bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic approach for identification and characterization of novel immunostimulatory proteins from soluble antigens of Leishmania donovani promastigotes
Authors: Gupta Shraddha Kumari , Sisodia Brijesh Singh , Sinha Sudhir , Hajela Krishnan , Naik Sita , Shasany Ajit Kumar , Dube Anuradha 
Published: February 2007

AbstractVisceral leishmaniasis (VL) caused by Leishmania donovani is a major parasitic disease prevalent in endemic regions of Bihar in India. In the absence of good chemotherapeutic options, there is a need to develop an effective vaccine against VL which should be dependent on the generation of a T helper type 1 (Th1) immune response. We have shown that soluble proteins from promastigote of a new clinical isolate of L. donovani (2001) ranging from 68 to 97.4 kDa (F2 fraction), induce Th1 responses in the peripheral blood mononuclear cells of cured Leishmania patients and hamsters and also showed significant prophylactic potential. To understand the nature of F2 proteins, it was further characterized using 2‐DE, MALDI‐TOF and MALDI‐TOF/TOF‐MS. In all, 63 spots were cut from a CBB stained gel for analysis and data was retrieved for 52 spots. A total of 33 proteins were identified including six hypothetical/unknown proteins. Major immunostimulatory proteins were identified as elongation factor‐2, p45, heat shock protein (HSP)70, HSP83, aldolase, enolase, triosephosphate isomerase, protein disulfideisomerase and calreticulin. This study substantiates the usefulness of proteomics in characterizing a complex protein fraction (F2) map of soluble L. donovani promastigote antigen identified as Th1 stimulatory for its potential as vaccine targets against VL.
Minimum model for the α‐helix–β‐hairpin transition in proteins
Authors: Imamura Hideo , Chen Jeff Z. Y. 
Published: February 2007

AbstractWe present a minimal model for proteins, which is able to capture the structural conversion between the α‐helix and β‐hairpin. In most regimes of the parameter space, the model produces a stable structure at a low temperature; in a few limited regimes of the parameter space, the model displays an β‐hairpin transition as the physical conditions vary. These variations include a perturbation on hydrogen bonding propensity at the middle of the modeled chain, or the change of the hydrophobicity of a designated pair along the chain. Using Monte Carlo simulations, we demonstrate the structural conversion by means of state diagrams, heat capacity maps, and free energy maps. Proteins 2007. © 2007 Wiley‐Liss, Inc.
PIER: Protein interface recognition for structural proteomics
Authors: Kufareva Irina , Budagyan Levon , Raush Eugene , Totrov Maxim , Abagyan Ruben 
Published: February 2007

AbstractRecent advances in structural proteomics call for development of fast and reliable automatic methods for prediction of functional surfaces of proteins with known three‐dimensional structure, including binding sites for known and unknown protein partners as well as oligomerization interfaces. Despite significant progress the problem is still far from being solved. Most existing methods rely, at least partially, on evolutionary information from multiple sequence alignments projected on protein surface. The common drawback of such methods is their limited applicability to the proteins with a sparse set of sequential homologs, as well as inability to detect interfaces in evolutionary variable regions. In this study, the authors developed an improved method for predicting interfaces from a single protein structure, which is based on local statistical properties of the protein surface derived at the level of atomic groups. The proposed Protein IntErface Recognition (PIER) method achieved the overall precision of 60% at the recall threshold of 50% at the residue level on a diverse benchmark of 490 homodimeric, 62 heterodimeric, and 196 transient interfaces (compared with 25% precision at 50% recall expected from random residue function assignment). For 70% of proteins in the benchmark, the binding patch residues were successfully detected with precision exceeding 50% at 50% recall. The calculation only took seconds for an average 300‐residue protein. The authors demonstrated that adding the evolutionary conservation signal only marginally influenced the overall prediction performance on the benchmark; moreover, for certain classes of proteins, using this signal actually resulted in a deteriorated prediction. Thorough benchmarking using other datasets from literature showed that PIER yielded improved performance as compared with several alignment‐free or alignment‐dependent predictions. The accuracy, efficiency, and dependence on structure alone make PIER a suitable tool for automated high‐throughput annotation of protein structures emerging from structural proteomics projects. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions
Authors: Snow Catherine , Qi Guoying , Hayward Steven 
Published: February 2007

AbstractEssential dynamics sampling simulations of the domain conformations of unliganded Escherichia coli adenylate kinase have been performed to determine whether the ligand‐induced closed‐domain conformation is accessible to the open unliganded enzyme. Adenylate kinase is a three‐ domain protein with a central CORE domain and twoflanking domains, the LID and the NMPbind domains. The sampling simulations were applied to the CORE and NMPbind domain pair and the CORE and LID domain pair separately. One aim is to compare the results to those of a similar study on the enzyme citrate synthase to determine whether a similar domain‐locking mechanism operates in adenylate kinase. Although for adenylate kinase the simulations suggest that the closed‐domain conformation of the unliganded enzyme is at a slightly higher free energy than the open for both domain pairs, the results are radically different to those found for citrate synthase. In adenylate kinase the targeted domain conformations could always be achieved, whereas this was not the case in citrate synthase due to an apparent free‐energy barrier between the open and closed conformations. Adenylate kinase has been classified as a protein that undergoes closure through a hinge mechanism, whereas citrate synthase has been assigned to the shear mechanism. This was quantified here in terms of the change in the number of interdomain contacting atoms upon closure which showed a considerable increase in adenylate kinase. For citrate synthase this number remained largely the same, suggesting that the domain faces slide over each other during closure. This suggests that shear and hinge mechanisms of domain closure may relate to the existence or absence of an appreciable barrier to closure for the unliganded protein, as the latter can hinge comparatively freely, whereas the former must follow a more constrained path. In general though it appears a bias toward keeping the unliganded enzyme in the open‐domain conformation may be a common feature of domain enzymes. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins
Authors: Baussand J. , Deremble C. , Carbone A. 
Published: February 2007

AbstractSeveral studies on large and small families of proteins proved in a general manner that hydrophobic amino acids are globally conserved even if they are subjected to high rate substitution. Statistical analysis of amino acids evolution within blocks of hydrophobic amino acids detected in sequences suggests their usage as a basic structural pattern to align pairs of proteins of less than 25% sequence identity, with no need of knowing their 3D structure. The authors present a new global alignment method and an automatic tool for Proteins with HYdrophobic Blocks ALignment (PHYBAL) based on the combinatorics of overlapping hydrophobic blocks. Two substitution matrices modeling a different selective pressure inside and outside hydrophobic blocks are constructed, the Inside Hydrophobic Blocks Matrix and the Outside Hydrophobic Blocks Matrix, and a 4D space of gap values is explored. PHYBAL performance is evaluated against Needleman and Wunsch algorithm run with Blosum 30, Blosum 45, Blosum 62, Gonnet, HSDM, PAM250, Johnson and Remote Homo matrices. PHYBAL behavior is analyzed on eight randomly selected pairs of proteins of >30% sequence identity that cover a large spectrum of structural properties. It is also validated on two large datasets, the 127 pairs of the Domingues dataset with >30% sequence identity, and 181 pairs issued from BAliBASE 2.0 and ranked by percentage of identity from 7 to 25%. Results confirm the importance of considering substitution matrices modeling hydrophobic contexts and a 4D space of gap values in aligning distantly related proteins. Two new notions of local and global stability are defined to assess the robustness of an alignment algorithm and the accuracy of PHYBAL. A new notion, the SAD‐coefficient, to assess the difficulty of structural alignment is also introduced. PHYBAL has been compared with Hydrophobic Cluster Analysis and HMMSUM methods. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Presence of cholinergic and calcium antagonist constituents in Saussurea lappa explains its use in constipation and spasm
Authors: Gilani Anwar H. , Shah Abdul J. , Yaeesh S. 
Published: February 2007

AbstractThis study was carried out to provide a scientific basis for the traditional use of Saussurea lappa, in constipation and spasms. Isolated tissue preparations were used to see if the aqueous‐methanol crude extract of the S. lappa root (Sl.Cr) contains gut stimulatory and inhibitory constituents. In isolated guinea‐pig ileum, a quiescent preparation, Sl.Cr caused a concentration‐dependent (0.3–5.0 mg/mL) spasmogenic effect, with the maximum effect reaching 91% of the acetylcholine maximum. A further increase in concentration caused a declining effect, indicating the presence of spasmolytic constituent(s). The spasmolytic effect was more marked in the spontaneously contracting rabbit jejunum and in the atropinized preparations. The spasmolytic effect was mediated through calcium channel blocking (CCB) activity, as evident by its inhibitory effect against high K+ (80 mm)‐induced contraction and displacement of the Ca++ concentration‐response curves to the right. These data indicate that the crude extract of Sl.Cr contains gut stimulatory constituent(s) of cholinergic‐type providing a scientific basis for its use in constipation. The presence of spasmolytic constituents of CCB‐type more evident in the spontaneous contracting gut preparation may explain its use in spasms. Copyright © 2007 John Wiley & Sons, Ltd.
Ultra‐performance liquid chromatography/tandem mass spectrometric quantification of structurally diverse drug mixtures using an ESI‐APCI multimode ionization source
Authors: Yu Kate , Di Li , Kerns Edward , Li Susan Q. , Alden Peter , Plumb Robert S. 
Published: February 2007

AbstractWe report in this paper an ultra‐performance liquid chromatography/tandem mass spectrometric (UPLC®/MS/MS) method utilizing an ESI‐APCI multimode ionization source to quantify structurally diverse analytes. Eight commercial drugs were used as test compounds. Each LC injection was completed in 1 min using a UPLC system coupled with MS/MS multiple reaction monitoring (MRM) detection. Results from three separate sets of experiments are reported. In the first set of experiments, the eight test compounds were analyzed as a single mixture. The mass spectrometer was switching rapidly among four ionization modes (ESI+, ESI−, APCI−, and APCI+) during an LC run. Approximately 8–10 data points were collected across each LC peak. This was insufficient for a quantitative analysis. In the second set of experiments, four compounds were analyzed as a single mixture. The mass spectrometer was switching rapidly among four ionization modes during an LC run. Approximately 15 data points were obtained for each LC peak. Quantification results were obtained with a limit of detection (LOD) as low as 0.01 ng/mL. For the third set of experiments, the eight test compounds were analyzed as a batch. During each LC injection, a single compound was analyzed. The mass spectrometer was detecting at a particular ionization mode during each LC injection. More than 20 data points were obtained for each LC peak. Quantification results were also obtained. This single‐compound analytical method was applied to a microsomal stability test. Compared with a typical HPLC method currently used for the microsomal stability test, the injection‐to‐injection cycle time was reduced to 1.5 min (UPLC method) from 3.5 min (HPLC method). The microsome stability results were comparable with those obtained by traditional HPLC/MS/MS. Copyright © 2007 John Wiley & Sons, Ltd.
Liquid chromatography/tandem mass spectrometry method for the simultaneous determination of olanzapine, risperidone, 9‐hydroxyrisperidone, clozapine, haloperidol and ziprasidone in rat plasma
Authors: Zhang Guodong , Terry Alvin V. , Bartlett Michael G. 
Published: February 2007

AbstractA simple, sensitive and rapid liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) method was developed and validated for simultaneous quantification of olanzapine, clozapine, ziprasidone, haloperidol, risperidone, and its active metabolite 9‐hydroxyrisperidone, in rat plasma using midazolam as internal standard (IS). The analytes were extracted from rat plasma using a single step liquid‐liquid extraction technique. The compounds were separated on a Waters Atlantis™ dC‐18 (30 mm × 2.1 mm i.d., 3 µm) column using a mobile phase of acetonitrile/5 mM ammonium formate (pH 6.1 adjusted with formic acid) with gradient elution. All of the analytes were detected in positive ion mode using multiple reaction monitoring (MRM). The method was validated and the specificity, linearity, lower limit of quantitation (LLOQ), precision, accuracy, recoveries and stability were determined. LLOQ was 0.1 ng/mL and correlation coefficient (R2) values for the linear range of 0.1–100 ng/mL were 0.997 or greater for all the analytes. The intra‐day and inter‐day precision and accuracy were better than 8.05%. The relative and absolute recovery was above 77% and matrix effects were low for all the analytes except for ziprasidone. This validated method has been successfully used to quantify the plasma concentration of the analytes after chronic treatment with antipsychotic drugs. Copyright © 2007 John Wiley & Sons, Ltd.
Characterization of major and minor alk(en)ylresorcinols from mango (Mangifera indica L.) peels by high‐performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry
Authors: Knödler Matthias , Berardini Nicolai , Kammerer Dietmar R. , Carle Reinhold , Schieber Andreas 
Published: February 2007

Abstract5‐Alkyl‐ and 5‐alkenylresorcinols, as well as their hydroxylated derivatives, were extracted from mango (Mangifera indica L.) peels, purified on polyamide and characterized by high‐performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry (HPLC/APcI‐MS) for the first time. Among the 15 compounds analyzed, 3 major and 12 minor C15‐, C17‐, and C19‐substituted resorcinols and related analogues, showing varying degrees of unsaturation, were characterized by their specific fragmentation patterns in collision‐induced dissociation experiments. This marks the first report on the occurrence of mono‐, di‐, and triunsaturated C15‐homologues, saturated and triunsaturated C17‐homologues, and mono‐ and diunsaturated C19‐homologues in mango peels. Additionally, several hydroxylated C15‐ and C17‐homologues, also not yet described in mango, and a C14‐monoene, unique because of its even‐numbered side chain, were tentatively identified on the basis of their fragmentation patterns. The results obtained in the present study indicate that HPLC‐DAD‐APcI‐MSn, combined with the newly developed solid‐phase extraction, is a powerful tool for the analysis of alk(en)ylresorcinols and could therefore be used for their determination in various matrices. Copyright © 2007 John Wiley & Sons, Ltd.
A Benchmark for Outdoor Vision SLAM Systems
Authors: Abdallah Samer M. , Asmar Daniel C. , Zelek John S. 
Published: February 2007

AbstractSimultaneous localization and mapping (SLAM) is a viable solution to autonomous robot navigation in outdoor settings when global positioning systems are unavailable or unreliable. While the traditional exteroceptive sensor for outdoor SLAM is a laser, cameras have also been proposed due to their low power consumption, low price, high bandwidth of information, and superior landmark segmentation capabilities. All outdoor Vision SLAM systems developed to date are implemented on different platforms, in different settings, using different dead‐reckoning sensors; a fact which makes it difficult to compare them and assess the state of the art of Vision SLAM. The contribution of this paper is in developing an infrastructure for a benchmark upon which past and future Vision SLAM system can be compared. This proposed benchmark is validated by testing its datasets on a Vision‐Inertial SLAM system. © 2007 Wiley Periodicals, Inc.
Disproportionate sampling for population subgroups in telephone surveys
Authors: Kalsbeek William D. , Boyle Walter R. , Agans Robert P. , White John E. 
Published: February 2007

AbstractPopulation studies often seek to examine phenomena in important population subgroups or to compare results among these and other subgroups. When subgroups of interest comprise a relatively small percentage of the population and acceptable subgroup member lists are not available to serve as sampling frames, it may be prohibitively expensive even by telephone to screen through a sample of the entire population. This paper considers some statistical effects of estimation from a class of two‐stratum telephone sample designs where part of the frame with a higher subgroup concentration is disproportionately sampled compared to the rest of the frame. Using proportionate sampling as a reference, the relative impact of this disproportionate design is determined for nominal and effective sample sizes, where the latter are tied to the effect of variation in sample weights that occurs in disproportionately allocated samples. Findings are illustrated using two recent telephone surveys. Whereas nominal subgroup sample sizes may be improved by disproportionate sampling, we conclude that both the survey designer and analyst should use this type of design cautiously in telephone surveys. Copyright © 2007 John Wiley & Sons, Ltd.
In situ non‐invasive EDXRF analysis to reconstruct stratigraphy and thickness of Renaissance pictorial multilayers
Authors: Bonizzoni L. , Galli A. , Poldi G. , Milazzo M. 
Published: February 2007

AbstractIn this paper, we report a few examples showing how energy dispersive XRF analysis (EDXRF) coupled with visible reflectance spectroscopy (vis‐RS) can be successfully applied for the investigation of wood or canvas paintings by performing stratigraphic analyses with non‐invasive techniques. The specific aim is to reconstruct layers and their thicknesses. The method has been tested in the laboratory on paint layers similar to traditional Renaissance ones. In situ analyses of a famous wood painting by Andrea Mantegna—‘Madonna col bambino e un coro di cherubini’, Pinacoteca di Brera, Milan—were also carried out. While illustrating the results concerning the identification of pigments and the discrimination of layer stratigraphy, advantages and limitation of this method are pointed out. Copyright © 2007 John Wiley & Sons, Ltd.
Multilayer interference mirrors as components for soft x‐ray WDS monochromators and tunable radiation sources
Authors: André J.‐M. , Jonnard P. , Benbalagh R. 
Published: February 2007

AbstractMultilayer interference mirrors (MIMs) are widely used as low‐resolution monochromators for soft x‐ray wavelength dispersive spectrometry (WDS). It is now possible to fabricate multilayer monochromators with medium resolution by etching MIMs with a large number of bilayers according to the profile of a lamellar grating. It will be shown both theoretically and experimentally that these multilayer gratings with appropriate characteristics can be used as monochromators for soft x‐rays, whose spectral resolving power is considerably improved with respect to mere interference mirrors. Moreover, tunable soft x‐ray sources based on the interaction of medium‐energy electron beams with periodic multilayer structures are presently being developed in several countries. The physical processes involved in this type of sources belong to the class of quasi‐Cerenkov emission. Among them are resonant transition radiation and parametric radiation. We present the basic concepts and the first experimental results concerning this new type of sources which should be very interesting for WDS. Copyright © 2007 John Wiley & Sons, Ltd.
Theoretical shapes of K x‐ray spectra for lead as predicted by MCDF calculations
Authors: Lewandowska‐Robak Maja , Polasik Marek 
Published: February 2007

AbstractSimulations of the shapes of Pb K x‐ray spectra have been performed for an experimental situation in which single and double L‐ and M‐shell ionization (apart from the single K‐shell ionization) of target atoms occurs. The simulations are based on the results of the calculations of the energies and probabilities of various Pb K x‐ray transitions, done with the multiconfiguration Dirac–Fock (MCDF) method with the inclusion of the transverse (Breit) interaction and quantum electro dynamic (QED) corrections. It has been found that most contributions to the simulated spectra considerably overlap other contributions. Thus, their extraction from the measured spectra, which provides data about the L‐ and M‐shell ionization probability in a collision process, will only be possible using the results of theoretical studies. Our studies can be crucial in both analysis of a number of observed Pb K x‐ray spectra and in designing new experiments concerning the K x‐ray spectra of multiply ionized heavy atoms induced in collisions with various light or heavy projectiles of different energies. Copyright © 2007 John Wiley & Sons, Ltd.
Wavelength despersive spectroscopy analysis at high spectral resolution: application to the study of Mo/Si multilayers
Authors: Jonnard Philippe , Maury Hélène , André Jean‐Michel 
Published: February 2007

AbstractWe show that x‐ray emission spectroscopy (XES) induced by electrons, analyzed at high spectral resolution by a WDS Johann‐type spectrometer, is a powerful technique to characterize in a nondestructive way the interlayers in Mo/Si multilayers. The analysis is performed using the IRIS (Instrument de Recherche sur les Interfaces et Surfaces) apparatus equipped with a curved crystal. Within those experimental conditions the spectral resolution E/ΔE is about 2000 in the 1800–1900 eV photon energy range. Because of the high resolution of the spectrometer, the evolution of the shape of the Si Kβ emission band (3p − 1s transition) as a function of the chemical environment of the Si atoms is easily evidenced. We study a series of Mo/Si multilayers, where the thickness of the Si layers is 2 nm and that of the Mo layers is 1, 2, 3 or 4 nm. It clearly appears that the emission band from the Si atoms within the multilayers is different from that of amorphous Si (a‐Si), which should be observed if no diffusion process takes place at the interfaces. By comparing the observed emission band to that of a‐Si and molybdenum silicides and using a simple diffusion model, we deduce the composition of the interlayers. Their thickness is deduced and estimated to be 0.4 ± 0.1 nm or 0.8 ± 0.2 nm depending on the samples. Copyright © 2007 John Wiley & Sons, Ltd.