 2006 John Wiley & Sons, Ltd.
A brokerage system for solar data archives
Authors: Zunino C. , Pompili I. , Sanna A. , Ciminiera L.
Published: November 2006

Scientific research and practical applications of solar physics require data and computational services to be integrated seamlessly and efficiently. The European Grid for Solar Observations (EGSO) leverages Grid‐oriented concepts and technology to provide a high‐performance infrastructure for solar applications. In this paper, an architecture for a data brokerage service is proposed. Brokers interact with providers and consumers in order to build a profile of both parties. In particular, a broker interacts with providers in order to gather information on the data potentially available to consumers, and with the consumers in order to identify the set of providers that are most likely to satisfy specific data needs. The brokerage technique is based on a multi‐tier management of metadata. Copyright © 2006 John Wiley & Sons, Ltd.
Toward a progress indicator for program compilation
Authors: Luo Gang , Chen Tong , Yu Hao
Published: November 2006

For user‐friendliness purposes, many modern software systems provide progress indicators for long‐running tasks. These progress indicators continuously estimate the percentage of the task that has been completed and when the task will finish. However, none of the existing program compilation tools provide a non‐trivial progress indicator, although it often takes minutes or hours to build a large program. In this paper, we investigate the problem of supporting such progress indicators. We first discuss the goals and challenges inherent in this problem. Then we present a set of techniques that are sufficient for implementing a simple yet useful progress indicator for program compilation. Finally, we report on an initial implementation of these techniques in GNU Make. Copyright © 2006 John Wiley & Sons, Ltd.
A new algorithm for encoding and decoding the Hilbert order
Authors: Chen Ningtao , Wang Nengchao , Shi Baochang
Published: November 2006

An iterative algorithm is described, based on the replication process of the Hilbert matrix, for encoding and decoding the Hilbert order. The time complexity of the proposed algorithm is smaller than those published previously, and the space complexity is bounded by a constant. Moreover, the new algorithm has a wider applicability when compared with existing algorithms for certain machine‐word lengths. A new variant of the Hilbert curve is suggested to overcome a shortcoming of the traditional Hilbert curve for the mapping problem. The proposed coding algorithms for the traditional Hilbert curve are also applicable to the new variant without increasing the time and space complexities. Copyright © 2006 John Wiley & Sons, Ltd.
Three‐dimensional sonographic determination of normal fetal mandibular and maxillary size during the second half of pregnancy
Authors: Roelfsema N. M. , Hop W. C. J. , Wladimiroff J. W.
Published: November 2006

Objective

To explore the various ways of obtaining fetal maxillary and mandibular size with three‐dimensional (3D) ultrasound, with a view to developing a tool for identifying minor anomalies in the lower facial region.

Methods

Serial 3D sonographic measurements of the fetal jaws were made in 126 normal singleton pregnancies at 18–34 weeks of gestation for determination of degree of maxillary and mandibular protrusion, maxillary and mandibular corpus lengths, mid‐ and lower facial depths and maxillary and mandibular curvature. In a sub study the reproducibility of the measurements was evaluated.

Results

The coefficient of variation in the reproducibility study varied between 7.1 and 10.5%. For all parameters except maxillary and mandibular protrusion, there was a significant gestational age‐related increase. Ratios of maxillary/mandibular protrusion, maxillary/mandibular corpus lengths, mid‐/lower facial depths and maxillary/mandibular curvature all showed a significant gestational age‐related decrease, with the most distinct decrease in the mid‐/lower facial depth ratio.

Conclusions

3D sonographic measurement of the fetal maxilla and mandible demonstrated an acceptable intraobserver variability for all measurements. The mid‐/lower facial depth ratio appears to be most valuable in determining abnormal mandibular development. Copyright © 2006 ISUOG. Published by John Wiley & Sons, Ltd.
Correlation between prenatal ultrasound and autopsy findings: a study of second‐trimester abortions
Authors: Kaasen A. , Tuveng J. , Heiberg A. , Scott H. , Haugen G.
Published: November 2006

Objective

To evaluate discrepancies between sonographic and autopsy findings following termination of pregnancy (TOP) in the second trimester.

Methods

This retrospective report is based on 288 consecutive second‐trimester abortions carried out because of fetal malformations diagnosed by ultrasound examination at a tertiary referral center. The correlation between the results from the ultrasound and autopsy examinations was evaluated.

Results

Autopsy was performed in 274 cases. In 160 of the 274 pregnancies (58.4%) there was full agreement between the two examination methods. Findings detected by autopsy (in addition to those leading to termination) were not observed by ultrasonography in 86 (31.4%) of the pregnancies; of the 64 malformations that occurred, 30 (46.9%) were judged as ‘detectable’. In 27 (9.9%) pregnancies, observations made by ultrasound (in addition to those leading to termination) were not confirmed at autopsy. In one pregnancy, postmortem radiology examination—but not autopsy—confirmed the ultrasound observations. No pregnancies were terminated because of false positive ultrasound observations. The correlation between ultrasound and autopsy findings was evaluated by three investigators; the inter‐rater agreement was high (κ = 0.85).

Conclusion

Discrepancies between ultrasound and autopsy findings were observed in about 40% of the pregnancies. These discrepancies confirm the need for autopsy following TOP. Copyright © 2006 ISUOG. Published by John Wiley & Sons, Ltd.
Phospholipase A1fromTrypanosoma cruziinfective stages generates lipid messengers that activate host cell protein kinase c
Authors: BELAUNZARÁN M. L. , WAINSZELBAUM M. J. , LAMMEL E. M. , GIMENEZ G. , ALOISE M. M. , FLORIN-CHRISTENSEN J. , ISOLA E. L. D.
Published: November 2006

Here we have studied phospholipase A1(Plase A1) fromTrypanosoma cruziinfective stages and it's possible role regarding the interaction with mammalian host cells. Plase A1was mainly detected as a membrane-bound activity in the infective amastigote and trypomastigote stages, being remarkably higher with respect to the non-infective epimastigotes. It is noteworthy that only the infective stages secreted Plase A1. Moreover, along the differentiation process from epimastigotes into metacyclic trypomastigotes, the secreted enzyme activity increased simultaneously with the appearance of metacyclic forms, as expected. Since this enzyme is predominantly membrane-associated and secreted by the infective stages, Vero cell lipid profile modifications were analysed after interaction with either intact infective parasites or purifiedT. cruziPlase A1. Significant changes in Vero cell lipid composition were observed, with the appearance of free fatty acids, diacylglycerol and lysophosphatidylcholine. Concomitantly with the generation of second lipid messengers, host cell protein kinase C activation was demonstrated. These results indicate thatT. cruziPlase A1could play a critical role in the early events of parasite-host cell interaction that precede invasion.
Comparison of alternative models for personality disorders
Authors: MOREY LESLIE C. , HOPWOOD CHRISTOPHER J. , GUNDERSON JOHN G. , SKODOL ANDREW E. , SHEA M. TRACIE , YEN SHIRLEY , STOUT ROBERT L. , ZANARINI MARY C. , GRILO CARLOS M. , SANISLOW CHARLES A. , McGLASHAN THOMAS H.
Published: November 2006

Background. The categorical classification system for personality disorder (PD) has been frequently criticized and several alternative dimensional models have been proposed.

Method. Antecedent, concurrent and predictive markers of construct validity were examined for three models of PDs: the Five-Factor Model (FFM), the Schedule for Nonadaptive and Adaptive Personality (SNAP) model and the DSM-IV in the Collaborative Study of Personality Disorders (CLPS) sample.

Results. All models showed substantial validity across a variety of marker variables over time. Dimensional models (including dimensionalized DSM-IV) consistently outperformed the conventional categorical diagnosis in predicting external variables, such as subsequent suicidal gestures and hospitalizations. FFM facets failed to improve upon the validity of higher-order factors upon cross-validation. Data demonstrated the importance of both stable trait and dynamic psychopathological influences in predicting external criteria over time.

Conclusions. The results support a dimensional representation of PDs that assesses both stable traits and dynamic processes.
Modelling outbreak control for pneumonic plague
Authors: MASSIN L. , LEGRAND J. , VALLERON A. J. , FLAHAULT A.
Published: November 2006

Although pneumonic plague is listed by the Centers of Disease Control in the leading ‘critical biological agents’, very few studies exist on this subject. In this study, a mathematical compartment model was used to describe the geographical and temporal spread of an epidemic of pneumonic plague following its use as a biological weapon. Univariate and multivariate analyses were performed in order to assess the key parameters for the control of an outbreak in France. If interventions were taken 10 days after an attack, a reference scenario of 1000 index cases in Paris would lead to 2500 deaths. The results of the study indicate that the rapidity of onset of interventions has the largest effect on the final size of the epidemic, followed by wearing masks, treating contacts preventively and quarantine. Limiting inter-regional mixing does little to reduce casualties, although it does confine them to a single region.
Generation of Reactive Oxygen and Antioxidant Species by Hydrodynamically Stressed Suspensions of Morinda citrifolia
Authors: Jeffers Paul , Kerins Sinead , Baker C. Jacyn , Kieran Patricia M.
Published: November 2006

The generation of reactive oxygen species (ROS) by plant cell suspension cultures, in response to the imposition of both biotic and abiotic stress, is well‐documented. This study investigated the generation of hydrogen peroxide by hydrodynamically stressed cultures of Morinda citrifolia, over a 5‐h period post‐stress imposition. Suspensions were exposed to repeated passages through a syringe, under laminar flow conditions, corresponding to cumulative energy dissipation levels of approximately 3–6 J kg‐1. Extracellular hydrogen peroxide was detected using a luminol‐based chemiluminescence assay. The addition of exogenous hydrogen peroxide facilitated the detection of low levels of hydrogen peroxide in the presence of antioxidants. Immediately after shear exposure, there was evidence of significant antioxidative capacity in the sheared cell cultures, which potentially masked any oxidative burst (OB), but which decreased over the following 40 min. This antioxidative capacity was determined to derive from the shearing process. Trials in which ground cellular debris was added to control suspensions suggested that some of the antioxidative capacity observed in stressed suspensions was directly associated with debris generated by the shearing process. Using UV‐vis spectrophotometry and HPLC, stress‐related increases in the levels of phenolic compounds were detected in suspension filtrates. Under the stress conditions investigated, maximum hydrogen peroxide levels of 11.5 μM were observed, 5 h after shear exposure. This study emphasizes the importance of considering both oxidative and antioxidative capacities as part of a holistic approach to the determination of the OB in hydrodynamically stressed plant cell suspension cultures.
Multivariate Characterization of Hydrogen Balmer Emission in Cataclysmic Variables
Authors: Sarty Gordon E. , Wu Kinwah
Published: November 2006

The ratios of hydrogen Balmer emission line intensities in cataclysmic variables are signatures of the physical processes that produce them. To quantify those signatures relative to classifications of cataclysmic variable types, we applied the multivariate statistical analysis methods of principal components analysis and discriminant function analysis to the spectroscopic emission data set of Williams (1983). The two analysis methods reveal two different sources of variation in the ratios of the emission lines. The source of variation seen in the principal components analysis was shown to be correlated with the binary orbital period. The source of variation seen in the discriminant function analysis was shown to be correlated with the equivalent width of the Hβ line. Comparison of the data scatterplot with scatterplots of theoretical models shows that Balmer line emission from T CrB systems is consistent with the photoionization of a surrounding nebula. Otherwise, models that we considered do not reproduce the wide range of Balmer decrements, including ‘inverted’ decrements, seen in the data.
Triaxial versus Spherical Dark Matter Halo Profiles
Authors: Knebe Alexander , Wießner Volkmar
Published: November 2006

When analyzing dark matter halos forming in cosmological n-body simulations, it is common practice to obtain the density profile utilizing spherical shells. However, it is also known that the systems under investigation are far from spherically symmetric but, rather, follow a triaxial mass distribution. In this study we present an estimator for the error introduced by spherically averaging an elliptical mass distribution. We systematically investigate the differences arising when using a triaxial density profile under the assumption of spherical symmetry. We show that the variance in the density can be as large as 50% in the outer parts of dark matter halos for extreme (but still credible) axis ratios of 0.55: 0.67: 1. The inner parts are less affected but still show a scatter at the 16% level for these prolate systems. For more moderate ellipticities, i.e. axis ratios of 0.73: 0.87: 1, the error is smaller but still as large as 10–20% depending on distance. We further provide a simple formula that allows estimation of this variance as a function of radius for arbitrary axis ratios. We conclude that highly prolate and/or oblate systems are better fit by analytical profiles that take into account the triaxial nature of cosmological objects.
Galactic Anisotropy of Cosmic Ray Intensity Observed by an Air Shower Experiment
Authors: Bahmanabadi Mahmud , Ghomi Mehdi Khakian , Sheidaei Farzaneh , Samimi Jalal
Published: November 2006

We have monitored multi-TeV cosmic rays by a small air shower array in Tehran (35°43′ N, 51°20′ E, 1200 m = 890 g cm−2). More than 1.1 × 106 extensive air shower events were recorded. These observations enabled us to analyse sidereal variation of the galactic cosmic ray intensity. The observed sidereal daily variation is compared to the expected variation which includes the Compton–Getting effect due to the motion of the earth in the Galaxy. In addition to the Compton–Getting effect, an anisotropy has been observed which is due to a unidirectional anisotropy of cosmic ray flow along the Galactic arms.
Cobalt Complexes of Tripodal Hexadentate Ligands: Electrochemically Driven Rearrangements
Authors: Bernhardt Paul V. , Kim Yang , Sujandi
Published: November 2006

The CoIII complexes of the hexadentate tripodal ligands HOsen (3-(2´-aminoethylamino)-2,2-bis((2´´-aminoethylamino)methyl)propan-1-ol) and HOten (3-(2´-aminoethylthia)-2,2-bis((2´´-aminoethylthia)methyl)propan-1-ol) have been synthesized and fully characterized. The crystal structures of [Co(HOsen)]Cl3∙H2O and [Co(HOten)](ClO4)Cl2 are reported and in both cases the ligands coordinate as tripodal hexadentate N6 and N3S3 donors, respectively. Cyclic voltammetry of the N3S3 coordinated complex [Co(HOten)]3+ is complicated and electrode dependent. On a Pt working electrode an irreversible CoIII/II couple (formal potential –157 mV versus Ag|AgCl) is seen, which is indicative of dissociation of the divalent complex formed at the electrode. The free HOten released by the dissociation of [Co(HOten)]2+ can be recaptured by Hg as shown by cyclic voltammetry experiments on a static Hg drop electrode (or in the presence of Hg2+ ions), which leads to the formation of an electroactive HgII complex of the N3S3 ligand (formal potential +60 mV versus Ag|AgCl). This behaviour is in contrast to the facile and totally reversible voltammetry of the hexaamine complex [Co(HOsen)]3+ (formal potential (CoIII/II) –519 mV versus Ag|AgCl), which is uncomplicated by any coupled chemical reactions. A kinetic and thermodynamic analysis of the [Co(HOten)]2+/[Hg(HOten)]2+ system is presented on the basis of digital simulation of the experimental voltammetric data.
Unusual Terpyridines as Ligands for Novel Light-Emitting Iridium(III) Complexes: Synthesis and Characterization
Authors: Winter Andreas , Ulbricht Christoph , Holder Elisabeth , Risch Nikolaus , Schubert Ulrich S.
Published: November 2006

Based on S-shaped terpyridines, a series of yellow, orange, and red-orange light-emitting iridium(iii) complexes has been synthesized. The respective compounds have been prepared by the bridge-splitting method starting from the dimeric precursor complexes [(ppy)2Ir-μ-Cl]2, [(ppy-CHO)2Ir-μ-Cl]2, and [(c6)2Ir-μ-Cl]2. The products have been fully characterized by one- and two-dimensional (1H–1H correlation) NMR spectroscopy, elemental analysis, and MALDI-TOF mass spectrometry revealing the successful coordination of the iridium(iii) centres to the S-shaped terpyridine ligands. Furthermore, the quantitative coordination has been verified by the photophysical and electrochemical properties of the mononuclear iridium(iii) complexes. The photoluminescence spectra have shown strong emissions with maxima between 538 and 600 nm. The study of the optical properties of these novel complexes has indicated that the colour shifts are mainly depending on the nature of the cyclometallating ligands.
Methyl 2-[N-(2′-Pyridylmethyl)carbamyl]pyridine-6-carboxylate: A Precursor for Unsymmetrical Diamide Ligands
Authors: Napitupulu Mery , Lawrance Geoffrey A. , Clarkson Guy J. , Moore Peter
Published: November 2006

Methyl 2-[N-(2′-pyridylmethyl)carbamyl]pyridine-6-carboxylate (H1), prepared by reaction of a 1:1 ratio of the methyl diester of pyridine-2,6-dicarboxylic acid and 2-aminomethylpyridine, can form 1:2 M:L complexes by acting as a tridentate ligand, as exemplified by a crystal structure analysis of [CoIII(1)2](ClO4) where each ligand is coordinated by the amido group and its two flanking pyridine groups, with the ester group, a relatively poor donor, remaining unbound. The acid formed upon ester hydrolysis, hydrogen 2-[N-(2′-pyridylmethyl)carbamyl]pyridine-6-carboxylate (H22), has been isolated as the ammonium salt, and forms a 2:2 M:L dimer [CuII2(2)2(OH2)2] where each ligand binds to one copper through the amido group, its flanking pyridine groups, and to the other copper by the carboxylate group, to form a 10-membered ring that incorporates both metals. Onward reaction of the monoester (H1) with a different amine leads to potentially pentadentate ligands centred on a 2,6-disubstituted pyridine but with unsymmetrical arms, as exemplified by synthesis of 2-[N-(2′-pyridylmethyl)carbamyl]-6-[N-(2′-pyridylethyl)carbamyl]pyridine (H23), 2-[N-(2′-pyridylmethyl)carbamyl]-6-[N-(1′-piperidinethyl)carbamyl]pyridine (H24), and 2-[N-(2′-pyridylmethyl)carbamyl]-6-[N-(2′-hydroxypropyl)carbamyl]pyridine (H25). Study of possible helicate formation with the unsymmetrical ligands has been initiated, with the ability to form polymetallic species probed by an ESI-MS study.
A structural model reveals energy transduction in dynein
Authors: Serohijos Adrian W. R. , Chen Yiwen , Ding Feng , Elston Timothy C. , Dokholyan Nikolay V.
Published: November 2006

Intracellular active transport is driven by ATP-hydrolyzing motor proteins that move along cytoskeletal filaments. In particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the Golgi, and mitosis. However, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. Using homology modeling and normal mode analysis, we propose a complete atomic structure and a mechanism for force generation by the motor protein dynein. In agreement with very recent electron microscopy (EM) reconstructions showing dynein as a ring-shaped heptamer, our model consists of six ATPases of the AAA (ATPases associated with various cellular activities) superfamily and a C-terminal domain, which is experimentally known to control motor function. Our model shows a coiled coil spanning the diameter of the motor that accounts for previously unidentified structures in EM studies and provides a potential mechanism for long-range communication between the AAA domains. Furthermore, normal mode analysis reveals that the subunits of the motor that contain the nucleotide binding sites exhibit minimal movement, whereas the rest of the motor is very mobile. Our analysis suggests the likely domain rearrangements of the motor unit that generate its power stroke. This study provides insights into the structure and function of dynein that can guide further experimental investigations into energy transduction in dynein.
The promyelocytic leukemia protein functions as a negative regulator of IFN-γ signaling
Authors: Choi Youn-Hee , Bernardi Rosa , Pandolfi Pier Paolo , Benveniste Etty N.
Published: November 2006

IFN-γ is an immunomodulatory cytokine and uses the STAT-1α transcription factor to mediate gene expression. The promyelocytic leukemia (PML) protein regulates transcription as an activator or repressor, depending on the gene under investigation. Herein, we examined the influence of PML on IFN-γ signaling, using PML wild-type (
Pml
+/+
) and deficient (
Pml
−/−
) mouse embryonic fibroblasts (MEF).
Pml
−/−
MEF exhibit enhanced IFN-γ-induced STAT-1α transcriptional activity compared with
Pml
+/+
cells. Moreover, reconstitution of PML in
Pml
−/−
MEF reduced STAT-1α transcriptional activity to levels comparable to
Pml
+/+
MEF. Numerous endogenous IFN-γ-regulated genes were up-regulated in
Pml
−/−
MEF compared with

Pml
+/+

MEF. IFN-γ-mediated STAT-1α DNA-binding activity was enhanced in

Pml
−/−

cells compared with
Pml
+/+
cells. Lastly, IFN-γ enhanced the formation of a PML–STAT-1α complex in the nucleus. These data suggest a novel function for PML in the IFN-γ signaling pathway by inhibiting STAT-1α DNA binding and transcriptional activity.
PKB and megalin determine the survival or death of renal proximal tubule cells
Authors: Caruso-Neves Celso , Pinheiro Ana Acacia S. , Cai Hui , Souza-Menezes Jackson , Guggino William B.
Published: November 2006

Renal proximal tubule cells have a remarkable ability to reabsorb large quantities of albumin through megalin-mediated endocytosis. This is an essential process for overall body homeostasis. Overstressing this endocytic system with a prolonged excess of albumin is injurious to proximal tubule cells. How these cells function and protect themselves from injury is unknown. Here, we show that megalin is the sensor that determines whether cells will be protected or injured by albumin. Megalin, through a novel mechanism, binds PKB in a D-3-phosphorylated phospholipid-insensitive manner, anchoring PKB in the luminal plasma membrane. Whereas low doses of albumin are protective, an overload of albumin decreases megalin expression followed by a reduction of plasma membrane PKB, PKB activity, and Bad phosphorylation induced by PKB. The result is albumin-induced apoptosis. These results reveal a model for PKB distribution in the plasma membrane and elucidate mechanisms involved in both the protective and toxic effects of albumin on proximal tubule cells. In addition, our findings suggest a mechanism for the progression of chronic kidney disease to end-stage renal disease.
The dynamics behind Titan's methane clouds
Authors: Mitchell Jonathan L. , Pierrehumbert Raymond T. , Frierson Dargan M. W. , Caballero Rodrigo
Published: November 2006

We present results of an axisymmetric global circulation model of Titan with a simplified suite of atmospheric physics forced by seasonally varying insolation. The recent discovery of midlatitude tropospheric clouds on Titan has caused much excitement about the roles of surface sources of methane and the global circulation in forming clouds. Although localized surface sources, such as methane geysers or “cryovolcanoes,” have been invoked to explain these clouds, we find in this work that clouds appear in regions of convergence by the mean meridional circulation and over the poles during solstices, where the solar forcing reaches its seasonal maximum. Other regions are inhibited from forming clouds because of dynamical transports of methane and strong subsidence. We find that for a variety of moist regimes, i.e., with the effect of methane thermodynamics included, the observed cloud features can be explained by the large-scale dynamics of the atmosphere. Clouds at the solsticial pole are found to be a robust feature of Titan's dynamics, whereas isolated midlatitude clouds are present exclusively in a variety of moist dynamical regimes. In all cases, even without including methane thermodynamics, our model ceases to produce polar clouds ≈4–6 terrestrial years after solstices.
Autoantibody-mediated demyelination depends on complement activation but not activatory Fc-receptors
Authors: Urich Eduard , Gutcher Ilona , Prinz Marco , Becher Burkhard
Published: November 2006

The precise mechanisms leading to CNS inflammation and myelin destruction in both multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE) remain the subject of intense debate. In both MS and EAE, autoantibodies (autoAbs) are thought to be involved in tissue destruction through recruiting Fc receptor (FcR)-bearing cells or direct cytotoxic effects through the activation of the complement pathway. Whereas intrathecal immunoglobulin (Ig) production and Ig deposition in inflammatory lesions is a hallmark of MS, mice deficient in B cells and Igs develop severe EAE. Paradoxically, mice of the same genetic background but deficient in FcRγ are EAE-resistant. We found that the functional expression of FcRγ on systemic accessory cells, but not CNS-resident cells, appears to be vital for the development of CNS inflammation, independent of antigen-presenting cell function or Ab involvement. On the other hand, we found that the injection of antimyelin oligodendrocyte glycoprotein-Abs drastically worsens disease severity, inflammation, and demyelination. Using FcRγ−/−and C1q−/−mice, we could definitively establish that the demyelinating capacity of such autoAbin vivorelies entirely on complement activation and is FcR-independent.
Activation of an oncogenic microRNA cistron by provirus integration
Authors: Wang Clifford L. , Wang Bruce B. , Bartha Gábor , Li Lauri , Channa Namitha , Klinger Mark , Killeen Nigel , Wabl Matthias
Published: November 2006

Retroviruses can cause tumors when they integrate near a protooncogene or tumor suppressor gene of the host. We infected >2,500 mice with the SL3-3 murine leukemia virus; in 22 resulting tumors, we found provirus integrations nearby or within the gene that contains the mir-17-92 microRNA (miRNA) cistron. Using quantitative real-time PCR, we showed that expression of miRNA was increased in these tumors, indicating that retroviral infection can induce expression of oncogenic miRNAs. Our results demonstrate that retroviral mutagenesis can be a potent tool for miRNA discovery.
Characterization of a core binding site for ADAMTS-13 in the A2 domain of von Willebrand factor
Authors: Wu Jing-Jiang , Fujikawa Kazuo , McMullen Brad A. , Chung Dominic W.
Published: November 2006

ADAMTS-13, a metalloprotease in plasma, specifically cleaves the Tyr-1605–Met-1606 bond in the A2 domain of von Willebrand factor (VWF) to regulate the polymer distribution of VWF in circulation, which is critical for primary hemostasis. A 73-aa peptide (VWF73) was previously identified as the minimal substrate cleavable by ADAMTS-13. In this study, VWF73 was enzymatically and chemically cleaved into shorter peptides, and the inhibition of cleavage of a VWF73-derived substrate by these purified peptides was measured in competition studies using a quantitative assay we recently reported. A 24-aa peptide encompassing Pro-1645–Lys-1668 (P′40–P′63) and situated 40 aa downstream from the cleavage site was the minimal peptide that could bind to and competitively inhibit ADAMTS-13 (
K
i
= 12 μM). This peptide and longer peptides encompassing this core sequence also inhibited the cleavage of multimeric VWF by ADAMTS-13. These results suggest the presence of a complementary extended binding site, or exosite, on ADAMTS-13. Mutation of Asp-1653 and Asp-1663 to Ala in this region significantly reduced the rate of cleavage of the substrate peptide, whereas the Glu1655Ala mutation caused an enhanced rate of cleavage. These results suggest that ionic interactions of the Pro-1645–Lys-1668 region with the exosite on ADAMTS-13 play a significant role in mediating substrate recognition.
Endogenous ARF6 Interacts with Rac1 upon Angiotensin II Stimulation to Regulate Membrane Ruffling and Cell Migration
Authors: Cotton Mathieu , Boulay Pierre-Luc , Houndolo Tanguy , Vitale Nicolas , Pitcher Julie A. , Claing Audrey
Published: November 2006

ARF6 and Rac1 are small GTPases known to regulate remodelling of the actin cytoskeleton. Here, we demonstrate that these monomeric G proteins are sequentially activated when HEK 293 cells expressing the angiotensin type 1 receptor (AT1R) are stimulated with angiotensin II (Ang II). After receptor activation, ARF6 and Rac1 transiently form a complex. Their association is, at least in part, direct and dependent on the nature of the nucleotide bound to both small G proteins. ARF6-GTP preferentially interacts with Rac1-GDP. AT1R expressing HEK293 cells ruffle, form membrane protrusions, and migrate in response to agonist treatment. ARF6, but not ARF1, depletion using small interfering RNAs recapitulates the ruffling and migratory phenotype observed after Ang II treatment. These results suggest that ARF6 depletion or Ang II treatment are functionally equivalent and point to a role for endogenous ARF6 as an inhibitor of Rac1 activity. Taken together, our findings reveal a novel function of endogenously expressed ARF6 and demonstrate that by interacting with Rac1, this small GTPase is a central regulator of the signaling pathways leading to actin remodeling.
A Regulated Adaptor Function of p40phox: Distinct p67phoxMembrane Targeting by p40phoxand by p47phox
Authors: Ueyama Takehiko , Tatsuno Toshihiko , Kawasaki Takumi , Tsujibe Satoshi , Shirai Yasuhito , Sumimoto Hideki , Leto Thomas L. , Saito Naoaki
Published: November 2006

In the phagocytic cell, NADPH oxidase (Nox2) system, cytoplasmic regulators (p47phox, p67phox, p40phox, and Rac) translocate and associate with the membrane-spanning flavocytochrome b558, leading to activation of superoxide production. We examined membrane targeting of phox proteins and explored conformational changes in p40phoxthat regulate its translocation to membranes upon stimulation. GFP-p40phoxtranslocates to early endosomes, whereas GFP-p47phoxtranslocates to the plasma membrane in response to arachidonic acid. In contrast, GFP-p67phoxdoes not translocate to membranes when expressed alone, but it is dependent on p40phoxand p47phoxfor its translocation to early endosomes or the plasma membrane, respectively. Translocation of GFP-p40phoxor GFP-p47phoxto their respective membrane-targeting sites is abolished by mutations in their phox (PX) domains that disrupt their interactions with their cognate phospholipid ligands. Furthermore, GFP-p67phoxtranslocation to either membrane is abolished by mutations that disrupt its interaction with p40phoxor p47phox. Finally, we detected a head-to-tail (PX–Phox and Bem1 [PB1] domain) intramolecular interaction within p40phoxin its resting state by deletion mutagenesis, cell localization, and binding experiments, suggesting that its PX domain is inaccessible to interact with phosphatidylinositol 3-phosphate without cell stimulation. Thus, both p40phoxand p47phoxfunction as diverse p67phox“carrier proteins” regulated by the unmasking of membrane-targeting domains in distinct mechanisms.
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
Authors: Rieping Wolfgang , Habeck Michael , Bardiaux Benjamin , Bernard Aymeric , Malliavin Thérèse E. , Nilges Michael
Published: November 2006

Summary: Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data. Here we present version 2.1 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation. We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN). The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages.

Availability: A distribution with the source code of ARIA 2.1 is freely available at

Contact:  nilges@pasteur.fr
QOMA: quasi-optimal multiple alignment of protein sequences
Authors: Zhang Xu , Kahveci Tamer
Published: November 2006

Motivation: We consider the problem of multiple alignment of protein sequences with the goal of achieving a large SP (Sum-of-Pairs) score.

Results: We introduce a new graph-based method. We name our method QOMA (Quasi-Optimal Multiple Alignment). QOMA starts with an initial alignment. It represents this alignment using a K-partite graph. It then improves the SP score of the initial alignment through local optimizations within a window that moves greedily on the alignment. QOMA uses two parameters to permit flexibility in time/accuracy trade off: (1) The size of the window for local optimization. (2) The sparsity of the K-partite graph. Unlike traditional progressive methods, QOMA is independent of the order of sequences. The experimental results on BAliBASE benchmarks show that QOMA produces higher SP score than the existing tools including ClustalW, Probcons, Muscle, T-Coffee and DCA. The difference is more significant for distant proteins.

Availability: The software is available from the authors upon request.

Contact: tamer@cise.ufl.edu

Supplementary information: Supplementary material is available at Bioinformatics online.
A predictive model for identifying proteins by a single peptide match
Authors: Higdon Roger , Kolker Eugene
Published: November 2006

Motivation: Tandem mass-spectrometry of trypsin digests, followed by database searching, is one of the most popular approaches in high-throughput proteomics studies. Peptides are considered identified if they pass certain scoring thresholds. To avoid false positive protein identification, ≥2 unique peptides identified within a single protein are generally recommended. Still, in a typical high-throughput experiment, hundreds of proteins are identified only by a single peptide. We introduce here a method for distinguishing between true and false identifications among single-hit proteins. The approach is based on randomized database searching and usage of logistic regression models with cross-validation. This approach is implemented to analyze three bacterial samples enabling recovery 68–98% of the correct single-hit proteins with an error rate of <2%. This results in a 22–65% increase in number of identified proteins. Identifying true single-hit proteins will lead to discovering many crucial regulators, biomarkers and other low abundance proteins.

Contact:  ekolker@biatech.org

Supplementary information: Supplementary Data are available at Bioinformatics online.
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Authors: Steggles L. Jason , Banks Richard , Shaw Oliver , Wipat Anil
Published: November 2006

Motivation: New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory.

Results: We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non–determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed.

Availability: The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at

Contact:  L.J.Steggles@ncl.ac.uk