bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of cytochromes b5 from insects and vertebrates
Authors: Wang Lijun , Cowley Aaron B. , Terzyan Simon , Zhang Xuejun , Benson David R. 
Published: February 2007

AbstractWe report a 1.55 Å X‐ray crystal structure of the heme‐binding domain of cytochrome b5 from Musca domestica (house fly; HF b5), and compare it with previously published structures of the heme‐binding domains of bovine microsomal cytochrome b5 (bMc b5) and rat outer mitochondrial membrane cytochrome b5 (rOM b5). The structural comparison was done in the context of amino acid sequences of all known homologues of the proteins under study. We show that insect b5s contain an extended hydrophobic patch at the base of the heme binding pocket, similar to the one previously shown to stabilize mammalian OM b5s relative to their Mc counterparts. The hydrophobic patch in insects includes a residue with a bulky hydrophobic side chain at position 71 (Met). Replacing Met71 in HF b5 with Ser, the corresponding residue in all known mammalian Mc b5s, is found to substantially destabilize the holoprotein. The destabilization is a consequence of two related factors: (1) a large decrease in apoprotein stability and (2) extension of conformational disruption in the apoprotein beyond the empty heme binding pocket (core 1) and into the heme‐independent folding core (core 2). Analogous changes have previously been shown to accompany replacement of Leu71 in rOM b5 with Ser. That the stabilizing role of Met71 in HF b5 is manifested primarily in the apo state is highlighted by the fact that its crystallographic Cα B factor is modestly larger than that of Ser71 in bMc b5, indicating that it slightly destabilizes local polypeptide conformation when heme is in its binding pocket. Finally, we show that the final unit of secondary structure in the cytochrome b5 heme‐binding domain, a 310 helix known as α6, differs substantially in length and packing interactions not only for different protein isoforms but also for given isoforms from different species. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Analysis of chameleon sequences and their implications in biological processes
Authors: Guo Jun‐Tao , Jaromczyk Jerzy W. , Xu Ying 
Published: February 2007

AbstractChameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon‐HS (Helix vs. Strand) and chameleon‐HE (Helix vs. Sheet), based on known structures in Protein Data Bank. Our survey shows that the longest chameleon‐HS is eight residues while the longest chameleon‐HE is seven residues. We have done a detailed analysis on the local and global environment that might contribute to the unique conformation of a chameleon sequence. We found that the existence of chameleon sequences does not present a problem for secondary structure prediction programs, including the first generation prediction programs, such as Chou–Fasman algorithm, and the third generation prediction programs that utilize evolution information. We have also investigated the possible implication of chameleon sequences in structural conservation and functional diversity of alternatively spliced protein isoforms. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Possible anxiolytic effect of two extracts of Passiflora quadrangularis L. in experimental models
Authors: de Castro Pollyanna Celso F. , Hoshino Alberto , Silva Jair Campos da , Mendes Fúlvio Rieli 
Published: February 2007

AbstractSeveral species of the genus Passiflora, known in Brazil as ‘maracujá’, have widespread use in folk medicine as sedatives and anxiolytics. The anxiolytic activities of aqueous and hydroalcohol extracts of Passiflora quadrangularis leaves were evaluated using the elevated plus‐maze, open field and holeboard tests. The hydroalcohol extract presented results suggestive of anxiolytic activity in dosages around 100, 250 and 500 mg/kg, as expressed by elevation of the time spent on the open arms in the plus‐maze; a decrease of freezing and an increase of deambulation and rearing in the open field test. The hydroalcohol extract showed results similar to diazepam on the holeboard. No positive results were found for the aqueous extract. Copyright © 2007 John Wiley & Sons, Ltd.
Shilajit: a review
Authors: Agarwal Suraj P. , Khanna Rajesh , Karmarkar Ritesh , Anwer Md. Khalid , Khar Roop K. 
Published: February 2007

AbstractShilajit is a pale‐brown to blackish‐brown exudation, of variable consistency, exuding from layers of rocks in many mountain ranges of the world, especially the Himalayas and Hindukush ranges of the Indian subcontinent. It has been found to consist of a complex mixture of organic humic substances and plant and microbial metabolites occurring in the rock rhizospheres of its natural habitat. Shilajit has been used as a rejuvenator and an adaptogen for thousands of years, in one form or another, as part of traditional systems of medicine in a number of countries. Many therapeutic properties have been ascribed to it, a number of which have been verified by modern scientific evaluation. Shilajit has been attributed with many miraculous healing properties. Copyright © 2007 John Wiley & Sons, Ltd.
New approach in asthma treatment using excitatory modulator
Authors: Hoang Ba X. , Shaw D. Graeme , Levine Stephen , Hoang Cuong , Pham Phuong 
Published: February 2007

AbstractThe impact of a herbal extract with excitatory modulator activity in the management of asthma was studied. An open and selective 3‐year follow‐up of 14 chronic refractory asthmatics aged between 22 and 70 was used. Participants received an extract of Sophora flavescens Ait. Medication use, a diary card of symptoms and respiratory function were recorded. The study was retrospective and all patients gave written informed consent. The quality of life, clinical symptoms and respiratory function improved during all periods of measurement. The use of inhaled corticosteroid and β‐agonists were reduced or eliminated. There were no significant adverse reactions reported. Therefore the extract of S. flavescens as an excitatory modulator appears to be a safe and may be an effective alternative treatment for refractory chronic asthma. Copyright © 2007 John Wiley & Sons, Ltd.
Ursolic acid: a potent Inhibitor of superoxides produced in the cellular system
Authors: Ali Muhammad S. , Ibrahim Syed A. , Jalil Saima , Choudhary Muhammad I. 
Published: February 2007

AbstractTriterpenoids of ursane class: ursolic acid, ilelatifol D, corosolic acid and euscaphic acid were isolated for the first time from Leonurus cardiaca, a member of the family Lamiaceae. The isolated compounds were tested for their cell‐based antiinflammatory potential by suppressing respiratory burst activity and superoxide scavenging property by using xanthine/xanthine oxidase system to produce superoxides in the cell‐free system. Ursolic acid was found to be an excellent inhibitor for the superoxides produced in the cellular system, while the same was inactive in the superoxide scavenging activity in cell‐free system. Copyright © 2007 John Wiley & Sons, Ltd.
Wound healing activity of root extracts of Berberis lyceum royle in rats
Authors: Asif A. , Kakub G. , Mehmood S. , Khunum R. , Gulfraz M. 
Published: February 2007

AbstractThe wound healing activities of the aqueous and methanol extracts of the root of Berberis lyceum were assessed using incision, excision and dead wound space models of wound repair in rats. After application of both extracts it was observed that the area of epithelialization increased, followed by an increase in wound contraction, skin breaking strength, tissue granulation, dry weight and hydroxyproline content. Histopathological studies of the granulation tissue also indicated that there was an increase in collagen formation in those rats treated with the methanol extract, compared with the control group animals. The methanol extract was more effective than the aqueous extract, but both showed significant results compared with the control. Copyright © 2007 John Wiley & Sons, Ltd.
Method development aspects for the quantitation of pharmaceutical compounds in human plasma with a matrix‐assisted laser desorption/ionization source in the multiple reaction monitoring mode
Authors: Kovarik Peter , Grivet Chantal , Bourgogne Emmanuel , Hopfgartner Gérard 
Published: February 2007

AbstractThe present work investigates various method development aspects for the quantitative analysis of pharmaceutical compounds in human plasma using matrix‐assisted laser desorption/ionization and multiple reaction monitoring (MALDI‐MRM). Talinolol was selected as a model analyte. Liquid‐liquid extraction (LLE) and protein precipitation were evaluated regarding sensitivity and throughput for the MALDI‐MRM technique and its applicability without and with chromatographic separation. Compared to classical electrospray liquid chromatography/mass spectrometry (LC/ESI‐MS) method development, with MALDI‐MRM the tuning of the analyte in single MS mode is more challenging due to interfering matrix background ions. An approach is proposed using background subtraction. With LLE and using a 200 µL human plasma aliquot acceptable precision and accuracy could be obtained in the range of 1 to 1000 ng/mL without any LC separation. Approximately 3 s were required for one analysis. A full calibration curve and its quality control samples (20 samples) can be analyzed within 1 min. Combining LC with the MALDI analysis allowed improving the linearity down to 50 pg/mL, while reducing the throughput potential only by two‐fold. Matrix effects are still a significant issue with MALDI but can be monitored in a similar way to that used for LC/ESI‐MS analysis. Copyright © 2007 John Wiley & Sons, Ltd.
Mass spectral studies of native and mass‐labeled perfluorooctanesulfonamides
Authors: Arsenault Gilles , Chittim Brock , McAlees Alan , McCrindle Robert , Potter Dave , Tashiro Colleen , Yeo Brian 
Published: February 2007

AbstractThis work examines the mass spectra of several environmentally relevant amides, perfluorooctanesulfonamide (FOSA), NMeFOSA, NEtFOSA, and NMe2FOSA, under electron ionization conditions. A previous mass spectral study of FOSA and NEtFOSA led the authors to propose possible structures for some of the fragment ions and fragmentation pathways that might explain their formation. In the present communication, further fragment ions are identified for these two compounds and alternative fragmentation pathways proposed. Mass spectral analyses of NMeFOSA and NMe2FOSA and of mass‐labeled NMeFOSA and NEtFOSA reinforce our conclusions about potential fragmentation pathways for these amides and the fragment ions expected. The mass spectral data presented here will help chemists to identify signals found in a gas chromatographic/mass spectrometric (GC/MS) analysis that stem from these perfluoroalkylsulfonamides. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of a two‐dimensional liquid chromatography/mass spectrometry approach with a chip‐based nanoelectrospray device for structural elucidation of metabolites in a human ADME study using a quadrupole time‐of‐flight mass spectrometer
Authors: Trunzer Markus , Graf Daniel , Kiffe Michael 
Published: February 2007

AbstractThe study of the metabolic fate of drugs is essential for the safety assessment of new compounds in the drug development process. However, the characterization and structural elucidation of metabolites from in vivo experiments is still a very challenging task. In this paper, we compare a two‐dimensional liquid chromatography/mass spectrometry (LC/MS) approach using either a capillary LC/MS system or the recently introduced chip‐based nanoelectrospray/MS system (Nanomate®) as the second dimension for structural elucidation of metabolites by MS. More than 30 radioactive fractions of a chromatographic separation from a human urine sample were analyzed and 54 metabolites could be identified. The long persisting and stable nanoelectrospray enabled the search for unknown metabolites by precursor‐ion scanning experiments followed by product‐ion scanning experiments of potential metabolites using a quadrupole time‐of‐flight (qTOF) mass spectrometer. The number of fragments produced by nanoelectrospray with product‐ion scanning was significantly higher compared to LC/MS experiments with in‐source fragmentation. Therefore, the assignment of possible modifications in metabolites to certain moieties of the drug could be investigated with higher accuracy. The capillary LC/MS system for the second dimension was more sensitive in the case of low abundant metabolites. These metabolites could not be detected by direct nanoelectrospray infusion, which limits the application of the Nanomate for trace metabolites. Copyright © 2007 John Wiley & Sons, Ltd.
Understanding HSV‐1 entry glycoproteins
Authors: Reske Adi , Pollara Gabriele , Krummenacher Claude , Chain Benjamin M. , Katz David R. 
Published: February 2007

AbstractHerpes Simplex Virus‐1 is a common infectious agent, but the precise detail of entry and infection of cells has only now begun to be clarified. Four viral surface glycoproteins (gB, gD, gH and gL) are required. This review summarises the known structure and function of each of these essential viral envelope glycoproteins, and explores what is known about their close cooperation with each other in mediating cellular membrane fusion. It is suggested that, following gD binding to one of its entry receptors, membrane fusion is mediated by gB and the heterodimer gH/gL. Significantly, these four entry glycoproteins also play a key role in the interaction between HSV and the host immune system. The glycoproteins serve an important role as targets of adaptive immunity. However, recent studies have demonstrated that the same proteins also play a key role in initiating the early innate immune response to HSV. Understanding the complex functions of these HSV proteins may be essential for successful development of vaccines for HSV. Copyright © 2007 John Wiley & Sons, Ltd.
A Self‐Consistent Bathymetric Mapping Algorithm
Authors: Roman Chris , Singh Hanumant 
Published: February 2007

AbstractThe achievable accuracy of bathymetric mapping in the deep ocean using robotic systems is most often limited by the available guidance or navigation information used to combine the measured sonar ranges during the map making process. This paper presents an algorithm designed to mitigate the affects of poor ground referenced navigation by applying the principles of map registration and pose filtering commonly used in simultaneous localization and mapping (SLAM) algorithms. The goal of the algorithm is to produce a self‐consistent point cloud representation of the bottom terrain with errors that are on a scale similar to the sonar range resolution rather than any direct positioning measurement. The presented algorithm operates causally and utilizes sensor data that are common to instrumented underwater robotic vehicles used for mapping and scientific explorations. Real world results are shown for data taken on several expeditions with the JASON remotely operated vehicle (ROV). Comparisons are made between more standard mapping approaches and the proposed method is shown to significantly improve the map quality and reveal scene information that would have otherwise been obscured due to poor direct navigation information. © 2007 Wiley Periodicals, Inc.
Real‐Time SLAM with Octree Evidence Grids for Exploration in Underwater Tunnels
Authors: Fairfield Nathaniel , Kantor George , Wettergreen David 
Published: February 2007

AbstractWe describe a simultaneous localization and mapping (SLAM) method for a hovering underwater vehicle that will explore underwater caves and tunnels, a true three‐dimensional (3D) environment. Our method consists of a Rao‐Blackwellized particle filter with a 3D evidence grid map representation. We describe a procedure for dynamically adjusting the number of particles to provide real‐time performance. We also describe how we adjust the particle filter prediction step to accommodate sensor degradation or failure. We present an efficient octree data structure that makes it feasible to maintain the hundreds of maps needed by the particle filter to accurately model large environments. This octree structure can exploit spatial locality and temporal shared ancestry between particles to reduce the processing and storage requirements. To test our SLAM method, we utilize data collected with manually deployed sonar mapping vehicles in the Wakulla Springs cave system in Florida and the Sistema Zacato´n in Mexico, as well as data collected by the DEPTHX vehicle in the test tank at the Austin Applied Research Laboratory. We demonstrate our mapping and localization approach with these real‐world datasets. © 2007 Wiley Periodicals, Inc.
Dense 3D Map Construction for Indoor Search and Rescue
Authors: Ellekilde Lars‐Peter , Huang Shoudong , Valls Miró Jaime , Dissanayake Gamini 
Published: February 2007

AbstractThe main contribution of this paper is a new simultaneous localization and mapping (SLAM) algorithm for building dense three‐dimensional maps using information acquired from a range imager and a conventional camera, for robotic search and rescue in unstructured indoor environments. A key challenge in this scenario is that the robot moves in 6D and no odometry information is available. An extended information filter (EIF) is used to estimate the state vector containing the sequence of camera poses and some selected 3D point features in the environment. Data association is performed using a combination of scale invariant feature transformation (SIFT) feature detection and matching, random sampling consensus (RANSAC), and least square 3D point sets fitting. Experimental results are provided to demonstrate the effectiveness of the techniques developed. © 2007 Wiley Periodicals, Inc.
Graphical SLAM for Outdoor Applications
Authors: Folkesson John , Christensen Henrik I. 
Published: February 2007

AbstractApplication of SLAM outdoors is challenged by complexity, handling of nonlinearities, and flexible integration of a diverse set of features. A graphical approach to SLAM is introduced that enables flexible data‐association. The method allows for handling of nonlinearities. The method also enables easy introduction of global constraints. Computational issues can be addressed as a graph reduction problem. A complete framework for graphical based SLAM is presented. The framework is demonstrated for a number of outdoor experiments using an ATRV robot equipped with a SICK laser scanner and a Cross‐Bow Inertial Unit. The experiments include handling of large outdoor environments with loop closing. The presented system operates at 5 Hz on a 800 MHz computer. © 2007 Wiley Periodicals, Inc.
SLAM with Panoramic Vision
Authors: Lemaire Thomas , Lacroix Simon 
Published: February 2007

AbstractThis article presents an approach to SLAM that takes advantage of panoramic images. Landmarks are interest points detected and matched in the images and mapped according to a bearings‐only SLAM approach. As they are acquired and processed, the panoramic images are also indexed and stored into a database. A database query procedure, independent of the robot and landmark position estimates, is able to detect loop closures by retrieving memorized images that are close to the current robot position. The bearings‐only estimation process is described, and results over a trajectory of a few hundreds of meters are presented and discussed. © 2007 Wiley Periodicals, Inc.
Building a Robust Implementation of Bearing‐only Inertial SLAM for a UAV
Authors: Bryson Mitch , Sukkarieh Salah 
Published: February 2007

AbstractThis paper presents the on‐going design and implementation of a robust inertial sensor based simultaneous localization and mapping (SLAM) algorithm for an unmanned aerial vehicle (UAV) using bearing‐only observations. A single color vision camera is used to observe the terrain from which image points corresponding to features in the environment are extracted. The SLAM algorithm estimates the complete six degrees‐of‐freedom motion of the UAV along with the three‐dimensional position of the features in the environment. An extended Kalman filter approach is used where a technique of delayed initialization is performed to initialize the three‐dimensional position of features from bearing‐only observations. Data association is achieved using a multihypothesis innovation gate based on the spatial uncertainty of each feature. Results are presented by running the algorithm off‐line using inertial sensor and vision data collected during a flight test of a UAV. © 2007 Wiley Periodicals, Inc.
Surface transient effects in ultralow‐energy Cs+ sputtering of Si
Authors: Chanbasha A. R. , Wee A. T. S. 
Published: February 2007

AbstractThis study examines the dependence of the sputter rate and the transient width (ztr) as a function of Cs+ primary ion energy (impact energy (Ep) = 320 eV, 500 eV and 1 keV) and incident angles between 0 and 70° . The instrument used was the ATOMIKA 4500 SIMS depth profiler and the sample was Si with ten delta layers of Si0.7 Ge0.3. We observed the narrowest transient widths of between 1.4 and 2.0 nm apparent depth. This was achieved at incident angles (θ) of 30–50° . An extended transient effect was observed when profiled at θ > 50° . Below this incident angle, the transient width is less than twice the penetration depth (ztr < 2Rnorm). At minimum ztr, ztr ≈ Rnorm. The detection sensitivity is best achieved at θ ≈ 30° for all energies investigated. The sputter rate is lowest at normal incidence, rising gradually to a maximum at θ ≈ 50–60° . This is similar to that observed with ultralow‐energy O2+ primary ion beams.1 At ultralow energies, reducing Ep does not have a significant effect in reducing ztr. We conclude that for Ep < 1 keV, the optimum condition to achieve minimum ztr while maintaining good sensitivity and high sputter rate is at θ ≈ 30° . Copyright © 2007 John Wiley & Sons, Ltd.
Experiences developing architectures for realizing thin‐client diagram editing tools
Authors: Grundy John , Hosking John , Cao Shuping , Zhao Denjin , Zhu Nianping , Tempero Ewan , Stoeckle Hermann 
Published: February 2007

AbstractDiagram‐centric applications such as software design tools, project planning tools and business process modelling tools are usually ‘thick‐client’ applications running as stand‐alone desktop applications. There are several advantages to providing such design tools as Web‐based or even PDA‐ and mobile‐phone‐based applications. These include ease of access and upgrade, provision of collaborative work support and Web‐based integration with other applications. However, building such thin‐client diagram editing tools is very challenging. We have developed several thin‐client diagram editing applications realized as a set of plug‐in extensions to a meta‐tool for visual design environment development. In this paper, we discuss key user interaction and software architecture issues, illustrate examples of interacting with our thin‐client diagram editing tools, describe our design and implementation approaches, and present the results of several different evaluations of the resultant applications. Our experiences will be useful for those interested in developing their own thin‐client diagram editing architectures and applications. Copyright © 2007 John Wiley & Sons, Ltd.